strand scale effet: Topics by Science.gov

Sample records for strand scale effet

Tissue strands as "bioink" for scale-up organ printing.

PubMed

Yu, Yin; Ozbolat, Ibrahim T

2014-01-01

Organ printing, takes tissue spheroids as building blocks together with additive manufacturing technique to engineer tissue or organ replacement parts. Although a wide array of cell aggregation techniques has been investigated, and gained noticeable success, the application of tissue spheroids for scale-up tissue fabrication is still worth investigation. In this paper, we introduce a new micro-fabrication technique to create tissue strands at the scale of 500-700μm as a "bioink" for future robotic tissue printing. Printable alginate micro-conduits are used as semi-permeable capsules for tissue strand fabrication. Mouse insulinoma beta TC3 cell tissue strands were formed upon 4 days post fabrication with reasonable mechanical strength, high cell viability close to 90%, and tissue specific markers expression. Fusion was readily observed between strands when placing them together as early as 24h. Also, tissue strands were deposited with human umbilical vein smooth muscle cells (HUVSMCs) vascular conduits together to fabricated miniature pancreatic tissue analog. Our study provided a novel technique using tissue strands as "bioink" for scale-up bioprinting of tissues or organs.
Use of 1–4 interaction scaling factors to control the conformational equilibrium between α-helix and β-strand

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pang, Yuan-Ping, E-mail: pang@mayo.edu

Highlights: • 1–4 interaction scaling factors are used to adjust conformational energy. • This article reports the effects of these factors on protein conformations. • Reducing these factors changes a helix to a strand in molecular dynamics simulation. • Increasing these factors causes the reverse conformational change. • These factors control the conformational equilibrium between helix and strand. - Abstract: 1–4 interaction scaling factors are used in AMBER forcefields to reduce the exaggeration of short-range repulsion caused by the 6–12 Lennard-Jones potential and a nonpolarizable charge model and to obtain better agreements of small-molecule conformational energies with experimental data. However,more » the effects of these scaling factors on protein secondary structure conformations have not been investigated until now. This article reports the finding that the 1–4 interactions among the protein backbone atoms separated by three consecutive covalent bonds are more repulsive in the α-helix conformation than in two β-strand conformations. Therefore, the 1–4 interaction scaling factors of protein backbone torsions ϕ and ψ control the conformational equilibrium between α-helix and β-strand. Molecular dynamics simulations confirm that reducing the ϕ and ψ scaling factors readily converts the α-helix conformation of AcO-(AAQAA){sub 3}-NH{sub 2} to a β-strand conformation, and the reverse occurs when these scaling factors are increased. These results suggest that the ϕ and ψ scaling factors can be used to generate the α-helix or β-strand conformation in situ and to control the propensities of a forcefield for adopting secondary structure elements.« less
Technical Status Review on Drag Prediction and Analysis from Computational Fluid Dynamics: State of the Art

DTIC Science & Technology

1989-06-01

Methodes de Panel) ct sur l’equation complete du potentiel avec ou sans incorporation des effets visqueux. sont couramment employees darn l’industrie...quo pour ce qui eat do Is privision do Is tralnie ia situation actuolle nett pas satisfaisante. Il est en effet plus facile d’obtonir do bonnos...d’un nouvel appareil civil ou militairo utilisont donc encore largaent les essais en soufflerie en Is1 C. minimum eat ensuite corrigE des effets
Factors affecting stranding of juvenile salmonids by wakes from ship passage in the Lower Columbia River

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pearson, Walter H.; Skalski, John R.

2011-09-01

The effects of deep-draft vessel traffic in confined riverine channels on shorelines and fish are of widespread concern. In the Pacific Northwest of the United States, wakes and subsequent beach run-up from ships transiting the Lower Columbia River have been observed to strand juvenile salmon and other fish. As part of a before-and-after study to assess stranding effects that may be associated with channel deepening, we measured 19 co-variables from observations of 126 vessel passages at three low-slope beaches and used multiple logistic regression to discern the significant factors influencing the frequency of stranding. Subyearling Chinook salmon were 82% ofmore » the fish stranded over all sites and seasons. Given a low-slope beach, stranding frequencies for juvenile salmon were significantly related to river location, salmon density in the shallows, a proxy for ship kinetic energy, tidal height, and two interactions. The beach types selected for our study do not include all the beach types along the Lower Columbia River so that the stranding probabilities described here cannot be extrapolated river-wide. A more sophisticated modeling effort, informed by additional field data, is needed to assess salmon losses by stranding for the entire lower river. Such modeling needs to include river-scale factors such as beach type, berms, proximity to navigation channel, and perhaps, proximity to tributaries that act as sources of out-migrating juvenile salmon. At both river and beach scales, no one factor produces stranding; rather interactions among several conditions produce a stranding event and give stranding its episodic nature.« less
Reduce Nb3Sn Strand Deformation when Fabricating High Jc Rutherford Cables

DOE Office of Scientific and Technical Information (OSTI.GOV)

Peng, Xuan

2012-12-17

During Phase I, our efforts were to reduce subelements deformation when fabricating Nb3Sn Rutherford cables. Our first focus is on 217-sublement tube type strand. We successfully made a few billets in OD tube with different Cu spacing between subelements, and supplied the strands to Fermi Lab for cabling. Through the rolling test characterization, these types of strands did not have enough bonding between subelements to withstand the deformation. We saw copper cracking between subelements in the deformed strands. We scaled up the billet from OD to 1.5 OD, and made two billets. This greatly improves the bonding. There is nomore » copper cracking in the deformed strands when we scaled up the diameter of the billets. Fermi Lab successfully made cables using one of this improved strands. In their cables, no Cu cracking and no filament bridging occurred. We also successfully made a couple of billets with hex OD and round ID subelements for 61-subelement restack. Due to the lack of bonding, we could not judge its cabling property properly. But we know through this experiment, we could keep the Nb round, once we select the proper Cu spacing.« less
Unresolved fine-scale structure in solar coronal loop-tops

DOE Office of Scientific and Technical Information (OSTI.GOV)

Scullion, E.; Van der Voort, L. Rouppe; Wedemeyer, S.

2014-12-10

New and advanced space-based observing facilities continue to lower the resolution limit and detect solar coronal loops in greater detail. We continue to discover even finer substructures within coronal loop cross-sections, in order to understand the nature of the solar corona. Here, we push this lower limit further to search for the finest coronal loop substructures, through taking advantage of the resolving power of the Swedish 1 m Solar Telescope/CRisp Imaging Spectro-Polarimeter (CRISP), together with co-observations from the Solar Dynamics Observatory/Atmospheric Image Assembly (AIA). High-resolution imaging of the chromospheric Hα 656.28 nm spectral line core and wings can, under certainmore » circumstances, allow one to deduce the topology of the local magnetic environment of the solar atmosphere where its observed. Here, we study post-flare coronal loops, which become filled with evaporated chromosphere that rapidly condenses into chromospheric clumps of plasma (detectable in Hα) known as a coronal rain, to investigate their fine-scale structure. We identify, through analysis of three data sets, large-scale catastrophic cooling in coronal loop-tops and the existence of multi-thermal, multi-stranded substructures. Many cool strands even extend fully intact from loop-top to footpoint. We discover that coronal loop fine-scale strands can appear bunched with as many as eight parallel strands within an AIA coronal loop cross-section. The strand number density versus cross-sectional width distribution, as detected by CRISP within AIA-defined coronal loops, most likely peaks at well below 100 km, and currently, 69% of the substructure strands are statistically unresolved in AIA coronal loops.« less
Recent observations of the formation of filaments

NASA Technical Reports Server (NTRS)

Martin, Sara F.

1986-01-01

Two examples of the formation of small filaments in H alpha are described and illustrated. In both cases, the formation is seen to be the spontaneous appearance of strands of absorbing mass that evolve from no previous structure. The initial development of the filaments appears to consist of the accumulation of these absorptive strands along approximately parallel paths in a channel between large-scale, opposite polarity magnetic fields on either side of the filaments. The strands exhibit continuous changes in shape and degree of absorption which can be due to successive condensations resulting in new strands, mass motions within the strands, and outflow of the mass from the strands. For at least several hours before the formation of both filaments, small-scale fragments of opposite polarity, line-of-sight magnetic flux adjacent to or immediately below the filaments, and at the ends of the filaments, were cancelling. This type of magnetic flux disappearance continued during the development of the filaments and is commonly observed in association with established filaments. Cancellation is interpreted as an important evolutionary change in the magnetic field that can lead to configurations suitable for the formation of filaments.
Effets thermoelectrique et thermomagnetique du yttrium barium copper oxide monocristallin

NASA Astrophysics Data System (ADS)

Ghamlouche, Hassan

1998-09-01

Des la decouverte des supraconducteurs a haute temperature critique, les recherches se sont intensifiees afin de comprendre les mecanismes qui sont a l'origine des proprietes de ces materiaux L'etat mixte, tout comme l'etat supraconducteur pur et l'etat normal, a fait l'objet de nombreux travaux de recherche. En particulier, la structure des vortex a l'etat mixte, et leur mouvement sous l'effet d'une force quelconque, etaient et restent le centre de preoccupation. Les effets thermoelectrique (Seebeck) et thermomagnetique (Nernst) sont parmi les differentes mesures qui peuvent donner de l'information sur les etats des vortex a l'etat mixte. L'avantage essentiel de ces deux effets est l'absence d'un courant electrique applique. Ce dernier peut donner des perturbations indesirables durant les mesures. D'autre pari, nous avons utilise la methode CA (Courant Alternatif) pour effectuer nos mesures. Cette methode est caracterisee par une meilleure resolution par rapport a la methode CC (Courant Continu) conventionnelle. Nous avons etudie autant des echantillons macles que des echantillons sans macles. D'abord nous avons teste notre montage a champ magnetique nul. Nous avons alors montre que le pic rapporte par certains dans l'effet Seebeck a la transition supraconductrice ne correspond pas a une realite physique mais a un artefact experimental. On avait associe ce pic aux fluctuations. Par la suite, nous avons mis en evidence et etudie pour la premiere fois avec les effets Seebeck et Nernst le phenomene de la fusion du reseau de vortex grace a des mesures sur les echantillons sans macles. Cette etude s'est faite pour deux concentrations d'oxygene differentes et pour un gradient de temperature parallele, consecutivement, aux deux axes cristallographiques dans le plan ab. Finalement, nous avons etudie l'effet des plans de maclage sur le mouvement des vortex. Ceci a ete realise en appliquant le gradient de temperature selon trois directions differentes (0, 45 et 90°) avec les plans de maclage. Nous avons observe, pour le premier angle un mouvement libre du vortex, pour le second angle une contribution de l'effet Nernst a l'effet Seebeck et pour la troisieme direction un phenomene d'activation. Dans ce dernier cas, les plans de maclage font un obstacle qui s'oppose au mouvement des vortex. De ce qui precede, nous concluons qu'avec la bonne resolution de notre technique nous sommes capables d'observer des phenomenes que la technique CC ne met pas en relief. D'autre part, la variete d'echantillons que nous avons etudies et les phenomenes que nous avons observes valorisent la presente etude.
Scaling up digital circuit computation with DNA strand displacement cascades.

PubMed

Qian, Lulu; Winfree, Erik

2011-06-03

To construct sophisticated biochemical circuits from scratch, one needs to understand how simple the building blocks can be and how robustly such circuits can scale up. Using a simple DNA reaction mechanism based on a reversible strand displacement process, we experimentally demonstrated several digital logic circuits, culminating in a four-bit square-root circuit that comprises 130 DNA strands. These multilayer circuits include thresholding and catalysis within every logical operation to perform digital signal restoration, which enables fast and reliable function in large circuits with roughly constant switching time and linear signal propagation delays. The design naturally incorporates other crucial elements for large-scale circuitry, such as general debugging tools, parallel circuit preparation, and an abstraction hierarchy supported by an automated circuit compiler.
A novel modeling to predict the critical current behavior of Nb3Sn PIT strand under transverse load based on a scaling law and Finite Element Analysis

NASA Astrophysics Data System (ADS)

Wang, Tiening; Chiesa, Luisa; Takayasu, Makoto; Bordini, Bernardo

2014-09-01

Superconducting Nb3Sn Powder-In-Tube (PIT) strands could be used for the superconducting magnets of the next generation Large Hadron Collider. The strands are cabled into the typical flat Rutherford cable configuration. During the assembly of a magnet and its operation the strands experience not only longitudinal but also transverse load due to the pre-compression applied during the assembly and the Lorentz load felt when the magnets are energized. To properly design the magnets and guarantee their safe operation, mechanical load effects on the strand superconducting properties are studied extensively; particularly, many scaling laws based on tensile load experiments have been established to predict the critical current dependence on strain. However, the dependence of the superconducting properties on transverse load has not been extensively studied so far. One of the reasons is that transverse loading experiments are difficult to conduct due to the small diameter of the strand (about 1 mm) and the data currently available do not follow a common measurement standard making the comparison between different data sets difficult. Recently at the University of Geneva, a new device has been developed to characterize the critical current of Nb3Sn strands under transverse loads. In this work we present a new 2D Finite Element Analysis (FEA) to predict the electro-mechanical response of a PIT strand that was tested at the University of Geneva when transverse load is applied. The FEA provides the strain map for the superconducting filaments when the load is applied. Those strain maps are then used to evaluate the critical current behavior of a PIT strand using a recently developed scaling law that correlates the superconducting properties of a wire with the strain invariants due to the load applied on the superconductor. The benefits and limitations of this method are discussed based on the comparison between the critical current simulation results obtained with the filament strain map and the experimental results available for PIT strands.
Molecular Precision at Micrometer Length Scales: Hierarchical Assembly of DNA-Protein Nanostructures.

PubMed

Schiffels, Daniel; Szalai, Veronika A; Liddle, J Alexander

2017-07-25

Robust self-assembly across length scales is a ubiquitous feature of biological systems but remains challenging for synthetic structures. Taking a cue from biology-where disparate molecules work together to produce large, functional assemblies-we demonstrate how to engineer microscale structures with nanoscale features: Our self-assembly approach begins by using DNA polymerase to controllably create double-stranded DNA (dsDNA) sections on a single-stranded template. The single-stranded DNA (ssDNA) sections are then folded into a mechanically flexible skeleton by the origami method. This process simultaneously shapes the structure at the nanoscale and directs the large-scale geometry. The DNA skeleton guides the assembly of RecA protein filaments, which provides rigidity at the micrometer scale. We use our modular design strategy to assemble tetrahedral, rectangular, and linear shapes of defined dimensions. This method enables the robust construction of complex assemblies, greatly extending the range of DNA-based self-assembly methods.
Statistical analysis of the Nb3Sn strand production for the ITER toroidal field coils

NASA Astrophysics Data System (ADS)

Vostner, A.; Jewell, M.; Pong, I.; Sullivan, N.; Devred, A.; Bessette, D.; Bevillard, G.; Mitchell, N.; Romano, G.; Zhou, C.

2017-04-01

The ITER toroidal field (TF) strand procurement initiated the largest Nb3Sn superconducting strand production hitherto. The industrial-scale production started in Japan in 2008 and finished in summer 2015. Six ITER partners (so-called Domestic Agencies, or DAs) are in charge of the procurement and involved eight different strand suppliers all over the world, of which four are using the bronze route (BR) process and four the internal-tin (IT) process. In total more than 500 tons have been produced including excess material covering losses during the conductor manufacturing process, in particular the cabling. The procurement is based on a functional specification where the main strand requirements like critical current, hysteresis losses, Cu ratio and residual resistance ratio are specified but not the strand production process or layout. This paper presents the analysis on the data acquired during the quality control (QC) process that was carried out to ensure the same conductor performance requirements are met by the different strand suppliers regardless of strand design. The strand QC is based on 100% billet testing and on applying statistical process control (SPC) limits. Throughout the production, samples adjacent to the strand pieces tested by the suppliers are cross-checked (‘verified’) by their respective DAs reference labs. The level of verification was lowered from 100% at the beginning of the procurement progressively to approximately 25% during the final phase of production. Based on the complete dataset of the TF strand production, an analysis of the SPC limits of the critical strand parameters is made and the related process capability indices are calculated. In view of the large-scale production and costs, key manufacturing parameters such as billet yield, number of breakages and piece-length distribution are also discussed. The results are compared among all the strand suppliers, focusing on the difference between BR and IT processes. Following the completion of the largest Nb3Sn strand production, our experience gained from monitoring the execution of the QC activities and from auditing the results from the measurements is summarised for future superconducting strand material procurement activities.
Effets de la taille finie du milieu non-linéaire sur le bruit quantique spatial généré par un oscillateur paramétrique optique confocal

NASA Astrophysics Data System (ADS)

Lopez, L.; Gatti, A.; Maitre, A.; Treps, N.; Gigan, S.; Fabre, C.

2004-11-01

Nous nous intéressons au comportement spatial des fluctuations quantiques à la sortie d'un oscillateur paramétrique optique dégénéré en modes transverses, sous le seuil. En vue de futures expériences, nous étudions les effets de la diffraction dans le milieu paramétrique sur le bruit quantique spatial. Nous montrons que l'on voit apparaître une aire de cohérence de taille finie pour les effets quantiques transverses.
Detecting the Length of Double-stranded DNA with Solid State Nanopores

NASA Astrophysics Data System (ADS)

Li, Jiali; Gershow, Marc; Stein, Derek; Qun, Cai; Brandin, Eric; Wang, Hui; Huang, Albert; Branton, Dan; Golovchenko, Jene

2003-03-01

We report on the use of nanometer scale diameter, solid-state nanopores as single molecule detectors of double stranded DNA molecules. These solid-state nanopores are fabricated in thin membranes of silicon nitride, by ion beam sculpting 1. They produce discrete electronic signals: current blockages, when an electrically biased nanopore is exposed to DNA molecules in aqueous salt solutions. We demonstrate examples of such electronic signals for 3k base pairs (bp) and 10k bp double stranded DNA molecules, which suggest that these molecules are individually translocating through the nanopore during the detection process. The translocating time for the 10k bp double stranded DNA is about 3 times longer than the 3k bp, demonstrating that a solid-state nanopore device can be used to detect the lengths of double stranded DNA molecules. Similarities and differences with signals obtained from single stranded DNA in a biological nanopores are discussed 2. 1. Li, J., Stein, D., McMullan, C., Branton, D. Aziz, M. J. and Golovchenko, J. Ion Beam Sculpting at nanometer length scales. Nature 412, 166-169 (2001). 2. Meller, A., L. Nivon, E. Brandin, Golovchenko, J. & Branton, D. Proc. Natl. Acad. Sci. USA 97, 1079-1084 (2000).
Biotechnological mass production of DNA origami

NASA Astrophysics Data System (ADS)

Praetorius, Florian; Kick, Benjamin; Behler, Karl L.; Honemann, Maximilian N.; Weuster-Botz, Dirk; Dietz, Hendrik

2017-12-01

DNA nanotechnology, in particular DNA origami, enables the bottom-up self-assembly of micrometre-scale, three-dimensional structures with nanometre-precise features. These structures are customizable in that they can be site-specifically functionalized or constructed to exhibit machine-like or logic-gating behaviour. Their use has been limited to applications that require only small amounts of material (of the order of micrograms), owing to the limitations of current production methods. But many proposed applications, for example as therapeutic agents or in complex materials, could be realized if more material could be used. In DNA origami, a nanostructure is assembled from a very long single-stranded scaffold molecule held in place by many short single-stranded staple oligonucleotides. Only the bacteriophage-derived scaffold molecules are amenable to scalable and efficient mass production; the shorter staple strands are obtained through costly solid-phase synthesis or enzymatic processes. Here we show that single strands of DNA of virtually arbitrary length and with virtually arbitrary sequences can be produced in a scalable and cost-efficient manner by using bacteriophages to generate single-stranded precursor DNA that contains target strand sequences interleaved with self-excising ‘cassettes’, with each cassette comprising two Zn2+-dependent DNA-cleaving DNA enzymes. We produce all of the necessary single strands of DNA for several DNA origami using shaker-flask cultures, and demonstrate end-to-end production of macroscopic amounts of a DNA origami nanorod in a litre-scale stirred-tank bioreactor. Our method is compatible with existing DNA origami design frameworks and retains the modularity and addressability of DNA origami objects that are necessary for implementing custom modifications using functional groups. With all of the production and purification steps amenable to scaling, we expect that our method will expand the scope of DNA nanotechnology in many areas of science and technology.
Biotechnological mass production of DNA origami.

PubMed

Praetorius, Florian; Kick, Benjamin; Behler, Karl L; Honemann, Maximilian N; Weuster-Botz, Dirk; Dietz, Hendrik

2017-12-06

DNA nanotechnology, in particular DNA origami, enables the bottom-up self-assembly of micrometre-scale, three-dimensional structures with nanometre-precise features. These structures are customizable in that they can be site-specifically functionalized or constructed to exhibit machine-like or logic-gating behaviour. Their use has been limited to applications that require only small amounts of material (of the order of micrograms), owing to the limitations of current production methods. But many proposed applications, for example as therapeutic agents or in complex materials, could be realized if more material could be used. In DNA origami, a nanostructure is assembled from a very long single-stranded scaffold molecule held in place by many short single-stranded staple oligonucleotides. Only the bacteriophage-derived scaffold molecules are amenable to scalable and efficient mass production; the shorter staple strands are obtained through costly solid-phase synthesis or enzymatic processes. Here we show that single strands of DNA of virtually arbitrary length and with virtually arbitrary sequences can be produced in a scalable and cost-efficient manner by using bacteriophages to generate single-stranded precursor DNA that contains target strand sequences interleaved with self-excising 'cassettes', with each cassette comprising two Zn 2+ -dependent DNA-cleaving DNA enzymes. We produce all of the necessary single strands of DNA for several DNA origami using shaker-flask cultures, and demonstrate end-to-end production of macroscopic amounts of a DNA origami nanorod in a litre-scale stirred-tank bioreactor. Our method is compatible with existing DNA origami design frameworks and retains the modularity and addressability of DNA origami objects that are necessary for implementing custom modifications using functional groups. With all of the production and purification steps amenable to scaling, we expect that our method will expand the scope of DNA nanotechnology in many areas of science and technology.
The Structure of Coronal Loops

NASA Technical Reports Server (NTRS)

Antiochos, Spiro K.

2009-01-01

It is widely believed that the simple coronal loops observed by XUV imagers, such as EIT, TRACE, or XRT, actually have a complex internal structure consisting of many (perhaps hundreds) of unresolved, interwoven "strands". According to the nanoflare model, photospheric motions tangle the strands, causing them to reconnect and release the energy required to produce the observed loop plasma. Although the strands, themselves, are unresolved by present-generation imagers, there is compelling evidence for their existence and for the nanoflare model from analysis of loop intensities and temporal evolution. A problem with this scenario is that, although reconnection can eliminate some of the strand tangles, it cannot destroy helicity, which should eventually build up to observable scales. we consider, therefore, the injection and evolution of helicity by the nanoflare process and its implications for the observed structure of loops and the large-scale corona. we argue that helicity does survive and build up to observable levels, but on spatial and temporal scales larger than those of coronal loops. we discuss the implications of these results for coronal loops and the corona, in general .
Bush v. Bin Laden: Effect of State Emotion on Perceived Threat is Mediated by Emotion Towards the Threat Agent (Bush vs. Ben Laden: l’Effet de l’Emotion etat sur la Menace Percue est Mediatisees par l’Emotion vis-a-vis de l’Agent Menacant)

DTIC Science & Technology

2009-07-01

auteurs discu- tent des implications des resultats pour les theories qui postulent un effet de I’emotion sur la perception du risque et pour com...effect of global negative emotion on perceived threat . The authors discuss implications of the findings for theories that postulate an effect of... auteurs ont mene une etude perception j emotion j experimentale afin d’examiner les effets d’etats emotionnels Specifi- ques (peur et colere) et globaux
Prediction de l’Eclatement Tourbillonnaire sur les Ailes Delta d’Avions Militaires (CFD Prediction of Vortex Breakdown on Delta Wings for Military Aircraft)

DTIC Science & Technology

2003-03-01

moins développé que le tourbillon expérimental. En moyenne, par effet de compensation entre la région de bord d’attaque et la région proche de ...que les effets d’anisotropie de la turbulence. Un premier élément de réponse peut être obtenu en utilisant un modèle de turbulence un plus élaboré, tel...que l’EARSM (Explicit Algebraïc Reynolds Stress Model) qui prend en compte les effets de rotation et d’anisotropie [Ref 6]. Nous verrons au paragraphe
Fractional Brownian motion and the critical dynamics of zipping polymers.

PubMed

Walter, J-C; Ferrantini, A; Carlon, E; Vanderzande, C

2012-03-01

We consider two complementary polymer strands of length L attached by a common-end monomer. The two strands bind through complementary monomers and at low temperatures form a double-stranded conformation (zipping), while at high temperature they dissociate (unzipping). This is a simple model of DNA (or RNA) hairpin formation. Here we investigate the dynamics of the strands at the equilibrium critical temperature T=T(c) using Monte Carlo Rouse dynamics. We find that the dynamics is anomalous, with a characteristic time scaling as τ∼L(2.26(2)), exceeding the Rouse time ∼L(2.18). We investigate the probability distribution function, velocity autocorrelation function, survival probability, and boundary behavior of the underlying stochastic process. These quantities scale as expected from a fractional Brownian motion with a Hurst exponent H=0.44(1). We discuss similarities to and differences from unbiased polymer translocation.

Le Laser A Argon Ionise : Applications Therapeutiques

NASA Astrophysics Data System (ADS)

Brunetaud, J. M.; Mosquet, L.; Mordon, S.; Rotteleur, G.

1984-03-01

Le laser a argon ionise est un laser a emission continue, reglee en general en multiraies de 487 a 544 nm. Le rayonnement de ce laser est bien absorbe par les tissus vivants, avec une action preferentielle au niveau des pigments rouges (hemoglobine, myoglobine) et noirs (melanine). Le laser a argon est princi-palement utilise en therapeutique pour ses effets thermiques : en fonction du choix des parametres (puissance optique, surface exposee, temps d'exposition) on peut obtenir une coagulation (temperature optimale au niveau des tissus 60Â° - 80Â°) ou une volatisation (temperature superieure a 100Â°). Si la zone volatilisee est tres etroite (inferieure a 0,5 mm) on obtient un effet de coupe. Par rapport aux deux autres lasers egalement utilises pour leurs effets thermiques (CO2 et Nd. YAG) l'argon a des effets intermediaires : la coagulation sera plus superficielle qu'avec le Nd. YAG et la volatisation plus profonde qu'avec le CO2. Lors de la coupe, la necrose sur les berges sera egalement plus importante qu'avec le CO2.
Fish stranding in freshwater systems: sources, consequences, and mitigation.

PubMed

Nagrodski, Alexander; Raby, Graham D; Hasler, Caleb T; Taylor, Mark K; Cooke, Steven J

2012-07-30

Fish can become stranded when water levels decrease, often rapidly, as a result of anthropogenic (e.g., canal drawdown, hydropeaking, vessel wakes) and natural (e.g., floods, drought, winter ice dynamics) events. We summarize existing research on stranding of fish in freshwater, discuss the sources, consequences, and mitigation options for stranding, and report current knowledge gaps. Our literature review revealed that ∼65.5% of relevant peer-reviewed articles were found to focus on stranding associated with hydropower operations and irrigation projects. In fact, anthropogenic sources of fish stranding represented 81.8% of available literature compared to only 19.9% attributed to natural fish stranding events. While fish mortality as a result of stranding is well documented, our analysis revealed that little is known about the sublethal and long-term consequences of stranding on growth and population dynamics. Furthermore, the contribution of stranding to annual mortality rates is poorly understood as are the potential ecosystem-scale impacts. Mitigation strategies available to deal with stranding include fish salvage, ramping rate limitations, and physical habitat works (e.g., to contour substrate to minimize stranding). However, a greater knowledge of the factors that cause fish stranding would promote the development and refinement of mitigation strategies that are economically and ecologically sustainable. Copyright © 2012 Elsevier Ltd. All rights reserved.
Effets Josephson generalises entre antiferroaimants et entre supraconducteurs antiferromagnetiques

NASA Astrophysics Data System (ADS)

Chasse, Dominique

L'effet Josephson est generalement presente comme le resultat de l'effet tunnel coherent de paires de Cooper a travers une jonction tunnel entre deux supraconducteurs, mais il est possible de l'expliquer dans un contexte plus general. Par exemple, Esposito & al. ont recemment demontre que l'effet Josephson DC peut etre decrit a l'aide du boson pseudo-Goldstone de deux systemes couples brisant chacun la symetrie abelienne U(1). Puisque cette description se generalise de facon naturelle a des brisures de symetries continues non-abeliennes, l'equivalent de l'effet Josephson devrait donc exister pour des types d'ordre a longue portee differents de la supraconductivite. Le cas de deux ferroaimants itinerants (brisure de symetrie 0(3)) couples a travers une jonction tunnel a deja ete traite dans la litterature Afin de mettre en evidence la generalite du phenomene et dans le but de faire des predictions a partir d'un modele realiste, nous etudions le cas d'une jonction tunnel entre deux antiferroaimants itinerants. En adoptant une approche Similaire a celle d'Ambegaokar & Baratoff pour une jonction Josephson, nous trouvons un courant d'aimantation alternee a travers la jonction qui est proportionnel a sG x sD ou fG et sD sont les vecteurs de Neel de part et d'autre de la jonction. La fonction sinus caracteristique du courant Josephson standard est donc remplacee.ici par un produit vectoriel. Nous montrons que, d'un point de vue microscopique, ce phenomene resulte de l'effet tunnel coherent de paires particule-trou de spin 1 et de vecteur d'onde net egal au vecteur d'onde antiferromagnetique Q. Nous trouvons egalement la dependance en temperature de l'analogue du courant critique. En presence d'un champ magnetique externe, nous obtenons l'analogue de l'effet Josephson AC et la description complete que nous en donnons s'applique aussi au cas d'une jonction tunnel entre ferroaimants (dans ce dernier cas, les traitements anterieurs de cet effet AC s'averent incomplets). Nous considerons ensuite le cas d'une jonction tunnel entre deux materiaux au sein desquels l'antiferromagnetisme itinerant et la supraconductivite de type d coexistent de facon homogene. Nous obtenons a nouveau un courant d'aimantation alternee proportionnel a sG x sD, mais l'amplitude de l'analogue du courant critique est modulee par l'energie Josephson de la jonction E oc cos Acp, ou Acp est la difference de phase entre les deux parametres d'ordre supraconducteurs. Symetriquement, le courant Josephson supraconducteur est proportionnel a sin Acp, mais le courant critique est module par l'energie de couplage entre les moments magnetiques alternes ES cx SG· SD.
Effet de la teneur en carbone sur la resistance du CA6NM a la propagation des fissures de fatigue

NASA Astrophysics Data System (ADS)

Akhiate, Aziz

L'amelioration des performances des roues de turbines hydrauliques a fait l'objet de plusieurs etudes. Dans ce memoire, on s'est interesse a l'effet de la teneur en carbone du materiau de base de type CA6NM des aubes de turbines sur la microstructure et les proprietes mecaniques en general et en particulier sur le comportement en fatigue propagation. De maniere a bien atteindre cet objectif, on a choisi trois differentes nuances d'acier a faible 0.018% C, moyenne 0.033% C et elevee 0.067% C teneurs en carbone. Le 0.018% C et 0.067% C ont ete fabriques par le meme facturier et ils ont subi des traitements thermiques differents. De meme, le 0.033% C a subi des traitements thermiques differents des deux autres apres avoir ete coule par un autre fabricant. Afin d'effacer l'historique des traitements thermiques prealablement effectues et d'avoir la meme taille de grains parents austenitiques (GPA), on a austenitise les trois nuances d'acier a la meme temperature 1040°C, a differentes periodes suivant la teneur en carbone. Apres avoir homogeneise la GPA, on a entame le revenu. Le carbone a une influence sur la microstructure revenue notamment la quantite d'austenite de reversion ainsi que sur sa stabilite thermique et mecanique. Pour mettre en evidence l'effet de la teneur en carbone, on a trouve raisonnable d'isoler les effets relies a la temperature de revenu, en particulier la formation d'austenite de reversion. En effet, on a choisi deux temperatures de revenu. La premiere temperature est a 550°C pendant 2h imposee aux trois materiaux afin d'avoir une microstructure sans austenite de reversion. La deuxieme temperature choisie est a 610°C pour avoir un maximum et une identique quantite d'austenite de reversion sans presence de martensite fraiche. A la lumiere de ces deux microstructures, nous pouvons etablir une relation entre les proprietes mecaniques du CA6NM et la teneur en carbone, ainsi qu'entre les effets de la presence ou non d'austenite de reversion sur les proprietes mecaniques. Les resultats montrent que l'effet de la teneur en carbone est plus significatif sur les proprietes mecaniques monotones de traction et de resilience des alliages sans austenite de reversion. En effet, la limite d'elasticite, la resistance a la traction et la durete augmentent avec la teneur en carbone par contre l'allongement diminue. D'autre part, l'augmentation de la temperature et de la duree de revenu diminuent leur durete.
pH-Driven Reversible Self-Assembly of Micron-Scale DNA Scaffolds.

PubMed

Green, Leopold N; Amodio, Alessia; Subramanian, Hari K K; Ricci, Francesco; Franco, Elisa

2017-12-13

Inspired by cytoskeletal scaffolds that sense and respond dynamically to environmental changes and chemical inputs with a unique capacity for reconfiguration, we propose a strategy that allows the dynamic and reversible control of the growth and breakage of micron-scale synthetic DNA structures upon pH changes. We do so by rationally designing a pH-responsive system composed of synthetic DNA strands that act as pH sensors, regulators, and structural elements. Sensor strands can dynamically respond to pH changes and route regulatory strands to direct the self-assembly of structural elements into tubular structures. This example represents the first demonstration of the reversible assembly and disassembly of micron-scale DNA scaffolds using an external chemical input other than DNA. The capacity to reversibly modulate nanostructure size may promote the development of smart devices for catalysis or drug-delivery applications.
Estimation of Prestress Force Distribution in Multi-Strand System of Prestressed Concrete Structures Using Field Data Measured by Electromagnetic Sensor

PubMed Central

Cho, Keunhee; Cho, Jeong-Rae; Kim, Sung Tae; Park, Sung Yong; Kim, Young-Jin; Park, Young-Hwan

2016-01-01

The recently developed smart strand can be used to measure the prestress force in the prestressed concrete (PSC) structure from the construction stage to the in-service stage. The higher cost of the smart strand compared to the conventional strand renders it unaffordable to replace all the strands by smart strands, and results in the application of only a limited number of smart strands in the PSC structure. However, the prestress forces developed in the strands of the multi-strand system frequently adopted in PSC structures differ from each other, which means that the prestress force in the multi-strand system cannot be obtained by simple proportional scaling using the measurement of the smart strand. Therefore, this study examines the prestress force distribution in the multi-strand system to find the correlation between the prestress force measured by the smart strand and the prestress force distribution in the multi-strand system. To that goal, the prestress force distribution was measured using electromagnetic sensors for various factors of the multi-strand system adopted on site in the fabrication of actual PSC girders. The results verified the possibility to assume normal distribution for the prestress force distribution per anchor head, and a method computing the mean and standard deviation defining the normal distribution is proposed. This paper presents a meaningful finding by proposing an estimation method of the prestress force based upon field-measured data of the prestress force distribution in the multi-strand system of actual PSC structures. PMID:27548172
Prévalence et caractéristiques des effets indésirables des antihypertenseurs chez les patients suivis en ambulatoire au Centre Hospitalier Universitaire Yalgado Ouédraogo

PubMed Central

Millogo, Georges Rosario Christian; Zongo, Ragomzingba Frank Edgard; Benao, Anita; Youl, Estelle Noëla Hoho; Bassoleth, Blaise Alexandre Bazona; Ouédraogo, Moussa; Zabsonré, Patrice; Guissou, Innocent Pierre

2018-01-01

La prise en charge médicamenteuse de l'hypertension artérielle (HTA) entraine des effets indésirables qui peuvent être gênants et ainsi influencer l'observance du patient. Nous avons étudié ces effets indésirables dans le service de cardiologie du Centre hospitalier universitaire Yalgado Ouédraogo afin de déterminer leurs fréquences et leurs caractéristiques. Il s'agissait d'une étude transversale de juillet à septembre 2015 chez les patients suivis en ambulatoire pour HTA. Les données ont été obtenues à partir de l'interrogatoire, des carnets de suivi des patients et des fiches de consultations. Au total 278 patients ont été inclus. La population d'étude incluait 69,1% de femmes. L'âge moyen était de 52,2 ans avec des extrêmes de 23 et 86 ans. Quatre vingt et sept virgule huit pourcent (87,8%) vivaient en milieu urbain. Le tabagisme, la dyslipidémie et les antécédents familiaux d'HTA représentaient respectivement 9%, 35,6% et 57,2%. Au plan thérapeutique, 43,2% étaient sous monothérapie, 35,6% sous bithérapie à l'initiation du traitement. Les inhibiteurs calciques (59,7%) étaient la classe thérapeutique la plus utilisée. La prévalence globale des effets indésirables était de 60,1%. Les inhibiteurs calciques étaient impliqués dans 53,6% suivis des diurétiques (48,6%) dans la survenue de l'effet indésirable. La prévalence spécifique par molécule était 28,1% pour l'amlodipine et 24,5% pour l'hydrochlorothiazide. La diurèse excessive (13,7%), la toux (12,9%) et les vertiges (11,5%) étaient les effets indésirables les plus fréquemment évoqués par les patients. Le système nerveux central et périphérique et le système ostéo-musculaire étaient les systèmes les plus atteints. Les effets indésirables sont un déterminant majeur de l'adhésion aux traitements antihypertenseur, car leur impact sur la vie quotidienne des patients peut s'avérer significatif. PMID:29875965
Development of a 10 m quasi-isotropic strand assembled from 2G wires

NASA Astrophysics Data System (ADS)

Kan, Changtao; Wang, Yinshun; Hou, Yanbing; Li, Yan; Zhang, Han; Fu, Yu; Jiang, Zhe

2018-03-01

Quasi-isotropic strands made of second generation (2G) high temperature superconducting (HTS) wires are attractive to applications of high-field magnets at low temperatures and power transmission cables at liquid nitrogen temperature in virtue of their high current carrying capability and well mechanical property. In this contribution, a 10 m length quasi-isotropic strand is manufactured and successfully tested in liquid nitrogen to verify the feasibility of an industrial scale production of the strand by the existing cabling technologies. The strand with copper sheath consists of 72 symmetrically assembled 2G wires. The uniformity of critical properties of long quasi-isotropic strands, including critical current and n-value, is very important for their using. Critical currents as well as n-values of the strand are measured every 1 m respectively and compared with the simulation results. Critical current and n-value of the strand are calculated basing on the self-consistent model solved by the finite element method (FEM). Effects of self-field on the critical current and n-value distributions in wires of the strand are analyzed in detail. The simulation results show good agreement with the experimental data and the 10 m quasi-isotropic strand has good critical properties uniformity.
Solid Propellant Test Motor Scaling

DTIC Science & Technology

2001-09-01

50 Figure 40. Comparison of Measured and Calculated Strand and Small Motor Burning Rates for Fundamental Studies of HTPB /AP Smokeless...Propellants...................................... 51 Figure 41. Agreement Between 2x4 Motor and Strand Burning Rate Data for Non-aluminized HTPB /AP...58 Figure 51. Comparison Between Results Obtained with Ultrasonic Method and Standard
Observation de l'interaction entre atome et surface en cellule de vapeur submicrométrique

NASA Astrophysics Data System (ADS)

Dutier, G.; Saltiel, S.; Bloch, D.; Ducloy, M.; Papoyan, A.; Sarkisyan, D.

2002-06-01

Sur une cellule de vapeur d'épaisseur submicrométrique ( 300 nm), les spectres d'absorption linéaire se révèlent très peu sensibles à l'effet Doppler (les effets transitoires favorisent fortement les atomes lents), et font apparaître les effets de l'interaction van der Waals à longue portée entre atome-surface. L'étude, entreprise d'abord sur la raie de résonance D1 de Cs, est poursuivie sur une transition à deux photons vers le niveau Cs 6(D{3/2}) résonnant avec la surface de YAG de la fenêtre. Elle ouvre diverses perspectives, notamment la détection d'états liés par un puits de potentiel induit par la surface.
Polymer chain dynamics under nanoscopic confinements.

PubMed

Kimmich, Rainer; Fatkullin, Nail; Mattea, Carlos; Fischer, Elmar

2005-02-01

It is shown that the confinement of polymer melts in nanopores leads to chain dynamics dramatically different from bulk behavior. This so-called corset effect occurs both above and below the critical molecular mass and induces the dynamic features predicted for reptation. A spinodal demixing technique was employed for the preparation of linear poly(ethylene oxide) (PEO) confined to nanoscopic strands that are in turn embedded in a quasi-solid and impenetrable methacrylate matrix. Both the molecular weight of the PEO and the mean diameter of the strands were varied to a certain degree. The chain dynamics of the PEO in the molten state was examined with the aid of field-gradient NMR diffusometry (time scale, 10(-2)-10(0) s) and field-cycling NMR relaxometry (time scale, 10(-9)-10(-4) s). The dominating mechanism for translational displacements probed in the nanoscopic strands by either technique is shown to be reptation. On the time scale of spin-lattice relaxation time measurements, the frequency dependence signature of reptation (i.e., T1 approximately nu(3/4)) showed up in all samples. A "tube" diameter of only 0.6 nm was concluded to be effective on this time scale even when the strand diameter was larger than the radius of gyration of the PEO random coils. This corset effect is traced back to the lack of the local fluctuation capacity of the free volume in nanoscopic confinements. The confinement dimension is estimated at which the crossover from confined to bulk chain dynamics is expected.
Large scale DNA microsequencing device

DOEpatents

Foote, Robert S.

1997-01-01

A microminiature sequencing apparatus and method provide means for simultaneously obtaining sequences of plural polynucleotide strands. The apparatus comprises a microchip into which plural channels have been etched using standard lithographic procedures and chemical wet etching. The channels include a reaction well and a separating section. Enclosing the channels is accomplished by bonding a transparent cover plate over the apparatus. A first oligonucleotide strand is chemically affixed to the apparatus through an alkyl chain. Subsequent nucleotides are selected by complementary base pair bonding. A target nucleotide strand is used to produce a family of labelled sequencing strands in each channel which are separated in the separating section. During or following separation the sequences are determined using appropriate detection means.
Large scale DNA microsequencing device

DOEpatents

Foote, Robert S.

1999-01-01

A microminiature sequencing apparatus and method provide means for simultaneously obtaining sequences of plural polynucleotide strands. The apparatus comprises a microchip into which plural channels have been etched using standard lithographic procedures and chemical wet etching. The channels include a reaction well and a separating section. Enclosing the channels is accomplished by bonding a transparent cover plate over the apparatus. A first oligonucleotide strand is chemically affixed to the apparatus through an alkyl chain. Subsequent nucleotides are selected by complementary base pair bonding. A target nucleotide strand is used to produce a family of labelled sequencing strands in each channel which are separated in the separating section. During or following separation the sequences are determined using appropriate detection means.
Large scale DNA microsequencing device

DOEpatents

Foote, R.S.

1999-08-31

A microminiature sequencing apparatus and method provide means for simultaneously obtaining sequences of plural polynucleotide strands. The apparatus comprises a microchip into which plural channels have been etched using standard lithographic procedures and chemical wet etching. The channels include a reaction well and a separating section. Enclosing the channels is accomplished by bonding a transparent cover plate over the apparatus. A first oligonucleotide strand is chemically affixed to the apparatus through an alkyl chain. Subsequent nucleotides are selected by complementary base pair bonding. A target nucleotide strand is used to produce a family of labelled sequencing strands in each channel which are separated in the separating section. During or following separation the sequences are determined using appropriate detection means. 11 figs.
Mesure Objective De L'attenuation et De L'effet D'occlusion Des Protecteurs Auditifs a Partir Des Potentiels Evoques Stationnaires et Multiples =

NASA Astrophysics Data System (ADS)

Valentin, Olivier

Selon l'Organisation mondiale de la sante, le nombre de travailleurs exposes quotidiennement a des niveaux de bruit prejudiciables a leur audition est passe de 120 millions en 1995 a 250 millions en 2004. Meme si la reduction du bruit a la source devrait etre toujours privilegiee, la solution largement utilisee pour lutter contre le bruit au travail reste la protection auditive individuelle. Malheureusement, le port des protecteurs auditifs n'est pas toujours respecte par les travailleurs car il est difficile de fournir un protecteur auditif dont le niveau d'attenuation effective est approprie a l'environnement de travail d'un individu. D'autre part, l'occlusion du canal auditif induit une modification de la perception de la parole, ce qui cree un inconfort incitant les travailleurs a retirer leurs protecteurs. Ces deux problemes existent parce que les methodes actuelles de mesure de l'effet d'occlusion et de l'attenuation sont limitees. Les mesures objectives basees sur des mesures microphoniques intra-auriculaires ne tiennent pas compte de la transmission directe du son a la cochlee par conduction osseuse. Les mesures subjectives au seuil de l'audition sont biaisees a cause de l'effet de masquage aux basses frequences induit par le bruit physiologique. L'objectif principal de ce travail de these de doctorat est d'ameliorer la mesure de l'attenuation et de l'effet d'occlusion des protecteurs auditifs intra-auriculaires. L'approche generale consiste a : (i) verifier s'il est possible de mesurer l'attenuation des protecteurs auditifs grâce au recueil des potentiels evoques stationnaires et multiples (PEASM) avec et sans protecteur auditif (protocole 1), (ii) adapter cette methodologie pour mesurer l'effet d'occlusion induit par le port de protecteur auditifs intra-auriculaires (protocole 2), et (iii) valider chaque protocole par l'intermediaire de mesures realisees sur sujets humains. Les resultats du protocole 1 demontrent que les PEASM peuvent etre utilises pour mesurer objectivement l'attenuation des protecteurs auditifs : les resultats obtenus a 500 Hz et 1 kHz demontrent que l'attenuation mesuree a partir des PEASM est relativement equivalente a l'attenuation calculee par la methode REAT, ce qui est en accord avec ce qui etait attendu puisque l'effet de masquage induit par le bruit physiologique aux basses frequences est relativement negligeable a ces frequences. Les resultats du protocole 2 demontrent que les PEASM peuvent etre egalement utilises pour mesurer objectivement l'effet d'occlusion induit par le port de protecteurs auditifs : l'effet d'occlusion mesure a partir des PEASM a 500 Hz est plus eleve que celui calcule par l'intermediaire de la methode subjective au seuil de l'audition, ce qui est en accord avec ce qui etait attendu puisqu'en dessous d'1 kHz, l'effet de masquage induit par le bruit physiologique aux basses frequences est source de biais pour les resultats obtenus par la methode subjective car il y a surestimation des seuils de l'audition en basse frequence lors du port de protecteurs auditifs. Toutefois, les resultats obtenus a 250 Hz sont en contradiction avec les resultats attendus. D'un point de vue scientifique, ce travail de these a permis de realiser deux nouvelles methodes innovantes pour mesurer objectivement l'attenuation et l'effet d'occlusion des protecteurs auditifs intra-auriculaires par electroencephalographie. D'un point de vue sante et securite au travail, les avancees presentees dans cette these pourraient aider a concevoir des protecteurs auditifs plus performants. En effet, si ces deux nouvelles methodes objectives etaient normalisees pour caracteriser les protecteurs auditifs intra-auriculaires, elles pourraient permettre : (i) de mieux apprehender l'efficacite reelle de la protection auditive et (ii) de fournir une mesure de l'inconfort induit par l'occlusion du canal auditif lors du port de protecteurs. Fournir un protecteur auditif dont l'efficacite reelle est adaptee a l'environnement de travail et dont le confort est optimise permettrait, sur le long terme, d'ameliorer les conditions des travailleurs en minimisant le risque lie a la degradation de leur appareil auditif. Les perspectives de travail proposees a la fin de cette these consistent principalement a : (i) exploiter ces deux methodes avec une gamme frequentielle plus etendue, (ii) explorer la variabilite intra-individuelle de chacune des methodes, (iii) comparer les resultats des deux methodes avec ceux obtenus par l'intermediaire de la methode "Microphone in Real Ear" (MIRE) et (iv) verifier la compatibilite de chacune des methodes avec tous les types de protecteurs auditifs. De plus, pour la methode de mesure de l'effet d'occlusion utilisant les PEASM, une etude complementaire est necessaire pour lever la contradiction observee a 250 Hz.
Large-scale analysis of antisense transcription in wheat using the Affymetrix GeneChip Wheat Genome Array

USDA-ARS?s Scientific Manuscript database

Natural antisense transcripts (NATs) are transcripts of the opposite DNA strand to the sense-strand either at the same locus (cis-encoded) or a different locus (trans-encoded). They can affect gene expression at multiple stages including transcription, RNA processing and transport, and translation....
Programmable self-assembly of three-dimensional nanostructures from 10,000 unique components

NASA Astrophysics Data System (ADS)

Ong, Luvena L.; Hanikel, Nikita; Yaghi, Omar K.; Grun, Casey; Strauss, Maximilian T.; Bron, Patrick; Lai-Kee-Him, Josephine; Schueder, Florian; Wang, Bei; Wang, Pengfei; Kishi, Jocelyn Y.; Myhrvold, Cameron; Zhu, Allen; Jungmann, Ralf; Bellot, Gaetan; Ke, Yonggang; Yin, Peng

2017-12-01

Nucleic acids (DNA and RNA) are widely used to construct nanometre-scale structures with ever increasing complexity, with possible application in fields such as structural biology, biophysics, synthetic biology and photonics. The nanostructures are formed through one-pot self-assembly, with early kilodalton-scale examples containing typically tens of unique DNA strands. The introduction of DNA origami, which uses many staple strands to fold one long scaffold strand into a desired structure, has provided access to megadalton-scale nanostructures that contain hundreds of unique DNA strands. Even larger DNA origami structures are possible, but manufacturing and manipulating an increasingly long scaffold strand remains a challenge. An alternative and more readily scalable approach involves the assembly of DNA bricks, which each consist of four short binding domains arranged so that the bricks can interlock. This approach does not require a scaffold; instead, the short DNA brick strands self-assemble according to specific inter-brick interactions. First-generation bricks used to create three-dimensional structures are 32 nucleotides long, consisting of four eight-nucleotide binding domains. Protocols have been designed to direct the assembly of hundreds of distinct bricks into well formed structures, but attempts to create larger structures have encountered practical challenges and had limited success. Here we show that DNA bricks with longer, 13-nucleotide binding domains make it possible to self-assemble 0.1-1-gigadalton, three-dimensional nanostructures from tens of thousands of unique components, including a 0.5-gigadalton cuboid containing about 30,000 unique bricks and a 1-gigadalton rotationally symmetric tetramer. We also assembled a cuboid that contains around 10,000 bricks and about 20,000 uniquely addressable, 13-base-pair ‘voxels’ that serves as a molecular canvas for three-dimensional sculpting. Complex, user-prescribed, three-dimensional cavities can be produced within this molecular canvas, enabling the creation of shapes such as letters, a helicoid and a teddy bear. We anticipate that with further optimization of structure design, strand synthesis and assembly procedure even larger structures could be accessible, which could be useful for applications such as positioning functional components.
Estimating At-Sea Mortality of Marine Turtles from Stranding Frequencies and Drifter Experiments

PubMed Central

Koch, Volker; Peckham, Hoyt; Mancini, Agnese; Eguchi, Tomoharu

2013-01-01

Strandings of marine megafauna can provide valuable information on cause of death at sea. However, as stranding probabilities are usually very low and highly variable in space and time, interpreting the results can be challenging. We evaluated the magnitude and distribution of at-sea mortality of marine turtles along the Pacific coast of Baja California Sur, México during 2010–11, using a combination of counting stranded animals and drifter experiments. A total of 594 carcasses were found during the study period, with loggerhead (62%) and green turtles (31%) being the most common species. 87% of the strandings occurred in the southern Gulf of Ulloa, a known hotspot of loggerhead distribution in the Eastern Pacific. While only 1.8% of the deaths could be definitively attributed to bycatch (net marks, hooks), seasonal variation in stranding frequencies closely corresponded to the main fishing seasons. Estimated stranding probabilities from drifter experiments varied among sites and trials (0.05–0.8), implying that only a fraction of dead sea turtles can be observed at beaches. Total mortality estimates for 15-day periods around the floater trials were highest for PSL, a beach in the southern Gulf of Ulloa, ranging between 11 sea turtles in October 2011 to 107 in August 2010. Loggerhead turtles were the most numerous, followed by green and olive ridley turtles. Our study showed that drifter trials combined with beach monitoring can provide estimates for death at sea to measure the impact of small-scale fisheries that are notoriously difficult to monitor for by-catch. We also provided recommendations to improve the precision of the mortality estimates for future studies and highlight the importance of estimating impacts of small–scale fisheries on marine megafauna. PMID:23483880
Shifting Plasma

NASA Image and Video Library

2017-05-09

Strands of plasma at the sun edge shifted and twisted back and forth over a 22-hour period, May 2-3, 2017. In this close-up from NASA Solar Dynamics Observatory, the strands are being manipulated by strong magnetic forces associated with active region. This kind of activity is not at all uncommon, but best viewed in profile. The images were taken in a wavelength of extreme ultraviolet light. To give a sense of scale, the strands hover above the sun more than several times the size of Earth. Movies are available at https://photojournal.jpl.nasa.gov/catalog/PIA21632
Marine mammal strandings and environmental changes: a 15-year study in the St. Lawrence ecosystem.

PubMed

Truchon, Marie-Hélène; Measures, Lena; L'Hérault, Vincent; Brêthes, Jean-Claude; Galbraith, Peter S; Harvey, Michel; Lessard, Sylvie; Starr, Michel; Lecomte, Nicolas

2013-01-01

Understanding the effects of climatic variability on marine mammals is challenging due to the complexity of ecological interactions. We used general linear models to analyze a 15-year database documenting marine mammal strandings (1994-2008; n = 1,193) and nine environmental parameters known to affect marine mammal survival, from regional (sea ice) to continental scales (North Atlantic Oscillation, NAO). Stranding events were more frequent during summer and fall than other seasons, and have increased since 1994. Poor ice conditions observed during the same period may have affected marine mammals either directly, by modulating the availability of habitat for feeding and breeding activities, or indirectly, through changes in water conditions and marine productivity (krill abundance). For most species (75%, n = 6 species), a low volume of ice was correlated with increasing frequency of stranding events (e.g. R(2)adj = 0.59, hooded seal, Cystophora cristata). This likely led to an increase in seal mortality during the breeding period, but also to increase habitat availability for seasonal migratory cetaceans using ice-free areas during winter. We also detected a high frequency of stranding events for mysticete species (minke whale, Balaenoptera acutorostrata) and resident species (beluga, Delphinapterus leucas), correlated with low krill abundance since 1994. Positive NAO indices were positively correlated with high frequencies of stranding events for resident and seasonal migratory cetaceans, as well as rare species (R(2)adj = 0.53, 0.81 and 0.34, respectively). This contrasts with seal mass stranding numbers, which were negatively correlated with a positive NAO index. In addition, an unusual multiple species mortality event (n = 114, 62% of total annual mortality) in 2008 was caused by a harmful algal bloom. Our findings provide an empirical baseline in understanding marine mammal survival when faced with climatic variability. This is a promising step in integrating stranding records to monitor the consequences of environmental changes in marine ecosystems over long time scales.

Marine Mammal Strandings and Environmental Changes: A 15-Year Study in the St. Lawrence Ecosystem

PubMed Central

Truchon, Marie-Hélène; Measures, Lena; L’Hérault, Vincent; Brêthes, Jean-Claude; Galbraith, Peter S.; Harvey, Michel; Lessard, Sylvie; Starr, Michel; Lecomte, Nicolas

2013-01-01

Understanding the effects of climatic variability on marine mammals is challenging due to the complexity of ecological interactions. We used general linear models to analyze a 15-year database documenting marine mammal strandings (1994–2008; n = 1,193) and nine environmental parameters known to affect marine mammal survival, from regional (sea ice) to continental scales (North Atlantic Oscillation, NAO). Stranding events were more frequent during summer and fall than other seasons, and have increased since 1994. Poor ice conditions observed during the same period may have affected marine mammals either directly, by modulating the availability of habitat for feeding and breeding activities, or indirectly, through changes in water conditions and marine productivity (krill abundance). For most species (75%, n = 6 species), a low volume of ice was correlated with increasing frequency of stranding events (e.g. R2 adj = 0.59, hooded seal, Cystophora cristata). This likely led to an increase in seal mortality during the breeding period, but also to increase habitat availability for seasonal migratory cetaceans using ice-free areas during winter. We also detected a high frequency of stranding events for mysticete species (minke whale, Balaenoptera acutorostrata) and resident species (beluga, Delphinapterus leucas), correlated with low krill abundance since 1994. Positive NAO indices were positively correlated with high frequencies of stranding events for resident and seasonal migratory cetaceans, as well as rare species (R2 adj = 0.53, 0.81 and 0.34, respectively). This contrasts with seal mass stranding numbers, which were negatively correlated with a positive NAO index. In addition, an unusual multiple species mortality event (n = 114, 62% of total annual mortality) in 2008 was caused by a harmful algal bloom. Our findings provide an empirical baseline in understanding marine mammal survival when faced with climatic variability. This is a promising step in integrating stranding records to monitor the consequences of environmental changes in marine ecosystems over long time scales. PMID:23544059
Gravitational lensing in observational cosmology

NASA Astrophysics Data System (ADS)

Nottale, L.

This paper reviews some previous theoretical and observational results concerning the various effects of gravitational lensing, and also presents still unpublished results in this field. The theoretical section deals with the Optical Scalar Equation (OSE) approach. We recall the form of these equations, which relate the deformations of the cross sectional area of a light beam to the material and energetic distribution it encounters, via the two basic contributions to lensing, the matter or Ricci term and the shear term. The introduction of a new distance, the optical distance, allows to write the OSE in a simplified way from which new solutions are easily derived. We demonstrate here that a general form may be obtained for the amplification formula in the exact relativistic treatment, provided the Universe is assumed to be Friedmannian in the mean. New results are also presented concerning the probability distribution of amplifications, the relation from matter term to shear terms (the first ones give the mean of the second ones) and the problem of energy conservation. We recall how our method let to an analytical formula yielding the amplification by any number of lenses placed anywhere along the line of sight and present new general solutions for lensing by large scale density inhomogeneities. The gravitational redshift effects are also considered, either due to the crossing by photons of inhomogeneities, or intrinsic to them ; generalized solutions to the last problem are given. Some observational evidence concerning various lensing effects, either statistical or applying to individual sources, are considered. We first recall how the dependence of the amplification formula on the various physical parameters points towards the optimisation of lensing by very rich clusters of galaxies lying at redshifts around 0.7, which may give rise to very large amplifications for reasonable values of the density parameter. Recent results concerning a statistical effect of amplification of Brightest Cluster Galaxies by foreground clusters are analysed, including the discussion of a selection effect precisely due to gravitational luminosity amplification. It results in an artificial increase of the deceleration parameter of the Universe measured from the Hubble diagram of these objects. We recall our proposal that the sample of distant 3C radiogalaxies of redshift > 1 is strongly perturbed by lensing effects, mostly by foreground clusters of galaxies (i.e. only the luminosity is changed without image multiplication), but also for some objects by galaxies, producing gravitational mirages. The case of 3C324, for which definite evidence for multiple imaging has been recently obtained, is described, including detailed modelling of the lensing configuration. We present a highly significant statistical effect of lensing on absorption line QSOs due to matter lying at the absorption redshifts. Microlensing is also considered, and we recall our recent proposal that the variability of some among the OVV QSOs turning to BL Lac at maximum brightness, like the eruptive object 0846 +51W1, is a consequence of microlensing by stars or compact objects constituting foreground galaxy halos. Finally, discrepant redshift associations are considered. We recall how the case of anomalous quintets of galaxies have been explained by the gravitational lensing effects of quartets halos on background galaxies. Then we present evidence that the Arp QSO-galaxy associations may be the result of the combined lensing effects of several superposed galaxies, groups and clusters. Cet article présente une revue de certains résultats théoriques et observationnels concernant les divers effets de lentille gravitationnelle, complétée par des résultats nouveaux non encore publiés. Dans la partie théorique, nous considérons essentiellement l'approche relativiste employant les équations scalaires optiques. La forme de ces équations est rappelée : elles relient les diverses déformations subies par la section d'un faisceau lumineux au cours de sa propagation, à la distribution matérielle et énergétique qu'il rencontre sur son trajet entre la source et l'observateur. Les deux contributions aux effets d'optique apparaissant dans ces équations (et leurs solutions) sont les termes de matière et les termes de cisaillement. Nous montrons comment une nouvelle distance peut être introduite, la distance optique, en fonction de laquelle les équations se simplifient et de nouvelles solutions analytiques peuvent être établies. En particulier, nous démontrons que la formule d'amplification gravitationnelle peut s'écrire sous une forme très générale sous la simple hypothèse que l'Univers est en moyenne de type Friedmann-Robertson-Walker. De nouveaux résultats sont aussi présentés concernant la distribution de probabilité des amplifications, les rapports entre termes de matière et termes de cisaillement (les premiers donnant la moyenne des seconds), et le problème de la conservation de l'énergie. Nous rappelons comment une formule analytique peut être obtenue pour des amplifications multiples et présentons des solutions nouvelles au problème de l'amplification par des hétérogénéités à très grande échelle. Enfin, les effets de décalages spectraux gravitationnels sont aussi considérés, qu'ils soient dus à des effets de traversée d'excès de densité, ou intrinsèques à ceux-ci ; dans ce dernier cas, une généralisation de solutions déjà connues est proposée. On considère ensuite le problème de la mise en évidence observationnelle des divers effets d'optique gravitationnelle, qu'ils soient de nature statistique ou qu'ils concernent des objets individuels. A la suite d'une analyse décrivant la dépendance de la formule d'amplification en fonction des différents paramètres y intervenant, nous insistons tout particulièrement sur le rôle cosmologique que jouent probablement les amas de galaxies très riches de décalages spectraux autour de 0,7 qui peuvent donner lieu à des amplifications quasi-infinies. La mise en évidence récente d'un effet statistique d'amplification par des amas d'avant-plan sur les galaxies les plus brillantes des amas est rappelée, ainsi que celle d'un important effet de sélection observationnel, précisément dû aux amplifications, qui augmente artificiellement la valeur de q0 mesurée à partir du diagramme de Hubble. L'extrapolation de cet effet à des objets plus lointains nous a conduit à proposer que les radiogalaxies lointaines du catalogue 3C de z < 1 étaient fortement affectées par les effets de lentille gravitationnelle, essentiellement par les amas (qui les amplifient la plupart du temps sans multiplication d'image), mais aussi dans certains cas par des galaxies qui peuvent alors provoquer des effets de mirage. Le cas de 3C324, pour lequel des preuves observationelles de multiplication d'image ont été récemment obtenues, est analysé en particulier ; un modèle détaillé en est présenté. Un autre effet statistique récemment démontré concerne les quasars à raies d'absorption, dont la luminosité est fortement corrélée à l'amplification prédite par de la matière située aux décalages spectraux d'absorption. On considère également les effets de microlentille : nous rappelons notre proposition récente que la variabilité de certains OVVs tels que le BL Lac éruptif 0846 + 51W1 est une conséquence du passage d'étoiles ou d'objets compacts du halo de galaxies intervenantes devant les régions centrales d'un quasar. Le lien entre effets d'optique gravitationnelle et associations de décalages spectraux discordants est évoqué. Le cas des quintets de galaxies discordant a été récemment expliqué par les effets (amplification, agrandissement, changement de densité superficielle d'objets lointains) des halos de groupes compacts de galaxies. Nous démontrons pour finir que les associations QSOsgalaxies de Arp peuvent s'expliquer par les effets de lentille gravitationnelle combinés de plusieurs galaxies, groupes et amas vus en superposition.
Metallographic autopsies of full-scale ITER prototype cable-in-conduit conductors after full testing in SULTAN: 1. The mechanical role of copper strands in a CICC

DOE PAGES

Sanabria, Carlos; Lee, Peter J.; Starch, William; ...

2015-06-22

Cables made with Nb 3Sn-based superconductor strands will provide the 13 T maximum peak magnetic field of the ITER Central Solenoid (CS) coils and they must survive up to 60,000 electromagnetic cycles. Accordingly, prototype designs of CS cable-in-conduit-conductors (CICC) were electromagnetically tested over multiple magnetic field cycles and warm-up-cool-down scenarios in the SULTAN facility at CRPP. We report here a post mortem metallographic analysis of two CS CICC prototypes which exhibited some rate of irreversible performance degradation during cycling. The standard ITER CS CICC cable design uses a combination of superconducting and Cu strands, and because the Lorentz force onmore » the strand is proportional to the transport current in the strand, removing the copper strands (while increasing the Cu:SC ratio of the superconducting strands) was proposed as one way of reducing the strand load. In this study we compare the two alternative CICCs, with and without Cu strands, keeping in mind that the degradation after SULTAN test was lower for the CICC without Cu strands. The post mortem metallographic evaluation revealed that the overall strand transverse movement was 20% lower in the CICC without Cu strands and that the tensile filament fractures found were less, both indications of an overall reduction in high tensile strain regions. Furthermore, it was interesting to see that the Cu strands in the mixed cable design (with higher degradation) helped reduce the contact stresses on the high pressure side of the CICC, but in either case, the strain reduction mechanisms were not enough to suppress cyclic degradation. Advantages and disadvantages of each conductor design are discussed here aimed to understand the sources of the degradation.« less
Compiler-aided systematic construction of large-scale DNA strand displacement circuits using unpurified components

NASA Astrophysics Data System (ADS)

Thubagere, Anupama J.; Thachuk, Chris; Berleant, Joseph; Johnson, Robert F.; Ardelean, Diana A.; Cherry, Kevin M.; Qian, Lulu

2017-02-01

Biochemical circuits made of rationally designed DNA molecules are proofs of concept for embedding control within complex molecular environments. They hold promise for transforming the current technologies in chemistry, biology, medicine and material science by introducing programmable and responsive behaviour to diverse molecular systems. As the transformative power of a technology depends on its accessibility, two main challenges are an automated design process and simple experimental procedures. Here we demonstrate the use of circuit design software, combined with the use of unpurified strands and simplified experimental procedures, for creating a complex DNA strand displacement circuit that consists of 78 distinct species. We develop a systematic procedure for overcoming the challenges involved in using unpurified DNA strands. We also develop a model that takes synthesis errors into consideration and semi-quantitatively reproduces the experimental data. Our methods now enable even novice researchers to successfully design and construct complex DNA strand displacement circuits.
Boundary Layer Simulation and Control in Wind Tunnels

DTIC Science & Technology

1988-04-01

de l’art dans le domaine de la simulation de la couche limite, ou le nombre de Reynolds n’est pas ou ne peut pas etre simule, examine les effets ...pour la definition de certains essais en soufflerie oil les effets visqueux sont d’une importance particuliere. CONTENTS Page PREFACE iii 1...transition associated with cylindrical bodies at high incidence in subsonic flow. Other relevant references are given therein. Figures 11 a-b, from Ref
Polymer dynamics under nanoscopic constraints: the "corset effect" as revealed by NMR relaxometry and diffusometry.

PubMed

Fatkullin, Nail; Fischer, Elmar; Mattea, Carlos; Beginn, Uwe; Kimmich, Rainer

2004-06-21

A spinodal demixing technique was employed for the preparation of linear poly(ethylene oxide) (PEO) confined in nanoscopic strands, which in turn are embedded in a quasi-solid methacrylate matrix impenetrable to PEO. Both the molecular weight of the PEO and the mean diameter of the strands are variable to a certain degree. Chain dynamics of the PEO in the molten state were examined with the aid of field-gradient NMR diffusometry and field-cycling NMR relaxometry. The dominating mechanism for translational displacements in the nanoscopic strands is shown to be reptation. A formalism for the evaluation of NMR diffusometry is presented, which permits the estimation of the mean PEO strand diameter. Samples of different composition revealed diameters in the range 9-58 nm, in reasonable agreement with electron micrographs. The time scale of the diffusion measurements was 10-300 ms. On the much shorter time scale of field-cycling NMR relaxometry, 10(-9)-10(-4)s, a frequency dispersion of the spin-lattice relaxation time characteristic for reptation clearly showed up in all samples. An effective tube diameter of only 0.6 nm was found even when the strand diameter was larger than the radius of gyration of the PEO chain random coils. The finding that the tube diameter effective on the short time scale of field-cycling NMR relaxometry is much smaller than the diameter of the confining structure is termed the "corset effect", and is traced back to the lack of local free-volume fluctuation capacity under nanoscale confinements. The order of magnitude of the 'pore' diameter, at which the cross-over from confined to bulk chain dynamics is expected, is estimated.
Large scale DNA microsequencing device

DOEpatents

Foote, R.S.

1997-08-26

A microminiature sequencing apparatus and method provide a means for simultaneously obtaining sequences of plural polynucleotide strands. The apparatus cosists of a microchip into which plural channels have been etched using standard lithographic procedures and chemical wet etching. The channels include a reaction well and a separating section. Enclosing the channels is accomplished by bonding a transparent cover plate over the apparatus. A first oligonucleotide strand is chemically affixed to the apparatus through an alkyl chain. Subsequent nucleotides are selected by complementary base pair bonding. A target nucleotide strand is used to produce a family of labelled sequencing strands in each channel which are separated in the separating section. During or following separation the sequences are determined using appropriate detection means. 17 figs.
Effets Seebeck et Nernst dans les cuprates: Etude de la reconstruction de la surface de Fermi sous champ magnetique intense

NASA Astrophysics Data System (ADS)

Laliberte, Francis

2010-06-01

Ce memoire presente des mesures de transport thermoelectrique, les effets Seebeck et Nernst, dans une serie d'echantillons de supraconducteurs a haute temperature critique. Des resultats obtenus recemment au Laboratoire National des Champs Magnetiques Intenses a Grenoble sur La1.7Eu0.2Sr0.1 CuO4, La1.675Eu0.2Sr0.125CuO 4, La1.64Eu0.2Sr0.16CuO4, La1.74Eu0.1Sr0.16CuO4 et La 1.4Nd0.4Sr0.2CuO4 sont analyses. Une attention particuliere est accordee aux equations de la theorie semi-classique du transport et leur validite est verifiee. La procedure experimentale et les materiaux utilises pour concevoir les montages de mesures sont expliques en detail. Enfin, un chapitre est dedie a l'explication et l'interpretation des resultats de transport thermoelectrique sur YBa2Cu3O6+delta publies au cours de l'hiver 2010 dans les revues Nature et Physical Review Letters. Les donnees d'effet Seebeck dans les echantillons de La 1.8-x,Eu0.2SrxCuO 4, ou un changement de signe est observe, permettent de conclure a la presence d'une poche d'electrons dans la surface de Fermi qui domine le transport a basse temperature dans la region sous-dopee du diagramme de phase. Cette conclusion est similaire a celle obtenue par des mesures d'effet Hall dans YBa 2Cu3O6+delta et elle cadre bien dans un scenario de reconstruction de la surface de Fermi. Les donnees d'effet Nernst recueillies indiquent que la contribution des fluctuations supraconductrices est limitee a un modeste intervalle de temperature au-dessus de la temperature critique.
Mechanical behaviors of multi-filament twist superconducting strand under tensile and cyclic loading

NASA Astrophysics Data System (ADS)

Wang, Xu; Li, Yingxu; Gao, Yuanwen

2016-01-01

The superconducting strand, serving as the basic unit cell of the cable-in-conduit-conductors (CICCs), is a typical multi-filament twist composite which is always subjected to a cyclic loading under the operating condition. Meanwhile, the superconducting material Nb3Sn in the strand is sensitive to strain frequently relating to the performance degradation of the superconductivity. Therefore, a comprehensive study on the mechanical behavior of the strand helps understanding the superconducting performance of the strained Nb3Sn strands. To address this issue, taking the LMI (internal tin) strand as an example, a three-dimensional structural finite element model, named as the Multi-filament twist model, of the strand with the real configuration of the LMI strand is built to study the influences of the plasticity of the component materials, the twist of the filament bundle, the initial thermal residual stress and the breakage and its evolution of the filaments on the mechanical behaviors of the strand. The effective properties of superconducting filament bundle with random filament breakage and its evolution versus strain are obtained based on the damage theory of fiber-reinforced composite materials proposed by Curtin and Zhou. From the calculation results of this model, we find that the occurrence of the hysteresis loop in the cyclic loading curve is determined by the reverse yielding of the elastic-plastic materials in the strand. Both the initial thermal residual stress in the strand and the pitch length of the filaments have significant impacts on the axial and hysteretic behaviors of the strand. The damage of the filaments also affects the axial mechanical behavior of the strand remarkably at large axial strain. The critical current of the strand is calculated by the scaling law with the results of the Multi-filament twist model. The predicted results of the Multi-filament twist model show an acceptable agreement with the experiment.
GENESUS: a two-step sequence design program for DNA nanostructure self-assembly.

PubMed

Tsutsumi, Takanobu; Asakawa, Takeshi; Kanegami, Akemi; Okada, Takao; Tahira, Tomoko; Hayashi, Kenshi

2014-01-01

DNA has been recognized as an ideal material for bottom-up construction of nanometer scale structures by self-assembly. The generation of sequences optimized for unique self-assembly (GENESUS) program reported here is a straightforward method for generating sets of strand sequences optimized for self-assembly of arbitrarily designed DNA nanostructures by a generate-candidates-and-choose-the-best strategy. A scalable procedure to prepare single-stranded DNA having arbitrary sequences is also presented. Strands for the assembly of various structures were designed and successfully constructed, validating both the program and the procedure.
Full-Scale Prestress Loss Monitoring of Damaged RC Structures Using Distributed Optical Fiber Sensing Technology

PubMed Central

Lan, Chunguang; Zhou, Zhi; Ou, Jinping

2012-01-01

For the safety of prestressed structures, prestress loss is a critical issue that will increase with structural damage, so it is necessary to investigate prestress loss of prestressed structures under different damage scenarios. Unfortunately, to date, no qualified techniques are available due to difficulty for sensors to survive in harsh construction environments of long service life and large span. In this paper, a novel smart steel strand based on the Brillouin optical time domain analysis (BOTDA) sensing technique was designed and manufactured, and then series of tests were used to characterize properties of the smart steel strands. Based on prestress loss principle analysis of damaged structures, laboratory tests of two similar beams with different damages were used to verify the concept of full-scale prestress loss monitoring of damaged reinforced concrete (RC) beams by using the smart steel strands. The prestress losses obtained from the Brillouin sensors are compared with that from conventional sensors, which provided the evolution law of prestress losses of damaged RC beams. The monitoring results from the proposed smart strand can reveal both spatial distribution and time history of prestress losses of damaged RC beams. PMID:22778590
Full-scale prestress loss monitoring of damaged RC structures using distributed optical fiber sensing technology.

PubMed

Lan, Chunguang; Zhou, Zhi; Ou, Jinping

2012-01-01

For the safety of prestressed structures, prestress loss is a critical issue that will increase with structural damage, so it is necessary to investigate prestress loss of prestressed structures under different damage scenarios. Unfortunately, to date, no qualified techniques are available due to difficulty for sensors to survive in harsh construction environments of long service life and large span. In this paper, a novel smart steel strand based on the Brillouin optical time domain analysis (BOTDA) sensing technique was designed and manufactured, and then series of tests were used to characterize properties of the smart steel strands. Based on prestress loss principle analysis of damaged structures, laboratory tests of two similar beams with different damages were used to verify the concept of full-scale prestress loss monitoring of damaged reinforced concrete (RC) beams by using the smart steel strands. The prestress losses obtained from the Brillouin sensors are compared with that from conventional sensors, which provided the evolution law of prestress losses of damaged RC beams. The monitoring results from the proposed smart strand can reveal both spatial distribution and time history of prestress losses of damaged RC beams.
THE INSTABILITY AND NON-EXISTENCE OF MULTI-STRANDED LOOPS WHEN DRIVEN BY TRANSVERSE WAVES

DOE Office of Scientific and Technical Information (OSTI.GOV)

Magyar, N.; Van Doorsselaere, T., E-mail: norbert.magyar@wis.kuleuven.be

2016-06-01

In recent years, omni-present transverse waves have been observed in all layers of the solar atmosphere. Coronal loops are often modeled as a collection of individual strands in order to explain their thermal behavior and appearance. We perform three-dimensional (3D) ideal magnetohydrodynamics simulations to study the effect of a continuous small amplitude transverse footpoint driving on the internal structure of a coronal loop composed of strands. The output is also converted into synthetic images, corresponding to the AIA 171 and 193 Å passbands, using FoMo. We show that the multi-stranded loop ceases to exist in the traditional sense of themore » word, because the plasma is efficiently mixed perpendicularly to the magnetic field, with the Kelvin–Helmholtz instability acting as the main mechanism. The final product of our simulation is a mixed loop with density structures on a large range of scales, resembling a power-law. Thus, multi-stranded loops are unstable to driving by transverse waves, and this raises strong doubts on the usability and applicability of coronal loop models consisting of independent strands.« less
Escherichia coli peptidoglycan structure and mechanics as predicted by atomic-scale simulations.

PubMed

Gumbart, James C; Beeby, Morgan; Jensen, Grant J; Roux, Benoît

2014-02-01

Bacteria face the challenging requirement to maintain their shape and avoid rupture due to the high internal turgor pressure, but simultaneously permit the import and export of nutrients, chemical signals, and virulence factors. The bacterial cell wall, a mesh-like structure composed of cross-linked strands of peptidoglycan, fulfills both needs by being semi-rigid, yet sufficiently porous to allow diffusion through it. How the mechanical properties of the cell wall are determined by the molecular features and the spatial arrangement of the relatively thin strands in the larger cellular-scale structure is not known. To examine this issue, we have developed and simulated atomic-scale models of Escherichia coli cell walls in a disordered circumferential arrangement. The cell-wall models are found to possess an anisotropic elasticity, as known experimentally, arising from the orthogonal orientation of the glycan strands and of the peptide cross-links. Other features such as thickness, pore size, and disorder are also found to generally agree with experiments, further supporting the disordered circumferential model of peptidoglycan. The validated constructs illustrate how mesoscopic structure and behavior emerge naturally from the underlying atomic-scale properties and, furthermore, demonstrate the ability of all-atom simulations to reproduce a range of macroscopic observables for extended polymer meshes.
Critical current scaling and the pivot-point in Nb3Sn strands

NASA Astrophysics Data System (ADS)

Tsui, Y.; Hampshire, D. P.

2012-05-01

Detailed measurements are provided of the engineering critical current density (Jc) and the index of transition (n-value) of two different types of advanced ITER Nb3Sn superconducting strand for fusion applications. The samples consist of one internal-tin strand (OST) and two bronze-route strands (BEAS I and BEAS II—reacted using different heat treatments). Tests on different sections of these wires show that prior to applying strain, Jc is homogeneous to better than 2% along the length of each strand. Jc data have been characterized as a function of magnetic field (B ≤ 14.5 T), temperature (4.2 K ≤ T ≤ 12 K) and applied axial strain ( - 1% ≤ ɛA ≤ 0.8%). Strain-cycling tests demonstrate that the variable strain Jc data are reversible to better than 2% when the applied axial strain is in the range of - 1% ≤ ɛA ≤ 0.5%. The wires are damaged when the intrinsic strain (ɛI) is ɛI ≥ 0.55% and ɛI ≥ 0.23% for the OST and BEAS strands, respectively. The strain dependences of the normalized Jc for each type of strand are similar to those of prototype strands of similar design measured in 2005 and 2008 to about 2% which makes them candidate strands for a round-robin interlaboratory comparison. The Jc data are described by Durham, ITER and Josephson-junction parameterizations to an accuracy of about 4%. For all of these scaling laws, the percentage difference between the data and the parameterization is larger when Jc is small, caused by high B, T or |ɛI|. The n-values can be described by a modified power law of the form n=1+r{I}_{{c}}^{s}, where r and s are approximately constant and Ic is the critical current. It has long been known that pivot-points (or cross-overs) in Jc occur at high magnetic field and temperature. Changing the magnetic field or temperature from one side of the pivot-point to the other changes the highest Jc sample to the lowest Jc sample and vice versa. The pivot-point follows the B-T phase boundary associated with the upper critical field and is usually attributed to the different tin content profiles and pinning properties of internal-tin and bronze-route strands. We report that the strain dependence of the pivot-point in these strands is quite different from that of the upper critical field and suggest that its origin in optimized high tin content strands is the proximity of the tetragonal Nb3Sn phase, which has low superconducting critical parameters.
Metallographic autopsies of full-scale ITER prototype cable-in-conduit conductors after full cyclic testing in SULTAN: II. Significant reduction of strand movement and strand damage in short twist pitch CICCs

DOE PAGES

Sanabria, Charlos; Lee, Peter J.; Starch, William; ...

2015-10-14

Prototype cable in conduit conductors (CICCs) destined for use in the Toroidal Field (TF) and Central Solenoid (CS) coils of the ITER experimental fusion reactor underwent severe cyclic loading in the SULTAN facility. Their autopsies revealed significant and permanent transverse strand migration due to the large Lorentz forces of the SULTAN test. The movement resulted in a 3 7% void fraction increase on the Low Pressure (LP) side of the longer twist pitch CICCs. However, short twist pitch conductors exhibited less than 1% void fraction increase in the LP side, as well as a complete absence of the Nb 3Snmore » filament fractures observed in the longer twist pitch conductors. We report here a detailed strand to cable analysis of short and longer “baseline” twist pitch CICCs. It was found that the use of Internal Tin strands in the longer “baseline” twist pitch CICCs can be beneficial possibly because of their superior stiffness—which better resist strand movement—while the use of Bronze Process strands showed more movement and poorer cyclic test performance. This was not the case for the short twist pitch CICC. Such conductor design seems to work well with both strand types. But it was found that despite the absence of filament fractures, the short twist pitch CICC made from the Internal Tin strands studied here developed severe strand distortion during cabling which resulted in diffusion barrier breaks and Sn contamination of the Cu stabilizer during the heat treatment. Furthermore, the short twist pitch CICC made from Bronze Process strands preserved diffusion barrier integrity.« less
Metallographic autopsies of full-scale ITER prototype cable-in-conduit conductors after full cyclic testing in SULTAN: II. Significant reduction of strand movement and strand damage in short twist pitch CICCs

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sanabria, Charlos; Lee, Peter J.; Starch, William

Prototype cable in conduit conductors (CICCs) destined for use in the Toroidal Field (TF) and Central Solenoid (CS) coils of the ITER experimental fusion reactor underwent severe cyclic loading in the SULTAN facility. Their autopsies revealed significant and permanent transverse strand migration due to the large Lorentz forces of the SULTAN test. The movement resulted in a 3 7% void fraction increase on the Low Pressure (LP) side of the longer twist pitch CICCs. However, short twist pitch conductors exhibited less than 1% void fraction increase in the LP side, as well as a complete absence of the Nb 3Snmore » filament fractures observed in the longer twist pitch conductors. We report here a detailed strand to cable analysis of short and longer “baseline” twist pitch CICCs. It was found that the use of Internal Tin strands in the longer “baseline” twist pitch CICCs can be beneficial possibly because of their superior stiffness—which better resist strand movement—while the use of Bronze Process strands showed more movement and poorer cyclic test performance. This was not the case for the short twist pitch CICC. Such conductor design seems to work well with both strand types. But it was found that despite the absence of filament fractures, the short twist pitch CICC made from the Internal Tin strands studied here developed severe strand distortion during cabling which resulted in diffusion barrier breaks and Sn contamination of the Cu stabilizer during the heat treatment. Furthermore, the short twist pitch CICC made from Bronze Process strands preserved diffusion barrier integrity.« less
Data centers as dispatchable loads to harness stranded power

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kim, Kibaek; Yang, Fan; Zavala, Victor M.

Here, we analyze how traditional data center placement and optimal placement of dispatchable data centers affect power grid efficiency. We use detailed network models, stochastic optimization formulations, and diverse renewable generation scenarios to perform our analysis. Our results reveal that significant spillage and stranded power will persist in power grids as wind power levels are increased. A counter-intuitive finding is that collocating data centers with inflexible loads next to wind farms has limited impacts on renewable portfolio standard (RPS) goals because it provides limited system-level flexibility. Such an approach can, in fact, increase stranded power and fossil-fueled generation. In contrast,more » optimally placing data centers that are dispatchable provides system-wide flexibility, reduces stranded power, and improves efficiency. In short, optimally placed dispatchable computing loads can enable better scaling to high RPS. In our case study, we find that these dispatchable computing loads are powered to 60-80% of their requested capacity, indicating that there are significant economic incentives provided by stranded power.« less
Data centers as dispatchable loads to harness stranded power

DOE PAGES

Kim, Kibaek; Yang, Fan; Zavala, Victor M.; ...

2016-07-20

Here, we analyze how traditional data center placement and optimal placement of dispatchable data centers affect power grid efficiency. We use detailed network models, stochastic optimization formulations, and diverse renewable generation scenarios to perform our analysis. Our results reveal that significant spillage and stranded power will persist in power grids as wind power levels are increased. A counter-intuitive finding is that collocating data centers with inflexible loads next to wind farms has limited impacts on renewable portfolio standard (RPS) goals because it provides limited system-level flexibility. Such an approach can, in fact, increase stranded power and fossil-fueled generation. In contrast,more » optimally placing data centers that are dispatchable provides system-wide flexibility, reduces stranded power, and improves efficiency. In short, optimally placed dispatchable computing loads can enable better scaling to high RPS. In our case study, we find that these dispatchable computing loads are powered to 60-80% of their requested capacity, indicating that there are significant economic incentives provided by stranded power.« less
Getting the balance right: a randomised controlled trial of physiotherapy and Exercise Interventions for ambulatory people with multiple sclerosis.

PubMed

Coote, Susan; Garrett, Maria; Hogan, Neasa; Larkin, Aidan; Saunders, Jean

2009-07-16

People with Multiple Sclerosis have a life long need for physiotherapy and exercise interventions due to the progressive nature of the disease and their greater risk of the complications of inactivity. The Multiple Sclerosis Society of Ireland run physiotherapy, yoga and exercise classes for their members, however there is little evidence to suggest which form of physical activity optimises outcome for people with the many and varied impairments associated with MS. This is a multi-centre, single blind, block randomised, controlled trial. Participants will be recruited via the ten regional offices of MS Ireland. Telephone screening will establish eligibility and stratification according to the mobility section of the Guys Neurological Disability Scale. Once a block of people of the same strand in the same geographical region have given consent, participants will be randomised. Strand A will concern individuals with MS who walk independently or use one stick to walk outside. Participants will be randomised to yoga, physiotherapy led exercise class, fitness instructor led exercise class or to a control group who don't change their exercise habits.Strand B will concern individuals with MS who walk with bilateral support or a rollator, they may use a wheelchair for longer distance outdoors. Participants will be randomised to 1:1 Physiotherapist led intervention, group intervention led by Physiotherapist, group yoga intervention or a control group who don't change their exercise habits. Participants will be assessed by physiotherapist who is blind to the group allocation at week 1, week 12 (following 10 weeks intervention or control), and at 12 week follow up. The primary outcome measure for both strands is the Multiple Sclerosis Impact Scale. Secondary outcomes are Modified Fatigue Impact Scale, 6 Minute Walk test, and muscle strength measured with hand held dynamometry. Strand B will also use Berg Balance Test and the Modified Ashworth Scale. Confounding variables such as sensation, coordination, proprioception, range of motion and other impairments will be recorded at initial assessment. Data analysis will analyse change in each group, and the differences between groups. Sub group analysis may be performed if sufficient numbers are recruited. ISRCTN77610415.

A Survey of Serious Aircraft Accidents Involving Fatigue Fracture. Volume 2. Rotary-Wing Aircraft (Etude sur des Accidents Importants d’Avions du aux Effets des Fractures de Fatigue. Volume 2. Effets sur des Helicopteres).

DTIC Science & Technology

1983-04-01

Convention on International Civil Aviation, Second Edition , March 1966. 5. WORLD AIRLINE ACCIDENT SUMMARY. Civil Aviation Authority, (Great Britain...people who either provided information, or who suggested other sources of information for the current edition of this survey. E.M.R. Alexander Civil...Waverley, New Zealand. F-28C Tail rotor drive shaft. Fatigue strength reduc- ed by softened condition & surface decarbur- isation. AISA 4130 steel. Ref: NZ
In vivo production of RNA nanostructures via programmed folding of single-stranded RNAs.

PubMed

Li, Mo; Zheng, Mengxi; Wu, Siyu; Tian, Cheng; Liu, Di; Weizmann, Yossi; Jiang, Wen; Wang, Guansong; Mao, Chengde

2018-06-06

Programmed self-assembly of nucleic acids is a powerful approach for nano-constructions. The assembled nanostructures have been explored for various applications. However, nucleic acid assembly often requires chemical or in vitro enzymatical synthesis of DNA or RNA, which is not a cost-effective production method on a large scale. In addition, the difficulty of cellular delivery limits the in vivo applications. Herein we report a strategy that mimics protein production. Gene-encoded DNA duplexes are transcribed into single-stranded RNAs, which self-fold into well-defined RNA nanostructures in the same way as polypeptide chains fold into proteins. The resulting nanostructure contains only one component RNA molecule. This approach allows both in vitro and in vivo production of RNA nanostructures. In vivo synthesized RNA strands can fold into designed nanostructures inside cells. This work not only suggests a way to synthesize RNA nanostructures on a large scale and at a low cost but also facilitates the in vivo applications.
Ingestion of bacterially expressed double-stranded RNA inhibits gene expression in planarians.

PubMed

Newmark, Phillip A; Reddien, Peter W; Cebrià, Francesc; Sánchez Alvarado, Alejandro

2003-09-30

Freshwater planarian flatworms are capable of regenerating complete organisms from tiny fragments of their bodies; the basis for this regenerative prowess is an experimentally accessible stem cell population that is present in the adult planarian. The study of these organisms, classic experimental models for investigating metazoan regeneration, has been revitalized by the application of modern molecular biological approaches. The identification of thousands of unique planarian ESTs, coupled with large-scale whole-mount in situ hybridization screens, and the ability to inhibit planarian gene expression through double-stranded RNA-mediated genetic interference, provide a wealth of tools for studying the molecular mechanisms that regulate tissue regeneration and stem cell biology in these organisms. Here we show that, as in Caenorhabditis elegans, ingestion of bacterially expressed double-stranded RNA can inhibit gene expression in planarians. This inhibition persists throughout the process of regeneration, allowing phenotypes with disrupted regenerative patterning to be identified. These results pave the way for large-scale screens for genes involved in regenerative processes.
Cable deformation simulation and a hierarchical framework for Nb3Sn Rutherford cables

DOE Office of Scientific and Technical Information (OSTI.GOV)

Arbelaez, D.; Prestemon, S. O.; Ferracin, P.

2009-09-13

Knowledge of the three-dimensional strain state induced in the superconducting filaments due to loads on Rutherford cables is essential to analyze the performance of Nb{sub 3}Sn magnets. Due to the large range of length scales involved, we develop a hierarchical computational scheme that includes models at both the cable and strand levels. At the Rutherford cable level, where the strands are treated as a homogeneous medium, a three-dimensional computational model is developed to determine the deformed shape of the cable that can subsequently be used to determine the strain state under specified loading conditions, which may be of thermal, magnetic,more » and mechanical origins. The results can then be transferred to the model at the strand/macro-filament level for rod restack process (RRP) strands, where the geometric details of the strand are included. This hierarchical scheme can be used to estimate the three-dimensional strain state in the conductor as well as to determine the effective properties of the strands and cables from the properties of individual components. Examples of the modeling results obtained for the orthotropic mechanical properties of the Rutherford cables are presented.« less
Les effets des interfaces sur les proprietes magnetiques et de transport des multicouches nickel/iron et cobalt/silver

NASA Astrophysics Data System (ADS)

Veres, Teodor

Cette these est consacree a l'etude de l'evolution structurale des proprietes magnetiques et de transport des multicouches Ni/Fe et nanostructures a base de Co et de l'Ag. Dans une premiere partie, essentiellement bibliographique, nous introduisons quelques concepts de base relies aux proprietes magnetiques et de transport des multicouches metalliques. Ensuite, nous presentons une breve description des methodes d'analyse des resultats. La deuxieme partie est consacree a l'etude des proprietes magnetiques et de transport des multicouches ferromagnetiques/ferromagnetiques Ni/Fe. Nous montrerons qu'une interpretation coherente de ces proprietes necessite la prise en consideration des effets des interfaces. Nous nous attacherons a mettre en evidence, a evaluer et a etudier les effets de ces interfaces ainsi que leur evolution, et ce, suite a des traitements thermiques tel que le depot a temperature elevee et l'irradiation ionique. Les analyses correlees de la structure et de la magnetoresistance nous permettront d'emettre des conclusions sur l'influence des couches tampons entre l'interface et le substrat ainsi qu'entre les couches elles-memes sur le comportement magnetique des couches F/F. La troisieme partie est consacree aux systemes a Magneto-Resistance Geante (MRG) a base de Co et Ag. Nous allons etudier l'evolution de la microstructure suite a l'irradiation avec des ions Si+ ayant une energie de 1 MeV, ainsi que les effets de ces changements sur le comportement magnetique. Cette partie debutera par l'analyse des proprietes d'une multicouche hybride, intermediaire entre les multicouches et les materiaux granulaires. Nous analyserons a l'aide des mesures de diffraction, de relaxation superparamagnetique et de magnetoresistance, les evolutions structurales produites par l'irradiation ionique. Nous etablirons des modeles qui nous aideront a interpreter les resultats pour une serie des multicouches qui couvrent un large eventail de differents comportements magnetiques et ceci en fonction de l'epaisseur de la couche magnetique de Co. Nous verrons que dans ces systemes les effets de l'irradiation ionique sont fortement influences par l'energie de surface ainsi que par l'enthalpie de formation, largement positive pour le systeme Co/Ag.
Assessment of the effect of No Stay, Bent Stay or Straight Stay when the Clothe the Soldier Rucksack is Worn with the Fragmentation Vest

DTIC Science & Technology

2006-02-01

effets de différents renforts de sac à dos (renforts droits, renforts courbés et aucun renfort) sur la...supérieures au seuil de tolérance de la peau et des muscles sous-jacents, et elles pourraient causer des lésions sur la peau et des ecchymoses. Assessment...présente évaluation portait sur cette pratique et visait à déterminer les effets de différents renforts de sac à dos (renforts droits, renforts courbés
A Survey of Serious Aircraft Accidents Involving Fatigue Fracture. Volume 1. Fixed-Wing Aircraft (Etude sur des Accidents Importants d’Avions du aux Effets des Fractures de Fatigue. Volume 1. Effets sur des Avions).

DTIC Science & Technology

1983-04-01

Bureau of Standards. NTS3 National Transportation Safety Board (USA). NTSB AAR NTSB Aircraft Accident Report. NZ AAR New Zealand Aircraft Accident Report...NZ AI New Zealand Accident Investigation Bureau. 0 -5- RAN Royal Australian Navy RAAI Royal Australian Air Force RAF Royal Air Force, UK S Substantial...Ice land Iraq Ireland Jamaica (1966 -1981) Japan (1973 - Feb. 81) Kenya Lethoso Malaysia Ma law i Mal ta Mexico Netherlands New Zealand Norway
Evaluation d'impact sur la santé et évaluation d'impact sur l'équité en santé : éventail de pratiques et questions de recherche.

PubMed

Villeval, Mélanie; Bidault, Elsa; Lang, Thierry

2016-09-01

L'Evaluation d'Impact sur la Santé (EIS) se développe au niveau international et est encore au stade émergent en France. Elle vise à évaluer les effets positifs et négatifs potentiels d'un projet, d'un programme ou d'une politique sur la santé. L'objectif est de produire des recommandations en direction des décideurs, afin d'en maximiser les effets positifs et d'en diminuer les effets négatifs. L'EIS est un moyen particulièrement intéressant d'action sur les déterminants de la santé au-delà des comportements individuels et du système de santé. Les politiques de logement, de transport, de solidarité, économiques, etc. ont, en effet, des impacts souvent non prévus sur la santé. Au-delà des effets sur la santé, l'EIS doit aussi permettre d'apprécier la distribution de ces effets dans la population.Si la préoccupation pour l'équité en santé est centrale dans l'EIS, elle reste cependant difficilement traduite en pratique. Face à cette difficulté, des démarches d'évaluation d'impact ont été développées pour renforcer la prise en compte de l'équité à chaque étape de l'EIS ou « Equity Focused Health Impact Assessment », ou prendre en compte les impacts sur les inégalités de santé de façon spécifique. Ainsi, l'Evaluation de l'Impact sur l'Equité en Santé (EIES) semble, par exemple, particulièrement intéressante pour évaluer l'impact sur les inégalités de projets dans le champ sanitaire.L'EIS et l'EIES posent de nombreuses questions de recherche, notamment autour de la réunion, dans une même démarche, du politique, du citoyen et de l'expert. La participation des populations vulnérables potentiellement affectées par la politique évaluée est une valeur centrale de l'EIS, mais pose des questions d'acceptabilité sociale. La collaboration avec les décideurs politiques est également un enjeu majeur. Les difficultés méthodologiques, notamment de quantification des impacts, peuvent constituer des freins à la promotion de la démarche auprès des décideurs. © The Author(s) 2015.
DOE Office of Scientific and Technical Information (OSTI.GOV)

Shin, J; Park, S; Jeong, J

Purpose: In particle therapy and radiobiology, the investigation of mechanisms leading to the death of target cancer cells induced by ionising radiation is an active field of research. Recently, several studies based on Monte Carlo simulation codes have been initiated in order to simulate physical interactions of ionising particles at cellular scale and in DNA. Geant4-DNA is the one of them; it is an extension of the general purpose Geant4 Monte Carlo simulation toolkit for the simulation of physical interactions at sub-micrometre scale. In this study, we present Geant4-DNA Monte Carlo simulations for the prediction of DNA strand breakage usingmore » a geometrical modelling of DNA structure. Methods: For the simulation of DNA strand breakage, we developed a specific DNA geometrical structure. This structure consists of DNA components, such as the deoxynucleotide pairs, the DNA double helix, the nucleosomes and the chromatin fibre. Each component is made of water because the cross sections models currently available in Geant4-DNA for protons apply to liquid water only. Also, at the macroscopic-scale, protons were generated with various energies available for proton therapy at the National Cancer Center, obtained using validated proton beam simulations developed in previous studies. These multi-scale simulations were combined for the validation of Geant4-DNA in radiobiology. Results: In the double helix structure, the deposited energy in a strand allowed to determine direct DNA damage from physical interaction. In other words, the amount of dose and frequency of damage in microscopic geometries was related to direct radiobiological effect. Conclusion: In this report, we calculated the frequency of DNA strand breakage using Geant4- DNA physics processes for liquid water. This study is now on-going in order to develop geometries which use realistic DNA material, instead of liquid water. This will be tested as soon as cross sections for DNA material become available in Geant4-DNA.« less
Development of a three-dimensional high-order strand-grids approach

NASA Astrophysics Data System (ADS)

Tong, Oisin

Development of a novel high-order flux correction method on strand grids is presented. The method uses a combination of flux correction in the unstructured plane and summation-by-parts operators in the strand direction to achieve high-fidelity solutions. Low-order truncation errors are cancelled with accurate flux and solution gradients in the flux correction method, thereby achieving a formal order of accuracy of 3, although higher orders are often obtained, especially for highly viscous flows. In this work, the scheme is extended to high-Reynolds number computations in both two and three dimensions. Turbulence closure is achieved with a robust version of the Spalart-Allmaras turbulence model that accommodates negative values of the turbulence working variable, and the Menter SST turbulence model, which blends the k-epsilon and k-o turbulence models for better accuracy. A major advantage of this high-order formulation is the ability to implement traditional finite volume-like limiters to cleanly capture shocked and discontinuous flows. In this work, this approach is explored via a symmetric limited positive (SLIP) limiter. Extensive verification and validation is conducted in two and three dimensions to determine the accuracy and fidelity of the scheme for a number of different cases. Verification studies show that the scheme achieves better than third order accuracy for low and high-Reynolds number flows. Cost studies show that in three-dimensions, the third-order flux correction scheme requires only 30% more walltime than a traditional second-order scheme on strand grids to achieve the same level of convergence. In order to overcome meshing issues at sharp corners and other small-scale features, a unique approach to traditional geometry, coined "asymptotic geometry," is explored. Asymptotic geometry is achieved by filtering out small-scale features in a level set domain through min/max flow. This approach is combined with a curvature based strand shortening strategy in order to qualitatively improve strand grid mesh quality.
Getting the Balance Right: A randomised controlled trial of physiotherapy and Exercise Interventions for ambulatory people with multiple sclerosis

PubMed Central

Coote, Susan; Garrett, Maria; Hogan, Neasa; Larkin, Aidan; Saunders, Jean

2009-01-01

Background People with Multiple Sclerosis have a life long need for physiotherapy and exercise interventions due to the progressive nature of the disease and their greater risk of the complications of inactivity. The Multiple Sclerosis Society of Ireland run physiotherapy, yoga and exercise classes for their members, however there is little evidence to suggest which form of physical activity optimises outcome for people with the many and varied impairments associated with MS. Methods and design This is a multi-centre, single blind, block randomised, controlled trial. Participants will be recruited via the ten regional offices of MS Ireland. Telephone screening will establish eligibility and stratification according to the mobility section of the Guys Neurological Disability Scale. Once a block of people of the same strand in the same geographical region have given consent, participants will be randomised. Strand A will concern individuals with MS who walk independently or use one stick to walk outside. Participants will be randomised to yoga, physiotherapy led exercise class, fitness instructor led exercise class or to a control group who don't change their exercise habits. Strand B will concern individuals with MS who walk with bilateral support or a rollator, they may use a wheelchair for longer distance outdoors. Participants will be randomised to 1:1 Physiotherapist led intervention, group intervention led by Physiotherapist, group yoga intervention or a control group who don't change their exercise habits. Participants will be assessed by physiotherapist who is blind to the group allocation at week 1, week 12 (following 10 weeks intervention or control), and at 12 week follow up. The primary outcome measure for both strands is the Multiple Sclerosis Impact Scale. Secondary outcomes are Modified Fatigue Impact Scale, 6 Minute Walk test, and muscle strength measured with hand held dynamometry. Strand B will also use Berg Balance Test and the Modified Ashworth Scale. Confounding variables such as sensation, coordination, proprioception, range of motion and other impairments will be recorded at initial assessment. Discussion Data analysis will analyse change in each group, and the differences between groups. Sub group analysis may be performed if sufficient numbers are recruited. Trial registration ISRCTN77610415 PMID:19607666
Three-dimensional bioprinting using self-assembling scalable scaffold-free “tissue strands” as a new bioink

PubMed Central

Yu, Yin; Moncal, Kazim K.; Li, Jianqiang; Peng, Weijie; Rivero, Iris; Martin, James A.; Ozbolat, Ibrahim T.

2016-01-01

Recent advances in bioprinting have granted tissue engineers the ability to assemble biomaterials, cells, and signaling molecules into anatomically relevant functional tissues or organ parts. Scaffold-free fabrication has recently attracted a great deal of interest due to the ability to recapitulate tissue biology by using self-assembly, which mimics the embryonic development process. Despite several attempts, bioprinting of scale-up tissues at clinically-relevant dimensions with closely recapitulated tissue biology and functionality is still a major roadblock. Here, we fabricate and engineer scaffold-free scalable tissue strands as a novel bioink material for robotic-assisted bioprinting technologies. Compare to 400 μm-thick tissue spheroids bioprinted in a liquid delivery medium into confining molds, near 8 cm-long tissue strands with rapid fusion and self-assemble capabilities are bioprinted in solid form for the first time without any need for a scaffold or a mold support or a liquid delivery medium, and facilitated native-like scale-up tissues. The prominent approach has been verified using cartilage strands as building units to bioprint articular cartilage tissue. PMID:27346373
Waveguides having patterned, flattened modes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Messerly, Michael J.; Pax, Paul H.; Dawson, Jay W.

Field-flattening strands may be added to and arbitrarily positioned within a field-flattening shell to create a waveguide that supports a patterned, flattened mode. Patterning does not alter the effective index or flattened nature of the mode, but does alter the characteristics of other modes. Compared to a telecom fiber, a hexagonal pattern of strands allows for a three-fold increase in the flattened mode's area without reducing the separation between its effective index and that of its bend-coupled mode. Hexagonal strand and shell elements prove to be a reasonable approximation, and, thus, to be of practical benefit vis-a-vis fabrication, to thosemore » of circular cross section. Patterned flattened modes offer a new and valuable path to power scaling.« less
Les effets bénéfiques de l'accompagnement du patient cancéreux: particularités du Maroc

PubMed Central

Lkhoyaali, Sihame; Aitelhaj, Meryem; Errihani, Hassan

2014-01-01

Au Maroc la majorité des patients âgés cancéreux sont pris en charge par leurs proches l'accompagnement des patients est à l'origine de conséquences émotionnelles psychiques et financières négatives mais en contrepartie il est à l'origine de plusieurs effets bénéfiques à savoir un resserrement des liens familiaux, une surestime du soi et il est la source d'un bien-être affectif et spirituel qui permet de faire face à la maladie. PMID:25722766
Development of a Dynamic Biomechanical Model for Load Carriage: Phase IV Part C1: Assessment of Pressure Measurement Systems on Flat Surfaces for use in Human Load Carriage

DTIC Science & Technology

2005-08-01

iv Sommaire Les études sur les effets de la pression de contact produite par une charge d’un sac à dos sont essentielles, étant...mobilité des soldats et amenuiser leur capacité de combat. Afin de mieux comprendre les effets de la pression d’un sac à dos sur le confort et la... de mesure de pression qui pourraient être utilisés pour établir les valeurs de tolérance de la peau aux pressions durant le transport d’une charge
Consequences experimentales des effets des fluctuations du vide sur la fluorescence parametrique et la generation du second harmonique en milieu confine

NASA Astrophysics Data System (ADS)

Robichaud, Luc

Les fluctuations du vide, qui consistent en l'apparition momentanee de particules, ce qui est permit par le principe d'incertitude de Heisenberg, joue un role primordial dans les processus photoniques, en particulier les processus non-lineaires. Par la manipulation de ces fluctuations du vide a l'aide de confinement optique, on retrouve deux phenomenes particuliers : l'intensification de la fluorescence parametrique (Walker, 2008) et l'inhibition de la generation du second harmonique (Collette, 2013). Dans ce travail, on presente les resultats dans le cas classique ; c'est-a-dire sans fluctuations du vide et confinement. Par la suite, on presente les effets des fluctuations du vide et du confinement, ce qui mene aux deux effets mentionnes. Dans le cas de la fluorescence parametrique, le bruit quantique sur le champ interne et externe est calcule, le role du desaccord de phase dans le modele est expose et une generalisation tridimensionnelle est etudiee afin de generaliser la conception du modele d'un cas unidimensionnel a un cas tridimensionnel planaire. Dans le cas de la generation du second harmonique, les difficultes d'un modele purement tridimensionnel sont exposees et ensuite le cas limite planaire est etudie.
The Promiscuity of [beta]-Strand Pairing Allows for Rational Design of [beta]-Sheet Face Inversion

DOE Office of Scientific and Technical Information (OSTI.GOV)

Makabe, Koki; Koide, Shohei

2009-06-17

Recent studies suggest the dominant role of main-chain H-bond formation in specifying {beta}-sheet topology. Its essentially sequence-independent nature implies a large degree of freedom in designing {beta}-sheet-based nanomaterials. Here we show rational design of {beta}-sheet face inversions by incremental deletions of {beta}-strands from the single-layer {beta}-sheet of Borrelia outer surface protein A. We show that a {beta}-sheet structure can be maintained when a large number of native contacts are removed and that one can design large-scale conformational transitions of a {beta}-sheet such as face inversion by exploiting the promiscuity of strand-strand interactions. High-resolution X-ray crystal structures confirmed the success ofmore » the design and supported the importance of main-chain H-bonds in determining {beta}-sheet topology. This work suggests a simple but effective strategy for designing and controlling nanomaterials based on {beta}-rich peptide self-assemblies.« less
Absorption by DNA single strands of adenine isolated in vacuo: The role of multiple chromophores

NASA Astrophysics Data System (ADS)

Nielsen, Lisbeth Munksgaard; Pedersen, Sara Øvad; Kirketerp, Maj-Britt Suhr; Nielsen, Steen Brøndsted

2012-02-01

The degree of electronic coupling between DNA bases is a topic being up for much debate. Here we report on the intrinsic electronic properties of isolated DNA strands in vacuo free of solvent, which is a good starting point for high-level excited states calculations. Action spectra of DNA single strands of adenine reveal sign of exciton coupling between stacked bases from blueshifted absorption bands (˜3 nm) relative to that of the dAMP mononucleotide (one adenine base). The bands are blueshifted by about 10 nm compared to those of solvated strands, which is a shift similar to that for the adenine molecule and the dAMP mononucleotide. Desolvation has little effect on the bandwidth, which implies that inhomogenous broadening of the absorption bands in aqueous solution is of minor importance compared to, e.g., conformational disorder. Finally, at high photon energies, internal conversion competes with electron detachment since dissociation of the bare photoexcited ions on the microsecond time scale is measured.
Stranded dolphin stomach contents represent the free-ranging population's diet

PubMed Central

Dunshea, Glenn; Barros, Nélio B.; Berens McCabe, Elizabeth J.; Gales, Nicholas J.; Hindell, Mark A.; Jarman, Simon N.; Wells, Randall S.

2013-01-01

Diet is a fundamental aspect of animal ecology. Cetacean prey species are generally identified by examining stomach contents of stranded individuals. Critical uncertainty in these studies is whether samples from stranded animals are representative of the diet of free-ranging animals. Over two summers, we collected faecal and gastric samples from healthy free-ranging individuals of an extensively studied bottlenose dolphin population. These samples were analysed by molecular prey detection and these data compared with stomach contents data derived from stranded dolphins from the same population collected over 22 years. There was a remarkable consistency in the prey species composition and relative amounts between the two datasets. The conclusions of past stomach contents studies regarding dolphin habitat associations, prey selection and proposed foraging mechanisms are supported by molecular data from live animals and the combined dataset. This is the first explicit test of the validity of stomach contents analysis for accurate population-scale diet determination of an inshore cetacean. PMID:23637389
Role of stranded gas in increasing global gas supplies

USGS Publications Warehouse

Attanasi, E.D.; Freeman, P.A.

2013-01-01

This report synthesizes the findings of three regional studies in order to evaluate, at the global scale, the contribution that stranded gas resources can make to global natural gas supplies. Stranded gas, as defined for this study, is natural gas in discovered conventional gas and oil fields that is currently not commercially producible for either physical or economic reasons. The regional studies evaluated the cost of bringing the large volumes of undeveloped gas in stranded gas fields to selected markets. In particular, stranded gas fields of selected Atlantic Basin countries, north Africa, Russia, and central Asia are screened to determine whether the volumes are sufficient to meet Europe’s increasing demand for gas imports. Stranded gas fields in Russia, central Asia, Southeast Asia, and Australia are also screened to estimate development, production, and transport costs and corresponding gas volumes that could be supplied to Asian markets in China, India, Japan, and South Korea. The data and cost analysis presented here suggest that for the European market and the markets examined in Asia, the development of stranded gas provides a way to meet projected gas import demands for the 2020-to-2040 period. Although this is a reconnaissance-type appraisal, it is based on volumes of gas that are associated with individual identified fields. Individual field data were carefully examined. Some fields were not evaluated because current technology was insufficient or it appeared the gas was likely to be held off the export market. Most of the evaluated stranded gas can be produced and delivered to markets at costs comparable to historical prices. Moreover, the associated volumes of gas are sufficient to provide an interim supply while additional technologies are developed to unlock gas diffused in shale and hydrates or while countries transition to making a greater use of renewable energy sources.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hong Junmei; Wei Na; Chalk, Alistair

RISC (RNA-induced silencing complex) is a central protein complex in RNAi, into which a siRNA strand is assembled to become effective in gene silencing. By using an in vitro RNAi reaction based on Drosophila embryo extract, an asymmetric model was recently proposed for RISC assembly of siRNA strands, suggesting that the strand that is more loosely paired at its 5' end is selectively assembled into RISC and results in target gene silencing. However, in the present study, we were unable to establish such a correlation in cell-based RNAi assays, as well as in large-scale RNAi data analyses. This suggests thatmore » the thermodynamic stability of siRNA is not a major determinant of gene silencing in mammalian cells. Further studies on fork siRNAs showed that mismatch at the 5' end of the siRNA sense strand decreased RISC assembly of the antisense strand, but surprisingly did not increase RISC assembly of the sense strand. More interestingly, measurements of melting temperature showed that the terminal stability of fork siRNAs correlated with the positions of the mismatches, but not gene silencing efficacy. In summary, our data demonstrate that there is no definite correlation between siRNA stability and gene silencing in mammalian cells, which suggests that instead of thermodynamic stability, other features of the siRNA duplex contribute to RISC assembly in RNAi.« less
Focusing on RISC assembly in mammalian cells.

PubMed

Hong, Junmei; Wei, Na; Chalk, Alistair; Wang, Jue; Song, Yutong; Yi, Fan; Qiao, Ren-Ping; Sonnhammer, Erik L L; Wahlestedt, Claes; Liang, Zicai; Du, Quan

2008-04-11

RISC (RNA-induced silencing complex) is a central protein complex in RNAi, into which a siRNA strand is assembled to become effective in gene silencing. By using an in vitro RNAi reaction based on Drosophila embryo extract, an asymmetric model was recently proposed for RISC assembly of siRNA strands, suggesting that the strand that is more loosely paired at its 5' end is selectively assembled into RISC and results in target gene silencing. However, in the present study, we were unable to establish such a correlation in cell-based RNAi assays, as well as in large-scale RNAi data analyses. This suggests that the thermodynamic stability of siRNA is not a major determinant of gene silencing in mammalian cells. Further studies on fork siRNAs showed that mismatch at the 5' end of the siRNA sense strand decreased RISC assembly of the antisense strand, but surprisingly did not increase RISC assembly of the sense strand. More interestingly, measurements of melting temperature showed that the terminal stability of fork siRNAs correlated with the positions of the mismatches, but not gene silencing efficacy. In summary, our data demonstrate that there is no definite correlation between siRNA stability and gene silencing in mammalian cells, which suggests that instead of thermodynamic stability, other features of the siRNA duplex contribute to RISC assembly in RNAi.
Measurement of longitudinal sulfur isotopic variations by laser ablation MC-ICP-MS in single human hair strands.

PubMed

Santamaria-Fernandez, Rebeca; Giner Martínez-Sierra, Justo; Marchante-Gayón, J M; García-Alonso, J Ignacio; Hearn, Ruth

2009-05-01

A new method for the measurement of longitudinal variations of sulfur isotope amount ratios in single hair strands using a laser ablation system coupled to a multicollector inductively coupled plasma mass spectrometer (LA-MC-ICP-MS) is reported here for the first time. Ablation parameters have been optimized for the measurement of sulfur isotope ratios in scalp human hair strands of 80-120-microm thickness and different washing procedures have been evaluated. The repeatability of the method has been tested and the ability to measure sulfur isotopic variations in 1,000-microm-long hair segments has been evaluated. A horse hair sample previously characterized for carbon and nitrogen isotope ratios in an interlaboratory study has been characterized by LA-MC-ICP-MS to be used as an in-house standard for the bracketing of human hair strands. (34)S/(32)S isotope amount ratios have been measured and corrected for instrumental mass bias adopting the external standardization approach using National Institute of Standards and Technology (NIST) RM8553 and full uncertainty budgets have been calculated using the Kragten approach. Results are reported as both (34)S/(32)S isotope amount ratios and deltaS(V-CDT) values (sulfur isotopic differences relative to a reference sample expressed in the Vienna Canyon Diablo Troilite (V-CDT) scale) calculated using NIST RM8553, NIST RM8554, and NIST RM8556 to anchor results to the V-CDT scale. The main advantage of the new method versus conventional gas source isotope ratio mass spectrometry measurements is that longitudinal variations in sulfur isotope amount ratios can be resolved. Proof of concept is shown with human scalp hair strands from three individuals, two UK residents and one traveler (long periods of time abroad). The method enables monitoring of longitudinal isotope ratio variations in single hair strands. Absolute ratios are reported and delta(34)S(V-CDT) values are plotted for comparison. Slight variations of <1.2 per thousand were detected in the hair strands from UK residents whereas the traveler presented a variation of >5 per thousand. Thus, the measurement of sulfur isotopic variations in hair samples has potential to be an indicator of geographical origin and recent movements and could be used in combination with isotope ratio measurements in water/foodstuffs from different geographical locations to provide important information in nutritional and geographical studies.
Development of a Dynamic Biomechanical Model for Load Carriage: Phase V: Development of the Biomechanical Model by Means of the Portable Measurement System

DTIC Science & Technology

2005-05-01

Résumé La performance opérationnelle des soldats dépend d’un certain nombre de facteurs, dont la charge de travail physiologique, les effets ...particulièrement à la charge de travail physiologique et aux effets biomécaniques, et à perfectionner la mise au point d’un modèle biomécanique dynamique (DBM...on a créé une couche de peau possédant des propriétés appropriées pour le modèle de torse et on a réalisé la modélisation de tous les composants
Using Practitioner Inquiry within and against Large-Scale Educational Reform

ERIC Educational Resources Information Center

Hines, Mary Beth; Conner-Zachocki, Jennifer

2015-01-01

This research study examines the impact of teacher research on participants in a large-scale educational reform initiative in the United States, No Child Left Behind, and its strand for reading teachers, Reading First. Reading First supported professional development for teachers in order to increase student scores on standardized tests. The…
Comparaison des effets des irradiations γ, X et UV dans les fibres optiques

NASA Astrophysics Data System (ADS)

Girard, S.; Ouerdane, Y.; Baggio, J.; Boukenter, A.; Meunier, J.-P.; Leray, J.-L.

2005-06-01

Les fibres optiques présentent de nombreux avantages incitant à les intégrer dans des applications devant résister aux environnements radiatifs associés aux domaines civil, spatial ou militaire. Cependant, leur exposition à un rayonnement entraîne la création de défauts ponctuels dans la silice amorphe pure ou dopée qui constitue les différentes parties de la fibre optique. Ces défauts causent, en particulier, une augmentation transitoire de l'atténuation linéique des fibres optiques responsable de la dégradation voire de la perte du signal propagé dans celles-ci. Dans cet article, nous comparons les effets de deux types d'irradiation: une impulsion X et une dose γ cumulée. Les effets de ces irradiations sont ensuite comparés avec ceux induits par une insolation ultraviolette (244 nm) sur les propriétés d'absorption des fibres optiques. Nous montrons qu'il existe des similitudes entre ces différentes excitations et qu'il est possible, sous certaines conditions, d'utiliser celles-ci afin d'évaluer la capacité de certaines fibres optiques à fonctionner dans un environnement nucléaire donné.
Antisuperconductors: Properties of Layered Compounds with Coupling

NASA Astrophysics Data System (ADS)

Carton, J.-P.; Lammert, P. E.; Prost, J.

1995-11-01

In this note, we consider properties of a hypothetical superconductor composed of Josephson-coupled microscopic layers with tunneling energy minimized at a phase difference of π. The non-zero phase offset in the ground state engenders an intriguing interplay between the superconductive ordering and structural lattice defects. Unusual magnetic properties are expected in the case of highly disordered crystals, which are consistent with observations of a “paramagnetic Meissner” or “Wohlleben” effect in high-T_c cuprate superconductors. Dans cette note, nous considérons les propriétés d'un supraconducteur hypothétique composé de couches microscopiques, couplées par effet Josephson, mais dont l'énergie de couplage est minimisée pour une différence de phase de π. L'état de base a des propriétés fascinantes dues à l'effet combiné de l'ordre supraconducteur et des défauts structuraux du cristal. Dans le cas de cristaux très désordonnés, on attend des propriétés magnétiques exceptionnelles, qui sont compatibles avec les observations dans quelques supraconducteurs cuprate haute-T_c d'un effet “Meissner paramagnétique” ou “Wohlleben”.
Etude par resistivite electrique du comportement d'un alliage amorphe Fe 40Ni 38Mo 4B 18 deforme par traction

NASA Astrophysics Data System (ADS)

Hoang, Long Phan; Sacovy, Paulette; Delaplace, Jean

1983-02-01

Des rubans d'alliages amorphes Metglas du type Fe 40Ni 38Mo 4B 18 à l'état brut de trempe ont été déformés par traction à la température ambiante et l'on a suivi les variations de la résistance électrique des échantillons au cours de la déformation. Il ressort de ces essais que la déformation plastique qui est de l'ordre de 0.5% avant rupture ne se produit pas de faĉon homogène dans l'échantillon. Les mesures électriques effectuées au cours de la déformation mettent en évidence dans le domaine élastique un effet d'élastorésistance, relativement important ( K ≠ 1); elles montrent que dans le domaine plastique la déformation permanente des échantillons s'accompagne d'une diminution de la résistivité électrique du matériau. Deux hypothèses sont discutées pour expliquer cet effet inattendu, l'un qui fait appel à l'existence de volumes libres, l'autre qui suppose une cristallisation localisée du matériau sous l'effet de la contrainte.
Engineering nanometre-scale coherence in soft matter

NASA Astrophysics Data System (ADS)

Liu, Chaoren; Xiang, Limin; Zhang, Yuqi; Zhang, Peng; Beratan, David N.; Li, Yueqi; Tao, Nongjian

2016-10-01

Electronic delocalization in redox-active polymers may be disrupted by the heterogeneity of the environment that surrounds each monomer. When the differences in monomer redox-potential induced by the environment are small (as compared with the monomer-monomer electronic interactions), delocalization persists. Here we show that guanine (G) runs in double-stranded DNA support delocalization over 4-5 guanine bases. The weak interaction between delocalized G blocks on opposite DNA strands is known to support partially coherent long-range charge transport. The molecular-resolution model developed here finds that the coherence among these G blocks follows an even-odd orbital-symmetry rule and predicts that weakening the interaction between G blocks exaggerates the resistance oscillations. These findings indicate how sequence can be exploited to change the balance between coherent and incoherent transport. The predictions are tested and confirmed using break-junction experiments. Thus, tailored orbital symmetry and structural fluctuations may be used to produce coherent transport with a length scale of multiple nanometres in soft-matter assemblies, a length scale comparable to that of small proteins.
First-time demonstration of measuring concrete prestress levels with metal packaged fibre optic sensors

NASA Astrophysics Data System (ADS)

Mckeeman, I.; Fusiek, G.; Perry, M.; Johnston, M.; Saafi, M.; Niewczas, P.; Walsh, M.; Khan, S.

2016-09-01

In this work we present the first large-scale demonstration of metal packaged fibre Bragg grating sensors developed to monitor prestress levels in prestressed concrete. To validate the technology, strain and temperature sensors were mounted on steel prestressing strands in concrete beams and stressed up to 60% of the ultimate tensile strength of the strand. We discuss the methods and calibration procedures used to fabricate and attach the temperature and strain sensors. The use of induction brazing for packaging the fibre Bragg gratings and welding the sensors to prestressing strands eliminates the use of epoxy, making the technique suitable for high-stress monitoring in an irradiated, harsh industrial environment. Initial results based on the first week of data after stressing the beams show the strain sensors are able to monitor prestress levels in ambient conditions.
Nanoparticules d'or: De l'imagerie par resonance magnetique a la radiosensibilisation

NASA Astrophysics Data System (ADS)

Hebert, Etienne M.

Cette thèse approfondit l'étude de nanoparticules d'or de 5 nm de diamètre recouvertes de diamideéthanethioldiethylènetriaminepentacétate de gadolinium (DTDTPA:Gd), un agent de contraste pour l'imagerie par résonance magnétique (IRM). En guise de ciblage passif, la taille des nanoparticules a été contrôlée afin d'utiliser le réseau de néovaisseaux poreux et perméable des tumeurs. De plus les tumeurs ont un drainage lymphatique déficient qui permet aux nanoparticules de demeurer plus longtemps dans le milieu interstitiel de la tumeur. Les expériences ont été effectuées sur des souris Balb/c femelles portant des tumeurs MC7-L1. La concentration de nanoparticules a pu être mesurée à l'IRM in vivo. La concentration maximale se retrouvait à la fin de l'infusion de 10 min. La concentration s'élevait à 0.3 mM dans la tumeur et de 0.12 mM dans le muscle environnant. Les nanoparticules étaient éliminées avec une demi-vie de 22 min pour les tumeurs et de 20 min pour le muscle environnant. Les nanoparticules ont été fonctionnalisées avec le peptide Tat afin de leur conférer des propriétés de ciblage actif La rétention de ces nanoparticules a ainsi été augmentée de 1600 %, passant d'une demi-vie d'élimination de 22 min à 350 min. La survie des souris a été mesurée à l'aide de courbes Kaplan-Meier et d'un modèle mathématique évalue l'efficacité de traitements. Le modèle nous permet, à l'aide de la vitesse de croissance des tumeurs et de l'efficacité des traitements, de calculer la courbe de survie des spécimens. Un effet antagoniste a été observé au lieu de l'effet synergétique attendu entre une infusion de Au@DTDTPA:Gd et l'irradiation aux rayons X. L'absence d'effet synergétique a été attribuée à l'épaisseur du recouvrement de DTDTPA:Gd qui fait écran aux électrons produits par l'or. De plus, le moyen d'ancrage du recouvrement utilise des thiols qui peuvent s'avérer être des capteurs de radicaux. De plus, contrairement a ce qui était escompté, un effet chimiothérapeutique de ces nanoparticules a été observé in vitro et in vivo. Par contre, le mécanisme précis de cet effet est encore à être expliquer, mais on sait déjà que les nanoparticules d'or affectent les fonctions des macrophages ainsi que l'angiogenèse. MOTS-CLÉS : Radiosensibilisateur, Nanoparticules d'or, Agent de contraste pour l'IRM, Électrons de basses énergies, Kaplan-Meier, Effet chimiothérapeutique.
Parametrisation D'effets Non-Standard EN Phenomenologie Electrofaible

NASA Astrophysics Data System (ADS)

Maksymyk, Ivan

Cette these pat articles porte sur la parametrisation d'effets non standard en physique electrofaible. Dans chaque analyse, nous avons ajoute plusieurs operateurs non standard au lagrangien du modele standard electrofaible. Les operateurs non standard decrivent les nouveaux effets decoulant d'un modele sous-jacent non-specefie. D'emblee, le nombre d'operateurs non standard que l'on peut inclure dans une telle analyse est illimite. Mais pour une classe specifique de modeles sous-jacents, les effets non standard peuvent etre decrits par un nombre raisonnable d'operateurs. Dans chaque analyse nous avons developpe des expressions pour des observables electrofaibles, en fonction des coefficients des operateurs nouveaux. En effectuant un "fit" statistique sur un ensemble de donnees experimentales precises, nous avons obtenu des contraintes phenomenologiques sur ces coefficients. Dans "Model-Independent Global Constraints on New Physics", nous avons adopte des hypotheses tres peu contraignantes relatives aux modeles sous-jacents. Nous avons tronque le lagrangien effectif a la dimension cinq (inclusivement). Visant la plus grande generalite possible, nous avons admis des interactions qui ne respectent pas les symetries discretes (soit C, P et CP) ainsi que des interactions qui ne conservent pas la saveur. Le lagrangien effectif contient une quarantaine d'operateurs nouveaux. Nous avons determine que, pour la plupart des coefficients des nouveaux operateurs, les contraintes sont assez serrees (2 ou 3%), mais il y a des exceptions interessantes. Dans "Bounding Anomalous Three-Gauge-Boson Couplings", nous avons determine des contraintes phenomenologiques sur les deviations des couplages a trois bosons de jauge par rapport aux interactions prescrites par le modele standard. Pour ce faire, nous avons calcule les contributions indirectes des CTBJ non standard aux observables de basse energie. Puisque le lagrangien effectif est non-renormalisable, certaines difficultes techniques se posent: pour regulariser les integrales de Feynman les chercheurs se sont generalement servi de la methode de coupure, mais cette methode peut mener a des resultats incorrects. Nous avons opte pour une technique alternative: la regularisation dimensionnelle et la "soustraction minimale avec decouplage". Dans "Beyond S, T and U" nous presentons le formalisme STUVWX, qui est une extension du formalisme STU de Peskin et Takeuchi. Ces formalismes sont bases sur l'hypothese que la theorie sous-jacente se manifeste au moyen de self -energies de bosons de jauge. Ce type d'effet s'appelle 'oblique'. A la base du formalisme STU se trouve la supposition que l'echelle de la nouvelle physique, M, est beaucoup plus grande que q, l'echelle a laquelle on effectue des mesures. Il en resulte que les effets obliques se parametrisent par les trois variables S, T et U. Par contre, dans le formalisme STUVWX, nous avons admis la possibilite que M~ q. Dans "A Global Fit to Extended Oblique Parameters", nous avons effectue deux fits statistiques sur un ensemble de mesures electrofaibles de haute precision. Dans le premier fit, nous avons pose V=W=X=0, obtenant ainsi des contraintes pour l'ensemble {S,T,U}. Dans le second fit, nous avons inclus tous les six parametres.
Characterization and electrochemical response of DNA functionalized 2nm gold nanoparticles confined in a nanochannel array.

PubMed

Peinetti, Ana S; Ceretti, Helena; Mizrahi, Martín; González, Graciela A; Ramírez, Silvana A; Requejo, Félix G; Montserrat, Javier M; Battaglini, Fernando

2018-06-01

Polyvalent gold nanoparticle oligonucleotide conjugates are subject of intense research. Even though 2nm diameter AuNPs have been previously modified with DNA, little is known about their structure and electrochemical behavior. In this work, we examine the influence of different surface modification strategies on the interplay between the meso-organization and the molecular recognition properties of a 27-mer DNA strand. This DNA strand is functionalized with different sulfur-containing moieties and immobilized on 2nm gold nanoparticles confined on a nanoporous alumina, working the whole system as an electrode array. Surface coverages were determined by EXAFS and the performance as recognition elements for impedance-based sensors is evaluated. Our results prove that low DNA coverages on the confined nanoparticles prompt to a more sensitive response, showing the relevance in avoiding the DNA strand overcrowding. The system was able to determine a concentration as low as 100pM of the complementary strand, thus introducing the foundations for the construction of label-free genosensors at the nanometer scale. Copyright © 2018 Elsevier B.V. All rights reserved.
Repair of clustered DNA damage caused by high LET radiation in human fibroblasts

NASA Technical Reports Server (NTRS)

Rydberg, B.; Lobrich, M.; Cooper, P. K.; Chatterjee, A. (Principal Investigator)

1998-01-01

It has recently been demonstrated experimentally that DNA damage induced by high LET radiation in mammalian cells is non-randomly distributed along the DNA molecule in the form of clusters of various sizes. The sizes of such clusters range from a few base-pairs to at least 200 kilobase-pairs. The high biological efficiency of high LET radiation for induction of relevant biological endpoints is probably a consequence of this clustering, although the exact mechanisms by which the clustering affects the biological outcome is not known. We discuss here results for induction and repair of base damage, single-strand breaks and double-strand breaks for low and high LET radiations. These results are discussed in the context of clustering. Of particular interest is to determine how clustering at different scales affects overall rejoining and fidelity of rejoining of DNA double-strand breaks. However, existing methods for measuring repair of DNA strand breaks are unable to resolve breaks that are close together in a cluster. This causes problems in interpretation of current results from high LET radiation and will require new methods to be developed.
A programming language for composable DNA circuits

PubMed Central

Phillips, Andrew; Cardelli, Luca

2009-01-01

Recently, a range of information-processing circuits have been implemented in DNA by using strand displacement as their main computational mechanism. Examples include digital logic circuits and catalytic signal amplification circuits that function as efficient molecular detectors. As new paradigms for DNA computation emerge, the development of corresponding languages and tools for these paradigms will help to facilitate the design of DNA circuits and their automatic compilation to nucleotide sequences. We present a programming language for designing and simulating DNA circuits in which strand displacement is the main computational mechanism. The language includes basic elements of sequence domains, toeholds and branch migration, and assumes that strands do not possess any secondary structure. The language is used to model and simulate a variety of circuits, including an entropy-driven catalytic gate, a simple gate motif for synthesizing large-scale circuits and a scheme for implementing an arbitrary system of chemical reactions. The language is a first step towards the design of modelling and simulation tools for DNA strand displacement, which complements the emergence of novel implementation strategies for DNA computing. PMID:19535415
A programming language for composable DNA circuits.

PubMed

Phillips, Andrew; Cardelli, Luca

2009-08-06

Recently, a range of information-processing circuits have been implemented in DNA by using strand displacement as their main computational mechanism. Examples include digital logic circuits and catalytic signal amplification circuits that function as efficient molecular detectors. As new paradigms for DNA computation emerge, the development of corresponding languages and tools for these paradigms will help to facilitate the design of DNA circuits and their automatic compilation to nucleotide sequences. We present a programming language for designing and simulating DNA circuits in which strand displacement is the main computational mechanism. The language includes basic elements of sequence domains, toeholds and branch migration, and assumes that strands do not possess any secondary structure. The language is used to model and simulate a variety of circuits, including an entropy-driven catalytic gate, a simple gate motif for synthesizing large-scale circuits and a scheme for implementing an arbitrary system of chemical reactions. The language is a first step towards the design of modelling and simulation tools for DNA strand displacement, which complements the emergence of novel implementation strategies for DNA computing.
New design of cable-in-conduit conductor for application in future fusion reactors

NASA Astrophysics Data System (ADS)

Qin, Jinggang; Wu, Yu; Li, Jiangang; Liu, Fang; Dai, Chao; Shi, Yi; Liu, Huajun; Mao, Zhehua; Nijhuis, Arend; Zhou, Chao; Yagotintsev, Konstantin A.; Lubkemann, Ruben; Anvar, V. A.; Devred, Arnaud

2017-11-01

The China Fusion Engineering Test Reactor (CFETR) is a new tokamak device whose magnet system includes toroidal field, central solenoid (CS) and poloidal field coils. The main goal is to build a fusion engineering tokamak reactor with about 1 GW fusion power and self-sufficiency by blanket. In order to reach this high performance, the magnet field target is 15 T. However, the huge electromagnetic load caused by high field and current is a threat for conductor degradation under cycling. The conductor with a short-twist-pitch (STP) design has large stiffness, which enables a significant performance improvement in view of load and thermal cycling. But the conductor with STP design has a remarkable disadvantage: it can easily cause severe strand indentation during cabling. The indentation can reduce the strand performance, especially under high load cycling. In order to overcome this disadvantage, a new design is proposed. The main characteristic of this new design is an updated layout in the triplet. The triplet is made of two Nb3Sn strands and one soft copper strand. The twist pitch of the two Nb3Sn strands is large and cabled first. The copper strand is then wound around the two superconducting strands (CWS) with a shorter twist pitch. The following cable stages layout and twist pitches are similar to the ITER CS conductor with STP design. One short conductor sample with a similar scale to the ITER CS was manufactured and tested with the Twente Cable Press to investigate the mechanical properties, AC loss and internal inspection by destructive examination. The results are compared to the STP conductor (ITER CS and CFETR CSMC) tests. The results show that the new conductor design has similar stiffness, but much lower strand indentation than the STP design. The new design shows potential for application in future fusion reactors.
Shifting Plasma

NASA Image and Video Library

2017-12-08

Strands of solar material at the sun's edge shifted and twisted back and forth over a 22-hour period in this footage captured May 2-3, 2017, by NASA’s Solar Dynamics Observatory. In this close-up, the strands are being manipulated by strong magnetic forces associated with active regions. To give a sense of scale, the strands that hover above the sun are more than several times the size of Earth. These images were taken in a wavelength of extreme ultraviolet light, which is typically invisible to our eyes, but was colorized here in red. go.nasa.gov/2qJzPD2 Credit: NASA/Goddard/SDO NASA image use policy. NASA Goddard Space Flight Center enables NASA’s mission through four scientific endeavors: Earth Science, Heliophysics, Solar System Exploration, and Astrophysics. Goddard plays a leading role in NASA’s accomplishments by contributing compelling scientific knowledge to advance the Agency’s mission. Follow us on Twitter Like us on Facebook Find us on Instagram
Influence of Controlled Cooling in Bimodal Scaffold Fabrication Using Polymers with Different Melting Temperatures.

PubMed

Lara-Padilla, Hernan; Mendoza-Buenrostro, Christian; Cardenas, Diego; Rodriguez-Garcia, Aida; Rodriguez, Ciro A

2017-06-11

The combination of different materials and capabilities to manufacture at several scales open new possibilities in scaffold design for bone regeneration. This work is focused on bimodal scaffolds that combine polylactic acid (PLA) melt extruded strands with polycaprolactone (PCL) electrospun fibers. This type of bimodal scaffold offers better mechanical properties, compared to the use of PCL for the extruded strands, and provides potential a means for controlled drug and/or growth factor delivery through the electrospun fibers. The technologies of fused deposition modeling (FDM) and electrospinning were combined to create 3D bimodal constructs. The system uses a controlled cooling system allowing the combination of polymers with different melting temperatures to generate integrated scaffold architecture. The thermoplastic polymers used in the FDM process enhance the mechanical properties of the bimodal scaffold and control the pore structure. Integrated layers of electrospun microfibers induce an increase of the surface area for cell culture purposes, as well as potential in situ controlled drug and/or growth factor delivery. The proposed bimodal scaffolds (PLA extruded strands and PCL electrospun fibers) show appropriate morphology and better mechanical properties when compared to the use of PCL extruded strands. On average, bimodal scaffolds with overall dimensions of 30 × 30 × 2.4 mm³ (strand diameter of 0.5 mm, strand stepover of 2.5 mm, pore size of 2 mm, and layer height of 0.3 mm) showed scaffold stiffness of 23.73 MPa and compression strength of 3.85 MPa. A cytotoxicity assay based human fibroblasts showed viability of the scaffold materials.
Influence of Controlled Cooling in Bimodal Scaffold Fabrication Using Polymers with Different Melting Temperatures

PubMed Central

Lara-Padilla, Hernan; Mendoza-Buenrostro, Christian; Cardenas, Diego; Rodriguez-Garcia, Aida; Rodriguez, Ciro A.

2017-01-01

The combination of different materials and capabilities to manufacture at several scales open new possibilities in scaffold design for bone regeneration. This work is focused on bimodal scaffolds that combine polylactic acid (PLA) melt extruded strands with polycaprolactone (PCL) electrospun fibers. This type of bimodal scaffold offers better mechanical properties, compared to the use of PCL for the extruded strands, and provides potential a means for controlled drug and/or growth factor delivery through the electrospun fibers. The technologies of fused deposition modeling (FDM) and electrospinning were combined to create 3D bimodal constructs. The system uses a controlled cooling system allowing the combination of polymers with different melting temperatures to generate integrated scaffold architecture. The thermoplastic polymers used in the FDM process enhance the mechanical properties of the bimodal scaffold and control the pore structure. Integrated layers of electrospun microfibers induce an increase of the surface area for cell culture purposes, as well as potential in situ controlled drug and/or growth factor delivery. The proposed bimodal scaffolds (PLA extruded strands and PCL electrospun fibers) show appropriate morphology and better mechanical properties when compared to the use of PCL extruded strands. On average, bimodal scaffolds with overall dimensions of 30 × 30 × 2.4 mm3 (strand diameter of 0.5 mm, strand stepover of 2.5 mm, pore size of 2 mm, and layer height of 0.3 mm) showed scaffold stiffness of 23.73 MPa and compression strength of 3.85 MPa. A cytotoxicity assay based human fibroblasts showed viability of the scaffold materials. PMID:28773000

DNA Damage Signals and Space Radiation Risk

NASA Technical Reports Server (NTRS)

Cucinotta, Francis A.

2011-01-01

Space radiation is comprised of high-energy and charge (HZE) nuclei and protons. The initial DNA damage from HZE nuclei is qualitatively different from X-rays or gamma rays due to the clustering of damage sites which increases their complexity. Clustering of DNA damage occurs on several scales. First there is clustering of single strand breaks (SSB), double strand breaks (DSB), and base damage within a few to several hundred base pairs (bp). A second form of damage clustering occurs on the scale of a few kbp where several DSB?s may be induced by single HZE nuclei. These forms of damage clusters do not occur at low to moderate doses of X-rays or gamma rays thus presenting new challenges to DNA repair systems. We review current knowledge of differences that occur in DNA repair pathways for different types of radiation and possible relationships to mutations, chromosomal aberrations and cancer risks.
Nanoflares, Spicules, and Other Small-Scale Dynamic Phenomena on the Sun

NASA Technical Reports Server (NTRS)

Klimchuk, James

2010-01-01

There is abundant evidence of highly dynamic phenomena occurring on very small scales in the solar atmosphere. For example, the observed pr operties of many coronal loops can only be explained if the loops are bundles of unresolved strands that are heated impulsively by nanoflares. Type II spicules recently discovered by Hinode are an example of small-scale impulsive events occurring in the chromosphere. The exist ence of these and other small-scale phenomena is not surprising given the highly structured nature of the magnetic field that is revealed by photospheric observations. Dynamic phenomena also occur on much lar ger scales, including coronal jets, flares, and CMEs. It is tempting to suggest that these different phenomena are all closely related and represent a continuous distribution of sizes and energies. However, this is a dangerous over simplification in my opinion. While it is tru e that the phenomena all involve "magnetic reconnection" (the changin g of field line connectivity) in some form, how this occurs depends s trongly on the magnetic geometry. A nanoflare resulting from the interaction of tangled magnetic strands within a confined coronal loop is much different from a major flare occurring at the current sheet form ed when a CME rips open an active region. I will review the evidence for ubiquitous small-scale dynamic phenomena on the Sun and discuss wh y different phenomena are not all fundamentally the same.
Systemes Fermioniques a Basse Dimension D'espace: Supraconductivite, Effet Hall Quantique et Statistique Fractionnaire

NASA Astrophysics Data System (ADS)

Sakhi, Said

Cette these est constituee de trois sujets de recherche distincts. Les deux premiers articles traitent du phenomene de supraconductivite dans un modele bidimensionnel, dans le troisieme article on etudie l'action effective d'un systeme electronique soumis a l'effet d'un champ magnetique (systeme de Hall) et le dernier article examine la quantification d'un systeme de particules identiques en deux dimensions d'espace et la possibilite des anyons. Le modele qu'on analyse dans les deux premiers articles est un systeme fermionique dont les particules chargees et de masse nulle interagissent entre elles avcc un couplage attractif et fort. L'analyse de l'action effective decrivant la physique a basse energie nous permet d'examiner la structure de l'espace de phase. A temperature nulle, le parametre d'ordre du systeme prend une valeur moyenne non nulle. Consequemment, la symetrie continue U(1) du modele est spontanement brisee et il en resulte l'apparition d'un mode de Goldstone. En presence d'un champ electromagnetique externe, ce mode disparait et le champ de jauge acquiert une masse donc l'effet Meissner caracteristique d'un supraconducteur. Bien que le modele ne soit pas renormalisable dans le sens perturbatif, on montre qu'il l'est dans le cadre du developpement en 1/N ou N est le nombre d'especes fermioniques. En outre, on montre que l'inclusion des effets thermiques change radicalement le mecanisme de supraconductivite. En effet, on montre que la brisure spontanee de la symetrie U(1) n'est plus possible a temperature finie a cause de tres severes divergences infrarouges. Par contre, la dynamique des tourbillons (vortex) existant dans le plan devient essentielle. On montre que le phenomene de supraconductivite resulte du confinement de ces objets topologiques et que la temperature critique s'identifie a celle de Kosterlitz -Thouless. Ce mecanisme de supraconductivite presente l'avantage d'aboutir a un rapport gap a la temperature critique plus eleve que celui du modele de BCS et la non violation de la symetrie par renversement du temps et de l'espace contrairement au modele anyonique. Dans le troisieme article, on a developpe une methode systematique pour calculer les determinants fermioniques en presence d'un champ magnetique perpendiculaire au plan de confinement des particules. Aussi bien les effets thermiques que ceux dus aux impuretes sont pris en consideration dans cette methode. La technique est illustree dans le cas du systeme de Hall quantique. Finalement, dans le dernier article, on discute la quantification d'un systeme de particules identiques dans le plan. Apres avoir correctement defini l'espace de phase classique du systeme, l'analyse fait ressortir deux parametres fondamentaux denotes par theta et alpha. Le premier parametre theta est associe a l'intensite du flux magnetique localise au vertex du cone et definit la statistique des particules. Pour des valeurs arbitraires de theta on parle d'anyons. L'autre parametre alpha est associe a l'extension auto-adjointe de l'hamiltonien et ressort de l'unitarite de la theorie. On montre par un exemple explicite que alpha peut etre vu comme le vestige d'une interaction a tres courte distance (haute energie) entre les particules du systeme. Finalement, on montre que le groupe de symetrie du systeme avec extension auto -adjointe n'est plus SO(2,1) car le generateur de dilatation de ce groupe n'est plus compatible avec un parametre alpha arbitraire. (Abstract shortened by UMI.).
L'effet Hall Quantique

NASA Astrophysics Data System (ADS)

Samson, Thomas

Nous proposons une methode permettant d'obtenir une expression pour la conductivite de Hall de structures electroniques bidimensionnelles et nous examinons celle -ci a la limite d'une temperature nulle dans le but de verifier l'effet Hall quantique. Nous allons nous interesser essentiellement a l'effet Hall quantique entier et aux effets fractionnaires inferieurs a un. Le systeme considere est forme d'un gaz d'electrons en interaction faible avec les impuretes de l'echantillon. Le modele du gaz d'electrons consiste en un gaz bidimensionnel d'electrons sans spin expose perpendiculairement a un champ magnetique uniforme. Ce dernier est decrit par le potentiel vecteur vec{rm A} defini dans la jauge de Dingle ou jauge symetrique. Conformement au formalisme de la seconde quantification, l'hamiltonien de ce gaz est represente dans la base des etats a un-corps de Dingle |n,m> et exprime ainsi en terme des operateurs de creation et d'annihilation correspondants a_sp{ rm n m}{dag} et a _{rm n m}. Nous supposons de plus que les electrons du niveau fondamental de Dingle interagissent entre eux via le potentiel coulombien. La methode utilisee fait appel a une equation mai tresse a N-corps, de nature quantique et statistique, et verifiant le second principe de la thermodynamique. A partir de celle-ci, nous obtenons un systeme d'equations differentielles appele hierarchie d'equations quantique dont la resolution nous permet de determiner une equation a un-corps, dite de Boltzmann quantique, et dictant l'evolution de la moyenne statistique de l'operateur non-diagonal a _sp{rm n m}{dag } a_{rm n}, _{rm m}, sous l'action du champ electrique applique vec{rm E}(t). C'est sa solution Tr(p(t) a _sp{rm n m}{dag} a_{rm n},_ {rm m}), qui definit la relation de convolution entre la densite courant de Hall vec{rm J}_{rm H }(t) et le champ electrique vec {rm E}(t) dont la transformee de Laplace-Fourier du noyau nous fournit l'expression de la conductivite de Hall desiree. Pour une valeur de facteur d'occupation (nombre d'electrons/degenerescence des etats de Dingle) superieure a un, c'est-a-dire en absence d'interaction electron-electron, il nous sera facile d'evaluer cette conductivite a la limite d'une temperature nulle et de demontrer qu'elle tend vers l'une des valeurs quantiques qe^2/h conformement a l'effet Hall quantique entier. Cependant, pour une valeur du facteur d'occupation inferieure a un, c'est-a-dire en presence d'interaction electron-electron, nous ne pourrons evaluer cette limite et obtenir les resultats escomptes a cause de l'impossibilite de determiner l'un des termes impliques. Neanmoins, ce dernier etant de nature statistique, il pourra etre aisement mis en fonction du propagateur du gaz d'electrons dont on doit maintenant determiner une expression en regime effet Hall quantique fractionnaire. Apres avoir demontre l'impuissance de la theorie des perturbations, basee sur le theoreme de Wick et la technique des diagrammes de Feynman, a accomplir cette tache correctement, nous proposons une seconde methode. Celle -ci fait appel au formalisme de l'integrale fonctionnelle et a l'utilisation d'une transformation de Hubbard-Stratonovich generalisee permettant de substituer a l'interaction a deux-corps une interaction effective a un-corps. L'expression finale obtenue bien que non completement resolue, devrait pouvoir etre estimee par une bonne approximation analytique ou au pire numeriquement.
An exponential scaling law for the strain dependence of the Nb3Sn critical current density

NASA Astrophysics Data System (ADS)

Bordini, B.; Alknes, P.; Bottura, L.; Rossi, L.; Valentinis, D.

2013-07-01

The critical current density of the Nb3Sn superconductor is strongly dependent on the strain applied to the material. In order to investigate this dependence, it is a common practice to measure the critical current of Nb3Sn strands for different values of applied axial strain. In the literature, several models have been proposed to describe these experimental data in the reversible strain region. All these models are capable of fitting the measurement results in the strain region where data are collected, but tend to predict unphysical trends outside the range of data, and especially for large strain values. In this paper we present a model of a new strain function, together with the results obtained by applying the new scaling law on relevant datasets. The data analyzed consisted of the critical current measurements at 4.2 K that were carried out under applied axial strain at Durham University and the University of Geneva on different strand types. With respect to the previous models proposed, the new scaling function does not present problems at large strain values, has a lower number of fitting parameters (only two instead of three or four), and is very stable, so that, starting from few experimental points, it can estimate quite accurately the strand behavior in a strain region where there are no data. A relationship is shown between the proposed strain function and the elastic strain energy, and an analogy is drawn with the exponential form of the McMillan equation for the critical temperature.
L’effet du yoga chez les patients atteints de cancer

PubMed Central

Côté, Andréanne; Daneault, Serge

2012-01-01

Résumé Objectif Déterminer si le yoga thérapeutique améliore la qualité de vie de patients atteints de cancer. Sources des données Recherche effectuée avec la base de données MEDLINE (1950–2010) en utilisant les mots-clés yoga, cancer et quality of life. Sélection des études Priorité accordée aux études cliniques randomisées contrôlées évaluant l’effet du yoga sur différents symptômes susceptibles de se présenter chez des patients atteints de cancer en Amérique du Nord. Synthèse Quatre études cliniques randomisées contrôlées ont d’abord été analysées, puis 2 études sans groupe-contrôle. Trois études réalisées en Inde et au Proche-Orient ont également apporté des éléments intéressants au plan méthodologique. Les interventions proposées comprenaient des séances de yoga d’une durée et d’une fréquence variables. Les paramètres mesurés variaient également d’une étude à l’autre. Plusieurs symptômes ont connu des améliorations significatives avec le yoga (meilleure qualité du sommeil, diminution des symptômes anxieux ou dépressifs, amélioration du bien-être spirituel, etc.). Il a aussi semblé que la qualité de vie, dans sa globalité ou dans certaines de ses composantes spécifiques, s’améliorait. Conclusion La variété des effets bénéfiques produits, l’absence d’effet secondaire et le rapport coût-bénéfice avantageux du yoga thérapeutique en fait une intervention intéressante à suggérer par les médecins de famille aux patients atteints de cancer. Certaines lacunes méthodologiques ont pu diminuer la puissance statistique des études présentées, à commencer par la taille restreinte des échantillons et par l’assiduité variable des patients soumis à l’intervention. Il est également possible que les échelles de mesure utilisées ne convenaient pas à ce type de situation et de clientèle pour qu’en soit dégagé un effet significatif. Toutefois, les commentaires favorables des participants recueillis au cours des études et leur degré d’appréciation et de bien-être donnent à penser qu’il faille poursuivre les recherches pour mieux en comprendre les mécanismes.
Site-Specific Dynamics of β-Sheet Peptides with (D) Pro-Gly Turns Probed by Laser-Excited Temperature-Jump Infrared Spectroscopy.

PubMed

Popp, Alexander; Scheerer, David; Chi, Heng; Keiderling, Timothy A; Hauser, Karin

2016-05-04

Turn residues and side-chain interactions play an important role for the folding of β-sheets. We investigated the conformational dynamics of a three-stranded β-sheet peptide ((D) P(D) P) and a two-stranded β-hairpin (WVYY-(D) P) by time-resolved temperature-jump (T-jump) infrared spectroscopy. Both peptide sequences contain (D) Pro-Gly residues that favor a tight β-turn. The three-stranded β-sheet (Ac-VFITS(D) PGKTYTEV(D) PGOKILQ-NH2 ) is stabilized by the turn sequences, whereas the β-hairpin (SWTVE(D) PGKYTYK-NH2 ) folding is assisted by both the turn sequence and hydrophobic cross-strand interactions. Relaxation times after the T-jump were monitored as a function of temperature and occur on a sub-microsecond time scale, (D) P(D) P being faster than WVYY-(D) P. The Xxx-(D) Pro tertiary amide provides a detectable IR band, allowing us to probe the dynamics site-specifically. The relative importance of the turn versus the intrastrand stability in β-sheet formation is discussed. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
Glass-like stress relaxation of a permanent gelatin network as a signature of pretransitional helix-coil fluctuations

NASA Astrophysics Data System (ADS)

Caroli, Christiane; Ronsin, Olivier; Lemaître, Anaël

2018-02-01

The stress response of permanently crosslinked gelatin gels was recently observed to display glass-like features, namely, a stretched-exponential behavior terminated by an exponential decay, the characteristic time scales of which increase dramatically with decreasing temperature. This phenomenon is studied here using a model of flexible polymer gel network where relaxation proceeds via elementary monomer exchanges between helix and coil segments. The relaxation dynamics of a full network simulation is found to be nearly identical to that of a model of independent strands, which shows that for flexible polymer gels in the range of elastic moduli of interest, both strand contour length disorder and elastic couplings are irrelevant. We thus focus on the independent strand model and find it not only to explain the observed functional form of the stress relaxation curves but also to yield predictions that match very satisfactorily the experimental measurements of final relaxation time and total stress drop. The system under study thus constitutes a rare case where the origin of glass-like behavior can be unambiguously identified, namely, as the signature of the enhancement of helix content fluctuations when approaching from above the mean-field helix-coil transition of strands.
Investigating Variation in Teaching with Technology-Rich Intervention: What Matters in Teaching and Teacher Training at Scale?

ERIC Educational Resources Information Center

Dunn, Margaret Breslin

2009-01-01

A main question this dissertation addresses is: what variation in teaching and teacher training matter? This question is examined within a specific but important context: the scale-up of a technology-rich intervention focused on the algebra strand of 8th grade mathematics. I conducted a multi-level case study by gathering and analyzing data at…
Anaerobic sludge digestion in the presence of lactobacillus additive

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ghosh, S.; Klass, D.L.

1980-01-01

A laboratory evaluation of a lactobacillus fermentation product was performed to study its effects as an additive on the anaerobic digestion of sewage sludge under conventional and overloaded high-rate conditions. The overloaded conditions were those experienced in commercial municipal digesters. It was concluded from this work that the use of the additive at low concentrations permits digester operation at least up to double the loading of untreated digesters and at higher methane yields and volatile solids reductions without affecting effluent quality. The additive also imparts iproved digester stability and rapid response to loading rate and detention time excursions and upsets.more » The beneficial effets of the additive observed in the laboratory remain to be established with other feeds such as biomass, and in large-scale commercial digestion tests that are now in progress.« less
Le rôle médiateur du fonctionnement familial dans la relation entre l’adversité familiale et l’adaptation sociale des enfants d’âge préscolaire1

PubMed Central

Felli, M. C.; Parent, S.; Zelazo, P. D.; Tremblay, R. E.; Séguin, J. R.

2017-01-01

Résumé À la petite enfance, l’adaptation sociale de l’enfant dépend en partie des risques auxquels il est exposé dans son environnement. Toutefois, les mécanismes par lesquels les facteurs de risque opèrent leurs influences sur l’adaptation sociale de l’enfant sont peu documentés. Ainsi, cette étude examine dans un premier temps l’effet principal de l’adversité familiale, un cumul de facteurs de risque, sur les problèmes de comportement intériorisés et extériorisés, ainsi que sur la sécurité d’attachement des enfants d’âge préscolaire. Dans un deuxième temps, elle évalue le rôle médiateur du fonctionnement familial dans le lien entre l’adversité familiale et les problèmes de comportement de même qu’entre l’adversité familiale et la sécurité d’attachement des enfants d’âge préscolaire. Les 572 participants à l’étude (n=572) sont âgés entre cinq et 42 mois lors des mesures de l’adversité familiale et de 42 mois lors de la mesure des problèmes de comportement et du fonctionnement familial. Quatre-vingt d’entre eux (n=80) ont fait l’objet d’une mesure de sécurité d’attachement à 48 mois. Les résultats indiquent, d’abord, un effet principal de l’adversité familiale sur les problèmes de comportement intériorisés et extériorisés. Un effet médiateur significatif du fonctionnement familial est ensuite rapporté dans le lien entre l’adversité familiale et les problèmes de comportement intériorisés et extériorisés. Aucun effet significatif n’est observé pour la sécurité d’attachement des enfants de 48 mois. PMID:28567062
Ultrashort Nucleic Acid Duplexes Exhibit Long Wormlike Chain Behavior with Force-Dependent Edge Effects

NASA Astrophysics Data System (ADS)

Whitley, Kevin D.; Comstock, Matthew J.; Chemla, Yann R.

2018-02-01

Despite their importance in biology and use in nanotechnology, the elastic behavior of nucleic acids on "ultrashort" (<15 nt ) length scales remains poorly understood. Here, we use optical tweezers combined with fluorescence imaging to observe directly the hybridization of oligonucleotides (7-12 nt) to a complementary strand under tension and to measure the difference in end-to-end extension between the single-stranded and duplex states. Data are consistent with long-polymer models at low forces (<8 pN ) but smaller than predicted at higher forces (>8 pN ), the result of the sequence-dependent duplex edge effects.
Dielectric dispersion for short double-strand DNA.

PubMed

Omori, Shinji; Katsumoto, Yoichi; Yasuda, Akio; Asami, Koji

2006-05-01

A complex dielectric constant for double-strand DNA molecules with a length of not greater than 120 base pairs in an aqueous solution containing 30 mM NaCl was systematically measured as a function of chain length in such a way that experimental uncertainties associated with the molecular-weight distribution of specimens were virtually excluded. In contrast to the past experimental and theoretical studies for much longer DNA molecules, both the molar specific dielectric increment and the relaxation time are proportional to the chain length. These scaling rules cannot be accounted for by any theory so far proposed that gives analytical expressions for those two quantities in the long-chain limit.
Detection of Strand Cleavage And Oxidation Damage Using Model DNA Molecules Captured in a Nanoscale Pore

NASA Technical Reports Server (NTRS)

Vercoutere, W.; Solbrig, A.; DeGuzman, V.; Deamer, D.; Akeson, M.

2003-01-01

We use a biological nano-scale pore to distinguish among individual DNA hairpins that differ by a single site of oxidation or a nick in the sugar-phosphate backbone. In earlier work we showed that the protein ion channel alpha-hemolysin can be used as a detector to distinguish single-stranded from double-stranded DNA, single base pair and single nucleotide differences. This resolution is in part a result of sensitivity to structural changes that influence the molecular dynamics of nucleotides within DNA. The strand cleavage products we examined here included a 5-base-pair (5-bp) hairpin with a 5-prime five-nucleotide overhang, and a complementary five-nucleotide oligomer. These produced predictable shoulder-spike and rapid near-full blockade signatures, respectively. When combined, strand annealing was monitored in real time. The residual current level dropped to a lower discrete level in the shoulder-spike blockade signatures, and the duration lengthened. However, these blockade signatures had a shorter duration than the unmodified l0bp hairpin. To test the pore sensitivity to nucleotide oxidation, we examined a 9-bp hairpin with a terminal 8-oxo-deoxyguanosine (8-oxo-dG), or a penultimate 8-oxo-dG. Each produced blockade signatures that differed from the otherwise identical control 9bp hairpins. This study showed that DNA structure is modified sufficiently by strand cleavage or oxidation damage at a single site to alter in a predictable manner the ionic current blockade signatures produced. This technique improves the ability to assess damage to DNA, and can provide a simple means to help characterize the risks of radiation exposure. It may also provide a method to test radiation protection.
MO-AB-BRA-04: Radiation Measurements with a DNA Double-Strand-Break Dosimeter

DOE Office of Scientific and Technical Information (OSTI.GOV)

Obeidat, M; Cline, K; Stathakis, S

Purpose: Many types of dosimeters are used to measure radiation, but none of them directly measures the biological effect of this dose. The purpose here is to create a dosimeter that can measure the probability of double-strand breaks (DSB) for DNA, which is directly related to the biological effect of radiation. Methods: The dosimeter has DNA strands, which are labeled on one end with biotin and on the other with fluorescein. The biotin attaches these strands to magnetic beads. We suspended the DNA dosimeter in phosphate-buffered saline (PBS) as it matches the internal environment of the body. We placed smallmore » volumes (50µL) of the DNA dosimeter into tubes and irradiated these samples in a water-equivalent plastic phantom with several doses (three samples per dose). After irradiating the samples, a magnet was placed against the tubes. The fluorescein attached to broken DNA strands was extracted (called the supernatant) and placed into a different tube. The fluorescein on the unbroken strands remained attached to the beads in the tube and was re-suspended with 50µL of PBS. A fluorescence reader was used to measure the fluorescence for both the re-suspended beads and supernatant. To prove that we are measuring DSB, we tested dosimeter response with two different lengths of attached DNA strands (1 and 4 kilo-base pair). Results: The probability of DSB at the dose levels of 5, 10, 25, and 50 Gy were 0.05, 0.08, 0.12, and 0.19, respectively, while the coefficients of variation were 0.14, 0.07, 0.02, and 0.01, respectively. The 4 kilo-base-pair dosimeter produced 5.3 times the response of the 1 kilo-base-pair dosimeter. Conclusion: The DNA dosimeter yields a measurable response to dose that scales with the DNA strand length. The goal now is to refine the dosimeter fabrication to reproducibly create a low coefficient of variation for the lower doses. This work was supported in part by Yarmouk University (Irbid, Jordan) and CPRIT (RP140105)« less
Internal stresses, dislocation mobility and ductility

NASA Astrophysics Data System (ADS)

Saada, G.

1991-06-01

The description of plastic deformation must take into account individual mechanisms and heterogeneity of plastic strain. Influence of dislocation interaction with forest dislocations and of cross slip are connected with the organization of dipole walls. The latter are described and their development is explained as a consequence of edge effects. Applications are discussed. La description de la déformation plastique doit prendre en compte les interactions individuelles des dislocations et l'hétérogénéité à grande échelle de la déformation plastique. Les interactions des dislocations mobiles avec la forêt de dislocations, le glissement dévié, ont pour effet la création de parois dipolaires. Celles-ci sont décrites et leur développement est appliqué à partir des effets de bord.
Effets de l'humidite sur la propagation du delaminage dans un composite carbone/epoxy sollicite en mode mixte I/II

NASA Astrophysics Data System (ADS)

LeBlanc, Luc R.

Les materiaux composites sont de plus en plus utilises dans des domaines tels que l'aerospatiale, les voitures a hautes performances et les equipements sportifs, pour en nommer quelques-uns. Des etudes ont demontre qu'une exposition a l'humidite nuit a la resistance des composites en favorisant l'initiation et la propagation du delaminage. De ces etudes, tres peu traitent de l'effet de l'humidite sur l'initiation du delaminage en mode mixte I/II et aucune ne traite des effets de l'humidite sur le taux de propagation du delaminage en mode mixte I/II dans un composite. La premiere partie de cette these consiste a determiner les effets de l'humidite sur la propagation du delaminage lors d'une sollicitation en mode mixte I/II. Des eprouvettes d'un composite unidirectionnel de carbone/epoxy (G40-800/5276-1) ont ete immergees dans un bain d'eau distillee a 70°C jusqu'a leur saturation. Des essais experimentaux quasi-statiques avec des chargements d'une gamme de mixites des modes I/II (0%, 25%, 50%, 75% et 100%) ont ete executes pour determiner les effets de l'humidite sur la resistance au delaminage du composite. Des essais de fatigue ont ete realises, avec la meme gamme de mixite des modes I/II, pour determiner 1'effet de 1'humidite sur l'initiation et sur le taux de propagation du delaminage. Les resultats des essais en chargement quasi-statique ont demontre que l'humidite reduit la resistance au delaminage d'un composite carbone/epoxy pour toute la gamme des mixites des modes I/II, sauf pour le mode I ou la resistance au delaminage augmente apres une exposition a l'humidite. Pour les chargements en fatigue, l'humidite a pour effet d'accelerer l'initiation du delaminage et d'augmenter le taux de propagation pour toutes les mixites des modes I/II. Les donnees experimentales recueillies ont ete utilisees pour determiner lesquels des criteres de delaminage en statique et des modeles de taux de propagation du delaminage en fatigue en mode mixte I/II proposes dans la litterature representent le mieux le delaminage du composite etudie. Une courbe de regression a ete utilisee pour determiner le meilleur ajustement entre les donnees experimentales et les criteres de delaminage en statique etudies. Une surface de regression a ete utilisee pour determiner le meilleur ajustement entre les donnees experimentales et les modeles de taux de propagation en fatigue etudies. D'apres les ajustements, le meilleur critere de delaminage en statique est le critere B-K et le meilleur modele de propagation en fatigue est le modele de Kenane-Benzeggagh. Afin de predire le delaminage lors de la conception de pieces complexes, des modeles numeriques peuvent etre utilises. La prediction de la longueur de delaminage lors des chargements en fatigue d'une piece est tres importante pour assurer qu'une fissure interlaminaire ne va pas croitre excessivement et causer la rupture de cette piece avant la fin de sa duree de vie de conception. Selon la tendance recente, ces modeles sont souvent bases sur l'approche de zone cohesive avec une formulation par elements finis. Au cours des travaux presentes dans cette these, le modele de progression du delaminage en fatigue de Landry & LaPlante (2012) a ete ameliore en y ajoutant le traitement des chargements en mode mixte I/II et en y modifiant l'algorithme du calcul de la force d'entrainement maximale du delaminage. Une calibration des parametres de zone cohesive a ete faite a partir des essais quasi-statiques experimentaux en mode I et II. Des resultats de simulations numeriques des essais quasi-statiques en mode mixte I/II, avec des eprouvettes seches et humides, ont ete compares avec les essais experimentaux. Des simulations numeriques en fatigue ont aussi ete faites et comparees avec les resultats experimentaux du taux de propagation du delaminage. Les resultats numeriques des essais quasi-statiques et de fatigue ont montre une bonne correlation avec les resultats experimentaux pour toute la gamme des mixites des modes I/II etudiee.
Surface Modification of Silicon Pillar Arrays To Enhance Fluorescence Detection of Uranium and DNA

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lincoln, Danielle R.; Charlton, Jennifer J.; Hatab, Nahla A.

There is an ever-growing need for detection methods that are both sensitive and efficient, such that reagent and sample consumption is minimized. Nanopillar arrays offer an attractive option to fill this need by virtue of their small scale in conjunction with their field enhancement intensity gains. This work investigates the use of nanopillar substrates for the detection of the uranyl ion and DNA, two analytes unalike but for their low quantum efficiencies combined with the need for high-throughput analyses. Here in this paper, the adaptability of these platforms was explored, as methods for the successful surface immobilization of both analytesmore » were developed and compared, resulting in a limit of detection for the uranyl ion of less than 1 ppm with a 0.2 μL sample volume. Moreover, differentiation between single-stranded and double-stranded DNA was possible, including qualitative identification between double-stranded DNA and DNA of the same sequence, but with a 10-base-pair mismatch.« less
cgDNAweb: a web interface to the cgDNA sequence-dependent coarse-grain model of double-stranded DNA.

PubMed

De Bruin, Lennart; Maddocks, John H

2018-06-14

The sequence-dependent statistical mechanical properties of fragments of double-stranded DNA is believed to be pertinent to its biological function at length scales from a few base pairs (or bp) to a few hundreds of bp, e.g. indirect read-out protein binding sites, nucleosome positioning sequences, phased A-tracts, etc. In turn, the equilibrium statistical mechanics behaviour of DNA depends upon its ground state configuration, or minimum free energy shape, as well as on its fluctuations as governed by its stiffness (in an appropriate sense). We here present cgDNAweb, which provides browser-based interactive visualization of the sequence-dependent ground states of double-stranded DNA molecules, as predicted by the underlying cgDNA coarse-grain rigid-base model of fragments with arbitrary sequence. The cgDNAweb interface is specifically designed to facilitate comparison between ground state shapes of different sequences. The server is freely available at cgDNAweb.epfl.ch with no login requirement.
Energy required to pinch a DNA plectoneme

NASA Astrophysics Data System (ADS)

Barde, Céline; Destainville, Nicolas; Manghi, Manoel

2018-03-01

DNA supercoiling plays an important role from a biological point of view. One of its consequences at the supramolecular level is the formation of DNA superhelices named plectonemes. Normally separated by a distance on the order of 10 nm, the two opposite double strands of a DNA plectoneme must be brought closer if a protein or protein complex implicated in genetic regulation is to be bound simultaneously to both strands, as if the plectoneme was locally pinched. We propose an analytic calculation of the energetic barrier, of elastic nature, required to bring closer the two loci situated on the opposed double strands. We examine how this energy barrier scales with the DNA supercoiling. For physically relevant values of elastic parameters and of supercoiling density, we show that the energy barrier is in the kBT range under physiological conditions, thus demonstrating that the limiting step to loci encounter is more likely the preceding plectoneme slithering bringing the two loci side by side.

Surface Modification of Silicon Pillar Arrays To Enhance Fluorescence Detection of Uranium and DNA

DOE PAGES

Lincoln, Danielle R.; Charlton, Jennifer J.; Hatab, Nahla A.; ...

2017-10-27

There is an ever-growing need for detection methods that are both sensitive and efficient, such that reagent and sample consumption is minimized. Nanopillar arrays offer an attractive option to fill this need by virtue of their small scale in conjunction with their field enhancement intensity gains. This work investigates the use of nanopillar substrates for the detection of the uranyl ion and DNA, two analytes unalike but for their low quantum efficiencies combined with the need for high-throughput analyses. Here in this paper, the adaptability of these platforms was explored, as methods for the successful surface immobilization of both analytesmore » were developed and compared, resulting in a limit of detection for the uranyl ion of less than 1 ppm with a 0.2 μL sample volume. Moreover, differentiation between single-stranded and double-stranded DNA was possible, including qualitative identification between double-stranded DNA and DNA of the same sequence, but with a 10-base-pair mismatch.« less
Effect of C(60) fullerene on the duplex formation of i-motif DNA with complementary DNA in solution.

PubMed

Jin, Kyeong Sik; Shin, Su Ryon; Ahn, Byungcheol; Jin, Sangwoo; Rho, Yecheol; Kim, Heesoo; Kim, Seon Jeong; Ree, Moonhor

2010-04-15

The structural effects of fullerene on i-motif DNA were investigated by characterizing the structures of fullerene-free and fullerene-bound i-motif DNA, in the presence of cDNA and in solutions of varying pH, using circular dichroism and synchrotron small-angle X-ray scattering. To facilitate a direct structural comparison between the i-motif and duplex structures in response to pH stimulus, we developed atomic scale structural models for the duplex and i-motif DNA structures, and for the C(60)/i-motif DNA hybrid associated with the cDNA strand, assuming that the DNA strands are present in an ideal right-handed helical conformation. We found that fullerene shifted the pH-induced conformational transition between the i-motif and the duplex structure, possibly due to the hydrophobic interactions between the terminal fullerenes and between the terminal fullerenes and an internal TAA loop in the DNA strand. The hybrid structure showed a dramatic reduction in cyclic hysteresis.
Force-extension behavior of DNA in the presence of DNA-bending nucleoid associated proteins

NASA Astrophysics Data System (ADS)

Dahlke, K.; Sing, C. E.

2018-02-01

Interactions between nucleoid associated proteins (NAPs) and DNA affect DNA polymer conformation, leading to phenomena such as concentration dependent force-extension behavior. These effects, in turn, also impact the local binding behavior of the protein, such as high forces causing proteins to unbind, or proteins binding favorably to locally bent DNA. We develop a coarse-grained NAP-DNA simulation model that incorporates both force- and concentration-dependent behaviors, in order to study the interplay between NAP binding and DNA conformation. This model system includes multi-state protein binding and unbinding, motivated by prior work, but is now dependent on the local structure of the DNA, which is related to external forces acting on the DNA strand. We observe the expected qualitative binding behavior, where more proteins are bound at lower forces than at higher forces. Our model also includes NAP-induced DNA bending, which affects DNA elasticity. We see semi-quantitative matching of our simulated force-extension behavior to the reported experimental data. By using a coarse-grained simulation, we are also able to look at non-equilibrium behaviors, such as dynamic extension of a DNA strand. We stretch a DNA strand at different rates and at different NAP concentrations to observe how the time scales of the system (such as pulling time and unbinding time) work in concert. When these time scales are similar, we observe measurable rate-dependent changes in the system, which include the number of proteins bound and the force required to extend the DNA molecule. This suggests that the relative time scales of different dynamic processes play an important role in the behavior of NAP-DNA systems.
Repeated mass strandings of Miocene marine mammals from Atacama Region of Chile point to sudden death at sea.

PubMed

Pyenson, Nicholas D; Gutstein, Carolina S; Parham, James F; Le Roux, Jacobus P; Chavarría, Catalina Carreño; Little, Holly; Metallo, Adam; Rossi, Vincent; Valenzuela-Toro, Ana M; Velez-Juarbe, Jorge; Santelli, Cara M; Rogers, David Rubilar; Cozzuol, Mario A; Suárez, Mario E

2014-04-22

Marine mammal mass strandings have occurred for millions of years, but their origins defy singular explanations. Beyond human causes, mass strandings have been attributed to herding behaviour, large-scale oceanographic fronts and harmful algal blooms (HABs). Because algal toxins cause organ failure in marine mammals, HABs are the most common mass stranding agent with broad geographical and widespread taxonomic impact. Toxin-mediated mortalities in marine food webs have the potential to occur over geological timescales, but direct evidence for their antiquity has been lacking. Here, we describe an unusually dense accumulation of fossil marine vertebrates from Cerro Ballena, a Late Miocene locality in Atacama Region of Chile, preserving over 40 skeletons of rorqual whales, sperm whales, seals, aquatic sloths, walrus-whales and predatory bony fish. Marine mammal skeletons are distributed in four discrete horizons at the site, representing a recurring accumulation mechanism. Taphonomic analysis points to strong spatial focusing with a rapid death mechanism at sea, before being buried on a barrier-protected supratidal flat. In modern settings, HABs are the only known natural cause for such repeated, multispecies accumulations. This proposed agent suggests that upwelling zones elsewhere in the world should preserve fossil marine vertebrate accumulations in similar modes and densities.
Repeated mass strandings of Miocene marine mammals from Atacama Region of Chile point to sudden death at sea

PubMed Central

Pyenson, Nicholas D.; Gutstein, Carolina S.; Parham, James F.; Le Roux, Jacobus P.; Chavarría, Catalina Carreño; Little, Holly; Metallo, Adam; Rossi, Vincent; Valenzuela-Toro, Ana M.; Velez-Juarbe, Jorge; Santelli, Cara M.; Rogers, David Rubilar; Cozzuol, Mario A.; Suárez, Mario E.

2014-01-01

Marine mammal mass strandings have occurred for millions of years, but their origins defy singular explanations. Beyond human causes, mass strandings have been attributed to herding behaviour, large-scale oceanographic fronts and harmful algal blooms (HABs). Because algal toxins cause organ failure in marine mammals, HABs are the most common mass stranding agent with broad geographical and widespread taxonomic impact. Toxin-mediated mortalities in marine food webs have the potential to occur over geological timescales, but direct evidence for their antiquity has been lacking. Here, we describe an unusually dense accumulation of fossil marine vertebrates from Cerro Ballena, a Late Miocene locality in Atacama Region of Chile, preserving over 40 skeletons of rorqual whales, sperm whales, seals, aquatic sloths, walrus-whales and predatory bony fish. Marine mammal skeletons are distributed in four discrete horizons at the site, representing a recurring accumulation mechanism. Taphonomic analysis points to strong spatial focusing with a rapid death mechanism at sea, before being buried on a barrier-protected supratidal flat. In modern settings, HABs are the only known natural cause for such repeated, multispecies accumulations. This proposed agent suggests that upwelling zones elsewhere in the world should preserve fossil marine vertebrate accumulations in similar modes and densities. PMID:24573855
156. Frank Deras Jr., Photographer December 1997 DETAIL VIEW OF ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

156. Frank Deras Jr., Photographer December 1997 DETAIL VIEW OF STRAND SHOE AND EYE BAR AT SAN FRANCISCO ANCHORAGE (HUMAN SCALE: TERRY COSTA, CALTRANS EMPLOYEE), FACING SOUTHEAST. - San Francisco Oakland Bay Bridge, Spanning San Francisco Bay, San Francisco, San Francisco County, CA
Inhomogeneous magnesium hydride synthesized by low temperature ion implantation: weak localization effect

NASA Astrophysics Data System (ADS)

Nédellec, P.; Dumoulin, L.; Burger, J. P.; Bernas, H.; Köstler, H.; Traverse, A.

1993-11-01

Metastable MgHx hydride was prepared by H ion implantation into Mg films at 5 K. The resistivity and magnetoresistance temperature dependence reveal weak localization effects due to atomic disorder. At low hydrogen concentrations, x le 0.3, the conductivity varies as σ sim log(T), typical of two-dimensional weak localization behaviour. The resistivity is also very sensitive to the sample inhomogeneity, due to H diffusion, which can be modelled by introducing a temperature-dependent geometrical percolating factor G. At higher H concentrations, 0.7 le x le 3, after annealing at 20 K, 50 K and 110 K, the samples also exhibit weak localization but with three-dimensional behaviour i.e. a σ sim sqrt{T}. Our analysis is consistent with the existence of an inhomogeneous system formed by a mixture of two phases with contrasted conduction properties, one of which is a well-behaved metal, while the other displays the localization properties. The results lead us to identify the former phase to a non percolating superconducting phase at low temperature. Des films d'hydrure MgHx sont préparés, hors de l'équilibre thermodynamique, par implantation d'ions H dans des films de Mg maintenus à 5 K. La mesure de la résistance et de la magnétorésistance en fonction de la température met en évidence des effets importants de localisation électronique due au désordre atomique. Pour les faibles concentrations d'hydrogène, x le 0,3, la conductivité varie comme σ sim log(T), variation caractéristique d'un comportement dominé par les effets de localisation électronique faible à 2 dimensions. La résistivité est très sensible aux effets d'inhomogénéité, liés à la diffusion de H. Nous avons modélisé ces effets en introduisant un coefficient géométrique variant avec la température. Pour les concentrations plus élevées (0, 7 le x le 3), après un recuit à 20 K, 50 K et 110 K, les films montrent également des effets de localisation mais la conductivité varie maintenant comme σ sim sqrt{T}, caractéristique d'un comportement tridimensionnel. L'analyse des résultats est compatible avec l'hypothèse d'un système inhomogène formé du mélange de deux phases avec des propriétés électriques contrastées : un “mauvais métal" et un “bon métal" qui, à basse température, pourrait présenter un état supraconducteur non percolant.
Des recommandations probantes pour surveiller l’innocuité des antipsychotiques de deuxième génération chez les enfants et les adolescents

PubMed Central

Pringsheim, Tamara; Panagiotopoulos, Constadina; Davidson, Jana; Ho, Josephine

2012-01-01

HISTORIQUE : Au Canada, l’utilisation d’antipsychotiques, notamment les antipsychotiques de deuxième génération (ADG), a augmenté de façon considérable depuis cinq ans chez les enfants ayant des troubles de santé mentale. Ces médicaments ont le potentiel de causer de graves complications métaboliques et neurologiques lorsqu’on les utilise de manière chronique. OBJECTIF : Synthétiser les données probantes relatives aux effets secondaires métaboliques et neurologiques précis associés à l’usage d’ADG chez les enfants et fournir des recommandations probantes sur la surveillance de ces effets secondaires. MÉTHODOLOGIE : Les auteurs ont procédé à une analyse systématique des essais cliniques contrôlés des ADG auprès d’enfants. Ils ont fait des recommandations à l’égard de la surveillance de l’innocuité des ADG d’après un modèle de classification fondé sur le système GRADE (système de notation de l’évaluation et de l’élaboration des recommandations). Lorsque les données probantes n’étaient pas suffisantes, ils fondaient leurs recommandations sur le consensus et l’avis d’experts. Un groupe consensuel multidisciplinaire a analysé toutes les données probantes pertinentes et est parvenu à un consensus à l’égard des recommandations. RÉSULTATS : Les recommandations probantes portant sur la surveillance de l’innocuité des ADG figurent dans les présentes lignes directrices. Les auteurs indiquent la qualité des recommandations relatives à des examens physiques et tests de laboratoire précis à l’égard de chaque ADG à des moments déterminés. CONCLUSION : De multiples essais aléatoires et contrôlés ont permis d’évaluer l’efficacité de bon nombre des ADG utilisés pour traiter les troubles de santé mentale en pédiatrie. Toutefois, leurs avantages ne sont pas sans risques : on observe à la fois des effets secondaires métaboliques et neurologiques chez les enfants traités au moyen d’ADG. Le risque de prise de poids, d’augmentation de l’indice de masse corporelle et de taux lipidiques anormaux est plus élevé à l’utilisation d’olanzapine, suivie de la clozapine et de la quétiapine. Quant au risque d’effets secondaires neurologiques des traitements, il est plus élevé à l’utilisation de rispéridone, d’olanzapine et d’aripiprazole. Des interventions de surveillance pertinentes des effets secondaires amélioreront la qualité des soins des enfants traités à l’aide de ces médicaments. PMID:24082813
Etude des melanges co-continus d'acide polylactique et d'amidon thermoplastique (PLA/TPS)

NASA Astrophysics Data System (ADS)

Chavez Garcia, Maria Graciela

Les melanges co-continus sont des melanges polymeriques ou chaque composant se trouve dans une phase continue. Pour cette raison, les caracteristiques de chacun des composants se combinent et il en resulte un materiau avec une morphologie et des proprietes particulieres. L'acide polylactique (PLA) et l'amidon thermoplastique (TPS) sont des biopolymeres qui proviennent de ressources renouvelables et qui sont biodegradables. Dans ce projet, differents melanges de PLA et TPS a une haute concentration de TPS ont ete prepares dans une extrudeuse bi-vis afin de generer des structures co-continues. Grace a la technique de lixiviation selective, le TPS est enleve pour creer une structure poreuse de PLA qui a pu etre analysee au moyen de la microtomographie R-X et de la microscopie electronique a balayage MEB. L'analyse des images 2D et 3D confirme la presence de la structure co-continue dans les melanges dont la concentration en TPS. se situe entre 66% et 80%. L'effet de deux plastifiants, le glycerol seul et le melange de glycerol et de sorbitol, dans la formulation de TPS est etudie dans ce travail. De plus, nous avons evalue l'effet du PLA greffe a l'anhydride maleique (PLAg) en tant que compatibilisant. On a trouve que la phase de TPS obtenue avec le glycerol est plus grande. L'effet de recuit sur la taille de phases est aussi analyse. Grace aux memes techniques d'analyse, on a etudie l'effet du procede de moulage par injection sur la morphologie. On a constate que les pieces injectees presentent une microstructure heterogene et differente entre la surface et le centre de la piece. Pres de la surface, une peau plus riche en PLA est presente et les phases de TPS y sont allongees sous forme de lamelles. Plus au centre de la piece, une morphologie plus cellulaire est observee pour chaque phase continue. L'effet des formulations sur les proprietes mecaniques a aussi ete etudie. Les pieces injectees dont la concentration de TPS est plus grande presentent une moindre resistance a la traction. La presence du compatibilisant dans la region co-continue affecte negativement cette resistance. En considerant que l'amidon est un biomateriau abondant, moins cher et plus rapidement biodegradable, son ajout dans le PLA presente l'avantage de reduire le cout tout en augmentant la vitesse de degradation du PLA. De plus, une structure continue poreuse de PLA produit par la technique de lixiviation selective a des applications potentielles soit comme materiau a degradation rapide ou encore, une fois la phase TPS retiree, comme substrat a porosite ouverte pour la fabrication de membranes, de supports cellulaires ou de filtres. Mots-cles : melanges immiscibles, acide polylactique, amidon thermoplastique, morphologie cocontinue, lixiviation selective, microtomographie R-X, materiau rigide poreux biodegradable.
Mapping yeast origins of replication via single-stranded DNA detection.

PubMed

Feng, Wenyi; Raghuraman, M K; Brewer, Bonita J

2007-02-01

Studies in th Saccharomyces cerevisiae have provided a framework for understanding how eukaryotic cells replicate their chromosomal DNA to ensure faithful transmission of genetic information to their daughter cells. In particular, S. cerevisiae is the first eukaryote to have its origins of replication mapped on a genomic scale, by three independent groups using three different microarray-based approaches. Here we describe a new technique of origin mapping via detection of single-stranded DNA in yeast. This method not only identified the majority of previously discovered origins, but also detected new ones. We have also shown that this technique can identify origins in Schizosaccharomyces pombe, illustrating the utility of this method for origin mapping in other eukaryotes.
Comportement instationnaire des thermoéléments à effet Peltier multi-étages

NASA Astrophysics Data System (ADS)

Monchoux, F.; Zély, D.; Cordier, A.

1995-01-01

The analysis of thermoelectric phenomena is possible based on non-equilibrium thermodynamics. Integration of the thermal balance equation leads to an analytical solution for the non-stationnary behaviour. The influence to Thomson effect is commmented. The model, introduced in the complete software TRNSYS, permits the modelling of complex systems including such elements in their thermal regulation. La thermodynamique des processus irréversibles permet l'analyse des phénomènes thermoélectriques. Par intégration de l'équation de bilan thermique, on a obtenu une solution analytique pour le régime non stationnaire donnant la température en tous points et le flux absorbé. On a analysé l'influence de l'effet Thomson. Le modèle a été inclu dans le code plus général TRNSYS qui permet la modélisation de systèmes complexes.
Isotope effect in the organic superconductor β_H-(BEDT-TTF)2I3 where BEDT-TTF is bis (ethylenedithiotetrathiafulvalene)

NASA Astrophysics Data System (ADS)

Auban-Senzier, P.; Bourbonnais, C.; Jérome, D.; Lenoir, C.; Batail, P.; Canadell, E.; Buisson, J. P.; Lefrant, S.

1993-03-01

We have performed the simultaneous investigation of the isotope effect on the superconducting transition and on the Raman spectra in the organic superconductor β_H-(BEDT-TTF)2I3 (T_c = 8 K). For this purpose, we substitute ^{13}C for ^{12}C on the carbon sites of the central double bond of BEDT-TTF molecule. The isotope shifts measured by Raman experiments can be fairly well explained by standard molecular dynamics. However, the critical temperature is lowered by 0.2 K in the ^{13}C enriched material. We analyse the possible sources of this remarkable downward shift which leads to an isotope coefficient higher than the BCS value. The extended-Hückel calculations of the density of states for the two HOMO bands of β_H-(BEDT-TTF)2I3 do show that, within the framework of a weak coupling theory, its sizeable variation on the scale of ω_D cannot account for the observed isotope effect. On the other hand, we discuss how inelastic electronic scattering observed in resistivity measurements just above T_c can lead through a pair breaking mechanism to a sizeable increase of the isotope coefficient. Nous présentons une étude simultanée d'effet isotopique sur la transition supraconductrice et les spectres Raman dans le supraconducteur organique β_H-(BEDT-TTF)2I3 (T_c = 8 K). Pour cela, nous avons synthétisé le composé dans lequel les atomes de carbone de la double liaison centrale de la molécule BEDT-TTF sont substitués par l'isotope ^{13}C. Les déplacements isotopiques mesurés par spectroscopie Raman sont bien expliqués par la dynamique moléculaire standard. Cependant, la température critique est abaissée de 0.2 K dans le matériau enrichi en ^{13}C. Nous étudions les origines possibles de cet effet qui permet d'obtenir un coefficient isotopique supérieur à la valeur BCS. Des calculs de la densité d'états effectués par la méthode de Hückel étendue pour les deux bandes HOMO du composé montrent que, dans le cadre d'une théorie de couplage faible, son importante variation à l'échelle de ω_D ne peut expliquer l'effet observé. D'autre part, nous expliquons comment la diffusion électronique inélastique observée en résistivité juste au-dessus de T_c peut conduire via un mécanisme de brisure de paires, à une augmentation significative du coefficient isotopique.
Comprehensive track-structure based evaluation of DNA damage by light ions from radiotherapy-relevant energies down to stopping

PubMed Central

Friedland, W.; Schmitt, E.; Kundrát, P.; Dingfelder, M.; Baiocco, G.; Barbieri, S.; Ottolenghi, A.

2017-01-01

Track structures and resulting DNA damage in human cells have been simulated for hydrogen, helium, carbon, nitrogen, oxygen and neon ions with 0.25–256 MeV/u energy. The needed ion interaction cross sections have been scaled from those of hydrogen; Barkas scaling formula has been refined, extending its applicability down to about 10 keV/u, and validated against established stopping power data. Linear energy transfer (LET) has been scored from energy deposits in a cell nucleus; for very low-energy ions, it has been defined locally within thin slabs. The simulations show that protons and helium ions induce more DNA damage than heavier ions do at the same LET. With increasing LET, less DNA strand breaks are formed per unit dose, but due to their clustering the yields of double-strand breaks (DSB) increase, up to saturation around 300 keV/μm. Also individual DSB tend to cluster; DSB clusters peak around 500 keV/μm, while DSB multiplicities per cluster steadily increase with LET. Remarkably similar to patterns known from cell survival studies, LET-dependencies with pronounced maxima around 100–200 keV/μm occur on nanometre scale for sites that contain one or more DSB, and on micrometre scale for megabasepair-sized DNA fragments. PMID:28345622
Improvement of DNA adenylation using T4 DNA ligase with a template strand and a strategically mismatched acceptor strand

PubMed Central

Patel, Maha P.; Baum, Dana A.; Silverman, Scott K.

2008-01-01

DNA with a 5′-adenylpyrophosphoryl cap (5′-adenylated DNA; AppDNA) is an activated form of DNA that is the biochemical intermediate of the reactions catalyzed by DNA ligase, RNA ligase, polynucleotide kinase, and other nucleic acid modifying enzymes. 5′-Adenylated DNA is also useful for in vitro selection experiments. Efficient preparation of 5′-adenylated DNA is therefore desirable for several biochemical applications. Here we have developed a DNA adenylation procedure that uses T4 DNA ligase and is more reliable than a previously reported approach that used the 5′-phosphorylated donor DNA substrate to be adenylated, a DNA template, and ATP but no acceptor strand. Our improved DNA adenylation procedure uses the above components as well as an acceptor strand that has a strategically chosen C-T acceptor-template mismatch directly adjacent to the adenylation site. This mismatch permits adenylation of the donor DNA substrate but largely suppresses subsequent ligation of the donor with the acceptor, as assayed on nine different DNA substrates that collectively have all four DNA nucleotides represented at each of the first two positions. The new DNA adenylation procedure is successful using either laboratory-prepared or commercial T4 DNA ligase and works well on the preparative (2 nmol) scale for all nine of the test DNA substrates. PMID:18022669
A Drift Model to Predict Where Marine Mammals Struck by Tidal Stream Turbines Might Strand

NASA Astrophysics Data System (ADS)

Bedington, M.; Dale, A. C.; Wilson, B.

2016-02-01

Tidal stream turbines will be a novel technology in Scottish waters, the risk of blade collision with marine mammals is an unknown environmental risk. In order to monitor this risk when scaling to commercial size arrays it is proposed to walk beaches for stranded carcases; where to conduct this monitoring for a given site can be informed by the use of an appropriately constructed drift model. A drift model has been created and investigated for case studies on the West Coast of Scotland. The model uses forcing fields from existing and specially set up current, wind and wave models. It considers the effect of carcase buoyancy, the combination of forcing fields and the coastline dynamics as well as the problems that arise from numerical approximations and uncertainty. Novel fieldwork using carcase like drifters has been undertaken to parametrise and inform the model, and to further understand the effect of wave transport on carcase sized objects, a feature not previously considered in drift work. The model is found to have sensitivity to the wind and wave parametrisations of carcases, as well as specification of stranding schemes. It shows heterogeneous stranding patterns which are site specific and allow a hierarchy of areas to be specified for monitoring. The uncertainties in this approach and the potential utility and drawbacks of using this sort of tool in environmental monitoring and mitigation are also discussed.
Preparation of Double-Stranded (Replicative Form) Bacteriophage M13 DNA.

PubMed

Green, Michael R; Sambrook, Joseph

2017-11-01

The double-stranded, closed-circular, replicative form (RF) of M13 DNA is present in high copy numbers in infected cells, and its physical characteristics are essentially identical to those of closed-circular plasmid DNAs. Any of the methods commonly used to purify plasmid DNA can therefore be used to isolate M13 RF DNA. This protocol describes the isolation of M13 RF DNA by alkaline lysis from small volumes (1-2 mL) of infected bacterial cultures. The yield of DNA (1-4 mg, depending on the size of the M13 clone) is more than enough for most purposes in molecular cloning. However, should more DNA be needed, the procedure can easily be scaled up. © 2017 Cold Spring Harbor Laboratory Press.
Business models and leadership styles in small medical device and bio-science businesses--examples in a region and their implications.

PubMed

Williams, D J; Hourd, P C

2004-01-01

This paper reviews the leadership styles and business models found in small technologically based businesses operating in the healthcare sector within one of the UK regions, the East Midlands. The most frequently encountered business model strands were 1) mixed economies: that fund development with service income; cross-sectoral product portfolios; and decoupled business portfolios led by a single entrepreneur and 2) scale sensitive "stay small" models including the avoidance of venture capital; "early exit"; and virtual business strands. There was found to be little correlation between leadership style and business model for the small number of businesses surveyed. The avoidance of venture capital is in direct contrast to adjacent regions.
Experimental results of 40-kA Nb[sub 3]Al cable-in-conduit conductor for fusion machines

DOE Office of Scientific and Technical Information (OSTI.GOV)

Takahashi, Y.; Sugimoto, M.; Isono, T.

1994-07-01

A 40-kA Nb[sub 3]Al cable-in-conduit conductor has been developed for the toroidal field coils of fusion reactors, because Nb[sub 3]Al has excellent mechanical performance. This conductor consists of 405 copper-stabilized multifilamentary strands inserted into a CuNi case circular conduit. The Nb[sub 3]Al strands are fabricated by the Jelly-roll process with a diameter of 1.22 mm. This conductor could be operated up to a current of 46 kA at an external field of 11.2 T. Accordingly, Nb[sub 3]Al promises to soon become a useful superconductor for large-scale high-field applications, such as fusion machines.
Interatomic Coulombic Decay Effects in Theoretical DNA Recombination Systems Involving Protein Interaction Sites

NASA Astrophysics Data System (ADS)

Vargas, E. L.; Rivas, D. A.; Duot, A. C.; Hovey, R. T.; Andrianarijaona, V. M.

2015-03-01

DNA replication is the basis for all biological reproduction. A strand of DNA will ``unzip'' and bind with a complimentary strand, creating two identical strands. In this study, we are considering how this process is affected by Interatomic Coulombic Decay (ICD), specifically how ICD affects the individual coding proteins' ability to hold together. ICD mainly deals with how the electron returns to its original state after excitation and how this affects its immediate atomic environment, sometimes affecting the connectivity between interaction sites on proteins involved in the DNA coding process. Biological heredity is fundamentally controlled by DNA and its replication therefore it affects every living thing. The small nature of the proteins (within the range of nanometers) makes it a good candidate for research of this scale. Understanding how ICD affects DNA molecules can give us invaluable insight into the human genetic code and the processes behind cell mutations that can lead to cancer. Authors wish to give special thanks to Pacific Union College Student Senate in Angwin, California, for their financial support.
A Simple Model for the Evolution of Multi-Stranded Coronal Loops

NASA Technical Reports Server (NTRS)

Fuentes, M. C. Lopez; Klimchuk, J. A.

2010-01-01

We develop and analyze a simple cellular automaton (CA) model that reproduces the main properties of the evolution of soft X-ray coronal loops. We are motivated by the observation that these loops evolve in three distinguishable phases that suggest the development, maintainance, and decay of a self-organized system. The model is based on the idea that loops are made of elemental strands that are heated by the relaxation of magnetic stress in the form of nanoflares. In this vision, usually called "the Parker conjecture" (Parker 1988), the origin of stress is the displacement of the strand footpoints due to photospheric convective motions. Modeling the response and evolution of the plasma we obtain synthetic light curves that have the same characteristic properties (intensity, fluctuations, and timescales) as the observed cases. We study the dependence of these properties on the model parameters and find scaling laws that can be used as observational predictions of the model. We discuss the implications of our results for the interpretation of recent loop observations in different wavelengths. Subject headings: Sun: corona - Sun: flares - Sun: magnetic topology - Sun: X-rays, gamma rays

Risk analysis reveals global hotspots for marine debris ingestion by sea turtles.

PubMed

Schuyler, Qamar A; Wilcox, Chris; Townsend, Kathy A; Wedemeyer-Strombel, Kathryn R; Balazs, George; van Sebille, Erik; Hardesty, Britta Denise

2016-02-01

Plastic marine debris pollution is rapidly becoming one of the critical environmental concerns facing wildlife in the 21st century. Here we present a risk analysis for plastic ingestion by sea turtles on a global scale. We combined global marine plastic distributions based on ocean drifter data with sea turtle habitat maps to predict exposure levels to plastic pollution. Empirical data from necropsies of deceased animals were then utilised to assess the consequence of exposure to plastics. We modelled the risk (probability of debris ingestion) by incorporating exposure to debris and consequence of exposure, and included life history stage, species of sea turtle and date of stranding observation as possible additional explanatory factors. Life history stage is the best predictor of debris ingestion, but the best-fit model also incorporates encounter rates within a limited distance from stranding location, marine debris predictions specific to the date of the stranding study and turtle species. There is no difference in ingestion rates between stranded turtles vs. those caught as bycatch from fishing activity, suggesting that stranded animals are not a biased representation of debris ingestion rates in the background population. Oceanic life-stage sea turtles are at the highest risk of debris ingestion, and olive ridley turtles are the most at-risk species. The regions of highest risk to global sea turtle populations are off of the east coasts of the USA, Australia and South Africa; the east Indian Ocean, and Southeast Asia. Model results can be used to predict the number of sea turtles globally at risk of debris ingestion. Based on currently available data, initial calculations indicate that up to 52% of sea turtles may have ingested debris. © 2015 John Wiley & Sons Ltd.
Metallographic autopsies of full-scale ITER prototype cable-in-conduit conductors after full cyclic testing in SULTAN: III. The importance of strand surface roughness in long twist pitch conductors

DOE PAGES

Sanabria, Charlie; Lee, Peter J.; Starch, William; ...

2016-05-31

As part of the ITER conductor qualification process, 3 m long Cable-in-Conduit Conductors (CICCs) were tested at the SULTAN facility under conditions simulating ITER operation so as to establish the current sharing temperature, T cs, as a function of multiple full Lorentz force loading cycles. After a comprehensive evaluation of both the Toroidal Field (TF) and the Central Solenoid (CS) conductors, it was found that T cs degradation was common in long twist pitch TF conductors while short twist pitch CS conductors showed some T cs increase. However, one kind of TF conductors containing superconducting strand fabricated by the Bochvarmore » Institute of Inorganic Materials (VNIINM) avoided T cs degradation despite having long twist pitch. In our earlier metallographic autopsies of long and short twist pitch CS conductors, we observed a substantially greater transverse strand movement under Lorentz force loading for long twist pitch conductors, while short twist pitch conductors had negligible transverse movement. With help from the literature, we concluded that the transverse movement was not the source of T cs degradation but rather an increase of the compressive strain in the Nb 3Sn filaments possibly induced by longitudinal movement of the wires. Like all TF conductors this TF VNIINM conductor showed large transverse motions under Lorentz force loading, but Tcs actually increased, as in all short twist pitch CS conductors. We here propose that the high surface roughness of the VNIINM strand may be responsible for the suppression of the compressive strain enhancement (characteristic of long twist pitch conductors). Furthermore, it appears that increasing strand surface roughness could improve the performance of long twist pitch CICCs.« less
Metallographic autopsies of full-scale ITER prototype cable-in-conduit conductors after full cyclic testing in SULTAN: III. The importance of strand surface roughness in long twist pitch conductors

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sanabria, Charlie; Lee, Peter J.; Starch, William

As part of the ITER conductor qualification process, 3 m long Cable-in-Conduit Conductors (CICCs) were tested at the SULTAN facility under conditions simulating ITER operation so as to establish the current sharing temperature, T cs, as a function of multiple full Lorentz force loading cycles. After a comprehensive evaluation of both the Toroidal Field (TF) and the Central Solenoid (CS) conductors, it was found that T cs degradation was common in long twist pitch TF conductors while short twist pitch CS conductors showed some T cs increase. However, one kind of TF conductors containing superconducting strand fabricated by the Bochvarmore » Institute of Inorganic Materials (VNIINM) avoided T cs degradation despite having long twist pitch. In our earlier metallographic autopsies of long and short twist pitch CS conductors, we observed a substantially greater transverse strand movement under Lorentz force loading for long twist pitch conductors, while short twist pitch conductors had negligible transverse movement. With help from the literature, we concluded that the transverse movement was not the source of T cs degradation but rather an increase of the compressive strain in the Nb 3Sn filaments possibly induced by longitudinal movement of the wires. Like all TF conductors this TF VNIINM conductor showed large transverse motions under Lorentz force loading, but Tcs actually increased, as in all short twist pitch CS conductors. We here propose that the high surface roughness of the VNIINM strand may be responsible for the suppression of the compressive strain enhancement (characteristic of long twist pitch conductors). Furthermore, it appears that increasing strand surface roughness could improve the performance of long twist pitch CICCs.« less
Risk Analysis Reveals Global Hotspots for Marine Debris Ingestion by Sea Turtles

NASA Astrophysics Data System (ADS)

Schuyler, Q. A.; Wilcox, C.; Townsend, K.; Wedemeyer-Strombel, K.; Balazs, G.; van Sebille, E.; Hardesty, B. D.

2016-02-01

Plastic marine debris pollution is rapidly becoming one of the critical environmental concerns facing wildlife in the 21st century. Here we present a risk analysis for plastic ingestion by sea turtles on a global scale. We combined global marine plastic distributions based on ocean drifter data with sea turtle habitat maps to predict exposure levels to plastic pollution. Empirical data from necropsies of deceased animals were then utilised to assess the consequence of exposure to plastics. We modelled the risk (probability of debris ingestion) by incorporating exposure to debris and consequence of exposure, and included life history stage, species of sea turtle, and date of stranding observation as possible additional explanatory factors. Life history stage is the best predictor of debris ingestion, but the best-fit model also incorporates encounter rates within a limited distance from stranding location, marine debris predictions specific to the date of the stranding study, and turtle species. There was no difference in ingestion rates between stranded turtles vs. those caught as bycatch from fishing activity, suggesting that stranded animals are not a biased representation of debris ingestion rates in the background population. Oceanic life-stage sea turtles are at the highest risk of debris ingestion, and olive ridley turtles are the most at-risk species. The regions of highest risk to global sea turtle populations are off of the east coasts of the USA, Australia, and South Africa; the east Indian Ocean, and Southeast Asia. Model results can be used to predict the number of sea turtles globally at risk of debris ingestion. Based on currently available data, initial calculations indicate that up to 52% of sea turtles may have ingested debris.
Explaining observed red and blue-shifts using multi-stranded coronal loops

NASA Astrophysics Data System (ADS)

Regnier, S.; Walsh, R. W.; Pearson, J.

2012-03-01

Magnetic plasma loops have been termed the building blocks of the solar atmosphere. However, it must be recognised that if the range of loop structures we can observe do consist of many ''sub-resolution'' elements, then current one-dimensional hydrodynamic models are really only applicable to an individual plasma element or strand. Thus a loop should be viewed is an amalgamation of these strands. They could operate in thermal isolation from one another with a wide range of temperatures occurring across the structural elements. This scenario could occur when the energy release mechanism consists of localised, discrete bursts of energy that are due to small scale reconnection sites within the coronal magnetic field- the nanoflare coronal heating mechanism. These energy bursts occur in a time-dependent manner, distributed along the loop/strand length, giving a heating function that depends on space and time. An important observational discovery with the Hinode/EIS spectrometer is the existence of red and blue-shifts in coronal loops depending on the location of the footpoints (inner or outer parts of the active region), and the temperature of the emission line in which the Doppler shifts are measured. Based on the multi-stranded model developed by Sarkar and Walsh (2008, ApJ, 683, 516), we show that red and blue-shifts exist in different simulated Hinode/EIS passbands: cooler lines (OV-SiVII) being dominated by red-shifts, whilst hotter lines (FeXV-CaXVII) are a combination of both. The distribution of blue-shifts depends on the energy input and not so much on the heating location. Characteristic Doppler shifts generated fit well with observed values. We also simulate the Hinode/EIS rasters to closely compare our simulation with the observations. Even if not statistically significant, loops can have footpoints with opposite Doppler shifts.
Spatial and temporal patterns of stranded intertidal marine debris: is there a picture of global change?

PubMed

Browne, Mark Anthony; Chapman, M Gee; Thompson, Richard C; Amaral Zettler, Linda A; Jambeck, Jenna; Mallos, Nicholas J

2015-06-16

Floating and stranded marine debris is widespread. Increasing sea levels and altered rainfall, solar radiation, wind speed, waves, and oceanic currents associated with climatic change are likely to transfer more debris from coastal cities into marine and coastal habitats. Marine debris causes economic and ecological impacts, but understanding the scope of these requires quantitative information on spatial patterns and trends in the amounts and types of debris at a global scale. There are very few large-scale programs to measure debris, but many peer-reviewed and published scientific studies of marine debris describe local patterns. Unfortunately, methods of defining debris, sampling, and interpreting patterns in space or time vary considerably among studies, yet if data could be synthesized across studies, a global picture of the problem may be avaliable. We analyzed 104 published scientific papers on marine debris in order to determine how to evaluate this. Although many studies were well designed to answer specific questions, definitions of what constitutes marine debris, the methods used to measure, and the scale of the scope of the studies means that no general picture can emerge from this wealth of data. These problems are detailed to guide future studies and guidelines provided to enable the collection of more comparable data to better manage this growing problem.
Directional emission from dye-functionalized plasmonic DNA superlattice microcavities

PubMed Central

Park, Daniel J.; Ku, Jessie C.; Sun, Lin; Lethiec, Clotilde M.; Stern, Nathaniel P.; Schatz, George C.; Mirkin, Chad A.

2017-01-01

Three-dimensional plasmonic superlattice microcavities, made from programmable atom equivalents comprising gold nanoparticles functionalized with DNA, are used as a testbed to study directional light emission. DNA-guided nanoparticle colloidal crystallization allows for the formation of micrometer-scale single-crystal body-centered cubic gold nanoparticle superlattices, with dye molecules coupled to the DNA strands that link the particles together, in the form of a rhombic dodecahedron. Encapsulation in silica allows one to create robust architectures with the plasmonically active particles and dye molecules fixed in space. At the micrometer scale, the anisotropic rhombic dodecahedron crystal habit couples with photonic modes to give directional light emission. At the nanoscale, the interaction between the dye dipoles and surface plasmons can be finely tuned by coupling the dye molecules to specific sites of the DNA particle-linker strands, thereby modulating dye–nanoparticle distance (three different positions are studied). The ability to control dye position with subnanometer precision allows one to systematically tune plasmon–excition interaction strength and decay lifetime, the results of which have been supported by electrodynamics calculations that span length scales from nanometers to micrometers. The unique ability to control surface plasmon/exciton interactions within such superlattice microcavities will catalyze studies involving quantum optics, plasmon laser physics, strong coupling, and nonlinear phenomena. PMID:28053232
How a short double-stranded DNA bends

NASA Astrophysics Data System (ADS)

Shin, Jaeoh; Lee, O.-Chul; Sung, Wokyung

2015-04-01

A recent experiment using fluorescence microscopy showed that double-stranded DNA fragments shorter than 100 base pairs loop with the probabilities higher by the factor of 102-106 than predicted by the worm-like chain (WLC) model [R. Vafabakhsh and T. Ha, Science 337, 1101(2012)]. Furthermore, the looping probabilities were found to be nearly independent of the loop size. The results signify a breakdown of the WLC model for DNA mechanics which works well on long length scales and calls for fundamental understanding for stressed DNA on shorter length scales. We develop an analytical, statistical mechanical model to investigate what emerges to the short DNA under a tight bending. A bending above a critical level initiates nucleation of a thermally induced bubble, which could be trapped for a long time, in contrast to the bubbles in both free and uniformly bent DNAs, which are either transient or unstable. The trapped bubble is none other than the previously hypothesized kink, which releases the bending energy more easily as the contour length decreases. It leads to tremendous enhancement of the cyclization probabilities, in a reasonable agreement with experiment.
Multi-scale coarse-graining for the study of assembly pathways in DNA-brick self-assembly.

PubMed

Fonseca, Pedro; Romano, Flavio; Schreck, John S; Ouldridge, Thomas E; Doye, Jonathan P K; Louis, Ard A

2018-04-07

Inspired by recent successes using single-stranded DNA tiles to produce complex structures, we develop a two-step coarse-graining approach that uses detailed thermodynamic calculations with oxDNA, a nucleotide-based model of DNA, to parametrize a coarser kinetic model that can reach the time and length scales needed to study the assembly mechanisms of these structures. We test the model by performing a detailed study of the assembly pathways for a two-dimensional target structure made up of 334 unique strands each of which are 42 nucleotides long. Without adjustable parameters, the model reproduces a critical temperature for the formation of the assembly that is close to the temperature at which assembly first occurs in experiments. Furthermore, the model allows us to investigate in detail the nucleation barriers and the distribution of critical nucleus shapes for the assembly of a single target structure. The assembly intermediates are compact and highly connected (although not maximally so), and classical nucleation theory provides a good fit to the height and shape of the nucleation barrier at temperatures close to where assembly first occurs.
Multi-scale coarse-graining for the study of assembly pathways in DNA-brick self-assembly

NASA Astrophysics Data System (ADS)

Fonseca, Pedro; Romano, Flavio; Schreck, John S.; Ouldridge, Thomas E.; Doye, Jonathan P. K.; Louis, Ard A.

2018-04-01

Inspired by recent successes using single-stranded DNA tiles to produce complex structures, we develop a two-step coarse-graining approach that uses detailed thermodynamic calculations with oxDNA, a nucleotide-based model of DNA, to parametrize a coarser kinetic model that can reach the time and length scales needed to study the assembly mechanisms of these structures. We test the model by performing a detailed study of the assembly pathways for a two-dimensional target structure made up of 334 unique strands each of which are 42 nucleotides long. Without adjustable parameters, the model reproduces a critical temperature for the formation of the assembly that is close to the temperature at which assembly first occurs in experiments. Furthermore, the model allows us to investigate in detail the nucleation barriers and the distribution of critical nucleus shapes for the assembly of a single target structure. The assembly intermediates are compact and highly connected (although not maximally so), and classical nucleation theory provides a good fit to the height and shape of the nucleation barrier at temperatures close to where assembly first occurs.
Effets non lineaires transversaux dans les guides d'ondes plans

NASA Astrophysics Data System (ADS)

Dumais, Patrick

Les effets non lineaires transversaux dus a l'effet Kerr optique non resonant sont etudies dans deux types de guides a geometrie plane. D'abord (au chapitre 2), l'emission de solitons spatiaux d'un guide de type canal est etudie historiquement, analytiquement et numeriquement dans le but d'en faire la conception et la fabrication, en AlGaAs, dans la region spectrale en deca de la moitie de la bande interdite de ce materiau, soit autour de 1,5 microns. Le composant, tel que concu, comporte une structure de multipuits quantiques. Le desordonnement local de cette structure permet une variation locale du coefficient Kerr dans le guide, ce qui mene a l'emission d'un soliton spatial au-dela d'une puissance optique de seuil. L'observation experimentale d'un changement en fonction de l'intensite du profil de champ a la sortie du guide realise est presentee. Deuxiemement (au chapitre 3) une technique de mesure du coefficient Kerr dans un guide plan est presentee. Cette technique consiste a mesurer le changement de transmission au travers d'un cache place a la sortie du guide en fonction de l'intensite crete a l'entree du guide plan. Une methode pour determiner les conditions optimales pour la sensibilite de la mesure est presentee, illustree de plusieurs exemples. Finalement, la realisation d'un oscillateur parametrique optique basee sur un cristal de niobate de lithium a domaines periodiquement inverses est presentee. La theorie des oscillateurs parametriques optiques est exposee avec une emphase sur la generation d'impulsions intenses a des longueurs d'onde autour de 1,5 microns a partir d'un laser Ti:saphir, dans le but d'obtenir une source pour faire les experiences sur l'emission solitonique.
Marine mammal strandings in the New Caledonia region, Southwest Pacific.

PubMed

Borsa, Philippe

2006-04-01

Four hundred twenty three marine mammals, in 72 stranding events, were recorded between 1877 and 2005 in New Caledonia, the Loyalty Islands, and Vanuatu in the southwest Pacific. Sixteen species were represented in this count, including: minke whale, Balaenoptera acutorostrata (1 single stranding), sei whale, B. borealis (1 single stranding), blue whale, B. musculus (1 single stranding), humpback whale, Megaptera novaeangliae (2 single strandings), giant sperm whale, Physeter macrocephalus (18 single strandings, 2 pair strandings), pygmy sperm whale, Kogia breviceps (5 single strandings), dwarf sperm whale, K. sima (2 single strandings, 1 triple stranding), Blainville's beaked whale, Mesoplodon densirostris (2 single strandings), short-finned pilot whale, Globicephala macrorhynchus (4 strandings, 56 individuals), melon-headed whale, Peponocephala electra (1 single stranding and 2 mass strandings totalling 231 individuals), common dolphin, Delphinus delphis (1 single stranding), spinner dolphin, Stenella longirostris (1 pair stranding and 2 mass strandings of groups of approximately 30 individuals each), Indian Ocean bottlenose dolphin, Tursiops aduncus (2 single strandings), dugong, Dugong dugon (14 single strandings), and New Zealand fur seal, Arctocephalus forsteri (3 single strandings). A stranded rorqual identified as an Antarctic minke whale (B. bonaerensis), with coloration patterns that did not match known descriptions, was also reported. Sei whale was recorded for the first time in the tropical Southwest Pacific region and Antarctic minke whale, melon-headed whale, and Indian Ocean bottlenose dolphin were recorded for the first time in New Caledonia. Strandings of sperm whales were most frequent in the spring, but also occurred in autumn months, suggesting a seasonal pattern of occurrence possibly related to seasonal migration. One stranded humpback whale bore the scars of a killer whale's attack and one dugong was injured by a shark. Scars left by propellers were noted on several stranded animals including one Antarctic minke whale, one pygmy sperm whale, one dwarf sperm whale, and four dugongs. Collisions with vessels were suspected to be a frequent cause of death for dugong.
Dynamics of Bottlebrush Networks

NASA Astrophysics Data System (ADS)

Cao, Zhen; Daniel, William; Vatankhah-Varnosfaderani, Mohammad; Sheiko, Sergei; Dobrynin, Andrey

The deformation dynamics of bottlebrush networks in a melt state is studied using a combination of theoretical, computational, and experimental techniques. Three main molecular relaxation processes are identified in these systems: (i) relaxation of the side chains, (ii) relaxation of the bottlebrush backbones on length scales shorter than the bottlebrush Kuhn length (bK) , and (iii) relaxation of the bottlebrush network strands between cross-links. The relaxation of side chains having a degree of polymerization (DP), nsc, dominates the network dynamics on the time scales τ0 < t <=τsc , where τ0 and τsc τ0 (nsc + 1)2 are the characteristic relaxation times of monomeric units and side chains, respectively. In this time interval, the shear modulus at small deformations decays with time as G0BB (t) t - 1 / 2. On time scales t >τsc, bottlebrush elastomers behave as networks of filaments with a shear modulus G0BB (t) (nsc + 1)- 1 / 4t - 1 / 2 . Finally, the response of the bottlebrush networks becomes time independent at times scales longer than the Rouse time of the bottlebrush network strands. In this time interval, the network shear modulus depends on the network molecular parameters as G0BB (t) (nsc + 1)-1N-1 . Analysis of the simulation data shows that the stress evolution in the bottlebrush networks during constant strain-rate deformation can be described by a universal function. NSF DMR-1409710, DMR-1407645, DMR-1624569, DMR-1436201.
A homogeneous nucleic acid hybridization assay based on strand displacement.

PubMed Central

Vary, C P

1987-01-01

A homogeneous nucleic acid hybridization assay which is conducted in solution and requires no separation steps is described. The assay is based on the concept of strand displacement. In the strand displacement assay, an RNA "signal strand" is hybridized within a larger DNA strand termed the "probe strand", which is, in turn, complementary to the target nucleic acid of interest. Hybridization of the target nucleic acid with the probe strand ultimately results in displacement of the RNA signal strand. Strand displacement, therefore, causes conversion of the RNA from double to single-stranded form. The single-strand specificity of polynucleotide phosphorylase (EC 2.7.7.8) allows discrimination between double-helical and single-stranded forms of the RNA signal strand. As displacement proceeds, free RNA signal strands are preferentially phosphorolyzed to component nucleoside diphosphates, including adenosine diphosphate. The latter nucleotide is converted to ATP by pyruvate kinase(EC 2.7.1.40). Luciferase catalyzed bioluminescence is employed to measure the ATP generated as a result of strand displacement. Images PMID:3309890
Strand Plasticity Governs Fatigue in Colloidal Gels

NASA Astrophysics Data System (ADS)

van Doorn, Jan Maarten; Verweij, Joanne E.; Sprakel, Joris; van der Gucht, Jasper

2018-05-01

The repeated loading of a solid leads to microstructural damage that ultimately results in catastrophic material failure. While posing a major threat to the stability of virtually all materials, the microscopic origins of fatigue, especially for soft solids, remain elusive. Here we explore fatigue in colloidal gels as prototypical inhomogeneous soft solids by combining experiments and computer simulations. Our results reveal how mechanical loading leads to irreversible strand stretching, which builds slack into the network that softens the solid at small strains and causes strain hardening at larger deformations. We thus find that microscopic plasticity governs fatigue at much larger scales. This gives rise to a new picture of fatigue in soft thermal solids and calls for new theoretical descriptions of soft gel mechanics in which local plasticity is taken into account.
Enzymatic Synthesis of Self-assembled Dicer Substrate RNA Nanostructures for Programmable Gene Silencing.

PubMed

Jang, Bora; Kim, Boyoung; Kim, Hyunsook; Kwon, Hyokyoung; Kim, Minjeong; Seo, Yunmi; Colas, Marion; Jeong, Hansaem; Jeong, Eun Hye; Lee, Kyuri; Lee, Hyukjin

2018-06-08

Enzymatic synthesis of RNA nanostructures is achieved by isothermal rolling circle transcription (RCT). Each arm of RNA nanostructures provides a functional role of Dicer substrate RNA inducing sequence specific RNA interference (RNAi). Three different RNAi sequences (GFP, RFP, and BFP) are incorporated within the three-arm junction RNA nanostructures (Y-RNA). The template and helper DNA strands are designed for the large-scale in vitro synthesis of RNA strands to prepare self-assembled Y-RNA. Interestingly, Dicer processing of Y-RNA is highly influenced by its physical structure and different gene silencing activity is achieved depending on its arm length and overhang. In addition, enzymatic synthesis allows the preparation of various Y-RNA structures using a single DNA template offering on demand regulation of multiple target genes.
Poly(o-phenylenediamine) colloid-quenched fluorescent oligonucleotide as a probe for fluorescence-enhanced nucleic acid detection.

PubMed

Tian, Jingqi; Li, Hailong; Luo, Yonglan; Wang, Lei; Zhang, Yingwei; Sun, Xuping

2011-02-01

In this Letter, we demonstrate that chemical oxidation polymerization of o-phenylenediamine (OPD) by potassium bichromate at room temperature results in the formation of submicrometer-scale poly(o-phenylenediamine) (POPD) colloids. Such colloids can absorb and quench dye-labeled single-stranded DNA (ssDNA) very effectively. In the presence of a target, a hybridization event occurs, which produces a double-stranded DNA (dsDNA) that detaches from the POPD surface, leading to recovery of dye fluorescence. With the use of an oligonucleotide (OND) sequence associated with human immunodeficiency virus (HIV) as a model system, we demonstrate the proof of concept that POPD colloid-quenched fluorescent OND can be used as a probe for fluorescence-enhanced nucleic acid detection with selectivity down to single-base mismatch.
Accurate quantification of microRNA via single strand displacement reaction on DNA origami motif.

PubMed

Zhu, Jie; Feng, Xiaolu; Lou, Jingyu; Li, Weidong; Li, Sheng; Zhu, Hongxin; Yang, Lun; Zhang, Aiping; He, Lin; Li, Can

2013-01-01

DNA origami is an emerging technology that assembles hundreds of staple strands and one single-strand DNA into certain nanopattern. It has been widely used in various fields including detection of biological molecules such as DNA, RNA and proteins. MicroRNAs (miRNAs) play important roles in post-transcriptional gene repression as well as many other biological processes such as cell growth and differentiation. Alterations of miRNAs' expression contribute to many human diseases. However, it is still a challenge to quantitatively detect miRNAs by origami technology. In this study, we developed a novel approach based on streptavidin and quantum dots binding complex (STV-QDs) labeled single strand displacement reaction on DNA origami to quantitatively detect the concentration of miRNAs. We illustrated a linear relationship between the concentration of an exemplary miRNA as miRNA-133 and the STV-QDs hybridization efficiency; the results demonstrated that it is an accurate nano-scale miRNA quantifier motif. In addition, both symmetrical rectangular motif and asymmetrical China-map motif were tested. With significant linearity in both motifs, our experiments suggested that DNA Origami motif with arbitrary shape can be utilized in this method. Since this DNA origami-based method we developed owns the unique advantages of simple, time-and-material-saving, potentially multi-targets testing in one motif and relatively accurate for certain impurity samples as counted directly by atomic force microscopy rather than fluorescence signal detection, it may be widely used in quantification of miRNAs.
EXTREME-ULTRAVIOLET OBSERVATIONAL CONSEQUENCES OF THE SPATIAL LOCALIZATION OF NANOFLARE HEATING WITHIN A MULTISTRANDED ATMOSPHERIC LOOP

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sarkar, Aveek; Walsh, Robert W.

2009-07-10

Determining the preferred spatial location of the energy input to solar coronal loops would be an important step forward toward a more complete understanding of the coronal heating problem. Following from the 2008 paper of Sarkar and Walsh, this paper presents a short (10{sup 9} cm {identical_to}10 Mm) 'global loop' as 125 individual strands, where each strand is modeled independently by a one-dimensional hydrodynamic simulation. The strands undergo small-scale episodic heating and are coupled together through the frequency distribution of the total energy input to the loop which follows a power-law distribution with index {approx}2.29. The spatial preference of themore » swarm of heating events from apex to footpoint is investigated. From a theoretical perspective, the resulting emission-measure-weighted temperature profiles along these two extreme cases do demonstrate a possible observable difference. Subsequently, the simulated output is folded through the Transition Region and Coronal Explorer (TRACE) instrument response functions and a rederivation of the temperature using different filter ratio techniques is performed. Given the multithermal scenario created by this many-strand loop model, a broad differential emission measure results; the subsequent double and triple filter ratios are very similar to those obtained from observations. However, any potential observational signature to differentiate between apex and footpoint dominant heating is possibly below instrumental thresholds. The consequences of using a broadband instrument like TRACE and Hinode-XRT in this way are discussed.« less
Structural evaluation of LIC-310-0396 and FAY-35-17-6.82 box beams with advanced strand deterioration : draft final report - phase II.

DOT National Transportation Integrated Search

2011-09-01

This report describes the results from the testing of a full scale three span 43 year old adjacent prestressed concrete box beam bridge. This research is the second phase of the overall project entitled Structural Evaluation of LIC-310-0396 Box Be...

The Development and Application of Novel Methods for the Solution of EMP Shielding Problems.

DTIC Science & Technology

1981-02-01

chiralit\\ into chemistr , and originated the branch of chemistr \\ on a molar scale in, for example. snails, flowers, and we no% call stereochemistr\\ More... Chemistr %. Nobel L ecture (Dec 12. 1915). als in Les Prix Nobel timprimenec Ro.Nalc P A Norstedi & denotes that the strand in position I crosses in front
Formation of template-switching artifacts by linear amplification.

PubMed

Chakravarti, Dhrubajyoti; Mailander, Paula C

2008-07-01

Linear amplification is a method of synthesizing single-stranded DNA from either a single-stranded DNA or one strand of a double-stranded DNA. In this protocol, molecules of a single primer DNA are extended by multiple rounds of DNA synthesis at high temperature using thermostable DNA polymerases. Although linear amplification generates the intended full-length single-stranded product, it is more efficient over single-stranded templates than double-stranded templates. We analyzed linear amplification over single- or double-stranded mouse H-ras DNA (exon 1-2 region). The single-stranded H-ras template yielded only the intended product. However, when the double-stranded template was used, additional artifact products were observed. Increasing the concentration of the double-stranded template produced relatively higher amounts of these artifact products. One of the artifact DNA bands could be mapped and analyzed by sequencing. It contained three template-switching products. These DNAs were formed by incomplete DNA strand extension over the template strand, followed by switching to the complementary strand at a specific Ade nucleotide within a putative hairpin sequence, from which DNA synthesis continued over the complementary strand.
Initiator-catalyzed self-assembly of duplex-looped DNA hairpin motif based on strand displacement reaction for logic operations and amplified biosensing.

PubMed

Bi, Sai; Yue, Shuzhen; Wu, Qiang; Ye, Jiayan

2016-09-15

Here we program an initiator-catalyzed self-assembly of duplex-looped DNA hairpin motif based on strand displacement reaction. Due to the recycling of initiator and performance in a cascade manner, this system is versatilely extended to logic operations, including the construction of concatenated logic circuits with a feedback function and a biocomputing keypad-lock security system. Compared with previously reported molecular security systems, the prominent feature of our keypad lock is that it can be spontaneously reset and recycled with no need of any external stimulus and human intervention. Moreover, through integrating with an isothermal amplification technique of rolling circle amplification (RCA), this programming catalytic DNA self-assembly strategy readily achieves sensitive and selective biosensing of initiator. Importantly, a magnetic graphene oxide (MGO) is introduced to remarkably reduced background, which plays an important role in enhancing the signal-to-noise ratio and improving the detection sensitivity. Therefore, the proposed sophisticated DNA strand displacement-based methodology with engineering dynamic functions may find broad applications in the construction of programming DNA nanostructures, amplification biosensing platform, and large-scale DNA circuits. Copyright © 2016 Elsevier B.V. All rights reserved.
Demonstration of the SeptiStrand benthic microbial fuel cell powering a magnetometer for ship detection

NASA Astrophysics Data System (ADS)

Arias-Thode, Y. Meriah; Hsu, Lewis; Anderson, Greg; Babauta, Jerome; Fransham, Roy; Obraztsova, Anna; Tukeman, Gabriel; Chadwick, D. Bart

2017-07-01

The Navy has a need for monitoring conditions and gathering information in marine environments. Sensors can monitor and report environmental parameters and potential activities such as animal movements, ships, or personnel. However, there has to be a means to power these sensors. One promising enabling technology that has been shown to provide long-term power production in underwater environments is the benthic microbial fuel cells (BMFC). BMFCs are devices that generate energy by coupling bioanodes and biocathodes through an external energy harvester. Recent studies have demonstrated success for usage of BMFCs in powering small instruments and other devices on the seafloor over limited periods of time. In this effort, a seven-stranded BMFC linear array of 30 m was designed to power a seafloor magnetometer to detect passing ship movements through Pearl Harbor, Hawaii. The BMFC system was connected to a flyback energy harvesting circuit that charged the battery powering the magnetometer. The deployment was demonstrated the BMFC supplied power to the battery for approximately 38 days. This is the first large-scale demonstration system for usage of the SeptiStrand BMFC technology to power a relevant sensor.
Effetive methods in educating extension agents and farmers on conservation farming technology

USDA-ARS?s Scientific Manuscript database

Adoption of new technologies requires transfer of information from developers to end users. Efficiency of the transfer process influences the rate of adoption and ultimate impact of the technology. Various channels are used to transfer technology from researchers to farmers. Two commonly used ones ...
Future of Software Engineering Standards

NASA Technical Reports Server (NTRS)

Poon, Peter T.

1997-01-01

In the new millennium, software engineering standards are expected to continue to influence the process of producing software-intensive systems which are cost-effetive and of high quality. These sytems may range from ground and flight systems used for planetary exploration to educational support systems used in schools as well as consumer-oriented systems.
Effet Bauschinger lors de la plasticité cyclique de l'aluminium pur monocristallin

NASA Astrophysics Data System (ADS)

Alhamany, A.; Chicois, J.; Fougères, R.; Hamel, A.

1992-08-01

This paper is concerned with the study of microscopic mechanisms which control the cyclic deformation of pure aluminium and especially with the analysis of the Bauschinger effect which appears in aluminium single crystals deformed by cyclic straining. Fatigue tests are performed on Al single crystals with the crystal axis parallel to [ overline{1}23] at room temperature, at plastic shear strain amplitudes in the range from 10^{-4} to 3× 10^{-3}. Mechanical saturation is not obtained at any strain level. Instead, a hardening-softening-secondary hardening sequence is found. The magnitude of the Bauschinger effect as the difference between yield stresses in traction and in compression, changes all along the fatigue loop and during the fatigue test. The Bauschinger effect disappears at two points of the fatigue loop, one in the traction part, the other in the compression one. At these points, the Bauschinger effect is inverted. Dislocation arrangement evolutions with fatigue conditions can explain the cyclic behaviour of Al single crystals. An heterogeneous dislocation distribution can be observed in the cyclically strained metal : dislocation tangles, long dislocation walls and dislocation cell walls, separated by dislocation poor channels appear in the material as a function of the cycle number. The long range internal stress necessary to ensure the compatibility of deformation between the hard and soft regions controls the observed Bauschinger effect. Ce travail s'inscrit dans le cadre de l'étude des mécanismes microsocopiques intervenant lors de la déformation cyclique de l'aluminium pur et concerne en particulier l'analyse de l'effet Bauschinger apparaissant au cours de la solliciation cyclique des monocristaux. L'étude a été menée à température ambiante sur des monocristaux d'aluminium pur orientés pour un glissement simple (axe [ overline{1}23] ), à des amplitudes de déformation plastique comprise entre 10^{-4} et quelques 10^{-3}. Nous n'avons pas obtenu de véritable saturation mécanique. Nous sommes en présence d'une séquence durcissement-adoucissement-durcissement secondaire. L'amplitude de l'effet Bauschinger considéré comme la différence entre les limites élastiques en traction et en compression mesurées selon une procédure appropriée, évolue le long d'une boucle de fatigue, s'annule pour deux points particuliers l'un en traction l'autre en compression. De part et d'autre de ces points, le signe de l'effet Bauschinger est inversé. Les microstructures des états fatigués sont caractérisés par une répartition hétérogène des dislocations constituée d'amas, de murs ou des parois, suivant le degré de déformation cyclique, séparés par des zones à faible densité de dislocations. Les contraintes internes liées aux incompatibilités de déformation résultant de cette répartition hétérogène des dislocations sont à l'origine de l'effet Bauschinger observé dans les monocristaux. Ces contraintes et l'évolution de la quantité de cellules de dislocations avec la fatigue expliquent le durcissement secondaire.
Influence of intra-molecular flexibility on the elastic property of double-stranded DNA film on a substrate

NASA Astrophysics Data System (ADS)

Wu, Jun-Zheng; Meng, Wei-Lie; Tang, Heng-Song; Zhang, Neng-Hui

2017-05-01

DNA film self-assembled or nanografted on a substrate, as a kind of soft matter, consists of fixed DNA chains endowed with negative charges and an aqueous solution full of cations, anions and water molecules. Their thermal/electrical/mechanical properties are closely related to the complex biodetection signals in nano-/micro-scale biosensors and other new genome technologies. This makes it important to properly characterize these properties. In this paper, the effect of flexible micro-scale configurations on the elastic moduli of DNA films is investigated. First, illuminated by Qiu’s sphere model, an alternative bead-chain model in terms of the Yukawa potential is presented for flexible intra-DNA configurations to describe interactions between DNA fragments. The effective charges of coarse-grained DNA beads could be derived, in which the empirical parameters are identified by curve fitting with Qiu’s experimental data. Second, the updated mesoscopic bead-chain model and the thought experiment of a continuum compression bar are used to compare the elastic moduli of double-stranded DNA (dsDNA) films prepared by self-assembling and nanografting techniques. Configurational sampling is achieved via Monte Carlo simulation. Our predictions quantitatively or qualitatively agree well with the relevant experiments on the effective charge of dsDNA from low to moderate monovalent counterion concentration, immobilization deflection of single-stranded DNA (ssDNA) or dsDNA microcantilever with the variation of salt concentration, and elastic modulus of ssDNA film in the air. The results reveal that different solution environment stimulates the diverse mechanical properties of dsDNA film on a substrate, and the end effect (i.e. terminal group effect) makes self-assembling dsDNA film stiffer in the sense of the same average packing density.
AEL Study of KERA Implementation in Four Rural Kentucky School Districts. 1993-94 Annual Report.

ERIC Educational Resources Information Center

Coe, Pamelia; And Others

A 5-year qualitative study of implementation of the Kentucky Education Reform Act (KERA) analyzes the effects on four rural school districts of large-scale changes in state policy. This annual report of the project focuses on five key KERA "strands." First, KERA mandates that grades K-3 be replaced with an ungraded primary program…
Organization of 'nanocrystal molecules' using DNA

NASA Astrophysics Data System (ADS)

Alivisatos, A. Paul; Johnsson, Kai P.; Peng, Xiaogang; Wilson, Troy E.; Loweth, Colin J.; Bruchez, Marcel P.; Schultz, Peter G.

1996-08-01

PATTERNING matter on the nanometre scale is an important objective of current materials chemistry and physics. It is driven by both the need to further miniaturize electronic components and the fact that at the nanometre scale, materials properties are strongly size-dependent and thus can be tuned sensitively1. In nanoscale crystals, quantum size effects and the large number of surface atoms influence the, chemical, electronic, magnetic and optical behaviour2-4. 'Top-down' (for example, lithographic) methods for nanoscale manipulation reach only to the upper end of the nanometre regime5; but whereas 'bottom-up' wet chemical techniques allow for the preparation of mono-disperse, defect-free crystallites just 1-10 nm in size6-10, ways to control the structure of nanocrystal assemblies are scarce. Here we describe a strategy for the synthesis of'nanocrystal molecules', in which discrete numbers of gold nanocrystals are organized into spatially defined structures based on Watson-Crick base-pairing interactions. We attach single-stranded DNA oligonucleotides of defined length and sequence to individual nanocrystals, and these assemble into dimers and trimers on addition of a complementary single-stranded DNA template. We anticipate that this approach should allow the construction of more complex two-and three-dimensional assemblies.
A new building block for DNA network formation by self-assembly and polymerase chain reaction.

PubMed

Bußkamp, Holger; Keller, Sascha; Robotta, Marta; Drescher, Malte; Marx, Andreas

2014-01-01

The predictability of DNA self-assembly is exploited in many nanotechnological approaches. Inspired by naturally existing self-assembled DNA architectures, branched DNA has been developed that allows self-assembly to predesigned architectures with dimensions on the nanometer scale. DNA is an attractive material for generation of nanostructures due to a plethora of enzymes which modify DNA with high accuracy, providing a toolbox for many different manipulations to construct nanometer scaled objects. We present a straightforward synthesis of a rigid DNA branching building block successfully used for the generation of DNA networks by self-assembly and network formation by enzymatic DNA synthesis. The Y-shaped 3-armed DNA construct, bearing 3 primer strands is accepted by Taq DNA polymerase. The enzyme uses each arm as primer strand and incorporates the branched construct into large assemblies during PCR. The networks were investigated by agarose gel electrophoresis, atomic force microscopy, dynamic light scattering, and electron paramagnetic resonance spectroscopy. The findings indicate that rather rigid DNA networks were formed. This presents a new bottom-up approach for DNA material formation and might find applications like in the generation of functional hydrogels.
Systems approach modelling of the interactive effects of fisheries, jellyfish and tourism in the Catalan coast

NASA Astrophysics Data System (ADS)

Tomlinson, Benjamin; Maynou, Francesc; Sabatés, Ana; Fuentes, Verónica; Canepa, Antonio; Sastre, Sergio

2018-02-01

Despite the large fluctuation in annual recordings of gelatinous plankton along the Catalan coast in the north western Mediterranean and the lack of long term data sets, there is a general perception that jellyfish abundances are increasing. Local authorities are concerned about the stranding events and arrivals of jellyfish to beaches and believe it could reduce the recreational appeal of the beaches - a valuable ecosystem service for the regional tourist industry. Previous studies also demonstrate the predation of jellyfish (Pelagia noctiluca ephyrae) upon some small pelagic fish larvae (Engraulis encrasicolus). Small pelagics are the principal source of revenue for the local fisheries. A social-ecological model was created in order to capture the effects of changes in abundance of P. noctiluca upon the local fisheries, the tourist industry and the wider economy. The following sub-models were constructed and connected following the systems approach framework methodology: an age-class based fisheries model; a jellyfish population matrix model; a jellyfish stranding model; a study on the impact of jellyfish strandings on beach users; and an economic input-output matrix. Various future scenarios for different abundances of jellyfish blooms were run. The "Expected blooms" scenario is similar to the quantity and size of blooms for 2000-2010. For a hypothetical "No blooms" scenario (standard background level of jellyfish but without any blooms) landings would increase by around 294 tonnes (5.1%) per year (averaged over 10 years) or approximately 0.19 M€ in profits per year (4.5%), and strandings would decrease by 49%. In a "Frequent blooms" scenario, landings would decrease by around 147 tonnes per year (2.5%) and decrease profits by 0.10 M€ per year (2.3%), and strandings would increase by 32%. Given the changes that these scenarios would cause on the regional gross domestic product and employment, this study concludes that the overall impact of either of these scenarios on the economy would not be significant at the regional scale.
Sequence-Specific DNA Photosplitting of Crosslinked DNAs Containing the 3-Cyanovinylcarbazole Nucleoside by Using DNA Strand Displacement.

PubMed

Nakamura, Shigetaka; Kawabata, Hayato; Fujimoto, Kenzo

2016-08-17

An oligodeoxynucleotide (ODN) containing the ultrafast reversible 3-cyanovinylcarbazole ((CNV) K) photo-crosslinker was photo-crosslinked to a complementary strand upon exposure to 366 nm irradiation and photosplit by use of 312 nm irradiation. In this paper we report that the photoreaction of (CNV) K on irradiation at 366 nm involves a photostationary state and that its reaction can be controlled by temperature. Guided by this new insight, we proposed and have now demonstrated previously unknown photosplitting of (CNV) K aided by DNA strand displacement as an alternative to heating. The photo-crosslinked double-stranded DNA (dsDNA) underwent >80 % photosplitting aided by DNA strand displacement on irradiation at 366 nm without heating. In this photosplitting based on DNA strand displacement, the relative thermal stability of the invader strand with respect to the template strands plays an important role, and an invader strand/template strand system that is more stable than the passenger strand/template strand system induces photosplitting without heating. This new strand-displacement-aided photosplitting occurred in a sequence-specific manner through irradiation at 366 nm in the presence of an invader strand. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
Accurate Quantification of microRNA via Single Strand Displacement Reaction on DNA Origami Motif

PubMed Central

Lou, Jingyu; Li, Weidong; Li, Sheng; Zhu, Hongxin; Yang, Lun; Zhang, Aiping; He, Lin; Li, Can

2013-01-01

DNA origami is an emerging technology that assembles hundreds of staple strands and one single-strand DNA into certain nanopattern. It has been widely used in various fields including detection of biological molecules such as DNA, RNA and proteins. MicroRNAs (miRNAs) play important roles in post-transcriptional gene repression as well as many other biological processes such as cell growth and differentiation. Alterations of miRNAs' expression contribute to many human diseases. However, it is still a challenge to quantitatively detect miRNAs by origami technology. In this study, we developed a novel approach based on streptavidin and quantum dots binding complex (STV-QDs) labeled single strand displacement reaction on DNA origami to quantitatively detect the concentration of miRNAs. We illustrated a linear relationship between the concentration of an exemplary miRNA as miRNA-133 and the STV-QDs hybridization efficiency; the results demonstrated that it is an accurate nano-scale miRNA quantifier motif. In addition, both symmetrical rectangular motif and asymmetrical China-map motif were tested. With significant linearity in both motifs, our experiments suggested that DNA Origami motif with arbitrary shape can be utilized in this method. Since this DNA origami-based method we developed owns the unique advantages of simple, time-and-material-saving, potentially multi-targets testing in one motif and relatively accurate for certain impurity samples as counted directly by atomic force microscopy rather than fluorescence signal detection, it may be widely used in quantification of miRNAs. PMID:23990889
Deuterium Isotope Effects During HMX Combustion: Chemical Kinetic Burn Rate Control Mechanism Verified

DTIC Science & Technology

1989-01-01

experience de gen dieses Experiments. Der 10 KDIE-Wert legt nahe. dab die combustion statique. La valeur de l’effet isotopique primaire laisse...anomaler combustion globale. Des 6tudes publifes par ailleurs confirment cette KDIE-Wert bei 10,4 MPa wirL angegeben. Diese KDIE-Experimente hypoth~se
Effets pathogènes d'un faible débit de dose : la relation « dose effet »

NASA Astrophysics Data System (ADS)

Masse, Roland

2002-10-01

There is no evidence of pathogenic effects in human groups exposed to less than 100 mSv at low dose-rate. The attributed effects are therefore the result of extrapolations from higher doses. The validity of such extrapolations is discussed from the point of view of epidemiology as well as cellular and molecular biology. The Chernobyl accident resulted in large excess of thyroid cancers in children; it also raised the point that some actual sanitary effects among distressed populations might be a direct consequence of low doses. Studies under the control of UN have not confirmed this point identifying no dose-effect relationship and " severe socio-economic and psychological pressures… poverty, poor diet and living conditions, and lifestyle factors" as the main cause for depressed health. Some hypothesis are considered for explaining the dose-dependence and high prevalence of non-cancer causes of death among human groups exposed to more than 300 mSv. To cite this article: R. Masse, C. R. Physique 3 (2002) 1049-1058.
Fiabilité des structures mécaniques adaptatives: effet de la panne des actionneurs ou des capteurs sur la stabilité

NASA Astrophysics Data System (ADS)

Fall, H.; Charon, W.; Kouta, R.

2002-12-01

Ces dernières décennies, des activités significatives dans le monde étaient dirigées autour du contrôle actif. Le but de ces recherches était essentiellement d'améliorer les performances, la fiabilité et la sécurité des systèmes. Notamment dans le cas des structures soumises à des vibrations aléatoires. D'importants travaux ont été consacré à l'utilisation des “matériaux intelligents” comme capteurs et actionneurs. Cette article propose l'analyse de la fiabilité des systèmes mécaniques en étudiant les pannes des actionneurs ou des capteurs. L'effet de ces pannes sur la stabilité et la performance du système y est démontré. Les méthodologies de conception y sont rappelées. Des exemples numériques sont fournis à travers le contrôle d'un panneau sous chargement dynamique pour illustrer la méthode proposée.
Development length of 0.6-inch prestressing strand in standard I-shaped pretensioned concrete beams

NASA Astrophysics Data System (ADS)

Barnes, Robert Wesley

The use of 0.6 in prestressing strand at a center-to-center spacing of 2 in allows for the optimal implementation of High Strength Concrete (HSC) in precast, prestressed concrete bridge superstructures. For this strand configuration, partial debonding of strands is a desirable alternative to the more traditional method of draping strands to alleviate extreme concrete stresses after prestress release. Recent experimental evidence suggests that existing code provisions addressing the anchorage of pretensioned strands do not adequately describe the behavior of these strands. In addition, the anchorage behavior of partially debonded strands is not fully understood. These uncertainties have combined to hinder the full exploitation of HSC in pretensioned concrete construction. A research study was conducted to determine the anchorage behavior of 0.6 in strands at 2 in spacing in full-size bridge members. The experimental program consisted of assessing transfer and development lengths in plant-cast AASHTO Type I I-beams. The influence of concrete compressive strengths ranging from 5700 to 14,700 psi was examined. In order to consider the full range of strand surface conditions found in practice, the prestressing strand featured either a bright mill finish or a rusted surface condition. The anchorage behavior of partially debonded strands was investigated by using a variety of strand debonding configurations---including debonded strand percentages as high as 75 percent. A limited investigation of the effect of horizontal web reinforcement on anchorage behavior was performed. Pull-out tests were performed in an attempt to correlate results with the bond quality of the strands used in the study. The correlation between strand draw-in and the anchorage behavior of prestressing strands was also examined. A review of the evolution and shortcomings of existing code provisions for the anchorage of prestressing strands is presented. Results of the experimental program are reported, along with recommended design procedures based on these results and those from other studies. The use of 0.6 in strand at 2 in spacing is concluded to be safe, and partial debonding of prestressing strands is shown to be an effective means of reducing stresses in the end regions of pretensioned girders.
The multiple personalities of Watson and Crick strands.

PubMed

Cartwright, Reed A; Graur, Dan

2011-02-08

In genetics it is customary to refer to double-stranded DNA as containing a "Watson strand" and a "Crick strand." However, there seems to be no consensus in the literature on the exact meaning of these two terms, and the many usages contradict one another as well as the original definition. Here, we review the history of the terminology and suggest retaining a single sense that is currently the most useful and consistent. The Saccharomyces Genome Database defines the Watson strand as the strand which has its 5'-end at the short-arm telomere and the Crick strand as its complement. The Watson strand is always used as the reference strand in their database. Using this as the basis of our standard, we recommend that Watson and Crick strand terminology only be used in the context of genomics. When possible, the centromere or other genomic feature should be used as a reference point, dividing the chromosome into two arms of unequal lengths. Under our proposal, the Watson strand is standardized as the strand whose 5'-end is on the short arm of the chromosome, and the Crick strand as the one whose 5'-end is on the long arm. Furthermore, the Watson strand should be retained as the reference (plus) strand in a genomic database. This usage not only makes the determination of Watson and Crick unambiguous, but also allows unambiguous selection of reference stands for genomics. This article was reviewed by John M. Logsdon, Igor B. Rogozin (nominated by Andrey Rzhetsky), and William Martin.
DNA forms of the geminivirus African cassava mosaic virus consistent with a rolling circle mechanism of replication.

PubMed Central

Saunders, K; Lucy, A; Stanley, J

1991-01-01

We have analysed DNA from African cassava mosaic virus (ACMV)-infected Nicotiana benthamiana by two-dimensional agarose gel electrophoresis and detected ACMV-specific DNAs by blot-hybridisation. ACMV DNA forms including the previously characterised single-stranded, open-circular, linear and supercoiled DNAs along with five previously uncharacterised heterogeneous DNAs (H1-H5) were resolved. The heterogeneous DNAs were characterised by their chromatographic properties on BND-cellulose and their ability to hybridise to strand-specific and double-stranded probes. The data suggest a rolling circle mechanism of DNA replication, based on the sizes and strand specificity of the heterogeneous single-stranded DNA forms and their electrophoretic properties in relation to genome length single-stranded DNAs. Second-strand synthesis on a single-stranded virus-sense template is evident from the position of heterogeneous subgenomic complementary-sense DNA (H3) associated with genome-length virus-sense template (VT) DNA. The position of heterogeneous virus-sense DNA (H5), ranging in size from one to two genome lengths, is consistent with its association with genome-length complementary-sense template (CT) DNA, reflecting virus-sense strand displacement during replication from a double-stranded intermediate. The absence of subgenomic complementary-sense DNA associated with the displaced virus-sense strand suggests that replication proceeds via an obligate single-stranded intermediate. The other species of heterogeneous DNAs comprised concatemeric single-stranded virus-sense DNA (H4), and double-stranded or partially single-stranded DNA (H1 and H2). Images PMID:2041773

Effets de la pollution de l’air sur la santé

PubMed Central

Abelsohn, Alan; Stieb, Dave M.

2011-01-01

Résumé Objectif Faire connaître aux médecins de famille les effets de la pollution atmosphérique sur la santé et indiquer quels conseils donner aux patients vulnérables pour qu’ils soient moins exposés. Sources de l’information On a consulté MEDLINE à l’aide des termes relatifs à la pollution atmosphérique et à ses effets indésirables. On a révisé les articles en anglais publiés entre janvier 2008 et décembre 2009. La plupart des études contenaient des preuves de niveau II. Principal message Au Canada, la pollution de l’air extérieur cause une morbidité et une mortalité importantes. Elle peut affecter le système respiratoire (exacerbation de l’asthme et de la maladie pulmonaire obstructive chronique) et le système cardiovasculaire (déclencher l’arythmie, l’insuffisance cardiaque et les AVC). La cote air santé (CAS) est un nouvel outil de communication mis au point par Santé Canada et Environnement Canada qui indique sur une échelle de 1 à 10, le risque pour la santé causé par la pollution atmosphérique. La CAS est largement diffusée dans les médias et cet outil pourrait être utile au médecin de famille pour inciter les patients à haut risque (comme ceux qui souffrent d’asthme, de maladie pulmonaire obstructive chronique ou d’insuffisance cardiaque) à réduire leur exposition à la pollution atmosphérique. Conclusion Le médecin de famille peut se servir de la CAS et de ses messages sur la santé pour enseigner aux asthmatiques et aux autres patients à risque élevé la façon de réduire les risques pour la santé causés par la pollution atmosphérique.
Le rôle du soutien parental dans la relation entre la victimisation homophobe, l’homophobie intériorisée et la détresse psychologique chez les jeunes de minorités sexuelles (JMS) : une approche de médiation modérée

PubMed Central

Bergeron, Félix-Antoine; Blais, Martin; Hébert, Martine

2016-01-01

Résumé Cet article explore le rôle modérateur du soutien parental dans les relations entre la victimisation homophobe, l’homophobie intériorisée et la détresse psychologique chez des jeunes de minorités sexuelles (JMS), que l’on dit aussi lesbiennes, gais, bisexuels ou en questionnement. Il vise à 1) documenter la prévalence des différentes formes de victimisation homophobe vécue par les JMS, et ce, selon le genre et l’âge et 2) à explorer l’effet modérateur du soutien parental dans la relation entre la victimisation homophobe, l’homophobie intériorisée et la détresse psychologique. Un échantillon de 228 JMS âgés de 14 à 22 ans, non exclusivement hétérosexuels, recrutés en milieu communautaire dans le cadre de l’enquête sur le Parcours Amoureux des Jeunes (PAJ) du Québec a été analysé. L’impact de la victimisation homophobe, du soutien parental, de l’homophobie intériorisée sur la détresse psychologique est exploré par un modèle de régression linéaire avec effets de médiation modérée. Le rôle modérateur du soutien parental est confirmé dans la relation entre la victimisation homophobe et la détresse psychologique. Ces variables peuvent constituer des leviers pour prévenir les effets négatifs des préjudices homophobes sur la santé mentale des JMS. PMID:26966851
75 FR 37382 - Notice of Antidumping Duty Order: Prestressed Concrete Steel Wire Strand from the People's...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-06-29

... strand (``PC strand'') from the People's Republic of China (``PRC''). On June 22, 2010, the ITC notified... investigation of PC strand from the PRC. See Prestressed Concrete Steel Wire Strand From the People's Republic... Determination''). Scope of the Order The scope of this investigation consists of PC strand, produced from wire...
Autonomous parvovirus LuIII encapsidates equal amounts of plus and minus DNA strands

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bates, R.C.; Snyder, C.E.; Banerjee, P.T.

1984-02-01

Autonomous parvoviruses are thought to uniquely encapsidate single-stranded DNA of minus polarity. In contrast, the defective adeno-associated viruses separately encapsidate equal amounts of plus and minus DNA strands. The uniqueness of minus strand encapsidation is reexamined for the autonomous parvoviruses. Although it was found that Kilham rat virus and H-1 virus encapsidate varying but small amounts of complementary-strand DNA, it was unexpected to find that LuIII virus encapsidated equal amounts of plus and minus DNA. The extracted LuIII DNA possessed properties of double-stranded replicative-form DNA, including insensitivity to S1 endonuclease, cleavage by restriction enzymes, and conversion to unit-length, single-stranded DNAmore » when electrophoresed under denaturing conditions. However, the inability of this DNA to form single-stranded DNA circles when denatured and then renatured in the presence of formamide and the lack of double-stranded DNA circle formation after treatment with exonuclease III and reannealing shows a lack of sequence homology of the 3' and 5' termini of LuIII DNA, in contrast to adeno-associated virus DNA. Digestion of LuIII double-stranded DNA with EcoRI and HincII and separation of plus and minus DNA strands on composite agarose-acrylamide gels identified a heterogeneity present only in the plus DNA strand. These results suggest that strand specificity of viral DNA encapsidation is not a useful property for differentiation between the autonomous and defective parvoviruses. Furthermore, encapsidation by LuIII of equal amounts of complementary DNA strands in contrast to encapsidation of minus strands by H-1 virus, when propagated in the same host cell type, suggests that selection of strands for encapsidation is a virus-coded rather than host-controlled event.« less
Rapid Polymer Transport in a Single Nanometer-Scale Pore

NASA Astrophysics Data System (ADS)

Kasianowicz, J. J.

1998-03-01

Protein ion channels are nanometer-scale pores that control the transport of ions and polymers across cell membranes. We compared the ability of charged and nonelectrolyte linear polymers to partition into a single channel reconstituted into a planar lipid bilayer membrane. The entry of each polymer (e.g. monodisperse length single-stranded homopolymeric RNA1 or poly(ethylene glycol)2,3) into the pore caused characteristic transient decreases in the channel's ionic conductance. The ionic current blockades yield detailed information about the physical properties of the polymers and the pore. The biological and technological significance of the results will be discussed.
Triple Helix Formation in a Topologically Controlled DNA Nanosystem.

PubMed

Yamagata, Yutaro; Emura, Tomoko; Hidaka, Kumi; Sugiyama, Hiroshi; Endo, Masayuki

2016-04-11

In the present study, we demonstrate single-molecule imaging of triple helix formation in DNA nanostructures. The binding of the single-molecule third strand to double-stranded DNA in a DNA origami frame was examined using two different types of triplet base pairs. The target DNA strand and the third strand were incorporated into the DNA frame, and the binding of the third strand was controlled by the formation of Watson-Crick base pairing. Triple helix formation was monitored by observing the structural changes in the incorporated DNA strands. It was also examined using a photocaged third strand wherein the binding of the third strand was directly observed using high-speed atomic force microscopy during photoirradiation. We found that the binding of the third strand could be controlled by regulating duplex formation and the uncaging of the photocaged strands in the designed nanospace. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
Etude thermo-hydraulique de l'ecoulement du moderateur dans le reacteur CANDU-6

NASA Astrophysics Data System (ADS)

Mehdi Zadeh, Foad

Etant donne la taille (6,0 m x 7,6 m) ainsi que le domaine multiplement connexe qui caracterisent la cuve des reacteurs CANDU-6 (380 canaux dans la cuve), la physique qui gouverne le comportement du fluide moderateur est encore mal connue de nos jours. L'echantillonnage de donnees dans un reacteur en fonction necessite d'apporter des changements a la configuration de la cuve du reacteur afin d'y inserer des sondes. De plus, la presence d'une zone intense de radiations empeche l'utilisation des capteurs courants d'echantillonnage. En consequence, l'ecoulement du moderateur doit necessairement etre etudie a l'aide d'un modele experimental ou d'un modele numerique. Pour ce qui est du modele experimental, la fabrication et la mise en fonction de telles installations coutent tres cher. De plus, les parametres de la mise a l'echelle du systeme pour fabriquer un modele experimental a l'echelle reduite sont en contradiction. En consequence, la modelisation numerique reste une alternative importante. Actuellement, l'industrie nucleaire utilise une approche numerique, dite de milieu poreux, qui approxime le domaine par un milieu continu ou le reseau des tubes est remplace par des resistances hydrauliques distribuees. Ce modele est capable de decrire les phenomenes macroscopiques de l'ecoulement, mais ne tient pas compte des effets locaux ayant un impact sur l'ecoulement global, tel que les distributions de temperatures et de vitesses a proximite des tubes ainsi que des instabilites hydrodynamiques. Dans le contexte de la surete nucleaire, on s'interesse aux effets locaux autour des tubes de calandre. En effet, des simulations faites par cette approche predisent que l'ecoulement peut prendre plusieurs configurations hydrodynamiques dont, pour certaines, l'ecoulement montre un comportement asymetrique au sein de la cuve. Ceci peut provoquer une ebullition du moderateur sur la paroi des canaux. Dans de telles conditions, le coefficient de reactivite peut varier de maniere importante, se traduisant par l'accroissement de la puissance du reacteur. Ceci peut avoir des consequences majeures pour la surete nucleaire. Une modelisation CFD (Computational Fluid Dynamics) detaillee tenant compte des effets locaux s'avere donc necessaire. Le but de ce travail de recherche est de modeliser le comportement complexe de l'ecoulement du moderateur au sein de la cuve d'un reacteur nucleaire CANDU-6, notamment a proximite des tubes de calandre. Ces simulations servent a identifier les configurations possibles de l'ecoulement dans la calandre. Cette etude consiste ainsi a formuler des bases theoriques a l'origine des instabilites macroscopiques du moderateur, c.-a-d. des mouvements asymetriques qui peuvent provoquer l'ebullition du moderateur. Le defi du projet est de determiner l'impact de ces configurations de l'ecoulement sur la reactivite du reacteur CANDU-6.
Proprietes ionochromes et photochromes de derives du polythiophene

NASA Astrophysics Data System (ADS)

Levesque, Isabelle

La synthese et la caracterisation de derives regioreguliers du polythiophene ont ete effectuees en solution et sur des films minces. La spectroscopie UV-visible de ces derives a permis de constater qu'ils peuvent posseder des proprietes chromiques particulieres selon le stimulus auquel ils sont soumis. Par exemple, une augmentation de la temperature permet en effet aux polymeres de passer d'une couleur violette a jaune, et ce, a l'etat solide aussi bien qu'en solution. Ces proprietes chromiques semblent regies par une transition conformationnelle (plane a non-plane) de la chaine principale. Ce travail avait pour but de mieux comprendre l'influence de l'organisation des chaines laterales sur les transitions chromiques. Deux derives synthetises possedant des chaines laterales sensibles aux cations alcalins se sont averes etre ionochromes en plus d'etre thermochromes. Il s'agit d'un polymere comportant des chaines laterales de type oligo(oxyethylene) et d'un autre comportant un groupement ether couronne specifique aux ions lithium. Les effets chromiques observes sont expliques par des interactions non-covalentes des cations avec les atomes d'oxygene des chaines laterales dans le cas du premier polymere, et par l'insertion de l'ion Li + dans la cavite de l'ether couronne dans le cas du second polymere. Ces interactions semblent provoquer une diminution de l'organisation induisant ainsi une torsion de la chaine principale. Les deux polymeres semblent specifiques a certains cations et pourraient donc servir comme detecteurs optiques. La specificite aux ions Li+ du second polymere pourrait aussi permettre la conduction ionique, en plus de la conductivite electronique caracteristique des polythiophenes, ce qui pourrait s'averer utile dans le cas de batteries legeres entierement faites de polymeres et de sels de lithium. D'autres derives comportant des chaines laterales de type azobenzene se sont averes etre photochromes en plus d'etre thermochromes. Le groupement lateral a la possibilite de changer de configuration de la forme trans a la forme cis lorsqu'il est soumis a une irradiation dans le domaine de l'ultraviolet ce qui provoque, selon toute evidence, un effet marque sur l'organisation des chaines laterales. Cela induit alors une torsion de la chaine principale thiophene entrainant une diminution de conjugaison marquee. Ces effets peuvent etre exploites entre autres dans l'ecriture optique. Il s'est avere que le polymere irradie peu conjugue peut etre force a retourner a son etat initial conjugue tres rapidement par un traitement electrochimique simple. En conclusion, on a pu prouver qu'une modification dans l'organisation des chaines laterales par un stimulus exterieur affecte considerablement la conformation de la chaine principale. Cela porte a croire que les chaines laterales stabilisent une conformation particuliere des polythiophenes.
The multiple personalities of Watson and Crick strands

PubMed Central

2011-01-01

Background In genetics it is customary to refer to double-stranded DNA as containing a "Watson strand" and a "Crick strand." However, there seems to be no consensus in the literature on the exact meaning of these two terms, and the many usages contradict one another as well as the original definition. Here, we review the history of the terminology and suggest retaining a single sense that is currently the most useful and consistent. Proposal The Saccharomyces Genome Database defines the Watson strand as the strand which has its 5'-end at the short-arm telomere and the Crick strand as its complement. The Watson strand is always used as the reference strand in their database. Using this as the basis of our standard, we recommend that Watson and Crick strand terminology only be used in the context of genomics. When possible, the centromere or other genomic feature should be used as a reference point, dividing the chromosome into two arms of unequal lengths. Under our proposal, the Watson strand is standardized as the strand whose 5'-end is on the short arm of the chromosome, and the Crick strand as the one whose 5'-end is on the long arm. Furthermore, the Watson strand should be retained as the reference (plus) strand in a genomic database. This usage not only makes the determination of Watson and Crick unambiguous, but also allows unambiguous selection of reference stands for genomics. Reviewers This article was reviewed by John M. Logsdon, Igor B. Rogozin (nominated by Andrey Rzhetsky), and William Martin. PMID:21303550
Strand-Specific Analysis of DNA Synthesis and Proteins Association with DNA Replication Forks in Budding Yeast.

PubMed

Yu, Chuanhe; Gan, Haiyun; Zhang, Zhiguo

2018-01-01

DNA replication initiates at DNA replication origins after unwinding of double-strand DNA(dsDNA) by replicative helicase to generate single-stranded DNA (ssDNA) templates for the continuous synthesis of leading-strand and the discontinuous synthesis of lagging-strand. Therefore, methods capable of detecting strand-specific information will likely yield insight into the association of proteins at leading and lagging strand of DNA replication forks and the regulation of leading and lagging strand synthesis during DNA replication. The enrichment and Sequencing of Protein-Associated Nascent DNA (eSPAN), which measure the relative amounts of proteins at nascent leading and lagging strands of DNA replication forks, is a step-wise procedure involving the chromatin immunoprecipitation (ChIP) of a protein of interest followed by the enrichment of protein-associated nascent DNA through BrdU immunoprecipitation. The isolated ssDNA is then subjected to strand-specific sequencing. This method can detect whether a protein is enriched at leading or lagging strand of DNA replication forks. In addition to eSPAN, two other strand-specific methods, (ChIP-ssSeq), which detects potential protein-ssDNA binding and BrdU-IP-ssSeq, which can measure synthesis of both leading and lagging strand, were developed along the way. These methods can provide strand-specific and complementary information about the association of the target protein with DNA replication forks as well as synthesis of leading and lagging strands genome wide. Below, we describe the detailed eSPAN, ChIP-ssSeq, and BrdU-IP-ssSeq protocols.
Biophysical dynamics in disorderly environments.

PubMed

Nelson, David R

2012-01-01

Three areas where time-independent disorder plays a key role in biological dynamics far from equilibrium are reviewed. We first discuss the anomalous localization dynamics that arises when a single species spreads in space and time via diffusion and fluid advection in the presence of frozen heterogeneities in the growth rate. Next we treat the unzipping of double-stranded DNA as a function of force and temperature, a challenge that must be surmounted every time a cell divides. Heterogeneity in the DNA sequence dominates the physics of single-molecule force-extension curves for a broad range of forces upon approaching a sharp unzipping transition. The dynamics of the unzipping fork exhibits anomalous drift and diffusion in a similar range above this transition, with energy barriers that scale as the square root of the genome size. Finally, we describe how activated peptidoglycan strand extension sites, called dislocations in materials science, can mediate the growth of bacterial cell walls. Enzymatically driven circumferential motions of a few dozen of these defects are sufficient to describe the exponential elongation rates observed in experiments on Escherichia coli in a nutrient-rich environment. However, long-range elastic forces transmitted by the peptidoglycan meshwork cause the moving dislocations to interact not only with each other, but also with a disorderly array of frozen, inactivated strand ends.
Coarse-grained molecular dynamics simulations of the tensile behavior of a thermosetting polymer.

PubMed

Yang, Shaorui; Qu, Jianmin

2014-07-01

Using a previously developed coarse-grained model, we conducted large-scale (∼ 85 × 85 × 85 nm(3)) molecular dynamics simulations of uniaxial-strain deformation to study the tensile behavior of an epoxy molding compound, epoxy phenol novolacs (EPN) bisphenol A (BPA). Under the uniaxial-strain deformation, the material is found to exhibit cavity nucleation and growth, followed by stretching of the ligaments separated by the cavities, until the ultimate failure through ligament scissions. The nucleation sites of cavities are rather random and the subsequent cavity growth accounts for much (87%) of the volumetric change during the uniaxial-strain deformation. Ultimate failure of the materials occurs when the cavity volume fraction reaches ∼ 60%. During the entire deformation process, polymer strands in the network are continuously extended to their linear states and broken in the postyielding strain hardening stage. When most of the strands are stretched to their taut configurations, rapid scission of a large number of strands occurs within a small strain increment, which eventually leads to fracture. Finally, through extensive numerical simulations of various loading conditions in addition to uniaxial strain, we find that yielding of the EPN-BPA can be described by the pressure-modified von Mises yield criterion.
Coarse-grained molecular dynamics simulations of the tensile behavior of a thermosetting polymer

NASA Astrophysics Data System (ADS)

Yang, Shaorui; Qu, Jianmin

2014-07-01

Using a previously developed coarse-grained model, we conducted large-scale (˜85×85×85nm3) molecular dynamics simulations of uniaxial-strain deformation to study the tensile behavior of an epoxy molding compound, epoxy phenol novolacs (EPN) bisphenol A (BPA). Under the uniaxial-strain deformation, the material is found to exhibit cavity nucleation and growth, followed by stretching of the ligaments separated by the cavities, until the ultimate failure through ligament scissions. The nucleation sites of cavities are rather random and the subsequent cavity growth accounts for much (87%) of the volumetric change during the uniaxial-strain deformation. Ultimate failure of the materials occurs when the cavity volume fraction reaches ˜60%. During the entire deformation process, polymer strands in the network are continuously extended to their linear states and broken in the postyielding strain hardening stage. When most of the strands are stretched to their taut configurations, rapid scission of a large number of strands occurs within a small strain increment, which eventually leads to fracture. Finally, through extensive numerical simulations of various loading conditions in addition to uniaxial strain, we find that yielding of the EPN-BPA can be described by the pressure-modified von Mises yield criterion.
Visualizing repetitive diffusion activity of double-strand RNA binding proteins by single molecule fluorescence assays.

PubMed

Koh, Hye Ran; Wang, Xinlei; Myong, Sua

2016-08-01

TRBP, one of double strand RNA binding proteins (dsRBPs), is an essential cofactor of Dicer in the RNA interference pathway. Previously we reported that TRBP exhibits repetitive diffusion activity on double strand (ds)RNA in an ATP independent manner. In the TRBP-Dicer complex, the diffusion mobility of TRBP facilitates Dicer-mediated RNA cleavage. Such repetitive diffusion of dsRBPs on a nucleic acid at the nanometer scale can be appropriately captured by several single molecule detection techniques. Here, we provide a step-by-step guide to four different single molecule fluorescence assays by which the diffusion activity of dsRBPs on dsRNA can be detected. One color assay, termed protein induced fluorescence enhancement enables detection of unlabeled protein binding and diffusion on a singly labeled RNA. Two-color Fluorescence Resonance Energy Transfer (FRET) in which labeled dsRBPs is applied to labeled RNA, allows for probing the motion of protein along the RNA axis. Three color FRET reports on the diffusion movement of dsRBPs from one to the other end of RNA. The single molecule pull down assay provides an opportunity to collect dsRBPs from mammalian cells and examine the protein-RNA interaction at single molecule platform. Copyright © 2016 Elsevier Inc. All rights reserved.
Identification of cis-acting elements on positive-strand subgenomic mRNA required for the synthesis of negative-strand counterpart in bovine coronavirus.

PubMed

Yeh, Po-Yuan; Wu, Hung-Yi

2014-07-30

It has been demonstrated that, in addition to genomic RNA, sgmRNA is able to serve as a template for the synthesis of the negative-strand [(-)-strand] complement. However, the cis-acting elements on the positive-strand [(+)-strand] sgmRNA required for (-)-strand sgmRNA synthesis have not yet been systematically identified. In this study, we employed real-time quantitative reverse transcription polymerase chain reaction to analyze the cis-acting elements on bovine coronavirus (BCoV) sgmRNA 7 required for the synthesis of its (-)-strand counterpart by deletion mutagenesis. The major findings are as follows. (1) Deletion of the 5'-terminal leader sequence on sgmRNA 7 decreased the synthesis of the (-)-strand sgmRNA complement. (2) Deletions of the 3' untranslated region (UTR) bulged stem-loop showed no effect on (-)-strand sgmRNA synthesis; however, deletion of the 3' UTR pseudoknot decreased the yield of (-)-strand sgmRNA. (3) Nucleotides positioned from -15 to -34 of the sgmRNA 7 3'-terminal region are required for efficient (-)-strand sgmRNA synthesis. (4) Nucleotide species at the 3'-most position (-1) of sgmRNA 7 is correlated to the efficiency of (-)-strand sgmRNA synthesis. These results together suggest, in principle, that the 5'- and 3'-terminal sequences on sgmRNA 7 harbor cis-acting elements are critical for efficient (-)-strand sgmRNA synthesis in BCoV.
Nanoscale Bio-engineering Solutions for Space Exploration: The Nanopore Sequencer

NASA Technical Reports Server (NTRS)

Stolc, Viktor; Cozmuta, Ioana

2004-01-01

Characterization of biological systems at the molecular level and extraction of essential information for nano-engineering design to guide the nano-fabrication of solid-state sensors and molecular identification devices is a computational challenge. The alpha hemolysin protein ion channel is used as a model system for structural analysis of nucleic acids like DNA. Applied voltage draws a DNA strand and surrounding ionic solution through the biological nanopore. The subunits in the DNA strand block ion flow by differing amounts. Atomistic scale simulations are employed using NASA supercomputers to study DNA translocation, with the aim to enhance single DNA subunit identification. Compared to protein channels, solid-state nanopores offer a better temporal control of the translocation of DNA and the possibility to easily tune its chemistry to increase the signal resolution. Potential applications for NASA missions, besides real-time genome sequencing include astronaut health, life detection and decoding of various genomes.
Label-Free Direct Electronic Detection of Biomolecules with Amorphous Silicon Nanostructures

PubMed Central

Lund, John; Mehta, Ranjana; Parviz, Babak A.

2007-01-01

We present the fabrication and characterization of a nano-scale sensor made of amorphous silicon for the label-free, electronic detection of three classes of biologically important molecules: ions, oligonucleotides, and proteins. The sensor structure has an active element which is a 50 nm wide amorphous silicon semicircle and has a total footprint of less than 4 μm2. We demonstrate the functionalization of the sensor with receptor molecules and the electronic detection of three targets: H+ ions, short single-stranded DNAs, and streptavidin. The sensor is able to reliably distinguish single base-pair mismatches in 12 base long strands of DNA and monitor the introduction and identification of straptavidin in real-time. The versatile sensor structure can be readily functionalized with a wide range of receptor molecules and is suitable for integration with high-speed electronic circuits as a post-process on an integrated circuit chip. PMID:17292148
Regulatory RNA design through evolutionary computation and strand displacement.

PubMed

Rostain, William; Landrain, Thomas E; Rodrigo, Guillermo; Jaramillo, Alfonso

2015-01-01

The discovery and study of a vast number of regulatory RNAs in all kingdoms of life over the past decades has allowed the design of new synthetic RNAs that can regulate gene expression in vivo. Riboregulators, in particular, have been used to activate or repress gene expression. However, to accelerate and scale up the design process, synthetic biologists require computer-assisted design tools, without which riboregulator engineering will remain a case-by-case design process requiring expert attention. Recently, the design of RNA circuits by evolutionary computation and adapting strand displacement techniques from nanotechnology has proven to be suited to the automated generation of DNA sequences implementing regulatory RNA systems in bacteria. Herein, we present our method to carry out such evolutionary design and how to use it to create various types of riboregulators, allowing the systematic de novo design of genetic control systems in synthetic biology.
Cell birth, cell death, cell diversity and DNA breaks: how do they all fit together?

NASA Technical Reports Server (NTRS)

Gilmore, E. C.; Nowakowski, R. S.; Caviness, V. S. Jr; Herrup, K.

2000-01-01

Substantial death of migrating and differentiating neurons occurs within the developing CNS of mice that are deficient in genes required for repair of double-stranded DNA breaks. These findings suggest that large-scale, yet previously unrecognized, double-stranded DNA breaks occur normally in early postmitotic and differentiating neurons. Moreover, they imply that cell death occurs if the breaks are not repaired. The cause and natural function of such breaks remains a mystery; however, their occurrence has significant implications. They might be detected by histological methods that are sensitive to DNA fragmentation and mistakenly interpreted to indicate cell death when no relationship exists. In a broader context, there is now renewed speculation that DNA recombination might be occurring during neuronal development, similar to DNA recombination in developing lymphocytes. If this is true, the target gene(s) of recombination and their significance remain to be determined.
Single molecule characterization of DNA binding and strand displacement reactions on lithographic DNA origami microarrays.

PubMed

Scheible, Max B; Pardatscher, Günther; Kuzyk, Anton; Simmel, Friedrich C

2014-03-12

The combination of molecular self-assembly based on the DNA origami technique with lithographic patterning enables the creation of hierarchically ordered nanosystems, in which single molecules are positioned at precise locations on multiple length scales. Based on a hybrid assembly protocol utilizing DNA self-assembly and electron-beam lithography on transparent glass substrates, we here demonstrate a DNA origami microarray, which is compatible with the requirements of single molecule fluorescence and super-resolution microscopy. The spatial arrangement allows for a simple and reliable identification of single molecule events and facilitates automated read-out and data analysis. As a specific application, we utilize the microarray to characterize the performance of DNA strand displacement reactions localized on the DNA origami structures. We find considerable variability within the array, which results both from structural variations and stochastic reaction dynamics prevalent at the single molecule level.

Dynamic DNA devices and assemblies formed by shape-complementary, non-base pairing 3D components

NASA Astrophysics Data System (ADS)

Gerling, Thomas; Wagenbauer, Klaus F.; Neuner, Andrea M.; Dietz, Hendrik

2015-03-01

We demonstrate that discrete three-dimensional (3D) DNA components can specifically self-assemble in solution on the basis of shape-complementarity and without base pairing. Using this principle, we produced homo- and heteromultimeric objects, including micrometer-scale one- and two-stranded filaments and lattices, as well as reconfigurable devices, including an actuator, a switchable gear, an unfoldable nanobook, and a nanorobot. These multidomain assemblies were stabilized via short-ranged nucleobase stacking bonds that compete against electrostatic repulsion between the components’ interfaces. Using imaging by electron microscopy, ensemble and single-molecule fluorescence resonance energy transfer spectroscopy, and electrophoretic mobility analysis, we show that the balance between attractive and repulsive interactions, and thus the conformation of the assemblies, may be finely controlled by global parameters such as cation concentration or temperature and by an allosteric mechanism based on strand-displacement reactions.
Nanoscale Bioengineering Solutions for Space Exploration the Nanopore Sequencer

NASA Technical Reports Server (NTRS)

Ioana, Cozmuta; Viktor, Stoic

2005-01-01

Characterization of biological systems at the molecular level and extraction of essential information for nano-engineering design to guide the nano-fabrication of solid-state sensors and molecular identification devices is a computational challenge. The alpha hemolysin protein ion channel is used as a model system for structural analysis of nucleic acids like DNA. Applied voltage draws a DNA strand and surrounding ionic solution through the biological nanopore. The subunits in the DNA strand block ion flow by differing amounts. Atomistic scale simulations are employed using NASA supercomputers to study DNA translocation. with the aim to enhance single DNA subunit identification. Compared to protein channels, solid-state nanopores offer a better temporal control of the translocation of DNA and the possibility to easily tune its chemistry to increase the signal resolution. Potential applications for NASA missions, besides real-time genome sequencing include astronaut health, life detection and decoding of various genomes. http://phenomrph.arc.nasa.gov/index.php
IC(B,T,STRAIN) Characterisation of a Nb3Sn Internal Tin Strand with Enhanced Specification for Use in Fusion Conductors

NASA Astrophysics Data System (ADS)

Pasztor, G.; Bruzzone, P.

2004-06-01

The dc performance of a recently produced internal tin route Nb3Sn strand with enhanced specification is studied extensively and compared with predecessor wires manufactured by the suppliers for the ITER Model Coils in 1996. The wire has been selected for use in a full size, developmental cable-in-conduit conductor sample, which is being tested in the SULTAN Test Facility. The critical current, Ic, and the index of the current/voltage characteristic, n, are measured over a broad range of field and temperature, using ITER standard sample holders, made of TiAlV grooved cylinders. The behavior of Ic versus applied tensile strain is also investigated at 4.2 K and 12 T, on straight specimens. Scaling law parameters are drawn from the fit of the experimental results. The implications of the test results to the design of the fusion conductors are discussed.
Coarse-grained simulation of DNA using LAMMPS : An implementation of the oxDNA model and its applications.

PubMed

Henrich, Oliver; Gutiérrez Fosado, Yair Augusto; Curk, Tine; Ouldridge, Thomas E

2018-05-10

During the last decade coarse-grained nucleotide models have emerged that allow us to study DNA and RNA on unprecedented time and length scales. Among them is oxDNA, a coarse-grained, sequence-specific model that captures the hybridisation transition of DNA and many structural properties of single- and double-stranded DNA. oxDNA was previously only available as standalone software, but has now been implemented into the popular LAMMPS molecular dynamics code. This article describes the new implementation and analyses its parallel performance. Practical applications are presented that focus on single-stranded DNA, an area of research which has been so far under-investigated. The LAMMPS implementation of oxDNA lowers the entry barrier for using the oxDNA model significantly, facilitates future code development and interfacing with existing LAMMPS functionality as well as other coarse-grained and atomistic DNA models.
Biological nano-functionalization of titanium-based biomaterial surfaces: a flexible toolbox

PubMed Central

Beutner, René; Michael, Jan; Schwenzer, Bernd; Scharnweber, Dieter

2010-01-01

Surface functionalization with bioactive molecules (BAMs) on a nanometre scale is a main field in current biomaterial research. The immobilization of a vast number of substances and molecules, ranging from inorganic calcium phosphate phases up to peptides and proteins, has been investigated throughout recent decades. However, in vitro and in vivo results are heterogeneous. This may be at least partially attributed to the limits of the applied immobilization methods. Therefore, this paper highlights, in the first part, advantages and limits of the currently applied methods for the biological nano-functionalization of titanium-based biomaterial surfaces. The second part describes a new immobilization system recently developed in our groups. It uses the nanomechanical fixation of at least partially single-stranded nucleic acids (NAs) into an anodic titanium oxide layer as an immobilization principle and their hybridization ability for the functionalization of the surface with BAMs conjugated to the respective complementary NA strands. PMID:19889692
Taking Up Space: Museum Exploration in the Twenty-First Century

ERIC Educational Resources Information Center

Sutton, Tiffany

2007-01-01

Museums have become a crucible for questions of the role that traditional art and art history should play in contemporary art. Friedrich Nietzsche argued in the nineteenth century that museums can be no more than mausoleums for effete (fine) art. Over the course of the twentieth century, however, curators dispelled such blanket pessimism by…
Issues and Prospects of Effetive Implementation of New Secondary School Curriculum in Nigeria

ERIC Educational Resources Information Center

Ahmadi, Ali A.; Lukman, Ajibola A.

2015-01-01

This paper digs into the issues surrounding effective implementation of new secondary school curriculum in Nigeria. This is based on the feeling that 21st century education is characterized with a dramatic technological revolution. The paper therefore portrays education in the 21st century as a total departure from the factory-model education of…
Optics of a Double Focussing Magnetic Sector by Fringe Effect; OPTIQUE D'UN SECTEUR MAGNETIQUE A DOUBLE FOCALISATION PAR EFFET DE FRANCES

DOE Office of Scientific and Technical Information (OSTI.GOV)

Krafft, J.

1960-01-01

A general study is made of the optical elements of a double-fccusing magnetic sector by the fringe effect, with a view to its application to the monochromation of the proton, deuteron, or triton beam of the 1.4 Mev accelerator. (auth)
Investigations into the Power MOSFET SEGR Phenomenon and its Physical Mechanism

NASA Technical Reports Server (NTRS)

Swift, G. M.; Edmonds, L. E.; Miyahira, T.; Nichols, D. K.; Johnston, A. H.

1997-01-01

The state of understanding of the destructive SEGR event in power MOSFETs is relatively mature with large published efforts, both experimental and theoretical. However, gasps remain in the uderstanding of the phenomenon, including unexplained anomalies, emperical-only dependencies on some important device and incident ion physical parameters, and limited insight into latent effets.
Biofilm formation on stainless steel and gold wires for bonded retainers in vitro and in vivo and their susceptibility to oral antimicrobials.

PubMed

Jongsma, Marije A; Pelser, Floris D H; van der Mei, Henny C; Atema-Smit, Jelly; van de Belt-Gritter, Betsy; Busscher, Henk J; Ren, Yijin

2013-05-01

Bonded retainers are used in orthodontics to maintain treatment result. Retention wires are prone to biofilm formation and cause gingival recession, bleeding on probing and increased pocket depths near bonded retainers. In this study, we compare in vitro and in vivo biofilm formation on different wires used for bonded retainers and the susceptibility of in vitro biofilms to oral antimicrobials. Orthodontic wires were exposed to saliva, and in vitro biofilm formation was evaluated using plate counting and live/dead staining, together with effects of exposure to toothpaste slurry alone or followed by antimicrobial mouthrinse application. Wires were also placed intra-orally for 72 h in human volunteers and undisturbed biofilm formation was compared by plate counting and live/dead staining, as well as by denaturing gradient gel electrophoresis for compositional differences in biofilms. Single-strand wires attracted only slightly less biofilm in vitro than multi-strand wires. Biofilms on stainless steel single-strand wires however, were much more susceptible to antimicrobials from toothpaste slurries and mouthrinses than on single-strand gold wires and biofilms on multi-strand wires. Also, in vivo significantly less biofilm was found on single-strand than on multi-strand wires. Microbial composition of biofilms was more dependent on the volunteer involved than on wire type. Biofilms on single-strand stainless steel wires attract less biofilm in vitro and are more susceptible to antimicrobials than on multi-strand wires. Also in vivo, single-strand wires attract less biofilm than multi-strand ones. Use of single-strand wires is preferred over multi-strand wires, not because they attract less biofilm, but because biofilms on single-strand wires are not protected against antimicrobials as in crevices and niches as on multi-strand wires.
Strand displacement by DNA polymerase III occurs through a tau-psi-chi link to single-stranded DNA-binding protein coating the lagging strand template.

PubMed

Yuan, Quan; McHenry, Charles S

2009-11-13

In addition to the well characterized processive replication reaction catalyzed by the DNA polymerase III holoenzyme on single-stranded DNA templates, the enzyme possesses an intrinsic strand displacement activity on flapped templates. The strand displacement activity is distinguished from the single-stranded DNA-templated reaction by a high dependence upon single-stranded DNA binding protein and an inability of gamma-complex to support the reaction in the absence of tau. However, if gamma-complex is present to load beta(2), a truncated tau protein containing only domains III-V will suffice. This truncated protein is sufficient to bind both the alpha subunit of DNA polymerase (Pol) III and chipsi. This is reminiscent of the minimal requirements for Pol III to replicate short single-stranded DNA-binding protein (SSB)-coated templates where tau is only required to serve as a scaffold to hold Pol III and chi in the same complex (Glover, B., and McHenry, C. (1998) J. Biol. Chem. 273, 23476-23484). We propose a model in which strand displacement by DNA polymerase III holoenzyme depends upon a Pol III-tau-psi-chi-SSB binding network, where SSB is bound to the displaced strand, stabilizing the Pol III-template interaction. The same interaction network is probably important for stabilizing the leading strand polymerase interactions with authentic replication forks. The specificity constant (k(cat)/K(m)) for the strand displacement reaction is approximately 300-fold less favorable than reactions on single-stranded templates and proceeds with a slower rate (150 nucleotides/s) and only moderate processivity (approximately 300 nucleotides). PriA, the initiator of replication restart on collapsed or misassembled replication forks, blocks the strand displacement reaction, even if added to an ongoing reaction.
Higher 5-hydroxymethylcytosine identifies immortal DNA strand chromosomes in asymmetrically self-renewing distributed stem cells.

PubMed

Huh, Yang Hoon; Cohen, Justin; Sherley, James L

2013-10-15

Immortal strands are the targeted chromosomal DNA strands of nonrandom sister chromatid segregation, a mitotic chromosome segregation pattern unique to asymmetrically self-renewing distributed stem cells (DSCs). By nonrandom segregation, immortal DNA strands become the oldest DNA strands in asymmetrically self-renewing DSCs. Nonrandom segregation of immortal DNA strands may limit DSC mutagenesis, preserve DSC fate, and contribute to DSC aging. The mechanisms responsible for specification and maintenance of immortal DNA strands are unknown. To discover clues to these mechanisms, we investigated the 5-methylcytosine and 5-hydroxymethylcytosine (5hmC) content on chromosomes in mouse hair follicle DSCs during nonrandom segregation. Although 5-methylcytosine content did not differ significantly, the relative content of 5hmC was significantly higher in chromosomes containing immortal DNA strands than in opposed mitotic chromosomes containing younger mortal DNA strands. The difference in relative 5hmC content was caused by the loss of 5hmC from mortal chromosomes. These findings implicate higher 5hmC as a specific molecular determinant of immortal DNA strand chromosomes. Because 5hmC is an intermediate during DNA demethylation, we propose a ten-eleven translocase enzyme mechanism for both the specification and maintenance of nonrandomly segregated immortal DNA strands. The proposed mechanism reveals a means by which DSCs "know" the generational age of immortal DNA strands. The mechanism is supported by molecular expression data and accounts for the selection of newly replicated DNA strands when nonrandom segregation is initiated. These mechanistic insights also provide a possible basis for another characteristic property of immortal DNA strands, their guanine ribonucleotide dependency.
Procedure for normalization of cDNA libraries

DOEpatents

Bonaldo, Maria DeFatima; Soares, Marcelo Bento

1997-01-01

This invention provides a method to normalize a cDNA library constructed in a vector capable of being converted to single-stranded circles and capable of producing complementary nucleic acid molecules to the single-stranded circles comprising: (a) converting the cDNA library in single-stranded circles; (b) generating complementary nucleic acid molecules to the single-stranded circles; (c) hybridizing the single-stranded circles converted in step (a) with complementary nucleic acid molecules of step (b) to produce partial duplexes to an appropriate Cot; (e) separating the unhybridized single-stranded circles from the hybridized single-stranded circles, thereby generating a normalized cDNA library.
Vacuum powder injector and method of impregnating fiber with powder

NASA Astrophysics Data System (ADS)

Working, Dennis C.

1993-05-01

A method and apparatus uniformly impregnate stranded material with dry powder such as low solubility, high melt flow polymer powder to produce, for example, composite prepregs. The stranded material is expanded in an impregnation chamber by an influx of air so that the powder, which may enter through the same inlet as the air, penetrates to the center of the stranded material. The stranded material then is contracted for holding the powder therein. The stranded material and powder may be pulled through the impregnation chamber in the same direction by vacuum. Larger particles of powder which do not fully penetrate the stranded material may be combed into the stranded material and powder which does not impregnate the stranded material may be collected and reused.
Vacuum powder injector and method of impregnating fiber with powder

NASA Technical Reports Server (NTRS)

Working, Dennis C. (Inventor)

1993-01-01

A method and apparatus uniformly impregnate stranded material with dry powder such as low solubility, high melt flow polymer powder to produce, for example, composite prepregs. The stranded material is expanded in an impregnation chamber by an influx of air so that the powder, which may enter through the same inlet as the air, penetrates to the center of the stranded material. The stranded material then is contracted for holding the powder therein. The stranded material and powder may be pulled through the impregnation chamber in the same direction by vacuum. Larger particles of powder which do not fully penetrate the stranded material may be combed into the stranded material and powder which does not impregnate the stranded material may be collected and reused.
3' Homologous Free Ends are Required for Stable Joint Molecule Formation by the RecA and Single-Stranded Binding Proteins of Escherichia coli

NASA Astrophysics Data System (ADS)

Konforti, Boyana B.; Davis, Ronald W.

1987-02-01

The RecA protein of Escherichia coli is important for genetic recombination in vivo and can promote synapsis and strand exchange in vitro. The DNA pairing and strand exchange reactions have been well characterized in reactions with circular single strands and linear duplexes, but little is known about these two processes using substrates more characteristic of those likely to exist in the cell. Single-stranded linear DNAs were prepared by separating strands of duplex molecules or by cleaving single-stranded circles at a unique restriction site created by annealing a short defined oligonucleotide to the circle. Analysis by gel electrophoresis and electron microscopy revealed that, in the presence of RecA and single-stranded binding proteins, a free 3' homologous end is essential for stable joint molecule formation between linear single-stranded and circular duplex DNA.
Determining orientation and direction of DNA sequences

DOEpatents

Goodwin, Edwin H.; Meyne, Julianne

2000-01-01

Determining orientation and direction of DNA sequences. A method by which fluorescence in situ hybridization can be made strand specific is described. Cell cultures are grown in a medium containing a halogenated nucleotide. The analog is partially incorporated in one DNA strand of each chromatid. This substitution takes place in opposite strands of the two sister chromatids. After staining with the fluorescent DNA-binding dye Hoechst 33258, cells are exposed to long-wavelength ultraviolet light which results in numerous strand nicks. These nicks enable the substituted strand to be denatured and solubilized by heat, treatment with high or low pH aqueous solutions, or by immersing the strands in 2.times.SSC (0.3M NaCl+0.03M sodium citrate), to name three procedures. It is unnecessary to enzymatically digest the strands using Exo III or another exonuclease in order to excise and solubilize nucleotides starting at the sites of the nicks. The denaturing/solubilizing process removes most of the substituted strand while leaving the prereplication strand largely intact. Hybridization of a single-stranded probe of a tandem repeat arranged in a head-to-tail orientation will result in hybridization only to the chromatid with the complementary strand present.
Single-cell template strand sequencing by Strand-seq enables the characterization of individual homologs.

PubMed

Sanders, Ashley D; Falconer, Ester; Hills, Mark; Spierings, Diana C J; Lansdorp, Peter M

2017-06-01

The ability to distinguish between genome sequences of homologous chromosomes in single cells is important for studies of copy-neutral genomic rearrangements (such as inversions and translocations), building chromosome-length haplotypes, refining genome assemblies, mapping sister chromatid exchange events and exploring cellular heterogeneity. Strand-seq is a single-cell sequencing technology that resolves the individual homologs within a cell by restricting sequence analysis to the DNA template strands used during DNA replication. This protocol, which takes up to 4 d to complete, relies on the directionality of DNA, in which each single strand of a DNA molecule is distinguished based on its 5'-3' orientation. Culturing cells in a thymidine analog for one round of cell division labels nascent DNA strands, allowing for their selective removal during genomic library construction. To preserve directionality of template strands, genomic preamplification is bypassed and labeled nascent strands are nicked and not amplified during library preparation. Each single-cell library is multiplexed for pooling and sequencing, and the resulting sequence data are aligned, mapping to either the minus or plus strand of the reference genome, to assign template strand states for each chromosome in the cell. The major adaptations to conventional single-cell sequencing protocols include harvesting of daughter cells after a single round of BrdU incorporation, bypassing of whole-genome amplification, and removal of the BrdU + strand during Strand-seq library preparation. By sequencing just template strands, the structure and identity of each homolog are preserved.
CTC1-mediated C-strand fill-in is an essential step in telomere length maintenance

PubMed Central

Feng, Xuyang; Hsu, Shih-Jui; Kasbek, Christopher; Chaiken, Mary

2017-01-01

Abstract To prevent progressive telomere shortening as a result of conventional DNA replication, new telomeric DNA must be added onto the chromosome end. The de novo DNA synthesis involves elongation of the G-rich strand of the telomere by telomerase. In human cells, the CST complex (CTC1-STN1-TEN1) also functions in telomere replication. CST first aids in duplication of the telomeric dsDNA. Then after telomerase has extended the G-rich strand, CST facilitates fill-in synthesis of the complementary C-strand. Here, we analyze telomere structure after disruption of human CTC1 and demonstrate that functional CST is essential for telomere length maintenance due to its role in mediating C-strand fill-in. Removal of CTC1 results in elongation of the 3΄ overhang on the G-rich strand. This leads to accumulation of RPA and telomeric DNA damage signaling. G-overhang length increases with time after CTC1 disruption and at early times net G-strand growth is apparent, indicating telomerase-mediated G-strand extension. In contrast, C-strand length decreases continuously, indicating a deficiency in C-strand fill-in synthesis. The lack of C-strand maintenance leads to gradual shortening of the telomeric dsDNA, similar to that observed in cells lacking telomerase. Thus, telomerase-mediated G-strand extension and CST-mediated C-strand fill-in are equally important for telomere length maintenance. PMID:28334750
The assessment of cold atmospheric plasma treatment of DNA in synthetic models of tissue fluid, tissue and cells

NASA Astrophysics Data System (ADS)

Szili, Endre J.; Gaur, Nishtha; Hong, Sung-Ha; Kurita, Hirofumi; Oh, Jun-Seok; Ito, Masafumi; Mizuno, Akira; Hatta, Akimitsu; Cowin, Allison J.; Graves, David B.; Short, Robert D.

2017-07-01

There is a growing literature database that demonstrates the therapeutic potential of cold atmospheric plasma (herein referred to as plasma). Given the breadth of proposed applications (e.g. from teeth whitening to cancer therapy) and vast gamut of plasma devices being researched, it is timely to consider plasma interactions with specific components of the cell in more detail. Plasma can produce highly reactive oxygen and nitrogen species (RONS) such as the hydroxyl radical (OH•), peroxynitrite (ONOO-) and superoxide (\\text{O}2- ) that would readily modify essential biomolecules such as DNA. These modifications could in principle drive a wide range of biological processes. Against this possibility, the reported therapeutic action of plasmas are not underpinned by a particularly deep knowledge of the potential plasma-tissue, -cell or -biomolecule interactions. In this study, we aim to partly address this issue by developing simple models to study plasma interactions with DNA, in the form of DNA-strand breaks. This is carried out using synthetic models of tissue fluid, tissue and cells. We argue that this approach makes experimentation simpler, more cost-effective and faster than compared to working with real biological materials and cells. Herein, a helium plasma jet source was utilised for these experiments. We show that the plasma jet readily induced DNA-strand breaks in the tissue fluid model and in the cell model, surprisingly without any significant poration or rupture of the phospholipid membrane. In the plasma jet treatment of the tissue model, DNA-strand breaks were detected in the tissue mass after pro-longed treatment (on the time-scale of minutes) with no DNA-strand breaks being detected in the tissue fluid model underneath the tissue model. These data are discussed in the context of the therapeutic potential of plasma.

Determining the folding and unfolding rate constants of nucleic acids by biosensor. Application to telomere G-quadruplex.

PubMed

Zhao, Yong; Kan, Zhong-yuan; Zeng, Zhi-xiong; Hao, Yu-hua; Chen, Hua; Tan, Zheng

2004-10-20

Nucleic acid molecules may fold into secondary structures, and the formation of such structures is involved in many biological processes and technical applications. The folding and unfolding rate constants define the kinetics of conformation interconversion and the stability of these structures and is important in realizing their functions. We developed a method to determine these kinetic parameters using an optical biosensor based on surface plasmon resonance. The folding and unfolding of a nucleic acid is coupled with a hybridization reaction by immobilization of the target nucleic acid on a sensor chip surface and injection of a complementary probe nucleic acid over the sensor chip surface. By monitoring the time course of duplex formation, both the folding and unfolding rate constants for the target nucleic acid and the association and dissociation rate constants for the target-probe duplex can all be derived from the same measurement. We applied this method to determine the folding and unfolding rate constants of the G-quadruplex of human telomere sequence (TTAGGG)(4) and its association and dissociation rate constants with the complementary strand (CCCTAA)(4). The results show that both the folding and unfolding occur on the time scale of minutes at physiological concentration of K(+). We speculate that this property might be important for telomere elongation. A complete set of the kinetic parameters for both of the structures allows us to study the competition between the formation of the quadruplex and the duplex. Calculations indicate that the formation of both the quadruplex and the duplex is strand concentration-dependent, and the quadruplex can be efficiently formed at low strand concentration. This property may provide the basis for the formation of the quadruplex in vivo in the presence of a complementary strand.
DNA Resection at Chromosome Breaks Promotes Genome Stability by Constraining Non-Allelic Homologous Recombination

PubMed Central

Koshland, Douglas

2012-01-01

DNA double-strand breaks impact genome stability by triggering many of the large-scale genome rearrangements associated with evolution and cancer. One of the first steps in repairing this damage is 5′→3′ resection beginning at the break site. Recently, tools have become available to study the consequences of not extensively resecting double-strand breaks. Here we examine the role of Sgs1- and Exo1-dependent resection on genome stability using a non-selective assay that we previously developed using diploid yeast. We find that Saccharomyces cerevisiae lacking Sgs1 and Exo1 retains a very efficient repair process that is highly mutagenic to genome structure. Specifically, 51% of cells lacking Sgs1 and Exo1 repair a double-strand break using repetitive sequences 12–48 kb distal from the initial break site, thereby generating a genome rearrangement. These Sgs1- and Exo1-independent rearrangements depend partially upon a Rad51-mediated homologous recombination pathway. Furthermore, without resection a robust cell cycle arrest is not activated, allowing a cell with a single double-strand break to divide before repair, potentially yielding multiple progeny each with a different rearrangement. This profusion of rearranged genomes suggests that cells tolerate any dangers associated with extensive resection to inhibit mutagenic pathways such as break-distal recombination. The activation of break-distal recipient repeats and amplification of broken chromosomes when resection is limited raise the possibility that genome regions that are difficult to resect may be hotspots for rearrangements. These results may also explain why mutations in resection machinery are associated with cancer. PMID:22479212
A two-dimensional 1H-NMR study of the dam methylase site: comparison between the hemimethylated GATC sequence, its unmethylated analogue and a hemimethylated CATG sequence. The sequence dependence of methylation upon base-pair lifetimes.

PubMed

Fazakerley, G V; Quignard, E; Teoule, R; Guy, A; Guschlbauer, W

1987-09-15

We report two-dimensional NOE (NOESY) spectra on the sequence d(GCGATCATGG).d(CCATGATCGC) which contains the unmethylated dam site. As expected the DNA adopts a B-form conformation but appears to be distorted at the TG step of the second strand. This distorsion, probably bending, is not seen on the opposite strand. When the first strand is methylated on adenine in the GATC or CATG sequence the NOESY spectra indicate little or no change in the conformation. However the single strand-duplex exchange is slowed down to the slow-exchange region on a proton NMR time scale. We have assigned the exchangeable imino and cytidine amino resonances of the three duplexes. From the imino linewidths as a function of temperature, we observe that the unmethylated and the hemimethylated Gm6ATC duplexes melt normally from the ends. However, this is not so for the hemimethylated Cm6ATG duplex which, apart from the terminal base pairs, melts cooperatively and at higher temperature. In spectra recorded in H2O a second duplex is observed, for the Gm6ATC sequence, which we have not been able to identify. It is however unlikely to be a hairpin structure. Ultraviolet-melting curves also indicate the presence of two transitions for this duplex. The effect of methylation upon base-pair lifetimes has been studied by comparing the above three duplexes. Little effect is observed upon methylation in the GATC sequence but a drastic increase in the lifetimes of all base pairs is observed upon methylation in the CATG sequence.
An autonomous molecular computer for logical control of gene expression.

PubMed

Benenson, Yaakov; Gil, Binyamin; Ben-Dor, Uri; Adar, Rivka; Shapiro, Ehud

2004-05-27

Early biomolecular computer research focused on laboratory-scale, human-operated computers for complex computational problems. Recently, simple molecular-scale autonomous programmable computers were demonstrated allowing both input and output information to be in molecular form. Such computers, using biological molecules as input data and biologically active molecules as outputs, could produce a system for 'logical' control of biological processes. Here we describe an autonomous biomolecular computer that, at least in vitro, logically analyses the levels of messenger RNA species, and in response produces a molecule capable of affecting levels of gene expression. The computer operates at a concentration of close to a trillion computers per microlitre and consists of three programmable modules: a computation module, that is, a stochastic molecular automaton; an input module, by which specific mRNA levels or point mutations regulate software molecule concentrations, and hence automaton transition probabilities; and an output module, capable of controlled release of a short single-stranded DNA molecule. This approach might be applied in vivo to biochemical sensing, genetic engineering and even medical diagnosis and treatment. As a proof of principle we programmed the computer to identify and analyse mRNA of disease-related genes associated with models of small-cell lung cancer and prostate cancer, and to produce a single-stranded DNA molecule modelled after an anticancer drug.
Evolution of Pull-Apart Basins and Their Scale Independence

NASA Astrophysics Data System (ADS)

Aydin, Atilla; Nur, Amos

1982-02-01

Pull-apart basins or rhomb grabens and horsts along major strike-slip fault systems in the world are generally associated with horizontal slip along faults. A simple model suggests that the width of the rhombs is controlled by the initial fault geometry, whereas the length increases with increasing fault displacement. We have tested this model by analyzing the shapes of 70 well-defined rhomb-like pull-apart basins and pressure ridges, ranging from tens of meters to tens of kilometers in length, associated with several major strike-slip faults in the western United States, Israel, Turkey, Iran, Guatemala, Venezuela, and New Zealand. In conflict with the model, we find that the length to width ratio of these basins is a constant value of approximately 3; these basins become wider as they grow longer with increasing fault offset. Two possible mechanisms responsible for the increase in width are suggested: (1) coalescence of neighboring rhomb grabens as each graben increases its length and (2) formation of fault strands parallel to the existing ones when large displacements need to be accommodated. The processes of formation and growth of new fault strands promote interaction among the new faults and between the new and preexisting faults on a larger scale. Increased displacement causes the width of the fault zone to increase resulting in wider pull-apart basins.
Higher 5-hydroxymethylcytosine identifies immortal DNA strand chromosomes in asymmetrically self-renewing distributed stem cells

PubMed Central

Huh, Yang Hoon; Cohen, Justin; Sherley, James L.

2013-01-01

Immortal strands are the targeted chromosomal DNA strands of nonrandom sister chromatid segregation, a mitotic chromosome segregation pattern unique to asymmetrically self-renewing distributed stem cells (DSCs). By nonrandom segregation, immortal DNA strands become the oldest DNA strands in asymmetrically self-renewing DSCs. Nonrandom segregation of immortal DNA strands may limit DSC mutagenesis, preserve DSC fate, and contribute to DSC aging. The mechanisms responsible for specification and maintenance of immortal DNA strands are unknown. To discover clues to these mechanisms, we investigated the 5-methylcytosine and 5-hydroxymethylcytosine (5hmC) content on chromosomes in mouse hair follicle DSCs during nonrandom segregation. Although 5-methylcytosine content did not differ significantly, the relative content of 5hmC was significantly higher in chromosomes containing immortal DNA strands than in opposed mitotic chromosomes containing younger mortal DNA strands. The difference in relative 5hmC content was caused by the loss of 5hmC from mortal chromosomes. These findings implicate higher 5hmC as a specific molecular determinant of immortal DNA strand chromosomes. Because 5hmC is an intermediate during DNA demethylation, we propose a ten-eleven translocase enzyme mechanism for both the specification and maintenance of nonrandomly segregated immortal DNA strands. The proposed mechanism reveals a means by which DSCs “know” the generational age of immortal DNA strands. The mechanism is supported by molecular expression data and accounts for the selection of newly replicated DNA strands when nonrandom segregation is initiated. These mechanistic insights also provide a possible basis for another characteristic property of immortal DNA strands, their guanine ribonucleotide dependency. PMID:24082118
Five-Strand versus Four-Strand Hamstring Tendon Graft Technique for Anterior Cruciate Ligament Reconstruction: A Biomechanical Comparison.

PubMed

Vaillant, Eric R; Parks, Brent G; Camire, Lyn M; Hinton, Richard Y

2017-11-01

The aim of this article is to compare diameter and stiffness, displacement, and strain in a five-strand versus four-strand hamstring graft for anterior cruciate ligament reconstruction. Eight matched pairs of lower extremities underwent four-strand or five-strand hamstring graft reconstruction. Diameter was significantly higher in the five-strand versus the four-strand construct ( p = 0.002). No significant difference was found between the groups in construct displacement or stiffness. Significantly higher strain was observed in the inner limb versus the outer limb in the four-strand construct ( p = 0.001) and in the inner limb versus the fifth limb in the 5-strand construct ( p = 0.004). A fifth limb added to a four-strand hamstring graft significantly increased graft diameter but did not significantly change stiffness or displacement, suggesting that attachment of additional graft material via suture did not provide for full incorporation of the added limb into the graft at time zero. The inner limb in both constructs absorbed significantly greater load than did other limbs. The use of suture to attach additional material to a four-strand hamstring graft may not contribute to improved biomechanical qualities of the graft at time zero. Thieme Medical Publishers 333 Seventh Avenue, New York, NY 10001, USA.
A Novel Computational Method to Reduce Leaky Reaction in DNA Strand Displacement.

PubMed

Li, Xin; Wang, Xun; Song, Tao; Lu, Wei; Chen, Zhihua; Shi, Xiaolong

2015-01-01

DNA strand displacement technique is widely used in DNA programming, DNA biosensors, and gene analysis. In DNA strand displacement, leaky reactions can cause DNA signals decay and detecting DNA signals fails. The mostly used method to avoid leakage is cleaning up after upstream leaky reactions, and it remains a challenge to develop reliable DNA strand displacement technique with low leakage. In this work, we address the challenge by experimentally evaluating the basic factors, including reaction time, ratio of reactants, and ion concentration to the leakage in DNA strand displacement. Specifically, fluorescent probes and a hairpin structure reporting DNA strand are designed to detect the output of DNA strand displacement, and thus can evaluate the leakage of DNA strand displacement reactions with different reaction time, ratios of reactants, and ion concentrations. From the obtained data, mathematical models for evaluating leakage are achieved by curve derivation. As a result, it is obtained that long time incubation, high concentration of fuel strand, and inappropriate amount of ion concentration can weaken leaky reactions. This contributes to a method to set proper reaction conditions to reduce leakage in DNA strand displacement.
5′CAG and 5′CTG Repeats Create Differential Impediment to the Progression of a Minimal Reconstituted T4 Replisome Depending on the Concentration of dNTPs

PubMed Central

Delagoutte, Emmanuelle; Baldacci, Giuseppe

2011-01-01

Instability of repetitive sequences originates from strand misalignment during repair or replicative DNA synthesis. To investigate the activity of reconstituted T4 replisomes across trinucleotide repeats (TNRs) during leading strand DNA synthesis, we developed a method to build replication miniforks containing a TNR unit of defined sequence and length. Each minifork consists of three strands, primer, leading strand template, and lagging strand template with a 5′ single-stranded (ss) tail. Each strand is prepared independently, and the minifork is assembled by hybridization of the three strands. Using these miniforks and a minimal reconstituted T4 replisome, we show that during leading strand DNA synthesis, the dNTP concentration dictates which strand of the structure-forming 5′CAG/5′CTG repeat creates the strongest impediment to the minimal replication complex. We discuss this result in the light of the known fluctuation of dNTP concentration during the cell cycle and cell growth and the known concentration balance among individual dNTPs. PMID:22096622
Developing Single-Molecule TPM Experiments for Direct Observation of Successful RecA-Mediated Strand Exchange Reaction

PubMed Central

Fan, Hsiu-Fang; Cox, Michael M.; Li, Hung-Wen

2011-01-01

RecA recombinases play a central role in homologous recombination. Once assembled on single-stranded (ss) DNA, RecA nucleoprotein filaments mediate the pairing of homologous DNA sequences and strand exchange processes. We have designed two experiments based on tethered particle motion (TPM) to investigate the fates of the invading and the outgoing strands during E. coli RecA-mediated pairing and strand exchange at the single-molecule level in the absence of force. TPM experiments measure the tethered bead Brownian motion indicative of the DNA tether length change resulting from RecA binding and dissociation. Experiments with beads labeled on either the invading strand or the outgoing strand showed that DNA pairing and strand exchange occurs successfully in the presence of either ATP or its non-hydrolyzable analog, ATPγS. The strand exchange rates and efficiencies are similar under both ATP and ATPγS conditions. In addition, the Brownian motion time-courses suggest that the strand exchange process progresses uni-directionally in the 5′-to-3′ fashion, using a synapse segment with a wide and continuous size distribution. PMID:21765895
Cause-specific temporal and spatial trends in green sea turtle strandings in the Hawaiian Archipelago (1982-2003)

USGS Publications Warehouse

Chaloupka, Milani; Work, Thierry M.; Balazs, George H.; Murakawa, Shawn K. K.; Morris, Robert

2008-01-01

We investigated cause-specific temporal and spatial trends in sea turtle strandings in the Hawaiian Archipelago. Five species of sea turtle were recorded in 3,861 strandings over a 22-year period (1982–2003). Green turtles comprised 97% of these strandings with size and gender composition reflecting the demographic structure of the resident green turtle population and relative green turtle abundance in Hawaiian waters. The cause of strandings was determined by necropsy based on a complete gross external and internal examination. Totally 75% of the 3,732 green turtle strandings were from Oahu where strandings occur year-round. The most common known cause of the green turtle strandings was the tumour-forming disease, fibropapillomatosis (28%) followed by hook-and-line fishing gear-induced trauma (7%), gillnet fishing gear-induced trauma (5%), boat strike (2.5%), and shark attack (2.7%). Miscellaneous causes comprised 5.4% of strandings whereas 49% of green turtle strandings could not be attributed to any known cause. Green turtle strandings attributable to boat strike were more likely from Kauai and Oahu while fibropapilloma strandings were more likely from Oahu and Maui. Hook-and-line gear strandings were more likely from Oahu due to higher per capita inshore fishing effort. The specific mortality rate (conditional probability) for fibropapillomatosis was 88%, 69% for gillnet gear and 52% for hook-and-line gear. The probability of a dead green turtle stranding increased from 1982 but levelled off by the mid-1990s. The declining mortality risk was because the prevalence and severity of fibropapillomatosis has decreased recently and so has the mortality risk attributable to gillnet gear. Despite exposure to disease and inshore fishing gears, the Hawaiian green turtle stock continues to recover following protection since the late 1970s. Nevertheless, measures to reduce incidental capture of sea turtles in coastal Hawaiian fisheries would be prudent, especially since strandings attributable to hook-and-line fishing gear have increased steadily since 1982.
Can a double stranded DNA be unzipped by pulling a single strand?: phases of adsorbed DNA.

PubMed

Kapri, Rajeev

2009-04-14

We study the unzipping of a double stranded DNA (dsDNA) by applying an external force on a single strand while leaving the other strand free. We find that the dsDNA can be unzipped to two single strands if the external force exceeds a critical value. We obtain the phase diagram, which is found to be different from the phase diagram of unzipping by pulling both the strands in opposite directions. In the presence of an attractive surface near DNA, the phase diagram gets modified drastically and shows richer surprises including a critical end point and a triple point.
Procedure for normalization of cDNA libraries

DOEpatents

Bonaldo, M.D.; Soares, M.B.

1997-12-30

This invention provides a method to normalize a cDNA library constructed in a vector capable of being converted to single-stranded circles and capable of producing complementary nucleic acid molecules to the single-stranded circles comprising: (a) converting the cDNA library in single-stranded circles; (b) generating complementary nucleic acid molecules to the single-stranded circles; (c) hybridizing the single-stranded circles converted in step (a) with complementary nucleic acid molecules of step (b) to produce partial duplexes to an appropriate Cot; (e) separating the unhybridized single-stranded circles from the hybridized single-stranded circles, thereby generating a normalized cDNA library. 1 fig.
The Stranding Anomaly as Population Indicator: The Case of Harbour Porpoise Phocoena phocoena in North-Western Europe

PubMed Central

Peltier, Helene; Baagøe, Hans J.; Camphuysen, Kees C. J.; Czeck, Richard; Dabin, Willy; Daniel, Pierre; Deaville, Rob; Haelters, Jan; Jauniaux, Thierry; Jensen, Lasse F.; Jepson, Paul D.; Keijl, Guido O.; Siebert, Ursula; Van Canneyt, Olivier; Ridoux, Vincent

2013-01-01

Ecological indicators for monitoring strategies are expected to combine three major characteristics: ecological significance, statistical credibility, and cost-effectiveness. Strategies based on stranding networks rank highly in cost-effectiveness, but their ecological significance and statistical credibility are disputed. Our present goal is to improve the value of stranding data as population indicator as part of monitoring strategies by constructing the spatial and temporal null hypothesis for strandings. The null hypothesis is defined as: small cetacean distribution and mortality are uniform in space and constant in time. We used a drift model to map stranding probabilities and predict stranding patterns of cetacean carcasses under H0 across the North Sea, the Channel and the Bay of Biscay, for the period 1990–2009. As the most common cetacean occurring in this area, we chose the harbour porpoise Phocoena phocoena for our modelling. The difference between these strandings expected under H0 and observed strandings is defined as the stranding anomaly. It constituted the stranding data series corrected for drift conditions. Seasonal decomposition of stranding anomaly suggested that drift conditions did not explain observed seasonal variations of porpoise strandings. Long-term stranding anomalies increased first in the southern North Sea, the Channel and Bay of Biscay coasts, and finally the eastern North Sea. The hypothesis of changes in porpoise distribution was consistent with local visual surveys, mostly SCANS surveys (1994 and 2005). This new indicator could be applied to cetacean populations across the world and more widely to marine megafauna. PMID:23614031
Database documentation of marine mammal stranding and mortality: current status review and future prospects.

PubMed

Chan, Derek K P; Tsui, Henry C L; Kot, Brian C W

2017-11-21

Databases are systematic tools to archive and manage information related to marine mammal stranding and mortality events. Stranding response networks, governmental authorities and non-governmental organizations have established regional or national stranding networks and have developed unique standard stranding response and necropsy protocols to document and track stranded marine mammal demographics, signalment and health data. The objectives of this study were to (1) describe and review the current status of marine mammal stranding and mortality databases worldwide, including the year established, types of database and their goals; and (2) summarize the geographic range included in the database, the number of cases recorded, accessibility, filter and display methods. Peer-reviewed literature was searched, focussing on published databases of live and dead marine mammal strandings and mortality and information released from stranding response organizations (i.e. online updates, journal articles and annual stranding reports). Databases that were not published in the primary literature or recognized by government agencies were excluded. Based on these criteria, 10 marine mammal stranding and mortality databases were identified, and strandings and necropsy data found in these databases were evaluated. We discuss the results, limitations and future prospects of database development. Future prospects include the development and application of virtopsy, a new necropsy investigation tool. A centralized web-accessed database of all available postmortem multimedia from stranded marine mammals may eventually support marine conservation and policy decisions, which will allow the use of marine animals as sentinels of ecosystem health, working towards a 'One Ocean-One Health' ideal.
Method and apparatus for testing a forward-moving strand

DOEpatents

Ducommun, Joel; Vulliens, Philippe

1980-01-01

In a method for testing a continuously forward-moving strand a light beam which passes along a plane that extends approximately perpendicularly to the longitudinal axis of the strand is introduced into the strand. The brightness value is measured on a place of the strand exterior which is distal from the light incidence place by means of at least one photoelectronic element disposed directly on the strand exterior and the measured result is evaluated in a gating circuit which is electrically connected to the photoelectronic element.
Triplex in-situ hybridization

DOEpatents

Fresco, Jacques R.; Johnson, Marion D.

2002-01-01

Disclosed are methods for detecting in situ the presence of a target sequence in a substantially double-stranded nucleic acid segment, which comprises: a) contacting in situ under conditions suitable for hybridization a substantially double-stranded nucleic acid segment with a detectable third strand, said third strand being capable of hybridizing to at least a portion of the target sequence to form a triple-stranded structure, if said target sequence is present; and b) detecting whether hybridization between the third strand and the target sequence has occured.
Deletions at short direct repeats and base substitutions are characteristic mutations for bleomycin-induced double- and single-strand breaks, respectively, in a human shuttle vector system

NASA Technical Reports Server (NTRS)

Dar, M. E.; Jorgensen, T. J.

1995-01-01

Using the radiomimetic drug, bleomycin, we have determined the mutagenic potential of DNA strand breaks in the shuttle vector pZ189 in human fibroblasts. The bleomycin treatment conditions used produce strand breaks with 3'-phosphoglycolate termini as > 95% of the detectable dose-dependent lesions. Breaks with this end group represent 50% of the strand break damage produced by ionizing radiation. We report that such strand breaks are mutagenic lesions. The type of mutation produced is largely determined by the type of strand break on the plasmid (i.e. single versus double). Mutagenesis studies with purified DNA forms showed that nicked plasmids (i.e. those containing single-strand breaks) predominantly produce base substitutions, the majority of which are multiples, which presumably originate from error-prone polymerase activity at strand break sites. In contrast, repair of linear plasmids (i.e. those containing double-strand breaks) mainly results in deletions at short direct repeat sequences, indicating the involvement of illegitimate recombination. The data characterize the nature of mutations produced by single- and double-strand breaks in human cells, and suggests that deletions at direct repeats may be a 'signature' mutation for the processing of DNA double-strand breaks.
A strand graph semantics for DNA-based computation

PubMed Central

Petersen, Rasmus L.; Lakin, Matthew R.; Phillips, Andrew

2015-01-01

DNA nanotechnology is a promising approach for engineering computation at the nanoscale, with potential applications in biofabrication and intelligent nanomedicine. DNA strand displacement is a general strategy for implementing a broad range of nanoscale computations, including any computation that can be expressed as a chemical reaction network. Modelling and analysis of DNA strand displacement systems is an important part of the design process, prior to experimental realisation. As experimental techniques improve, it is important for modelling languages to keep pace with the complexity of structures that can be realised experimentally. In this paper we present a process calculus for modelling DNA strand displacement computations involving rich secondary structures, including DNA branches and loops. We prove that our calculus is also sufficiently expressive to model previous work on non-branching structures, and propose a mapping from our calculus to a canonical strand graph representation, in which vertices represent DNA strands, ordered sites represent domains, and edges between sites represent bonds between domains. We define interactions between strands by means of strand graph rewriting, and prove the correspondence between the process calculus and strand graph behaviours. Finally, we propose a mapping from strand graphs to an efficient implementation, which we use to perform modelling and simulation of DNA strand displacement systems with rich secondary structure. PMID:27293306
Streptavidin-coated magnetic beads for DNA strand separation implicate a multitude of problems during cell-SELEX.

PubMed

Paul, Angela; Avci-Adali, Meltem; Ziemer, Gerhard; Wendel, Hans P

2009-09-01

Using whole living cells as a target for SELEX (systematic evolution of ligands by exponential enrichment) experiments represents a promising method to generate cell receptor-specific aptamers. These aptamers have a huge potential in diagnostics, therapeutics, imaging, regenerative medicine, and target validation. During the SELEX for selecting DNA aptamers, one important step is the separation of 2 DNA strands to yield one of the 2 strands as single-stranded DNA aptamer. This is being done routinely by biotin labeling of the complementary DNA strand to the desired aptamer and then separating the DNA strand by using streptavidin-coated magnetic beads. After immobilization of the double-stranded DNA on these magnetic beads and alkaline denaturation, the non-biotinylated strand is being eluted and the biotinylated strand is retarded. Using Western blot analysis, we demonstrated the detachment of covalent-bonded streptavidin from the bead surface after alkaline treatment. The eluates were also contaminated with undesired biotinylated strands. Furthermore, a streptavidin-induced aggregation of target cells was demonstrated by flow cytometry and microscopic methods. Cell-specific enrichment of aptamers was not possible due to clustering and patching effects triggered by streptavidin. Therefore, the use of streptavidin-coated magnetic beads for DNA strand separation should be examined thoroughly, especially for cell-SELEX applications.

Tensile and dimensional properties of wood strands made from plantation southern pine lumber

Treesearch

Qinglin Wu; Zhiyong Cai; Jong N. Lee

2005-01-01

Working stresses and performance of strand composite lumber largely depend upon the properties of each individual strand. Southern pine strands from plantation lumber grown in southern Louisiana were investigated in this study in order to understand strand behaviors. The effects of hot-pressing and resin application on tensile modulus, strength, and dimensional...
The Cultivation of Ivy. A Saga of the College in America.

ERIC Educational Resources Information Center

Thelin, John R

The popular image of the Ivy League is one of a slightly awesome bastion of the well-born, well-bred, and soon-to-be-powerful or, less charitably, a haven for "the effete, unAmerican, and hopelessly bookish." This pervasive idea of collegiate personality is analyzed, tracing the evolution of the Ivy League from an incongruous array of…
Human Benchmarking of Expert Systems. Literature Review

DTIC Science & Technology

1990-01-01

effetiveness of the development procedures used in order to predict whether the aplication of similar approaches will likely have effective and...they used in their learning and problem solving. We will describe these approaches later. Reasoning. Reasoning usually includes inference. Because to ... in the software engineering process. For example, existing approaches to software evaluation in the military are based on a model of conventional
Symetrie en energie des spectres de l'onde de densite de charge dans le 2-hydrogene seleniure de niobium

NASA Astrophysics Data System (ADS)

Behmand, Behnaz

Les mecanismes qui menent a la supraconductivite dans les supraconducteurs a haute temperature critique sont encore aujourd'hui mal compris contrairement a ceux dans les supraconducteurs conventionnels. Dans les hauts-Tc, certaines modulations de la densite d'etats electroniques coexistant avec la phase supraconductrice ont ete observees, ce qui engendre des questionnements sur leur role dans la supraconductivite. En fait, plusieurs types de modulation de la densite d'etats electroniques existent, comme par exemple l'onde de densite de charge et l'onde de densite de paires. Ces deux modulations, d'origines differentes et mesurables avec la technique de spectroscopie par effet tunnel, peuvent etre differenciees avec une etude de leur symetrie. Ce memoire consistera donc a presenter l'etude de la symetrie de l'onde de densite de charge dans le 2H-NbSe2 qui est presente dans la phase supraconductrice a 300 mK. Par contre, certaines difficultes liees au principe de mesure, soit l'effet de normalisation, nuisent a l'identification de cette symetrie. La methode, pour contourner ce probleme sera alors l'element clef de ce travail.
Accident D’Electrisation et Hemorragie Cerebro-Meningee : A Propos D’une Observation

PubMed Central

Chaibdraa, A.; Medjellakh, M.S.; Saouli, A.; Bentakouk, M.C.

2008-01-01

Summary L'électrisation est un évènement accidentel qui diffère des autres pathologies occasionnant des brûlures graves, à cause de ses spécificités qui traduisent d'une part la destruction du revêtement cutané, mais également les effets directs ou indirects du courant électrique sur tout tissu de l'organisme rencontré lors de son passage, en particulier le tissu nerveux. Les manifestations neurologiques centrales sont nombreuses, en relation avec les effets de l'électricité sur le parenchyme cérébral ou une lésion associée à l'électrisation. Nous rapportons l'observation d'une hémorragie cérébro-meningée survenant au 3ème jour d'une électrisation grave. Cette complication est bien documentée dans la littérature traitant des accidents d'électrisation post-foudroiement. N'ayant pas rencontré de cas similaire publié lors des accidents dus au courant industriel, nous présentons cette observation, qui soulève le problème du mécanisme physiopathologique de survenue, difficile à trancher. PMID:21991125
Nouvelles approches en theorie du champ moyen dynamique: le cas du pouvoir thermoelectrique et celui de l'effet orbital d'un champ magnetique

NASA Astrophysics Data System (ADS)

Arsenault, Louis-Francois

Les applications reliees a la generation d'energie motivent la recherche de materiaux ayant un fort pouvoir thermoelectrique (S). De plus, S nous renseigne sur certaines proprietes fondamentales des materiaux, comme, par exemple, la transition entre l'etat coherent et incoherent des quasi-particules lorsque la temperature augmente. Empiriquement, la presence de fortes interactions electron-electron peut mener a un pouvoir thermoelectrique geant. Nous avons donc etudie le modele le plus simple qui tient compte de ces fortes interactions, le modele de Hubbard. La theorie du champ moyen dynamique (DMFT) est tout indiquee dans ce cas. Nous nous sommes concentres sur un systeme tridimensionnel (3d) cubique a face centree (fcc), et ce, pour plusieurs raisons. A) Ce type de cristal est tres commun dans la nature. B) La DMFT donne de tres bons resultats en 3d et donc ce choix sert aussi de preuve de principe de la methode. C) Finalement, a cause de la frustration electronique intrinseque au fcc, celui-ci ne presente pas de symetrie particule-trou, ce qui est tres favorable a l'apparition d'une grande valeur de S. Ce travail demontre que lorsque le materiau est un isolant a demi-remplissage a cause des fortes interactions (isolant de Mott), il est possible d'obtenir de grands pouvoirs thermoelectriques en le dopant legerement. C'est un resultat pratique important. Du point de vue methodologique, nous avons montre comment la limite de frequence infinie de S et l'approche dite de Kelvin, qui considere la limite de frequence nulle avant la limite thermodynamique pour S, donnent des estimations fiables de la vraie limite continue (DC) dans les domaines de temperature appropriee. Ces deux approches facilitent grandement les calculs en court-circuit ant la necessite de recourir a de problematiques prolongements analytiques. Nous avons trouve que la methode de calcul a frequence infinie fonctionne bien lorsque les echelles d'energie sont relativement faibles. En d'autres termes, cette approche donne une bonne representation de S lorsque le systeme devient coherent. Les calculs montrent aussi que la formule Kelvin est precise lorsque la fonction spectrale des electrons devient incoherente, soit a plus haute temperature. Dans la limite Kelvin, S est essentiellement l'entropie par particule, tel que propose il y a longtemps. Nos resultats demontrent ainsi que la vision purement entropique de S est la bonne dans le regime incoherent, alors que dans le regime coherent, l'approche a frequence infinie est meilleure. Nous avons utilise une methode a la fine pointe, soit le Monte-Carlo quantique en temps continu pour resoudre la DMFT. Pour permettre une exploration rapide du diagramme de phase, nous avons du developper une nouvelle version de la methode des perturbations iterees pour qu'elle soit applicable aussi a forte interaction au-dela de la valeur critique de la transition de Mott. Un autre sujet a aussi ete aborde. L'effet orbital du champ magnetique dans les systemes electroniques fortement correles est une question tres importante et peu developpee. Cela est d'autant plus essentiel depuis la decouverte des oscillations quantiques dans les supraconducteurs a haute temperature (haut- Tc). Par desir de developper une methode la moins biaisee possible, nous avons derive la DMFT lorsqu'un champ se couplant a l'operateur energie cinetique par la substitution de Peierls est present. Ce type d'approche est necessaire pour comprendre entre autres l'effet de la physique de Mott sur des phenomenes tels que les oscillations quantiques. Nous avons obtenu un resultat tres important en demontrant rigoureusement que la relation d'auto-coherence de la DMFT et le systeme intermediaire d'impurete quantique restent les memes. L'effet du champ peut etre contenu dans la fonction de Green locale, ce qui constitue la grande difference avec le cas habituel. Ceci permet de continuer a utiliser les solutionneurs d'impuretes standards, qui sont de plus en plus puissants. Nous avons aussi developpe la methode pour le cas d'un empilement de plans bidimensionnels selon z, ce qui permet d'etudier l'effet orbital du champ dans des nanostructures et meme dans les materiaux massifs, si le nombre de plans est suffisant pour obtenir la limite tridimensionnelle. Mots cles : Pouvoir thermoelectrique, Theorie du Champ Moyen Dynamique, Modele de Hubbard, Effet orbital du champ magnetique, Electrons fortement correles, Materiaux quantiques, Theorie des perturbations iterees
RNA signal amplifier circuit with integrated fluorescence output.

PubMed

Akter, Farhima; Yokobayashi, Yohei

2015-05-15

We designed an in vitro signal amplification circuit that takes a short RNA input that catalytically activates the Spinach RNA aptamer to produce a fluorescent output. The circuit consists of three RNA strands: an internally blocked Spinach aptamer, a fuel strand, and an input strand (catalyst), as well as the Spinach aptamer ligand 3,5-difluoro-4-hydroxylbenzylidene imidazolinone (DFHBI). The input strand initially displaces the internal inhibitory strand to activate the fluorescent aptamer while exposing a toehold to which the fuel strand can bind to further displace and recycle the input strand. Under a favorable condition, one input strand was able to activate up to five molecules of the internally blocked Spinach aptamer in 185 min at 30 °C. The simple RNA circuit reported here serves as a model for catalytic activation of arbitrary RNA effectors by chemical triggers.
Separation of 1-23-kb complementary DNA strands by urea-agarose gel electrophoresis.

PubMed

Hegedüs, Eva; Kókai, Endre; Kotlyar, Alexander; Dombrádi, Viktor; Szabó, Gábor

2009-09-01

Double-stranded (ds), as well as denatured, single-stranded (ss) DNA samples can be analyzed on urea-agarose gels. Here we report that after denaturation by heat in the presence of 8 M urea, the two strands of the same ds DNA fragment of approximately 1-20-kb size migrate differently in 1 M urea containing agarose gels. The two strands are readily distinguished on Southern blots by ss-specific probes. The different migration of the two strands could be attributed to their different, base composition-dependent conformation impinging on the electrophoretic mobility of the ss molecules. This phenomenon can be exploited for the efficient preparation of strand-specific probes and for the separation of the complementary DNA strands for subsequent analysis, offering a new tool for various cell biological research areas.
Click nucleic acid ligation: applications in biology and nanotechnology.

PubMed

El-Sagheer, Afaf H; Brown, Tom

2012-08-21

Biochemical strategies that use a combination of synthetic oligonucleotides, thermostable DNA polymerases, and DNA ligases can produce large DNA constructs up to 1 megabase in length. Although these ambitious targets are feasible biochemically, comparable technologies for the chemical synthesis of long DNA strands lag far behind. The best available chemical approach is the solid-phase phosphoramidite method, which can be used to assemble DNA strands up to 150 bases in length. Beyond this point, deficiencies in the chemistry make it impossible to produce pure DNA. A possible alternative approach to the chemical synthesis of large DNA strands is to join together carefully purified synthetic oligonucleotides by chemical methods. Click ligation by the copper-catalyzed azide-alkyne (CuAAC) reaction could facilitate this process. In this Account, we describe the synthesis, characterization, and applications of oligonucleotides prepared by click ligation. The alkyne and azide oligonucleotide strands can be prepared by standard protocols, and the ligation reaction is compatible with a wide range of chemical modifications to DNA and RNA. We have employed click ligation to synthesize DNA constructs up to 300 bases in length and much longer sequences are feasible. When the resulting triazole linkage is placed in a PCR template, various DNA polymerases correctly copy the entire base sequence. We have also successfully demonstrated both in vitro transcription and rolling circle amplification through the modified linkage. This linkage has shown in vivo biocompatibility: an antibiotic resistance gene containing triazole linkages functions in E. coli . Using click ligation, we have synthesized hairpin ribozymes up to 100 nucleotides in length and a hammerhead ribozyme with the triazole linkage located at the substrate cleavage site. At the opposite end of the length scale, click-ligated, cyclic mini-DNA duplexes have been used as models to study base pairing. Cyclic duplexes have potential therapeutic applications. They have extremely high thermodynamic stability, have increased resistance to enzymatic degradation, and have been investigated as decoys for regulatory proteins. For potential nanotechnology applications, we have synthesized double stranded DNA catenanes by click ligation. Other researchers have studied covalently fixed multistranded DNA constructs including triplexes and quadruplexes.
A framework for community ownership of a text messaging programme to improve adherence to antiretroviral therapy and client-provider communication: a mixed methods study.

PubMed

Mbuagbaw, Lawrence; Bonono-Momnougui, Renee-Cecile; Thabane, Lehana; Kouanfack, Charles; Smieja, Marek; Ongolo-Zogo, Pierre

2014-09-26

Mobile phone text messaging has been shown to improve adherence to antiretroviral therapy and to improve communication between patients and health care workers. It is unclear which strategies are most appropriate for scaling up text messaging programmes. We sought to investigate acceptability and readiness for ownership (community members designing, sending and receiving text messages) of a text message programme among a community of clients living with human immunodeficiency virus (HIV) in Yaoundé, Cameroon and to develop a framework for implementation. We used the mixed-methods sequential exploratory design. In the qualitative strand we conducted 7 focus group discussions (57 participants) to elicit themes related to acceptability and readiness. In the quantitative strand we explored the generalizability of these themes in a survey of 420 clients. Qualitative and quantitative data were merged to generate meta-inferences. Both qualitative and quantitative strands showed high levels of acceptability and readiness despite low rates of participation in other community-led projects. In the qualitative strand, compared to the quantitative strand, more potential service users were willing to pay for a text messaging service, preferred participation of health personnel in managing the project and preferred that the project be based in the hospital rather than in the community. Some of the limitations identified to implementing a community-owned project were lack of management skills in the community, financial, technical and literacy challenges. Participants who were willing to pay were more likely to find the project acceptable and expressed positive feelings about community readiness to own a text messaging project. Community ownership of a text messaging programme is acceptable to the community of clients at the Yaoundé Central Hospital. Our framework for implementation includes components for community members who take on roles as services users (demonstrating clear benefits, allowing a trial period and ensuring high levels of confidentiality) or service providers (training in project management and securing sustainable funding). Such a project can be evaluated using participation rate, clinical outcomes, satisfaction with the service, cost and feedback from users.
75 FR 38977 - Pre-Stressed Concrete Steel Wire Strand from the People's Republic of China: Notice of Amended...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-07-07

... Wire Strand from the People's Republic of China: Notice of Amended Final Affirmative Countervailing... issuing a countervailing duty order on pre-stressed concrete steel wire strand (PC strand) from the People... determination of material injury to a U.S. industry. See Pre-Stressed Concrete Steel Wire Strand from the People...
Language Variation and Change in the Australian Curriculum English: Integrating Sub-Strands through a Pedagogy of Metalogue

ERIC Educational Resources Information Center

Willis, Linda-Dianne; Exley, Beryl

2016-01-01

The Language Strand of the Australian Curriculum: English (Australian Curriculum, Assessment & Reporting Authority (ACARA), 2016b) includes the sub-strand of "Language Variation and Change". This sub-strand is a marked space for discovery and discussion of the history and politics of language use. As such, this sub-strand points to…
A Novel Computational Method to Reduce Leaky Reaction in DNA Strand Displacement

PubMed Central

Li, Xin; Wang, Xun; Song, Tao; Lu, Wei; Chen, Zhihua; Shi, Xiaolong

2015-01-01

DNA strand displacement technique is widely used in DNA programming, DNA biosensors, and gene analysis. In DNA strand displacement, leaky reactions can cause DNA signals decay and detecting DNA signals fails. The mostly used method to avoid leakage is cleaning up after upstream leaky reactions, and it remains a challenge to develop reliable DNA strand displacement technique with low leakage. In this work, we address the challenge by experimentally evaluating the basic factors, including reaction time, ratio of reactants, and ion concentration to the leakage in DNA strand displacement. Specifically, fluorescent probes and a hairpin structure reporting DNA strand are designed to detect the output of DNA strand displacement, and thus can evaluate the leakage of DNA strand displacement reactions with different reaction time, ratios of reactants, and ion concentrations. From the obtained data, mathematical models for evaluating leakage are achieved by curve derivation. As a result, it is obtained that long time incubation, high concentration of fuel strand, and inappropriate amount of ion concentration can weaken leaky reactions. This contributes to a method to set proper reaction conditions to reduce leakage in DNA strand displacement. PMID:26491602
Molecular investigation of evaporation of biodroplets containing single-strand DNA on graphene surface.

PubMed

Akbari, Fahimeh; Foroutan, Masumeh

2018-02-14

In this study, the water droplet behaviour of four different types of single-strand DNA with homogeneous base sequence on a graphene substrate during evaporation of the droplet was investigated using molecular dynamics (MD) simulation. The simulation results indicated that the evaporation depended on the DNA sequence. The observed changes can be divided into four parts: (i) vaporization mode, (ii) evaporation flux, (iii) mechanism of single-strand placement on the surface, and (iv) consideration of remaining single strands after evaporation. Our simulation observations indicated different evaporation modes for thymine biodroplets as compared to those for other biodroplets. The evaporation of the thymine biodroplets occurred with an increase in the contact angle, while that of the other biodroplets occur in a constant contact angle mode. Moreover, thymine biodroplets generate the lowest contact line compared to other single strands, and it is always placed far away from the centre of the droplets during evaporation. Investigating variations in the evaporation flux shows that thymine has the highest evaporation flux and guanine has the lowest. Moreover, during initial evaporation, the flux of evaporation increases at the triple point of the biodroplets containing thymine single strands, while it decreases in the other biodroplets. The following observation was obtained from the study of the placement of single strands on the substrate: guanine and thymine interacted slower than other single strands during evaporation with graphene, adenine single strand had a higher folding during evaporation, and guanine single strand showed the lowest end-to-end distance. The investigation of single-strand DNA after evaporation shows that adenine produces the most stable structure at the end of evaporation. In addition, cytosine is the most stretched single-strand DNA due to its lack of internal π-π stacking and hydrogen bonding. Therefore, cytosine single strand is more accessible for use in microarrays to detect target single strands.
Correlated Template-Switching Events during Minus-Strand DNA Synthesis: a Mechanism for High Negative Interference during Retroviral Recombination

PubMed Central

Anderson, Jeffrey A.; Teufel, Ronald J.; Yin, Philip D.; Hu, Wei-Shau

1998-01-01

Two models for the mechanism of retroviral recombination have been proposed: forced copy choice (minus-strand recombination) and strand displacement-assimilation (plus-strand recombination). Each minus-strand recombination event results in one template switch, whereas each plus-strand recombination event results in two template switches. Recombinant proviruses with one and more than one template switches were previously observed. Recombinants with one template switch were generated by minus-strand recombination, while recombinants containing more than one template switch may have been generated by plus-strand recombination or by correlated minus-strand recombination. We recently observed that retroviral recombination exhibits high negative interference whereby the frequency of recombinants containing multiple template-switching events is higher than expected. To delineate the mechanism that generates recombinants with more than one template switch, we devised a system that permits only minus-strand recombination. Two highly homologous vectors, WH204 and WH221, containing eight different restriction site markers were used. The primer binding site (PBS) of WH221 was deleted; although reverse transcription cannot initiate from WH221 RNA, it can serve as a template for DNA synthesis in heterozygotic virions. After one round of retroviral replication, the structures of the recombinant proviruses were examined. Recombinants containing two, three, four, and five template switches were observed at 1.4-, 10-, 65-, and 50-fold-higher frequencies, respectively, than expected. This indicates that minus-strand recombination events are correlated and can generate proviruses with multiple template switches efficiently. The frequencies of recombinants containing multiple template switches were similar to those observed in the previous system, which allowed both minus- and plus-strand recombination. Thus, the previously reported high negative interference during retroviral recombination can be caused by correlated template switches during minus-strand DNA synthesis. In addition, all examined recombinants contained an intact PBS, indicating that most of the plus-strand DNA transfer occurs after completion of the strong-stop DNA. PMID:9445017
Replication of tobacco mosaic virus RNA.

PubMed Central

Buck, K W

1999-01-01

The replication of tobacco mosaic virus (TMV) RNA involves synthesis of a negative-strand RNA using the genomic positive-strand RNA as a template, followed by the synthesis of positive-strand RNA on the negative-strand RNA templates. Intermediates of replication isolated from infected cells include completely double-stranded RNA (replicative form) and partly double-stranded and partly single-stranded RNA (replicative intermediate), but it is not known whether these structures are double-stranded or largely single-stranded in vivo. The synthesis of negative strands ceases before that of positive strands, and positive and negative strands may be synthesized by two different polymerases. The genomic-length negative strand also serves as a template for the synthesis of subgenomic mRNAs for the virus movement and coat proteins. Both the virus-encoded 126-kDa protein, which has amino-acid sequence motifs typical of methyltransferases and helicases, and the 183-kDa protein, which has additional motifs characteristic of RNA-dependent RNA polymerases, are required for efficient TMV RNA replication. Purified TMV RNA polymerase also contains a host protein serologically related to the RNA-binding subunit of the yeast translational initiation factor, eIF3. Study of Arabidopsis mutants defective in RNA replication indicates that at least two host proteins are needed for TMV RNA replication. The tomato resistance gene Tm-1 may also encode a mutant form of a host protein component of the TMV replicase. TMV replicase complexes are located on the endoplasmic reticulum in close association with the cytoskeleton in cytoplasmic bodies called viroplasms, which mature to produce 'X bodies'. Viroplasms are sites of both RNA replication and protein synthesis, and may provide compartments in which the various stages of the virus mutiplication cycle (protein synthesis, RNA replication, virus movement, encapsidation) are localized and coordinated. Membranes may also be important for the configuration of the replicase with respect to initiation of RNA synthesis, and synthesis and release of progeny single-stranded RNA. PMID:10212941
The cost of getting CCS wrong: Uncertainty, infrastructure design, and stranded CO 2

DOE PAGES

Middleton, Richard Stephen; Yaw, Sean Patrick

2018-01-11

Carbon capture, and storage (CCS) infrastructure will require industry—such as fossil-fuel power, ethanol production, and oil and gas extraction—to make massive investment in infrastructure. The cost of getting these investments wrong will be substantial and will impact the success of CCS technology. Multiple factors can and will impact the success of commercial-scale CCS, including significant uncertainties regarding capture, transport, and injection-storage decisions. Uncertainties throughout the CCS supply chain include policy, technology, engineering performance, economics, and market forces. In particular, large uncertainties exist for the injection and storage of CO 2. Even taking into account upfront investment in site characterization, themore » final performance of the storage phase is largely unknown until commercial-scale injection has started. We explore and quantify the impact of getting CCS infrastructure decisions wrong based on uncertain injection rates and uncertain CO 2 storage capacities using a case study managing CO 2 emissions from the Canadian oil sands industry in Alberta. We use SimCCS, a widely used CCS infrastructure design framework, to develop multiple CCS infrastructure scenarios. Each scenario consists of a CCS infrastructure network that connects CO 2 sources (oil sands extraction and processing) with CO 2 storage reservoirs (acid gas storage reservoirs) using a dedicated CO 2 pipeline network. Each scenario is analyzed under a range of uncertain storage estimates and infrastructure performance is assessed and quantified in terms of cost to build additional infrastructure to store all CO 2. We also include the role of stranded CO 2, CO 2 that a source was expecting to but cannot capture due substandard performance in the transport and storage infrastructure. Results show that the cost of getting the original infrastructure design wrong are significant and that comprehensive planning will be required to ensure that CCS becomes a successful climate mitigation technology. Here, we show that the concept of stranded CO 2 can transform a seemingly high-performing infrastructure design into the worst case scenario.« less
The Use of Carcasses for the Analysis of Cetacean Population Genetic Structure: A Comparative Study in Two Dolphin Species

PubMed Central

Bilgmann, Kerstin; Möller, Luciana M.; Harcourt, Robert G.; Kemper, Catherine M.; Beheregaray, Luciano B.

2011-01-01

Advances in molecular techniques have enabled the study of genetic diversity and population structure in many different contexts. Studies that assess the genetic structure of cetacean populations often use biopsy samples from free-ranging individuals and tissue samples from stranded animals or individuals that became entangled in fishery or aquaculture equipment. This leads to the question of how representative the location of a stranded or entangled animal is with respect to its natural range, and whether similar results would be obtained when comparing carcass samples with samples from free-ranging individuals in studies of population structure. Here we use tissue samples from carcasses of dolphins that stranded or died as a result of bycatch in South Australia to investigate spatial population structure in two species: coastal bottlenose (Tursiops sp.) and short-beaked common dolphins (Delphinus delphis). We compare these results with those previously obtained from biopsy sampled free-ranging dolphins in the same area to test whether carcass samples yield similar patterns of genetic variability and population structure. Data from dolphin carcasses were gathered using seven microsatellite markers and a fragment of the mitochondrial DNA control region. Analyses based on carcass samples alone failed to detect genetic structure in Tursiops sp., a species previously shown to exhibit restricted dispersal and moderate genetic differentiation across a small spatial scale in this region. However, genetic structure was correctly inferred in D. delphis, a species previously shown to have reduced genetic structure over a similar geographic area. We propose that in the absence of corroborating data, and when population structure is assessed over relatively small spatial scales, the sole use of carcasses may lead to an underestimate of genetic differentiation. This can lead to a failure in identifying management units for conservation. Therefore, this risk should be carefully assessed when planning population genetic studies of cetaceans. PMID:21655285
The cost of getting CCS wrong: Uncertainty, infrastructure design, and stranded CO 2

DOE Office of Scientific and Technical Information (OSTI.GOV)

Middleton, Richard Stephen; Yaw, Sean Patrick

Carbon capture, and storage (CCS) infrastructure will require industry—such as fossil-fuel power, ethanol production, and oil and gas extraction—to make massive investment in infrastructure. The cost of getting these investments wrong will be substantial and will impact the success of CCS technology. Multiple factors can and will impact the success of commercial-scale CCS, including significant uncertainties regarding capture, transport, and injection-storage decisions. Uncertainties throughout the CCS supply chain include policy, technology, engineering performance, economics, and market forces. In particular, large uncertainties exist for the injection and storage of CO 2. Even taking into account upfront investment in site characterization, themore » final performance of the storage phase is largely unknown until commercial-scale injection has started. We explore and quantify the impact of getting CCS infrastructure decisions wrong based on uncertain injection rates and uncertain CO 2 storage capacities using a case study managing CO 2 emissions from the Canadian oil sands industry in Alberta. We use SimCCS, a widely used CCS infrastructure design framework, to develop multiple CCS infrastructure scenarios. Each scenario consists of a CCS infrastructure network that connects CO 2 sources (oil sands extraction and processing) with CO 2 storage reservoirs (acid gas storage reservoirs) using a dedicated CO 2 pipeline network. Each scenario is analyzed under a range of uncertain storage estimates and infrastructure performance is assessed and quantified in terms of cost to build additional infrastructure to store all CO 2. We also include the role of stranded CO 2, CO 2 that a source was expecting to but cannot capture due substandard performance in the transport and storage infrastructure. Results show that the cost of getting the original infrastructure design wrong are significant and that comprehensive planning will be required to ensure that CCS becomes a successful climate mitigation technology. Here, we show that the concept of stranded CO 2 can transform a seemingly high-performing infrastructure design into the worst case scenario.« less
Sulfolobus chromatin proteins modulate strand displacement by DNA polymerase B1

PubMed Central

Sun, Fei; Huang, Li

2013-01-01

Strand displacement by a DNA polymerase serves a key role in Okazaki fragment maturation, which involves displacement of the RNA primer of the preexisting Okazaki fragment into a flap structure, and subsequent flap removal and fragment ligation. We investigated the role of Sulfolobus chromatin proteins Sso7d and Cren7 in strand displacement by DNA polymerase B1 (PolB1) from the hyperthermophilic archaeon Sulfolobus solfataricus. PolB1 showed a robust strand displacement activity and was capable of synthesizing thousands of nucleotides on a DNA-primed 72-nt single-stranded circular DNA template. This activity was inhibited by both Sso7d and Cren7, which limited the flap length to 3–4 nt at saturating concentrations. However, neither protein inhibited RNA displacement on an RNA-primed single-stranded DNA minicircle by PolB1. Strand displacement remained sensitive to modulation by the chromatin proteins when PolB1 was in association with proliferating cell nuclear antigen. Inhibition of DNA instead of RNA strand displacement by the chromatin proteins is consistent with the finding that double-stranded DNA was more efficiently bound and stabilized than an RNA:DNA duplex by these proteins. Our results suggest that Sulfolobus chromatin proteins modulate strand displacement by PolB1, permitting efficient removal of the RNA primer while inhibiting excessive displacement of the newly synthesized DNA strand during Okazaki fragment maturation. PMID:23821667

Method for producing labeled single-stranded nucleic acid probes

DOEpatents

Dunn, John J.; Quesada, Mark A.; Randesi, Matthew

1999-10-19

Disclosed is a method for the introduction of unidirectional deletions in a cloned DNA segment. More specifically, the method comprises providing a recombinant DNA construct comprising a DNA segment of interest inserted in a cloning vector, the cloning vector having an f1 endonuclease recognition sequence adjacent to the insertion site of the DNA segment of interest. The recombinant DNA construct is then contacted with the protein pII encoded by gene II of phage f1 thereby generating a single-stranded nick. The nicked DNA is then contacted with E. coli Exonuclease III thereby expanding the single-stranded nick into a single-stranded gap. The single-stranded gapped DNA is then contacted with a single-strand-specific endonuclease thereby producing a linearized DNA molecule containing a double-stranded deletion corresponding in size to the single-stranded gap. The DNA treated in this manner is then incubated with DNA ligase under conditions appropriate for ligation. Also disclosed is a method for producing single-stranded DNA probes. In this embodiment, single-stranded gapped DNA, produced as described above, is contacted with a DNA polymerase in the presence of labeled nucleotides to fill in the gap. This DNA is then linearized by digestion with a restriction enzyme which cuts outside the DNA segment of interest. The product of this digestion is then denatured to produce a labeled single-stranded nucleic acid probe.
Using DNA origami nanostructures to determine absolute cross sections for UV photon-induced DNA strand breakage.

PubMed

Vogel, Stefanie; Rackwitz, Jenny; Schürman, Robin; Prinz, Julia; Milosavljević, Aleksandar R; Réfrégiers, Matthieu; Giuliani, Alexandre; Bald, Ilko

2015-11-19

We have characterized ultraviolet (UV) photon-induced DNA strand break processes by determination of absolute cross sections for photoabsorption and for sequence-specific DNA single strand breakage induced by photons in an energy range from 6.50 to 8.94 eV. These represent the lowest-energy photons able to induce DNA strand breaks. Oligonucleotide targets are immobilized on a UV transparent substrate in controlled quantities through attachment to DNA origami templates. Photon-induced dissociation of single DNA strands is visualized and quantified using atomic force microscopy. The obtained quantum yields for strand breakage vary between 0.06 and 0.5, indicating highly efficient DNA strand breakage by UV photons, which is clearly dependent on the photon energy. Above the ionization threshold strand breakage becomes clearly the dominant form of DNA radiation damage, which is then also dependent on the nucleotide sequence.
Mechanism of asymmetric polymerase assembly at the eukaryotic replication fork

PubMed Central

Georgescu, Roxana E; Langston, Lance; Yao, Nina Y; Yurieva, Olga; Zhang, Dan; Finkelstein, Jeff; Agarwal, Tani; O’Donnell, Mike E

2015-01-01

Eukaryotes use distinct polymerases for leading- and lagging-strand replication, but how they target their respective strands is uncertain. We reconstituted Saccharomyces cerevisiae replication forks and found that CMG helicase selects polymerase (Pol) ε to the exclusion of Pol δ on the leading strand. Even if Pol δ assembles on the leading strand, Pol ε rapidly replaces it. Pol δ–PCNA is distributive with CMG, in contrast to its high stability on primed ssDNA. Hence CMG will not stabilize Pol δ, instead leaving the leading strand accessible for Pol ε and stabilizing Pol ε. Comparison of Pol ε and Pol δ on a lagging-strand model DNA reveals the opposite. Pol δ dominates over excess Pol ε on PCNA-primed ssDNA. Thus, PCNA strongly favors Pol δ over Pol ε on the lagging strand, but CMG over-rides and flips this balance in favor of Pol ε on the leading strand. PMID:24997598
Crude oil as a stranding cause among loggerhead sea turtles (Caretta caretta) in the Canary Islands, Spain (1998-2011).

PubMed

Camacho, María; Calabuig, Pascual; Luzardo, Octavio P; Boada, Luis D; Zumbado, Manuel; Orós, Jorge

2013-07-01

We report the number of strandings caused by crude oil among loggerhead turtles (Caretta caretta) in the Canary Islands between 1998 and 2011 and analyze the impact of the designation of the Canary Islands as a Particularly Sensitive Sea Area (PSSA) in 2005. Among 1,679 stranded loggerhead turtles, 52 turtles stranded due to crude oil (3.1%). The survival rate of the turtles stranded by crude oil was 88%. All turtles that died because of crude oil stranding had signs of ingestion of crude oil and lesions, included esophageal impaction, necrotizing gastroenteritis, necrotizing hepatitis, and tubulonephrosis. The number of strandings caused by crude oil after 2005 was significantly lower than it was before 2006. We show that the designation of the Canary Islands as a PSSA in 2005 by the International Maritime Organization was associated with a reduction of sea turtle strandings caused by crude oil.
Development of strand burner for solid propellant burning rate studies

NASA Astrophysics Data System (ADS)

Aziz, A.; Mamat, R.; Ali, W. K. Wan

2013-12-01

It is well-known that a strand burner is an apparatus that provides burning rate measurements of a solid propellant at an elevated pressure in order to obtain the burning characteristics of a propellant. This paper describes the facilities developed by author that was used in his studies. The burning rate characteristics of solid propellant have be evaluated over five different chamber pressures ranging from 1 atm to 31 atm using a strand burner. The strand burner has a mounting stand that allows the propellant strand to be mounted vertically. The strand was ignited electrically using hot wire, and the burning time was recorded by electronic timer. Wire technique was used to measure the burning rate. Preliminary results from these techniques are presented. This study shows that the strand burner can be used on propellant strands to obtain accurate low pressure burning rate data.
Extended Minus-Strand DNA as Template for R-U5-Mediated Second-Strand Transfer in Recombinational Rescue of Primer Binding Site-Modified Retroviral Vectors

PubMed Central

Mikkelsen, Jacob Giehm; Lund, Anders H.; Dybkær, Karen; Duch, Mogens; Pedersen, Finn Skou

1998-01-01

We have previously demonstrated recombinational rescue of primer binding site (PBS)-impaired Akv murine leukemia virus-based vectors involving initial priming on endogenous viral sequences and template switching during cDNA synthesis to obtain PBS complementarity in second-strand transfer of reverse transcription (Mikkelsen et al., J. Virol. 70:1439–1447, 1996). By use of the same forced recombination system, we have now found recombinant proviruses of different structures, suggesting that PBS knockout vectors may be rescued through initial priming on endogenous virus RNA, read-through of the mutated PBS during minus-strand synthesis, and subsequent second-strand transfer mediated by the R-U5 complementarity of the plus strand and the extended minus-strand DNA acceptor template. Mechanisms for R-U5-mediated second-strand transfer and its possible role in retrovirus replication and evolution are discussed. PMID:9499117
Dynamics of Leading-strand Lesion Skipping by the Replisome

PubMed Central

Yeeles, Joseph T.P.; Marians, Kenneth J.

2013-01-01

SUMMARY The E. coli replisome stalls transiently when it encounters a lesion in the leading-strand template, skipping over the damage by reinitiating replication at a new primer synthesized downstream by the primase. We report here that template unwinding and lagging-strand synthesis continue downstream of the lesion at a reduced rate after replisome stalling, that one replisome is capable of skipping multiple lesions, and that the rate limiting steps of replication restart involve the synthesis and activation of the new primer downstream. We also find little support for the concept that polymerase uncoupling, where extensive lagging-strand synthesis proceeds downstream in the absence of leading-strand synthesis, involves physical separation of the leading-strand polymerase from the replisome. Instead, our data indicate that extensive uncoupled replication likely results from a failure of the leading-strand polymerase still associated with the DNA helicase and the lagging-strand polymerase that are proceeding downstream to reinitiate synthesis. PMID:24268579
Forward modeling transient brightenings and microflares around an active region observed with Hi-C

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kobelski, Adam R.; McKenzie, David E., E-mail: kobelski@solar.physics.montana.edu

Small-scale flare-like brightenings around active regions are among the smallest and most fundamental of energetic transient events in the corona, providing a testbed for models of heating and active region dynamics. In a previous study, we modeled a large collection of these microflares observed with Hinode/X-Ray Telescope (XRT) using EBTEL and found that they required multiple heating events, but could not distinguish between multiple heating events on a single strand, or multiple strands each experiencing a single heating event. We present here a similar study, but with extreme-ultraviolet data of Active Region 11520 from the High Resolution Coronal Imager (Hi-C)more » sounding rocket. Hi-C provides an order of magnitude improvement to the spatial resolution of XRT, and a cooler temperature sensitivity, which combine to provide significant improvements to our ability to detect and model microflare activity around active regions. We have found that at the spatial resolution of Hi-C (≈0.''3), the events occur much more frequently than expected (57 events detected, only 1 or 2 expected), and are most likely made from strands of the order of 100 km wide, each of which is impulsively heated with multiple heating events. These findings tend to support bursty reconnection as the cause of the energy release responsible for the brightenings.« less
FEMCAM Analysis of SULTAN Test Results for ITER Nb3SN Cable-conduit Conductors

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yuhu Zhai, Pierluigi Bruzzone, Ciro Calzolaio

2013-03-19

Performance degradation due to filament fracture of Nb3 Sn cable-in-conduit conductors (CICCs) is a critical issue in large-scale magnet designs such as ITER which is currently being constructed in the South of France. The critical current observed in most SULTAN TF CICC samples is significantly lower than expected and the voltage-current characteristic is seen to have a much broader transition from a single strand to the CICC. Moreover, most conductors exhibit the irreversible degradation due to filament fracture and strain relaxation under electromagnetic cyclic loading. With recent success in monitoring thermal strain distribution and its evolution under the electromagnetic cyclicmore » loading from in situ measurement of critical temperature, we apply FEMCAM which includes strand filament breakage and local current sharing effects to SULTAN tested CICCs to study Nb3 Sn strain sensitivity and irreversible performance degradation. FEMCAM combines the thermal bending effect during cool down and the EM bending effect due to locally accumulating Lorentz force during magnet operation. It also includes strand filament fracture and related local current sharing for the calculation of cable n value. In this paper, we model continuous performance degradation under EM cyclic loading based on strain relaxation and the transition broadening upon cyclic loading to the extreme cases seen in SULTAN test data to better quantify conductor performance degradation.« less
Assessment of cultural competence in Texas nursing faculty.

PubMed

Marzilli, Collen

2016-10-01

Cultural competence [CC] is an essential component of nursing education and nursing practice yet there is a gap in the research evaluating CC in faculty and how to practically develop this skillset for faculty members. To explore CC in faculty as evaluated with the Nurses' Cultural Competence Scale [NCCS] and apply the findings to the Purnell Model of Cultural Competence [PMCC] to guide professional development opportunities for faculty members. This was a concurrent mixed-methods study. Faculty members teaching in Texas nursing programs were recruited for the study. Quantitative data was collected using an online survey tool and qualitative data was collected over the phone. 89 Texas faculty members completed the quantitative strand and a subset of 10 faculty members completed the qualitative strand. Descriptive statistics were used to examine the quantitative data and Strauss and Corbin's methodology guided the evaluation of the qualitative data. These two strands were used to support the results. Faculty in Texas are moderately culturally competent. The qualitative findings support the application of the PMCC to the areas identified by the NCCS. The PMCC may be applied to the application of culture and values in nursing professional education as supported by the NCCS. Recommendations are to include the PMCC as a structure for the creation of professional development opportunities for faculty. Copyright © 2016 Elsevier Ltd. All rights reserved.
Effect of Barrel Material on Critical Current Measurements of High-Jc RRP Nb3Sn Wires

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ghosh, A.

Nb{sub 3}Sn strands extracted from a 20-strand rectangular Rutherford cable were reacted on either stainless steel or Ti-alloy barrels and the critical current, I{sub c}, in the field range of 8-11.5 T was measured on ITER-type barrels made from Ti-6Al-4V alloy, 304 stainless steel and G-10. Measurements on the 'standard' Ti-alloy barrel using the test procedure employed at BNL are shown to reproduce I{sub c} for extracted strands to {+-}2%. The I{sub c} data for the sample mounted on the 'standard' Ti-alloy are fit to the deviatoric strain scaling model developed for Nb{sub 3}Sn by the University of Twente groupmore » using an arbitrary pre-strain. Using the parameters for this fit, the I{sub c} data for the other barrels are fitted by only adjusting the strain. Using this procedure, the strain difference due to the barrel material is determined. Assuming a thermal pre-strain of -0.2% for the sample measured on the Ti-alloy barrel, the use of stainless steel barrel increases the compressive strain by -0.07%, that of G-10 by -0.10%. With the wire soldered to the stainless steel barrel, the strain increases to -0.15%. Details of this study are presented.« less
3D-structured illumination microscopy reveals clustered DNA double-strand break formation in widespread γH2AX foci after high LET heavy-ion particle radiation.

PubMed

Hagiwara, Yoshihiko; Niimi, Atsuko; Isono, Mayu; Yamauchi, Motohiro; Yasuhara, Takaaki; Limsirichaikul, Siripan; Oike, Takahiro; Sato, Hiro; Held, Kathryn D; Nakano, Takashi; Shibata, Atsushi

2017-12-12

DNA double-strand breaks (DSBs) induced by ionising radiation are considered the major cause of genotoxic mutations and cell death. While DSBs are dispersed throughout chromatin after X-rays or γ-irradiation, multiple types of DNA damage including DSBs, single-strand breaks and base damage can be generated within 1-2 helical DNA turns, defined as a complex DNA lesion, after high Linear Energy Transfer (LET) particle irradiation. In addition to the formation of complex DNA lesions, recent evidence suggests that multiple DSBs can be closely generated along the tracks of high LET particle irradiation. Herein, by using three dimensional (3D)-structured illumination microscopy, we identified the formation of 3D widespread γH2AX foci after high LET carbon-ion irradiation. The large γH2AX foci in G 2 -phase cells encompassed multiple foci of replication protein A (RPA), a marker of DSBs undergoing resection during homologous recombination. Furthermore, we demonstrated by 3D analysis that the distance between two individual RPA foci within γH2AX foci was approximately 700 nm. Together, our findings suggest that high LET heavy-ion particles induce clustered DSB formation on a scale of approximately 1 μm 3 . These closely localised DSBs are considered to be a risk for the formation of chromosomal rearrangement after heavy-ion irradiation.
Fibrillation auriculaire et activité physique

PubMed Central

Bosomworth, N. John

2015-01-01

Résumé Objectif Examiner les données probantes portant sur les effets de divers niveaux d’activité physique sur l’incidence de fibrillation auriculaire (FA) dans la population générale et chez les athlètes d’endurance. Sources des données Une recherche a initialement été menée sur PubMed à l’aide des titres MeSH ou des mots-de-texte anglais (avec descripteur de zone de recherche TIAB [title and abstract]) atrial fibrillation et exercise ou physical activity ou athlet* ou sport*, sans filtre additionnel. Le système GRADE (grading of recommendations, assessment, development, and evaluation) a été utilisé pour tirer les conclusions au sujet de la qualité et du niveau de preuve. Sélection des études Aucune étude d’intervention n’est ressortie de la recherche. Les études d’observation ont alors été jugées acceptables et, bien que des études prospectives de cohortes à long terme de plus grande envergure auraient été préférables, des essais cas-témoins ou transversaux ont aussi été inclus dans cette révision. Synthèse Les données disponibles laissent croire à un lien proportionnel à la dose entre l’exercice plus intense et l’incidence réduite de FA chez les femmes. Il en va de même pour les hommes dont le niveau d’activité physique est de faible à modéré. Chez les hommes seulement, l’activité intense est associée à un risque accru de FA et ce, dans la plupart des études, mais pas la totalité d’entre elles. Ce risque est modéré, le rapport de risque instantané étant de 1,29 dans l’une des études de meilleure qualité. Le risque de FA chez la plupart des personnes régulièrement actives est plus faible que le risque observé dans la population sédentaire appariée. Conclusion La fibrillation auriculaire est probablement moins fréquente à mesure que le niveau d’activité physique augmente, la relation dose-réponse étant démontrable. À toutes les intensités, l’exercice doit être encouragé pour ses effets sur le bien-être physique et la réduction de la mortalité. Chez les hommes qui pratiquent des activités vigoureuses, les effets bénéfiques sur la FA pourraient disparaître et le risque pourrait surpasser celui observé dans la population sédentaire; cependant les données probantes à cet effet ne sont ni robustes ni constantes. Ces hommes devraient être mis au courant de cette hausse modeste du risque s’ils choisissent de poursuivre leurs activités physiques vigoureuses.
Tensile and thickness swelling properties of strands from Southern hardwoods and Southern pine : effect of hot-pressing and resin application

Treesearch

Zhiyong Cai; Qinglin Wu; Guangping Han; Jong N. Lee

2007-01-01

Tensile and the moisture-induced thickness swelling properties of wood strands are among the most fundamental parameters in modeling and predicting engineering constants of strand-based composites such as oriented strandboard (OSB). The effects of hot-pressing and resin-curing on individual strand properties were investigated in this study. Strands from four Louisiana-...
Force-Induced Rupture of a DNA Duplex: From Fundamentals to Force Sensors.

PubMed

Mosayebi, Majid; Louis, Ard A; Doye, Jonathan P K; Ouldridge, Thomas E

2015-12-22

The rupture of double-stranded DNA under stress is a key process in biophysics and nanotechnology. In this article, we consider the shear-induced rupture of short DNA duplexes, a system that has been given new importance by recently designed force sensors and nanotechnological devices. We argue that rupture must be understood as an activated process, where the duplex state is metastable and the strands will separate in a finite time that depends on the duplex length and the force applied. Thus, the critical shearing force required to rupture a duplex depends strongly on the time scale of observation. We use simple models of DNA to show that this approach naturally captures the observed dependence of the force required to rupture a duplex within a given time on duplex length. In particular, this critical force is zero for the shortest duplexes, before rising sharply and then plateauing in the long length limit. The prevailing approach, based on identifying when the presence of each additional base pair within the duplex is thermodynamically unfavorable rather than allowing for metastability, does not predict a time-scale-dependent critical force and does not naturally incorporate a critical force of zero for the shortest duplexes. We demonstrate that our findings have important consequences for the behavior of a new force-sensing nanodevice, which operates in a mixed mode that interpolates between shearing and unzipping. At a fixed time scale and duplex length, the critical force exhibits a sigmoidal dependence on the fraction of the duplex that is subject to shearing.
Estimation of Prestress Force Distribution in the Multi-Strand System of Prestressed Concrete Structures

PubMed Central

Cho, Keunhee; Park, Sung Yong; Cho, Jeong-Rae; Kim, Sung Tae; Park, Young-Hwan

2015-01-01

Prestressed concrete (PSC) is one of the most reliable, durable and widely used construction materials, which overcomes the weakness of concrete in tension by the introduction of a prestress force. Smart strands enabling measurement of the prestress force have recently been developed to maintain PSC structures throughout their lifetime. However, the smart strand cannot give a representative indication of the whole prestress force when used in multi-strand systems since each strand sustains a different prestress force. In this paper, the actual distribution of the prestress force in a multi-strand system is examined using elastomagnetic (EM) sensors to develop a method for tracking representative indicators of the prestress force using smart strands. PMID:26083230
[Results of flexor tendon sutures of the fingers with 2-strand (40 tendons) and 4-strand (64 tendons) core sutures].

PubMed

Winkel, R; Kalbhenn, O; Hoffmann, R

2012-06-01

This retrospective examination compares the results of finger flexor tendon sutures with 2 strands and 4 strands. It was checked, whether and how 2 more strands influenced the rupture rate, the movement of the finger and the contentment of the patients. From 1996 to 2000 for the core suture of the flexor tendon of fingers we used 2 strands. 35 patients with 40 tendon sutures of 73 patients were examined. From 2001 to 2005 we used for the core suture 2 loop threads. 53 patients with 64 tendon sutures from a total of 111 patients were examined. At least 12 months had passed between operation and the examination. The rupture rate and the range of movement of each finger joint and the total mobility of the affected fingers were evaluated. Each case was compared to the uninjured opposite hand. The functional result was judged according to the score of Buck-Gramcko. The patient's contentment was recorded by the DASH (disability of arm, shoulder and hand) score. Effects of gender, age, accompanying injuries, zone of the injury and their influence on the results were analysed. The Buck-Gramcko score showed in the 2-strand group a distribution from summarised 70% "excellent" and "good" and 30% "fair" and "poor". In the 4-strand-group the relation was 93.7% "excellent" and "good", 6.3% "fair", one "poor". In the 2-strand group 2/40 (5%) of the tendon sutures ruptured, in the 4-strand group 1/64 (1.6%) ruptured. The average DASH value in the 2-strands-group was 16.6/100, in the 4-strands-group 18.1/100 when 0 is the best possible result and 100 the worst. The patient judgement in the 2-strand group was summarised to 70% for "excellent" and "good" and 30% "fair" and "poor". In the 4-strand group the patient's judgment was summarised in 75% "excellent" and "good" and in 25% "fair". The results of flexor tendon sutures with 4-strand core sutures have been superior to the results with 2-strand core suture according to range of motion of the fingers (P <0.005). © Georg Thieme Verlag KG Stuttgart · New York.
A novel single fluorophore-labeled double-stranded oligonucleotide probe for fluorescence-enhanced nucleic acid detection based on the inherent quenching ability of deoxyguanosine bases and competitive strand-displacement reaction.

PubMed

Zhang, Yingwei; Tian, Jingqi; Li, Hailong; Wang, Lei; Sun, Xuping

2012-01-01

We develop a novel single fluorophore-labeled double-stranded oligonucleotide (OND) probe for rapid, nanostructure-free, fluorescence-enhanced nucleic acid detection for the first time. We further demonstrate such probe is able to well discriminate single-base mutation in nucleic acid. The design takes advantage of an inherent quenching ability of guanine bases. The short strand of the probe is designed with an end-labeled fluorophore that is placed adjacent to two guanines as the quencher located on the long opposite strand, resulting in great quenching of dye fluorescence. In the presence of a target complementary to the long strand of the probe, a competitive strand-displacement reaction occurs and the long strand forms a more stable duplex with the target, resulting in the two strands of the probe being separated from each other. As a consequence of this displacement, the fluorophore and the quencher are no longer in close proximity and dye fluorescence increases, signaling the presence of target.
Offshore Earthquakes Do Not Influence Marine Mammal Stranding Risk on the Washington and Oregon Coasts.

PubMed

Grant, Rachel A; Savirina, Anna; Hoppitt, Will

2018-01-26

The causes of marine mammals stranding on coastal beaches are not well understood, but may relate to topography, currents, wind, water temperature, disease, toxic algal blooms, and anthropogenic activity. Offshore earthquakes are a source of intense sound and disturbance and could be a contributing factor to stranding probability. We tested the hypothesis that the probability of marine mammal stranding events on the coasts of Washington and Oregon, USA is increased by the occurrence of offshore earthquakes in the nearby Cascadia subduction zone. The analysis carried out here indicated that earthquakes are at most, a very minor predictor of either single, or large (six or more animals) stranding events, at least for the study period and location. We also tested whether earthquakes inhibit stranding and again, there was no link. Although we did not find a substantial association of earthquakes with strandings in this study, it is likely that there are many factors influencing stranding of marine mammals and a single cause is unlikely to be responsible. Analysis of a subset of data for which detailed descriptions were available showed that most live stranded animals were pups, calves, or juveniles, and in the case of dead stranded mammals, the commonest cause of death was trauma, disease, and emaciation.
Optical Properties of Laminarin Using Terahertz Time-Domain Spectroscopy (abstract)

NASA Astrophysics Data System (ADS)

Shin, Hee Jun; Maeng, Inhee; Oh, Seung Jae; Kim, Sung In; Kim, Ha Won; Son, Joo-Hiuk

2009-04-01

Terahertz spectroscopy is important in the study of biomolecular structure because the vibration and rotation energy of large molecules such as DNA, proteins, and polysaccharides are laid in terahertz regions. Terahertz time-domain spectroscopy (THz-TDS), using terahertz pulses generated and detected by femto-second pulses laser, has been used in the study of biomolecular dynamics, as well as carrier dynamics of semiconductors. Laminarin is a polysaccharide of glucose in brown algae. It is made up of β(1-3)-glucan and β(1-6)-glucan. β-glucan is an anticancer material that activates the immune reaction of human cells and inhibits proliferation of cancer cells. β-glucan with a single-strand structure has been reported to activate the immune reaction to a greater extent than β-glucan with a triple-strand helix structure. We used THz-TDS to characterize the difference between single-strand and triple-strand β-glucan. We obtained single-strand β-glucan by chemical treatment of triple-strand β-glucan. We measured the frequency dependent optical constants of Laminarin using THz-TDS. Power absorption of the triple-strand helix is larger than the single-strand helix in terahertz regions. The refractive index of the triple-strand helix is also larger than that of the single-strand helix.

The Impact of Turtle Excluder Devices and Fisheries Closures on Loggerhead and Kemp's Ridley Strandings in the Western Gulf of Mexico

USGS Publications Warehouse

Lewison, R.L.; Crowder, L.B.; Shaver, D.J.

2003-01-01

The Sea Turtle Stranding and Salvage Network has been monitoring turtle strandings for more than 20 years in the United States. High numbers of strandings in the early to mid-1980s prompted regulations to require turtle excluder devices (TEDs) on shrimping vessels (trawlers). Following year-round TED implementation in 1991, however, stranding levels in the Gulf of Mexico increased. We evaluated the efficacy of TEDs and other management actions (e.g., fisheries closures) on loggerhead (Caretta caretta) and Kemp's ridley (Lepidochelys kempii) turtle populations by analyzing a long-term, stranding data set from the western Gulf of Mexico. Our analyses suggest that both sea turtle population growth and shrimping activity have contributed to the observed increase in strandings. Compliance with regulations requiring turtle excluder devices was a significant factor in accounting for annual stranding variability: low compliance was correlated with high levels of strandings. Our projections suggest that improved compliance with TED regulations will reduce strandings to levels that, in conjunction with other protective measures, should promote population recoveries for loggerhead and Kemp's ridley turtles. Local, seasonal fisheries closures, concurrent with TED enforcement, could reduce strandings to even lower levels. A seasonal closure adjacent to a recently established Kemp's ridley nesting beach may also reduce mortality of nesting adults and thus promote long-term population persistence by fostering the establishment of a robust secondary nesting site.
DOE Office of Scientific and Technical Information (OSTI.GOV)

Emanuela Barzi et al.

Fermilab is developing 11 T superconducting dipole magnets for future accelerators based on Nb{sub 3}Sn conductor. Within the High Field Magnet Project, the first prototypes feature 1 meter long two-layer shell-type coils and common coils. For the former, keystoned Rutherford-type cable made of 28 Nb{sub 3}Sn strands 1 mm in diameter are used, whereas for the latter a 60-strand flat cable was chosen. Multifilamentary Nb{sub 3}Sn strands produced with various technologies by industry were used for the development and testing of the prototype cable. An experimental cabling machine with up to 28-strand capacity that has been recently purchased, installed andmore » commissioned at Fermilab, has allowed further advances in strand and cable studies. Cables of 27 and 28 strands of various structures (single strands or assemblies of sub-strands), with aspect ratios from 7 to 17, packing factors from 85 to 95%, with and without a stainless steel core were made out of Copper, NbTi, and Modified Jelly Roll (OST), Powder-in-Tube (SMI) and Internal Tin (Mitsubishi) Nb{sub 3}Sn strands. optimal parameters were determined with respect to mechanical and electrical properties, including critical current degradation, interstrand resistance, etc. Round strands of the same billets used in the cables were deformed by rolling them down to various thicknesses. Their critical current Ic was then measured and compared with that of the strands extracted from cables having different packing factors. This paper summarizes the results of such R and D efforts at Fermilab.« less
Evaluation de L’Effet du Vieillissement des Equipages sur les Consequences du Decalage Horaire (Evaluation of Crew Members Aging on Jet-Lag Consequences)

DTIC Science & Technology

2000-08-01

Ergonomia , 1987, 30, 13 79- physique que psychologique. Cela tend A damontrer que 1393. dans des conditions militaires op~rationnelles, les 2...melatonin. Ergonomia , 1987, 30, 1379- 1393. 2 - BLOIS R, FEINBERG I., GAILLARD J.M., KUPFER D.J. and WEBB W.B. Sleep in normal and pathological aging
Electromagnetic Noise Interference and Compatibility

DTIC Science & Technology

1975-11-01

RADIO INTERFERENCE by C.Fengler 7 LES CHARGES ELECTROSTATIQUES ET LES PERTURBATIONS QU’ELLES ENTRAINENT DANS LES LIAISONS RADIOELECTRIQUES par...PAR LA TRANSMISSION DANS UN SYSTFJE INTEGRE AEROPORTE par r,.David et M.Vanneizel 31 Not available at time of priating Reference DIGITAL DATA...TRANSMISSION IN AIRCRAFT: EMC-PROBLEMS AND POSSIBLE SOLUTIONS by R.Rode 32 GENERATIONS El EFFETS DES TENSIONS PARASITES DE CONDUCTION ET DE RAVONNEMENT ENTRE
Impuretés et systèmes corrélés. Des chaînes aux cuprates supraconducteurs

NASA Astrophysics Data System (ADS)

Bobroff, J.

2005-01-01

Impurities and correlated systems Discovery of high TC superconductors has opened the new field of strongly correlated fermions physics. In these compounds, mostly transition metal oxides, strong correlations between electrons affect sharply their electronic properties. In order to determine accurately these correlations and their possible link with superconductivity, we study the effect of local defects such as non magnetic impurities. In fact, in the more simple case of insulating spin chains and ladders, these impurities induce a staggered magnetism in their neighborhood which reveals the underlying electronic correlations. Similar effects are observed in high TC superconductors, using local probes such as nuclear magnetic resonance. These observations allow to get a better understanding of both normal and superconducting state of these oxides, both full of surprises. La découverte des supraconducteurs à haute température critique a ouvert la voie à une nouvelle physique, celle des fermions fortement corrélés. Dans ces systèmes, le plus souvent des oxydes de métaux de transition, les fortes corrélations entre électrons affectent profondément leurs propriétés électroniques et induisent de nouveaux états originaux : liquides de spins, supraconductivité, etc. Pour mesurer ces corrélations et ainsi déterminer leur lien éventuel avec la supraconductivité, nous proposons d'étudier l'effet de défauts ponctuels tels que des impuretés non magnétiques. En effet, dans le cas plus simple de chaînes ou d'échelles de spin isolantes, ces impuretés induisent dans leur voisinage immédiat un magnétisme alterné révélateur des corrélations électroniques. Des effets semblables sont observés dans les supraconducteurs à haute température critique, grâce à des sondes locales comme la résonance magnétique nucléaire. Ces observations permettent de mieux comprendre à la fois l'état normal et supraconducteur de ces oxydes, tous deux riches en surprises.
Les hémodialysés HVC sont-ils vraiment des patients difficiles à traiter?

PubMed Central

Krati, Khadija; Cherquaoui, Hind; Oubaha, Sofia; Samlani, Zouhour

2015-01-01

L'hépatite C demeure la principale infection virale chez l'hémodialysé, dont la prise en charge thérapeutique ainsi que la gestion de ses effets secondaires restent difficiles. Il s'agit d'une étude rétrospective portant sur tous les patients atteints d'hépatite C chronique ayant une insuffisance rénale chronique sous hémodialyse, suivis au service de gastroentérologie au CHU Mohamed VI de Marrakech sur une période de Janvier 2004 à Décembre 2014. Sur un total de 355 cas d'hépatite virale C, 13 patients étaient hémodialysés (3,66%). Dix patients ont été traités, soit 76,94% des cas. Le traitement n’était pas indiqué chez 2 patients ayant une fibrose minime sans cytolyse. Il était contre-indiqué chez une patiente multitarée. Deux malades ont eu une réponse virologique rapide et 5 une réponse virologique précoce. Le taux de réponse virologique soutenue était de 40%, 30% des patients étaient non répondeurs. Le traitement fut arrêté chez 2 patientes pour effets secondaires sévères. Un seul patient a été candidat à une transplantation rénale. En analyse multivariée, la réponse virologique soutenue a été significativement associée à certains facteurs prédictifs de bonne réponse thérapeutique: Age jeune ≤40 ans (P=0,0057), fibrose minime F1-F2 (P=0,03), génotype non 1 (P=0,0064), charge virale préthérapeutique <800000 UI/ml (P=0,013), et l'absence d'arrêt thérapeutique (P=0,028). La gestion efficace des effets secondaires du traitement de HVC permet d'obtenir chez l'hémodialysé un taux de réponse virologique soutenue avoisinant celui de la population générale. PMID:27022433
Durcissement superficiel de la fonte grise Ft25 induit par un traitement de surface dans le moule

NASA Astrophysics Data System (ADS)

Bouitna, Mohamed; Boutarek-Zaourar, Naïma; Mansour, Samir; Chentouf, Samir Mourad; Mossang, Eric

2018-02-01

L'objectif de cette étude est la consolidation en surface de la fonte grise lamellaire Ft25 par un dépôt riche en manganèse en développant une méthode combinant en une seule opération l'élaboration et le traitement de surface dans le moule. Les effets de la granulométrie du ferro-manganèse (80 % Mn + 20 % Fe), ainsi que l'épaisseur des pièces en fontes sur les couches formées ont été étudiés. On a retenu trois granulométries du ferro-manganèse de 0,18 mm, 0,25 mm et 0,5 mm pour le traitement des pièces en fontes présentant des épaisseurs de 25 mm, 100 mm et 200 mm. Parmi les résultats obtenus, on distingue une consolidation des propriétés en surface induite par la formation d'une couche riche en manganèse continue et homogène. L'effet de la granulométrie du ferro-manganèse sur l'épaisseur de la couche traitée a été mis en évidence. La variation de l'épaisseur des couches formées diminue avec l'augmentation de la granulométrie du ferro-manganèse. Pour une pièce de 100 mm d'épaisseur, la couche formée est estimée à 350 μm pour une granulométrie de 0,18 alors qu'elle n'est que de 180 μm pour une granulométrie de 0,5. L'effet de l'épaisseur de la pièce n'est en revanche pas assez prononcé sur la taille des couches formées. Une amélioration nette de la résistance, à l'usure de la fonte traitée en relation avec les transformations en surface, a été mise en évidence.
Les neuropathies liées au VIH/SIDA: une étude clinique chez les patients infectés par le VIH au Centre d'Excellence VIH/SIDA de l'Université de Lubumbashi

PubMed Central

Kabongo, Joe Katabwa; Kaputu-Kalala-Malu, Célestin; Luboya, Oscar; Mutombo, Valerien; Ntambwe, Abel; Mapatano, Mala Ali; Mukendi, Kavulu Mayamba

2015-01-01

Introduction En vue d'améliorer la prise en charge des patients souffrant de neuropathie (NP) associées à l'infection HIV, nous avons essayé de déterminer le profil clinique des personnes souffrant de NP au cours du suivi thérapeutique de leur infection HIV. Méthodes Il s'agit d'une étude transversale (n= 101) menée au centre d'excellence depuis 1 an. Notre analyse est essentiellement clinique. Par un examen clinique minutieux, nous avons recherché tous les symptômes et signes cliniques des NP. Subjectivement, les douleurs dominent le tableau. Pour affiner leur diagnostic, nous avons utilisé l’échelle DN4 (Diagnostic des douleurs neuropathiques) et l’échelle EVA (Evaluation de la gravité des douleurs). Nous avons ensuite analysé nos données en fonction de certains autres facteurs épidémiologiques tels que le taux des CD4, le traitement anti-HIV etc. Résultats Les 101 patients représentent 3,12% de la cohorte générale; 53,3% des patients présentent une abolition des réflexes ostéotendineux des membres inférieurs; 77,89% présentent une hypoesthésie thermo algique en chaussette et en gants; 25% ont présenté une amyotrophie des membres inférieurs; 76,5% ont été soumis à un traitement antirétroviral contenant la stavudine; 11,7% ont pris la didanosine (DDI) et Abacavir (ABC). 84% ont une moyenne de CD4 de 292 cel/mm3. Conclusion La NP altère la qualité de vie de nos patients et diminue l'adhérence au traitement antirétroviral. Plusieurs facteurs sont incriminés dans la survenue de la NP, l'effet direct des antirétroviraux, l'effet inflammatoire dysimmunitaire, l'effet infectieux lié aux infections opportunistes. D'autres facteurs seront recherchés et analysés ultérieurement. PMID:26185582
Photochemical Acceleration of DNA Strand Displacement by Using Ultrafast DNA Photo-crosslinking.

PubMed

Nakamura, Shigetaka; Hashimoto, Hirokazu; Kobayashi, Satoshi; Fujimoto, Kenzo

2017-10-18

DNA strand displacement is an essential reaction in genetic recombination, biological processes, and DNA nanotechnology. In particular, various DNA nanodevices enable complicated calculations. However, it takes time before the output is obtained, so acceleration of DNA strand displacement is required for a rapid-response DNA nanodevice. Herein, DNA strand displacement by using DNA photo-crosslinking to accelerate this displacement is evaluated. The DNA photo-crosslinking of 3-cyanovinylcarbazole ( CNV K) was accelerated at least 20 times, showing a faster DNA strand displacement. The rate of photo-crosslinking is a key factor and the rate of DNA strand displacement is accelerated through ultrafast photo-crosslinking. The rate of DNA strand displacement was regulated by photoirradiation energy. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.
Salton Seismic Imaging Project Line 5—the San Andreas Fault and Northern Coachella Valley Structure, Riverside County, California

NASA Astrophysics Data System (ADS)

Rymer, M. J.; Fuis, G.; Catchings, R. D.; Goldman, M.; Tarnowski, J. M.; Hole, J. A.; Stock, J. M.; Matti, J. C.

2012-12-01

The Salton Seismic Imaging Project (SSIP) is a large-scale, active- and passive-source seismic project designed to image the San Andreas Fault (SAF) and the adjacent basins (Imperial and Coachella Valleys) in southern California. Here, we focus on SSIP Line 5, one of four 2-D NE-SW-oriented seismic profiles that were acquired across the Coachella Valley. The 38-km-long SSIP-Line-5 seismic profile extends from the Santa Rosa Ranges to the Little San Bernardino Mountains and crosses both strands of the SAF, the Mission Creek (MCF) and Banning (BF) strands, near Palm Desert. Data for Line 5 were generated from nine buried explosive sources (most spaced about 2 to 8 km apart) and were recorded on approximately 281 Texan seismographs (average spacing 138 m). First-arrival refractions were used to develop a refraction tomographic velocity image of the upper crust along the seismic profile. The seismic data were also stacked and migrated to develop low-fold reflection images of the crust. From the surface to about 8 km depth, P-wave velocities range from about 2 km/s to more than 7.5 km/s, with the lowest velocities within a well-defined (~2-km-deep, 15-km-wide) basin (< 4 km/s), and the highest velocities below the transition from the Coachella Valley to the Santa Rosa Ranges on the southwest and within the Little San Bernardino Mountains on the northeast. The MCF and BF strands of the SAF bound an approximately 2.5-km-wide horst-type structure on the northeastern side of the Coachella Valley, beneath which the upper crust is characterized by a pronounced low-velocity zone that extends to the bottom of the velocity image. Rocks within the low-velocity zone have significantly lower velocities than those to the northeast and the southwest at the same depths. Conversely, the velocities of rocks on both sides of the Coachella Valley are greater than 7 km/s at depths exceeding about 4 km. The relatively narrow zone of shallow high-velocity rocks between the surface traces of the MCF and BF strands is associated with a zone of uplifted strata. Along SSIP Line 5, we infer that the MCF and BF strands are steeply dipping and merge at about 2 km depth. We base our interpretation on a prominent basement low-velocity zone (fault zone) that is centered southwest of the MCF and BF strands and extends to at least 8 km depth.
Interpreting the spatio-temporal patterns of sea turtle strandings: Going with the flow

USGS Publications Warehouse

Hart, K.M.; Mooreside, P.; Crowder, L.B.

2006-01-01

Knowledge of the spatial and temporal distribution of specific mortality sources is crucial for management of species that are vulnerable to human interactions. Beachcast carcasses represent an unknown fraction of at-sea mortalities. While a variety of physical (e.g., water temperature) and biological (e.g., decomposition) factors as well as the distribution of animals and their mortality sources likely affect the probability of carcass stranding, physical oceanography plays a major role in where and when carcasses strand. Here, we evaluate the influence of nearshore physical oceanographic and wind regimes on sea turtle strandings to decipher seasonal trends and make qualitative predictions about stranding patterns along oceanfront beaches. We use results from oceanic drift-bottle experiments to check our predictions and provide an upper limit on stranding proportions. We compare predicted current regimes from a 3D physical oceanographic model to spatial and temporal locations of both sea turtle carcass strandings and drift bottle landfalls. Drift bottle return rates suggest an upper limit for the proportion of sea turtle carcasses that strand (about 20%). In the South Atlantic Bight, seasonal development of along-shelf flow coincides with increased numbers of strandings of both turtles and drift bottles in late spring and early summer. The model also predicts net offshore flow of surface waters during winter - the season with the fewest relative strandings. The drift bottle data provide a reasonable upper bound on how likely carcasses are to reach land from points offshore and bound the general timeframe for stranding post-mortem (< two weeks). Our findings suggest that marine turtle strandings follow a seasonal regime predictable from physical oceanography and mimicked by drift bottle experiments. Managers can use these findings to reevaluate incidental strandings limits and fishery takes for both nearshore and offshore mortality sources. ?? 2005 Elsevier Ltd. All rights reserved.
Long-Term Seasonal and Interannual Patterns of Marine Mammal Strandings in Subtropical Western South Atlantic

PubMed Central

Prado, Jonatas H. F.; Mattos, Paulo H.; Silva, Kleber G.; Secchi, Eduardo R.

2016-01-01

Understanding temporal patterns of marine mammal occurrence is useful for establishing conservation strategies. We used a 38 yr-long dataset spanning 1976 to 2013 to describe temporal patterns and trends in marine mammal strandings along a subtropical stretch of the east coast of South America. This region is influenced by a transitional zone between tropical and temperate waters and is considered an important fishing ground off Brazil. Generalized Additive Models were used to evaluate the temporal stranding patterns of the most frequently stranded species. Forty species were documented in 12,540 stranding events. Franciscana (n = 4,574), South American fur seal, (n = 3,419), South American sea lion (n = 2,049), bottlenose dolphins (n = 293) and subantarctic fur seal (n = 219) were the most frequently stranded marine mammals. The seasonality of strandings of franciscana and bottlenose dolphin coincided with periods of higher fishing effort and strandings of South American and subantarctic fur seals with post-reproductive dispersal. For South American sea lion the seasonality of strandings is associated with both fishing effort and post-reproductive dispersal. Some clear seasonal patterns were associated with occurrence of cold- (e.g. subantarctic fur seal) and warm-water (e.g. rough-toothed dolphin) species in winter and summer, respectively. Inter-annual increases in stranding rate were observed for franciscana and South American fur seal and these are likely related to increased fishing effort and population growth, respectively. For subantarctic fur seal the stranding rate showed a slight decline while for bottlenose dolphin it remained steady. No significant year to year variation in stranding rate was observed for South American sea lion. The slight decrease in frequency of temperate/polar marine mammals and the increased occurrence of subtropical/tropical species since the late 1990s might be associated with environmental changes linked to climate change. This long-term study indicates that temporal stranding patterns of marine mammals might be explained by either fishing-related or environmental factors. PMID:26814667
Long-Term Seasonal and Interannual Patterns of Marine Mammal Strandings in Subtropical Western South Atlantic.

PubMed

Prado, Jonatas H F; Mattos, Paulo H; Silva, Kleber G; Secchi, Eduardo R

2016-01-01

Understanding temporal patterns of marine mammal occurrence is useful for establishing conservation strategies. We used a 38 yr-long dataset spanning 1976 to 2013 to describe temporal patterns and trends in marine mammal strandings along a subtropical stretch of the east coast of South America. This region is influenced by a transitional zone between tropical and temperate waters and is considered an important fishing ground off Brazil. Generalized Additive Models were used to evaluate the temporal stranding patterns of the most frequently stranded species. Forty species were documented in 12,540 stranding events. Franciscana (n = 4,574), South American fur seal, (n = 3,419), South American sea lion (n = 2,049), bottlenose dolphins (n = 293) and subantarctic fur seal (n = 219) were the most frequently stranded marine mammals. The seasonality of strandings of franciscana and bottlenose dolphin coincided with periods of higher fishing effort and strandings of South American and subantarctic fur seals with post-reproductive dispersal. For South American sea lion the seasonality of strandings is associated with both fishing effort and post-reproductive dispersal. Some clear seasonal patterns were associated with occurrence of cold- (e.g. subantarctic fur seal) and warm-water (e.g. rough-toothed dolphin) species in winter and summer, respectively. Inter-annual increases in stranding rate were observed for franciscana and South American fur seal and these are likely related to increased fishing effort and population growth, respectively. For subantarctic fur seal the stranding rate showed a slight decline while for bottlenose dolphin it remained steady. No significant year to year variation in stranding rate was observed for South American sea lion. The slight decrease in frequency of temperate/polar marine mammals and the increased occurrence of subtropical/tropical species since the late 1990s might be associated with environmental changes linked to climate change. This long-term study indicates that temporal stranding patterns of marine mammals might be explained by either fishing-related or environmental factors.
Phenotypic diversification by enhanced genome restructuring after induction of multiple DNA double-strand breaks.

PubMed

Muramoto, Nobuhiko; Oda, Arisa; Tanaka, Hidenori; Nakamura, Takahiro; Kugou, Kazuto; Suda, Kazuki; Kobayashi, Aki; Yoneda, Shiori; Ikeuchi, Akinori; Sugimoto, Hiroki; Kondo, Satoshi; Ohto, Chikara; Shibata, Takehiko; Mitsukawa, Norihiro; Ohta, Kunihiro

2018-05-18

DNA double-strand break (DSB)-mediated genome rearrangements are assumed to provide diverse raw genetic materials enabling accelerated adaptive evolution; however, it remains unclear about the consequences of massive simultaneous DSB formation in cells and their resulting phenotypic impact. Here, we establish an artificial genome-restructuring technology by conditionally introducing multiple genomic DSBs in vivo using a temperature-dependent endonuclease TaqI. Application in yeast and Arabidopsis thaliana generates strains with phenotypes, including improved ethanol production from xylose at higher temperature and increased plant biomass, that are stably inherited to offspring after multiple passages. High-throughput genome resequencing revealed that these strains harbor diverse rearrangements, including copy number variations, translocations in retrotransposons, and direct end-joinings at TaqI-cleavage sites. Furthermore, large-scale rearrangements occur frequently in diploid yeasts (28.1%) and tetraploid plants (46.3%), whereas haploid yeasts and diploid plants undergo minimal rearrangement. This genome-restructuring system (TAQing system) will enable rapid genome breeding and aid genome-evolution studies.
Chromosome territories reposition during DNA damage-repair response

PubMed Central

2013-01-01

Background Local higher-order chromatin structure, dynamics and composition of the DNA are known to determine double-strand break frequencies and the efficiency of repair. However, how DNA damage response affects the spatial organization of chromosome territories is still unexplored. Results Our report investigates the effect of DNA damage on the spatial organization of chromosome territories within interphase nuclei of human cells. We show that DNA damage induces a large-scale spatial repositioning of chromosome territories that are relatively gene dense. This response is dose dependent, and involves territories moving from the nuclear interior to the periphery and vice versa. Furthermore, we have found that chromosome territory repositioning is contingent upon double-strand break recognition and damage sensing. Importantly, our results suggest that this is a reversible process where, following repair, chromosome territories re-occupy positions similar to those in undamaged control cells. Conclusions Thus, our report for the first time highlights DNA damage-dependent spatial reorganization of whole chromosomes, which might be an integral aspect of cellular damage response. PMID:24330859
Strand development and splice device : final report, February 3, 2009.

DOT National Transportation Integrated Search

2010-02-01

"A new device for gripping prestressing strands was developed and tested. The device could provide a means of anchoring the terminal end of a strand in order to provide a mechanism for developing bonded strand at the service limit state, to provide t...
Replicase activity of purified recombinant protein P2 of double-stranded RNA bacteriophage phi6.

PubMed

Makeyev, E V; Bamford, D H

2000-01-04

In nature, synthesis of both minus- and plus-sense RNA strands of all the known double-stranded RNA viruses occurs in the interior of a large protein assembly referred to as the polymerase complex. In addition to other proteins, the complex contains a putative polymerase possessing characteristic sequence motifs. However, none of the previous studies has shown template-dependent RNA synthesis directly with an isolated putative polymerase protein. In this report, recombinant protein P2 of double-stranded RNA bacteriophage phi6 was purified and demonstrated in an in vitro enzymatic assay to act as the replicase. The enzyme efficiently utilizes phage-specific, positive-sense RNA substrates to produce double-stranded RNA molecules, which are formed by newly synthesized, full-length minus-strands base paired with the plus-strand templates. P2-catalyzed replication is also shown to be very effective with a broad range of heterologous single-stranded RNA templates. The importance and implications of these results are discussed.
Offshore Earthquakes Do Not Influence Marine Mammal Stranding Risk on the Washington and Oregon Coasts

PubMed Central

Grant, Rachel A.; Savirina, Anna

2018-01-01

Simple Summary Marine mammals stranding on coastal beaches is not unusual. However, there appears to be no single cause for this, with several causes being probable, such as starvation, contact with humans (for example boat strike or entanglement with fishing gear), disease, and parasitism. We evaluated marine mammal stranding off the Washington and Oregon coasts and looked at offshore earthquakes as a possible contributing factor. Our analysis showed that offshore earthquakes did not make marine mammals more likely to strand. We also analysed a subset of data from the north of Washington State and found that non-adult animals made up a large proportion of stranded animals, and for dead animals the commonest cause of death was disease, traumatic injury, or starvation. Abstract The causes of marine mammals stranding on coastal beaches are not well understood, but may relate to topography, currents, wind, water temperature, disease, toxic algal blooms, and anthropogenic activity. Offshore earthquakes are a source of intense sound and disturbance and could be a contributing factor to stranding probability. We tested the hypothesis that the probability of marine mammal stranding events on the coasts of Washington and Oregon, USA is increased by the occurrence of offshore earthquakes in the nearby Cascadia subduction zone. The analysis carried out here indicated that earthquakes are at most, a very minor predictor of either single, or large (six or more animals) stranding events, at least for the study period and location. We also tested whether earthquakes inhibit stranding and again, there was no link. Although we did not find a substantial association of earthquakes with strandings in this study, it is likely that there are many factors influencing stranding of marine mammals and a single cause is unlikely to be responsible. Analysis of a subset of data for which detailed descriptions were available showed that most live stranded animals were pups, calves, or juveniles, and in the case of dead stranded mammals, the commonest cause of death was trauma, disease, and emaciation. PMID:29373509
Process of infection with bacteriophage phi chi 174. XL. Viral DNA replication of phi chi 174 mutants blocked in progeny single-stranded DNA synthesis.

PubMed Central

Fukuda, A; Sinsheimer, R L

1976-01-01

Mutation in several different cistrons of bacteriophage phi chi 174 blocks net progeny single-stranded DNA synthesis at the late period of infection (15). For the study of the functions of these cistrons in single-stranded DNA synthesis, asymmetric replication of replicative form DNA was examined at the late period of infection with amber mutants of these cistrons. While the normal, rapid process of asymmetric single-stranded viral DNA synthesis is blocked at the late period of these mutant infections, an asymmetric synthesis of the viral strand of replicative-form DNA is observed in this period, though at a reduced level, together with degradation of prelabeled viral strand. Some intermediate replicative-form molecules were also detected. Asymmetric synthesis of the viral strand of replicative-form DNA at the late period of phi chi infection is completely inhibited in the presence of a low concentration (35mug/ml) of chloramphenicol (which also blocks net single-stranded viral DNA synthesis). These results are discussed in terms of the possible role of the specific viral proteins for normal single-stranded DNA synthesis. PMID:1255871
Improving strand pairing prediction through exploring folding cooperativity

PubMed Central

Jeong, Jieun; Berman, Piotr; Przytycka, Teresa M.

2008-01-01

The topology of β-sheets is defined by the pattern of hydrogen-bonded strand pairing. Therefore, predicting hydrogen bonded strand partners is a fundamental step towards predicting β-sheet topology. At the same time, finding the correct partners is very difficult due to long range interactions involved in strand pairing. Additionally, patterns of aminoacids observed in β-sheet formations are very general and therefore difficult to use for computational recognition of specific contacts between strands. In this work, we report a new strand pairing algorithm. To address above mentioned difficulties, our algorithm attempts to mimic elements of the folding process. Namely, in addition to ensuring that the predicted hydrogen bonded strand pairs satisfy basic global consistency constraints, it takes into account hypothetical folding pathways. Consistently with this view, introducing hydrogen bonds between a pair of strands changes the probabilities of forming hydrogen bonds between other pairs of strand. We demonstrate that this approach provides an improvement over previously proposed algorithms. We also compare the performance of this method to that of a global optimization algorithm that poses the problem as integer linear programming optimization problem and solves it using ILOG CPLEX™ package. PMID:18989036

The Human DNA glycosylases NEIL1 and NEIL3 Excise Psoralen-Induced DNA-DNA Cross-Links in a Four-Stranded DNA Structure.

PubMed

Martin, Peter R; Couvé, Sophie; Zutterling, Caroline; Albelazi, Mustafa S; Groisman, Regina; Matkarimov, Bakhyt T; Parsons, Jason L; Elder, Rhoderick H; Saparbaev, Murat K

2017-12-12

Interstrand cross-links (ICLs) are highly cytotoxic DNA lesions that block DNA replication and transcription by preventing strand separation. Previously, we demonstrated that the bacterial and human DNA glycosylases Nei and NEIL1 excise unhooked psoralen-derived ICLs in three-stranded DNA via hydrolysis of the glycosidic bond between the crosslinked base and deoxyribose sugar. Furthermore, NEIL3 from Xenopus laevis has been shown to cleave psoralen- and abasic site-induced ICLs in Xenopus egg extracts. Here we report that human NEIL3 cleaves psoralen-induced DNA-DNA cross-links in three-stranded and four-stranded DNA substrates to generate unhooked DNA fragments containing either an abasic site or a psoralen-thymine monoadduct. Furthermore, while Nei and NEIL1 also cleave a psoralen-induced four-stranded DNA substrate to generate two unhooked DNA duplexes with a nick, NEIL3 targets both DNA strands in the ICL without generating single-strand breaks. The DNA substrate specificities of these Nei-like enzymes imply the occurrence of long uninterrupted three- and four-stranded crosslinked DNA-DNA structures that may originate in vivo from DNA replication fork bypass of an ICL. In conclusion, the Nei-like DNA glycosylases unhook psoralen-derived ICLs in various DNA structures via a genuine repair mechanism in which complex DNA lesions can be removed without generation of highly toxic double-strand breaks.
Efficient and simpler method to construct normalized cDNA libraries with improved representations of full-length cDNAs

DOEpatents

Soares, Marcelo Bento; Bonaldo, Maria de Fatima

1998-01-01

This invention provides a method to normalize a cDNA library comprising: (a) constructing a directionally cloned library containing cDNA inserts wherein the insert is capable of being amplified by polymerase chain reaction; (b) converting a double-stranded cDNA library into single-stranded DNA circles; (c) generating single-stranded nucleic acid molecules complementary to the single-stranded DNA circles converted in step (b) by polymerase chain reaction with appropriate primers; (d) hybridizing the single-stranded DNA circles converted in step (b) with the complementary single-stranded nucleic acid molecules generated in step (c) to produce partial duplexes to an appropriate Cot; and (e) separating the unhybridized single-stranded DNA circles from the hybridized DNA circles, thereby generating a normalized cDNA library. This invention also provides a method to normalize a cDNA library wherein the generating of single-stranded nucleic acid molecules complementary to the single-stranded DNA circles converted in step (b) is by excising cDNA inserts from the double-stranded cDNA library; purifying the cDNA inserts from cloning vectors; and digesting the cDNA inserts with an exonuclease. This invention further provides a method to construct a subtractive cDNA library following the steps described above. This invention further provides normalized and/or subtractive cDNA libraries generated by the above methods.
Method for introducing unidirectional nested deletions

DOEpatents

Dunn, J.J.; Quesada, M.A.; Randesi, M.

1999-07-27

Disclosed is a method for the introduction of unidirectional deletions in a cloned DNA segment. More specifically, the method comprises providing a recombinant DNA construct comprising a DNA segment of interest inserted in a cloning vector. The cloning vector has an f1 endonuclease recognition sequence adjacent to the insertion site of the DNA segment of interest. The recombinant DNA construct is then contacted with the protein pII encoded by gene II of phage f1 thereby generating a single-stranded nick. The nicked DNA is then contacted with E. coli Exonuclease III thereby expanding the single-stranded nick into a single-stranded gap. The single-stranded gapped DNA is then contacted with a single-strand-specific endonuclease thereby producing a linearized DNA molecule containing a double-stranded deletion corresponding in size to the single-stranded gap. The DNA treated in this manner is then incubated with DNA ligase under conditions appropriate for ligation. Also disclosed is a method for producing single-stranded DNA probes. In this embodiment, single-stranded gapped DNA, produced as described above, is contacted with a DNA polymerase in the presence of labeled nucleotides to fill in the gap. This DNA is then linearized by digestion with a restriction enzyme which cuts outside the DNA segment of interest. The product of this digestion is then denatured to produce a labeled single-stranded nucleic acid probe. 1 fig.
Efficient and simpler method to construct normalized cDNA libraries with improved representations of full-length cDNAs

DOEpatents

Soares, M.B.; Fatima Bonaldo, M. de

1998-12-08

This invention provides a method to normalize a cDNA library comprising: (a) constructing a directionally cloned library containing cDNA inserts wherein the insert is capable of being amplified by polymerase chain reaction; (b) converting a double-stranded cDNA library into single-stranded DNA circles; (c) generating single-stranded nucleic acid molecules complementary to the single-stranded DNA circles converted in step (b) by polymerase chain reaction with appropriate primers; (d) hybridizing the single-stranded DNA circles converted in step (b) with the complementary single-stranded nucleic acid molecules generated in step (c) to produce partial duplexes to an appropriate Cot; and (e) separating the unhybridized single-stranded DNA circles from the hybridized DNA circles, thereby generating a normalized cDNA library. This invention also provides a method to normalize a cDNA library wherein the generating of single-stranded nucleic acid molecules complementary to the single-stranded DNA circles converted in step (b) is by excising cDNA inserts from the double-stranded cDNA library; purifying the cDNA inserts from cloning vectors; and digesting the cDNA inserts with an exonuclease. This invention further provides a method to construct a subtractive cDNA library following the steps described above. This invention further provides normalized and/or subtractive cDNA libraries generated by the above methods. 25 figs.
Radioresistance of GGG Sequences to Prompt Strand Break Formation from Direct-Type Radiation Damage

PubMed Central

Black, Paul J.; Miller, Adam S.; Hayes, Jeffrey J.

2016-01-01

Purpose As humans, we are constantly exposed to ionizing radiation from natural, man-made and cosmic sources which can damage DNA, leading to deleterious effects including cancer incidence. In this work we introduce a method to monitor strand breaks resulting from damage due to the direct effect of ionizing radiation and provide evidence for sequence-dependent effects leading to strand breaks. Materials and methods To analyze only DNA strand breaks caused by radiation damage due to the direct effect of ionizing radiation, we combined an established technique to generate dehydrated DNA samples with a technique to analyze single strand breaks on short oligonucleotide sequences via denaturing gel electrophoresis. Results We find that direct damage primarily results in a reduced number of strand breaks in guanine triplet regions (GGG) when compared to isolated guanine (G) bases with identical flanking base context. In addition, we observe strand break behavior possibly indicative of protection of guanine bases when flanked by pyrimidines, and sensitization of guanine to strand break when flanked by adenine (A) bases in both isolated G and GGG cases. Conclusions These observations provide insight into the strand break behavior in GGG regions damaged via the direct effect of ionizing radiation. In addition, this could be indicative of DNA sequences that are naturally more susceptible to strand break due to the direct effect of ionizing radiation. PMID:27349757
Method for introducing unidirectional nested deletions

DOEpatents

Dunn, John J.; Quesada, Mark A.; Randesi, Matthew

1999-07-27

Disclosed is a method for the introduction of unidirectional deletions in a cloned DNA segment. More specifically, the method comprises providing a recombinant DNA construct comprising a DNA segment of interest inserted in a cloning vector, the cloning vector having an f1 endonuclease recognition sequence adjacent to the insertion site of the DNA segment of interest. The recombinant DNA construct is then contacted with the protein pII encoded by gene II of phage f1 thereby generating a single-stranded nick. The nicked DNA is then contacted with E. coli Exonuclease III thereby expanding the single-stranded nick into a single-stranded gap. The single-stranded gapped DNA is then contacted with a single-strand-specific endonuclease thereby producing a linearized DNA molecule containing a double-stranded deletion corresponding in size to the single-stranded gap. The DNA treated in this manner is then incubated with DNA ligase under conditions appropriate for ligation. Also disclosed is a method for producing single-stranded DNA probes. In this embodiment, single-stranded gapped DNA, produced as described above, is contacted with a DNA polymerase in the presence of labeled nucleotides to fill in the gap. This DNA is then linearized by digestion with a restriction enzyme which cuts outside the DNA segment of interest. The product of this digestion is then denatured to produce a labeled single-stranded nucleic acid probe.
Translocation of double strand DNA into a biological nanopore

NASA Astrophysics Data System (ADS)

Chatkaew, Sunita; Mlayeh, Lamia; Leonetti, Marc; Homble, Fabrice

2009-03-01

Translocation of double strand DNA across a unique mitochondrial biological nanopore (VDAC) is observed by an electrophysiological method. Characteristics of opened and sub-conductance states of VDAC are studied. When the applied electric potential is beyond ± 20 mV, VDAC transits to a sub-conductance state. Plasmids (circular double strand DNA) with a diameter greater than that of the channel shows the current reduction into the channel during the interaction but the state with zero-current is not observed. On the contrary, the interaction of linear double strand DNA with the channel shows the current reduction along with the zero-current state. These show the passages of linear double strand DNA across the channel and the electrostatic effect due to the surface charges of double strand DNA and channel for circular and linear double strand DNA.
Stable loop in the crystal structure of the intercalated four-stranded cytosine-rich metazoan telomere

NASA Technical Reports Server (NTRS)

Kang, C.; Berger, I.; Lockshin, C.; Ratliff, R.; Moyzis, R.; Rich, A.

1995-01-01

In most metazoans, the telomeric cytosine-rich strand repeating sequence is d(TAACCC). The crystal structure of this sequence was solved to 1.9-A resolution. Four strands associate via the cytosine-containing parts to form a four-stranded intercalated structure held together by C.C+ hydrogen bonds. The base-paired strands are parallel to each other, and the two duplexes are intercalated into each other in opposite orientations. One TAA end forms a highly stabilized loop with the 5' thymine Hoogsteen-base-paired to the third adenine. The 5' end of this loop is in close proximity to the 3' end of one of the other intercalated cytosine strands. Instead of being entirely in a DNA duplex, this structure suggests the possibility of an alternative conformation for the cytosine-rich telomere strands.
Inter-strand current sharing and ac loss measurements in superconducting YBCO Roebel cables

DOE PAGES

Majoros, M.; Sumption, M. D.; Collings, E. W.; ...

2015-04-08

A Roebel cable, one twist pitch long, was modified from its as-received state by soldering copper strips between the strands to provide inter-strand connections enabling current sharing. Various DC transport currents (representing different percentages of its critical current) were applied to a single strand of such a modified cable at 77 K in a liquid nitrogen bath. Simultaneous monitoring of I–V curves in different parts of the strand as well as in its interconnections with other strands was made using a number of sensitive Keithley nanovoltmeters in combination with a multichannel high-speed data acquisition card, all controlled via LabView software.more » Current sharing onset was observed at about 1.02 of strand I c. At a strand current of 1.3I c about 5% of the current was shared through the copper strip interconnections. A finite element method modeling was performed to estimate the inter-strand resistivities required to enable different levels of current sharing. The relative contributions of coupling and hysteretic magnetization (and loss) were compared, and for our cable and tape geometry, and at dB/dt=1 T s -1, and our inter-strand resistance of 0.77 mΩ, (enabling a current sharing of 5% at 1.3I c) the coupling component was 0.32% of the hysteretic component. However, inter-strand contact resistance values of 100–1000 times smaller (close to those of NbTi and Nb 3Sn based accelerator cables) would make the coupling components comparable in size to the hysteretic components.« less
Inter-strand current sharing and ac loss measurements in superconducting YBCO Roebel cables

DOE PAGES

sumption, Mike; Majoros, Milan; Collings, E. W.; ...

2014-11-07

A Roebel cable, one twist pitch long, was modified from its as-received state by soldering copper strips between the strands to provide inter-strand connections enabling current sharing. Various DC transport currents (representing different percentages of its critical current) were applied to a single strand of such a modified cable at 77 K in a liquid nitrogen bath. Simultaneous monitoring of I–V curves in different parts of the strand as well as in its interconnections with other strands was made using a number of sensitive Keithley nanovoltmeters in combination with a multichannel high-speed data acquisition card, all controlled via LabView software.more » Current sharing onset was observed at about 1.02 of strand I c. At a strand current of 1.3I c about 5% of the current was shared through the copper strip interconnections. A finite element method modeling was performed to estimate the inter-strand resistivities required to enable different levels of current sharing. The relative contributions of coupling and hysteretic magnetization (and loss) were compared, and for our cable and tape geometry, and at dB/dt=1 T s -1, and our inter-strand resistance of 0.77 mΩ, (enabling a current sharing of 5% at 1.3I c ) the coupling component was 0.32% of the hysteretic component. However, inter-strand contact resistance values of 100–1000 times smaller (close to those of NbTi and Nb 3Sn based accelerator cables) would make the coupling components comparable in size to the hysteretic components.« less
Inter-strand current sharing and ac loss measurements in superconducting YBCO Roebel cables

DOE Office of Scientific and Technical Information (OSTI.GOV)

Majoros, M.; Sumption, M. D.; Collings, E. W.

A Roebel cable, one twist pitch long, was modified from its as-received state by soldering copper strips between the strands to provide inter-strand connections enabling current sharing. Various DC transport currents (representing different percentages of its critical current) were applied to a single strand of such a modified cable at 77 K in a liquid nitrogen bath. Simultaneous monitoring of I–V curves in different parts of the strand as well as in its interconnections with other strands was made using a number of sensitive Keithley nanovoltmeters in combination with a multichannel high-speed data acquisition card, all controlled via LabView software.more » Current sharing onset was observed at about 1.02 of strand I c. At a strand current of 1.3I c about 5% of the current was shared through the copper strip interconnections. A finite element method modeling was performed to estimate the inter-strand resistivities required to enable different levels of current sharing. The relative contributions of coupling and hysteretic magnetization (and loss) were compared, and for our cable and tape geometry, and at dB/dt=1 T s -1, and our inter-strand resistance of 0.77 mΩ, (enabling a current sharing of 5% at 1.3I c) the coupling component was 0.32% of the hysteretic component. However, inter-strand contact resistance values of 100–1000 times smaller (close to those of NbTi and Nb 3Sn based accelerator cables) would make the coupling components comparable in size to the hysteretic components.« less
Inter-strand current sharing and ac loss measurements in superconducting YBCO Roebel cables

DOE Office of Scientific and Technical Information (OSTI.GOV)

sumption, Mike; Majoros, Milan; Collings, E. W.

A Roebel cable, one twist pitch long, was modified from its as-received state by soldering copper strips between the strands to provide inter-strand connections enabling current sharing. Various DC transport currents (representing different percentages of its critical current) were applied to a single strand of such a modified cable at 77 K in a liquid nitrogen bath. Simultaneous monitoring of I–V curves in different parts of the strand as well as in its interconnections with other strands was made using a number of sensitive Keithley nanovoltmeters in combination with a multichannel high-speed data acquisition card, all controlled via LabView software.more » Current sharing onset was observed at about 1.02 of strand I c. At a strand current of 1.3I c about 5% of the current was shared through the copper strip interconnections. A finite element method modeling was performed to estimate the inter-strand resistivities required to enable different levels of current sharing. The relative contributions of coupling and hysteretic magnetization (and loss) were compared, and for our cable and tape geometry, and at dB/dt=1 T s -1, and our inter-strand resistance of 0.77 mΩ, (enabling a current sharing of 5% at 1.3I c ) the coupling component was 0.32% of the hysteretic component. However, inter-strand contact resistance values of 100–1000 times smaller (close to those of NbTi and Nb 3Sn based accelerator cables) would make the coupling components comparable in size to the hysteretic components.« less
Quality control mechanisms exclude incorrect polymerases from the eukaryotic replication fork

PubMed Central

Schauer, Grant D.; O’Donnell, Michael E.

2017-01-01

The eukaryotic genome is primarily replicated by two DNA polymerases, Pol ε and Pol δ, that function on the leading and lagging strands, respectively. Previous studies have established recruitment mechanisms whereby Cdc45-Mcm2-7-GINS (CMG) helicase binds Pol ε and tethers it to the leading strand, and PCNA (proliferating cell nuclear antigen) binds tightly to Pol δ and recruits it to the lagging strand. The current report identifies quality control mechanisms that exclude the improper polymerase from a particular strand. We find that the replication factor C (RFC) clamp loader specifically inhibits Pol ε on the lagging strand, and CMG protects Pol ε against RFC inhibition on the leading strand. Previous studies show that Pol δ is slow and distributive with CMG on the leading strand. However, Saccharomyces cerevisiae Pol δ–PCNA is a rapid and processive enzyme, suggesting that CMG may bind and alter Pol δ activity or position it on the lagging strand. Measurements of polymerase binding to CMG demonstrate Pol ε binds CMG with a Kd value of 12 nM, but Pol δ binding CMG is undetectable. Pol δ, like bacterial replicases, undergoes collision release upon completing replication, and we propose Pol δ–PCNA collides with the slower CMG, and in the absence of a stabilizing Pol δ–CMG interaction, the collision release process is triggered, ejecting Pol δ on the leading strand. Hence, by eviction of incorrect polymerases at the fork, the clamp machinery directs quality control on the lagging strand and CMG enforces quality control on the leading strand. PMID:28069954
CMG helicase and DNA polymerase ε form a functional 15-subunit holoenzyme for eukaryotic leading-strand DNA replication.

PubMed

Langston, Lance D; Zhang, Dan; Yurieva, Olga; Georgescu, Roxana E; Finkelstein, Jeff; Yao, Nina Y; Indiani, Chiara; O'Donnell, Mike E

2014-10-28

DNA replication in eukaryotes is asymmetric, with separate DNA polymerases (Pol) dedicated to bulk synthesis of the leading and lagging strands. Pol α/primase initiates primers on both strands that are extended by Pol ε on the leading strand and by Pol δ on the lagging strand. The CMG (Cdc45-MCM-GINS) helicase surrounds the leading strand and is proposed to recruit Pol ε for leading-strand synthesis, but to date a direct interaction between CMG and Pol ε has not been demonstrated. While purifying CMG helicase overexpressed in yeast, we detected a functional complex between CMG and native Pol ε. Using pure CMG and Pol ε, we reconstituted a stable 15-subunit CMG-Pol ε complex and showed that it is a functional polymerase-helicase on a model replication fork in vitro. On its own, the Pol2 catalytic subunit of Pol ε is inefficient in CMG-dependent replication, but addition of the Dpb2 protein subunit of Pol ε, known to bind the Psf1 protein subunit of CMG, allows stable synthesis with CMG. Dpb2 does not affect Pol δ function with CMG, and thus we propose that the connection between Dpb2 and CMG helps to stabilize Pol ε on the leading strand as part of a 15-subunit leading-strand holoenzyme we refer to as CMGE. Direct binding between Pol ε and CMG provides an explanation for specific targeting of Pol ε to the leading strand and provides clear mechanistic evidence for how strand asymmetry is maintained in eukaryotes.
CMG helicase and DNA polymerase ε form a functional 15-subunit holoenzyme for eukaryotic leading-strand DNA replication

PubMed Central

Langston, Lance D.; Zhang, Dan; Yurieva, Olga; Georgescu, Roxana E.; Finkelstein, Jeff; Yao, Nina Y.; Indiani, Chiara; O’Donnell, Mike E.

2014-01-01

DNA replication in eukaryotes is asymmetric, with separate DNA polymerases (Pol) dedicated to bulk synthesis of the leading and lagging strands. Pol α/primase initiates primers on both strands that are extended by Pol ε on the leading strand and by Pol δ on the lagging strand. The CMG (Cdc45-MCM-GINS) helicase surrounds the leading strand and is proposed to recruit Pol ε for leading-strand synthesis, but to date a direct interaction between CMG and Pol ε has not been demonstrated. While purifying CMG helicase overexpressed in yeast, we detected a functional complex between CMG and native Pol ε. Using pure CMG and Pol ε, we reconstituted a stable 15-subunit CMG–Pol ε complex and showed that it is a functional polymerase–helicase on a model replication fork in vitro. On its own, the Pol2 catalytic subunit of Pol ε is inefficient in CMG-dependent replication, but addition of the Dpb2 protein subunit of Pol ε, known to bind the Psf1 protein subunit of CMG, allows stable synthesis with CMG. Dpb2 does not affect Pol δ function with CMG, and thus we propose that the connection between Dpb2 and CMG helps to stabilize Pol ε on the leading strand as part of a 15-subunit leading-strand holoenzyme we refer to as CMGE. Direct binding between Pol ε and CMG provides an explanation for specific targeting of Pol ε to the leading strand and provides clear mechanistic evidence for how strand asymmetry is maintained in eukaryotes. PMID:25313033
Assembly and structural analysis of a covalently closed nano-scale DNA cage

PubMed Central

Andersen, Felicie F.; Knudsen, Bjarne; Oliveira, Cristiano Luis Pinto; Frøhlich, Rikke F.; Krüger, Dinna; Bungert, Jörg; Agbandje-McKenna, Mavis; McKenna, Robert; Juul, Sissel; Veigaard, Christopher; Koch, Jørn; Rubinstein, John L.; Guldbrandtsen, Bernt; Hede, Marianne S.; Karlsson, Göran; Andersen, Anni H.; Pedersen, Jan Skov; Knudsen, Birgitta R.

2008-01-01

The inherent properties of DNA as a stable polymer with unique affinity for partner molecules determined by the specific Watson–Crick base pairing makes it an ideal component in self-assembling structures. This has been exploited for decades in the design of a variety of artificial substrates for investigations of DNA-interacting enzymes. More recently, strategies for synthesis of more complex two-dimensional (2D) and 3D DNA structures have emerged. However, the building of such structures is still in progress and more experiences from different research groups and different fields of expertise are necessary before complex DNA structures can be routinely designed for the use in basal science and/or biotechnology. Here we present the design, construction and structural analysis of a covalently closed and stable 3D DNA structure with the connectivity of an octahedron, as defined by the double-stranded DNA helices that assembles from eight oligonucleotides with a yield of ∼30%. As demonstrated by Small Angle X-ray Scattering and cryo-Transmission Electron Microscopy analyses the eight-stranded DNA structure has a central cavity larger than the apertures in the surrounding DNA lattice and can be described as a nano-scale DNA cage, Hence, in theory it could hold proteins or other bio-molecules to enable their investigation in certain harmful environments or even allow their organization into higher order structures. PMID:18096620
The diversity of the human hair colour assessed by visual scales and instrumental measurements. A worldwide survey.

PubMed

Lozano, I; Saunier, J B; Panhard, S; Loussouarn, G

2017-02-01

To study (i) the diversity of the natural colour of the human hair through both visual assessment of hair tone levels and colorimetric measurements of hair strands collected from 2057 human male and female volunteers, from 23 regions of the world and (ii) the correlation between visual assessments and colorimetric measurements. Hair strands were analysed by a spectrocolorimeter under the L*, a*, b* referential system and scored in vivo by experts before sampling, through standardized visual reference scales based on a 1-10 range. Results show that from a typological aspect, black or dark brown hairs largely predominate among studied ethnic groups, whereas Caucasian or derived populations exhibit the widest palette of medium to fair shades, partly explaining some past interbreeding among populations. Instrumental measurements clearly confirm that a given colour of a pigmented hair, at the exclusion of red hairs, is mostly governed by two components, L* and b*, from the L*, a*, b* reference system. The comparisons between visual assessments and instrumental data show that these appear closely linked. Darker hairs show close or subtle variations in L*, a*, b* parameters, making their individual colour differentiation calling for technical improvements in colorimetric measurements. The latter are likely governed by other physical factors such as shape, diameter and shine. © 2016 Society of Cosmetic Scientists and the Société Française de Cosmétologie.
An autonomous molecular computer for logical control of gene expression

PubMed Central

Benenson, Yaakov; Gil, Binyamin; Ben-Dor, Uri; Adar, Rivka; Shapiro, Ehud

2013-01-01

Early biomolecular computer research focused on laboratory-scale, human-operated computers for complex computational problems1–7. Recently, simple molecular-scale autonomous programmable computers were demonstrated8–15 allowing both input and output information to be in molecular form. Such computers, using biological molecules as input data and biologically active molecules as outputs, could produce a system for ‘logical’ control of biological processes. Here we describe an autonomous biomolecular computer that, at least in vitro, logically analyses the levels of messenger RNA species, and in response produces a molecule capable of affecting levels of gene expression. The computer operates at a concentration of close to a trillion computers per microlitre and consists of three programmable modules: a computation module, that is, a stochastic molecular automaton12–17; an input module, by which specific mRNA levels or point mutations regulate software molecule concentrations, and hence automaton transition probabilities; and an output module, capable of controlled release of a short single-stranded DNA molecule. This approach might be applied in vivo to biochemical sensing, genetic engineering and even medical diagnosis and treatment. As a proof of principle we programmed the computer to identify and analyse mRNA of disease-related genes18–22 associated with models of small-cell lung cancer and prostate cancer, and to produce a single-stranded DNA molecule modelled after an anticancer drug. PMID:15116117
English Language Arts Curriculum Guide, Intermediate Elementary Level: Grade 4.

ERIC Educational Resources Information Center

Saporito, Leo C., Ed.; And Others

Prepared for use in grade four, this language arts curriculum guide bases its reading strand on "Roads to Everywhere" (Ginn 100), the English strand on "Roberts English Series" (Harcourt), the spelling strand on "Sound and Sense in Spelling" (Harcourt), and the handwriting strand on "Better Handwriting for…
77 FR 2958 - Prestressed Concrete Steel Wire Strand From Thailand: Correction to Notice of Opportunity To...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-01-20

... DEPARTMENT OF COMMERCE International Trade Administration [A-549-820] Prestressed Concrete Steel Wire Strand From Thailand: Correction to Notice of Opportunity To Request Administrative Review AGENCY... prestressed concrete steel wire strand (``PC Strand'') from Thailand. See Antidumping or Countervailing Duty...

75 FR 4104 - Prestressed Concrete Steel Wire Strand From China

Federal Register 2010, 2011, 2012, 2013, 2014

2010-01-26

... Concrete Steel Wire Strand From China AGENCY: United States International Trade Commission. ACTION... wire strand, provided for in subheading 7312.10.30 of the Harmonized Tariff Schedule of the United... merchandise as PC strand, produced from wire of nonstainless, non-galvanized steel, which is suitable for use...
Yeast Pif1 Accelerates Annealing of Complementary DNA Strands

PubMed Central

2015-01-01

Pif1 is a helicase involved in the maintenance of nuclear and mitochondrial genomes in eukaryotes. Here we report a new activity of Saccharomyces cerevisiae Pif1, annealing of complementary DNA strands. We identified preferred substrates for annealing as those that generate a duplex product with a single-stranded overhang relative to a blunt end duplex. Importantly, we show that Pif1 can anneal DNA in the presence of ATP and Mg2+. Pif1-mediated annealing also occurs in the presence of single-stranded DNA binding proteins. Additionally, we show that partial duplex substrates with 3′-single-stranded overhangs such as those generated during double-strand break repair can be annealed by Pif1. PMID:25393406
Yeast Pif1 accelerates annealing of complementary DNA strands.

PubMed

Ramanagoudr-Bhojappa, Ramanagouda; Byrd, Alicia K; Dahl, Christopher; Raney, Kevin D

2014-12-09

Pif1 is a helicase involved in the maintenance of nuclear and mitochondrial genomes in eukaryotes. Here we report a new activity of Saccharomyces cerevisiae Pif1, annealing of complementary DNA strands. We identified preferred substrates for annealing as those that generate a duplex product with a single-stranded overhang relative to a blunt end duplex. Importantly, we show that Pif1 can anneal DNA in the presence of ATP and Mg(2+). Pif1-mediated annealing also occurs in the presence of single-stranded DNA binding proteins. Additionally, we show that partial duplex substrates with 3'-single-stranded overhangs such as those generated during double-strand break repair can be annealed by Pif1.
Mechanism for accurate, protein-assisted DNA annealing by Deinococcus radiodurans DdrB

PubMed Central

Sugiman-Marangos, Seiji N.; Weiss, Yoni M.; Junop, Murray S.

2016-01-01

Accurate pairing of DNA strands is essential for repair of DNA double-strand breaks (DSBs). How cells achieve accurate annealing when large regions of single-strand DNA are unpaired has remained unclear despite many efforts focused on understanding proteins, which mediate this process. Here we report the crystal structure of a single-strand annealing protein [DdrB (DNA damage response B)] in complex with a partially annealed DNA intermediate to 2.2 Å. This structure and supporting biochemical data reveal a mechanism for accurate annealing involving DdrB-mediated proofreading of strand complementarity. DdrB promotes high-fidelity annealing by constraining specific bases from unauthorized association and only releases annealed duplex when bound strands are fully complementary. To our knowledge, this mechanism provides the first understanding for how cells achieve accurate, protein-assisted strand annealing under biological conditions that would otherwise favor misannealing. PMID:27044084
75 FR 36678 - Prestressed Concrete Steel Wire Strand From China; Determinations

Federal Register 2010, 2011, 2012, 2013, 2014

2010-06-28

... Concrete Steel Wire Strand From China; Determinations On the basis of the record \\1\\ developed in the... prestressed concrete steel wire strand (PC strand), provided for in subheading 7312.10.30 of the Harmonized... Spring Wire Corp. (Bedford Heights, OH); Insteel Wire Products Co. (Mt. Airy, NC); and Sumiden Wire...
The Parameter of Preposition Stranding: A View from Child English

ERIC Educational Resources Information Center

Sugisaki, Koji; Snyder, William

2006-01-01

In this squib we examine the time course of children's acquisition of English to evaluate the basic insights of Kayne's (1981; 1984) proposals on preposition stranding. Kayne argued that the availability of preposition stranding (P-stranding) in English is parametrically linked to the availability of double object datives and the prepositional…
Probe and method for DNA detection

DOEpatents

Yeh, Hsin-Chih; Werner, James Henry; Sharma, Jaswinder Kumar; Martinez, Jennifer Suzanne

2013-07-02

A hybridization probe containing two linear strands of DNA lights up upon hybridization to a target DNA using silver nanoclusters that have been templated onto one of the DNA strands. Hybridization induces proximity between the nanoclusters on one strand and an overhang on the other strand, which results in enhanced fluorescence emission from the nanoclusters.
7 CFR 1755.370 - RUS specification for seven wire galvanized steel strand.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 7 Agriculture 11 2012-01-01 2012-01-01 false RUS specification for seven wire galvanized steel... steel strand. (a) RUS incorporates by reference ASTM A475-78, Standard Specification for Zinc-Coated Steel Wire Strand, issued May 1978. All seven wire galvanized steel strand purchased after April 1, 1990...
7 CFR 1755.370 - RUS specification for seven wire galvanized steel strand.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 7 Agriculture 11 2014-01-01 2014-01-01 false RUS specification for seven wire galvanized steel... steel strand. (a) RUS incorporates by reference ASTM A475-78, Standard Specification for Zinc-Coated Steel Wire Strand, issued May 1978. All seven wire galvanized steel strand purchased after April 1, 1990...
7 CFR 1755.370 - RUS specification for seven wire galvanized steel strand.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 7 Agriculture 11 2013-01-01 2013-01-01 false RUS specification for seven wire galvanized steel... steel strand. (a) RUS incorporates by reference ASTM A475-78, Standard Specification for Zinc-Coated Steel Wire Strand, issued May 1978. All seven wire galvanized steel strand purchased after April 1, 1990...
Action of CMG with strand-specific DNA blocks supports an internal unwinding mode for the eukaryotic replicative helicase

PubMed Central

Langston, Lance; O’Donnell, Mike

2017-01-01

Replicative helicases are ring-shaped hexamers that encircle DNA for duplex unwinding. The currently accepted view of hexameric helicase function is by steric exclusion, where the helicase encircles one DNA strand and excludes the other, acting as a wedge with an external DNA unwinding point during translocation. Accordingly, strand-specific blocks only affect these helicases when placed on the tracking strand, not the excluded strand. We examined the effect of blocks on the eukaryotic CMG and, contrary to expectations, blocks on either strand inhibit CMG unwinding. A recent cryoEM structure of yeast CMG shows that duplex DNA enters the helicase and unwinding occurs in the central channel. The results of this report inform important aspects of the structure, and we propose that CMG functions by a modified steric exclusion process in which both strands enter the helicase and the duplex unwinding point is internal, followed by exclusion of the non-tracking strand. DOI: http://dx.doi.org/10.7554/eLife.23449.001 PMID:28346143
Improved silencing properties using small internally segmented interfering RNAs

PubMed Central

Bramsen, Jesper B.; Laursen, Maria B.; Damgaard, Christian K.; Lena, Suzy W.; Ravindra Babu, B.; Wengel, Jesper; Kjems, Jørgen

2007-01-01

RNA interference is mediated by small interfering RNAs (siRNAs) that upon incorporation into the RNA-induced silencing complex (RISC) can target complementary mRNA for degradation. Standard siRNA design usually feature a 19–27 base pair contiguous double-stranded region that is believed to be important for RISC incorporation. Here, we describe a novel siRNA design composed of an intact antisense strand complemented with two shorter 10–12 nt sense strands. This three-stranded construct, termed small internally segmented interfering RNA (sisiRNA), is highly functional demonstrating that an intact sense strand is not a prerequisite for RNA interference. Moreover, when using the sisiRNA design only the antisense strand is functional in activated RISC thereby completely eliminating unintended mRNA targeting by the sense strand. Interestingly, the sisiRNA design supports the function of chemically modified antisense strands, which are non-functional within the context of standard siRNA designs. This suggests that the sisiRNA design has a clear potential of improving the pharmacokinetic properties of siRNA in vivo. PMID:17726057
Fundamental Design based on Current Distribution in Coaxial Multi-Layer Cable-in-Conduit Conductor

NASA Astrophysics Data System (ADS)

Hamajima, Takataro; Tsuda, Makoto; Yagai, Tsuyoshi; Takahata, Kazuya; Imagawa, Shinsaku

An imbalanced current distribution is often observed in cable-in-conduit (CIC) superconductors which are composed of multi-staged, triplet type sub-cables, and hence deteriorates the performance of the coils. Therefore, since it is very important to obtain a homogeneous current distribution in the superconducting strands, we propose a coaxial multi-layer type CIC conductor. We use a circuit model for all layers in the coaxial multi-layer CIC conductor, and derive a generalized formula governing the current distribution as explicit functions of the superconductor construction parameters, such as twist pitch, twist direction, radius of each layer, and number of superconducting (SC) strands and copper (Cu) strands. We apply the formula to design the coaxial multi-layer CIC which has the same number of SC strands and Cu strands of the CIC for Central Solenoid of ITER. We can design three kinds of the coaxial multi-layer CIC depending on distribution of SC and Cu strands on all layers. It is shown that the SC strand volume should be optimized as a function of SC and Cu strand distribution on the layers.
Sub-Ensemble Monitoring of DNA Strand Displacement Using Multiparameter Single-Molecule FRET.

PubMed

Baltierra-Jasso, Laura E; Morten, Michael J; Magennis, Steven W

2018-03-05

Non-enzymatic DNA strand displacement is an important mechanism in dynamic DNA nanotechnology. Here, we show that the large parameter space that is accessible by single-molecule FRET is ideal for the simultaneous monitoring of multiple reactants and products of DNA strand exchange reactions. We monitored the strand displacement from double-stranded DNA (dsDNA) by single-stranded DNA (ssDNA) at 37 °C; the data were modelled as a second-order reaction approaching equilibrium, with a rate constant of 10 m -1 s -1 . We also followed the displacement from a DNA three-way junction (3WJ) by ssDNA. The presence of three internal mismatched bases in the middle of the invading strand did not prevent displacement from the 3WJ, but reduced the second-order rate constant by about 50 %. We attribute strand exchange in the dsDNA and 3WJ to a zero-toehold pathway from the blunt-ended duplex arms. The single-molecule approach demonstrated here will be useful for studying complex DNA networks. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.
Variation of mutational burden in healthy human tissues suggests non-random strand segregation and allows measuring somatic mutation rates.

PubMed

Werner, Benjamin; Sottoriva, Andrea

2018-06-01

The immortal strand hypothesis poses that stem cells could produce differentiated progeny while conserving the original template strand, thus avoiding accumulating somatic mutations. However, quantitating the extent of non-random DNA strand segregation in human stem cells remains difficult in vivo. Here we show that the change of the mean and variance of the mutational burden with age in healthy human tissues allows estimating strand segregation probabilities and somatic mutation rates. We analysed deep sequencing data from healthy human colon, small intestine, liver, skin and brain. We found highly effective non-random DNA strand segregation in all adult tissues (mean strand segregation probability: 0.98, standard error bounds (0.97,0.99)). In contrast, non-random strand segregation efficiency is reduced to 0.87 (0.78,0.88) in neural tissue during early development, suggesting stem cell pool expansions due to symmetric self-renewal. Healthy somatic mutation rates differed across tissue types, ranging from 3.5 × 10-9/bp/division in small intestine to 1.6 × 10-7/bp/division in skin.
Linear nicking endonuclease-mediated strand-displacement DNA amplification.

PubMed

Joneja, Aric; Huang, Xiaohua

2011-07-01

We describe a method for linear isothermal DNA amplification using nicking endonuclease-mediated strand displacement by a DNA polymerase. The nicking of one strand of a DNA target by the endonuclease produces a primer for the polymerase to initiate synthesis. As the polymerization proceeds, the downstream strand is displaced into a single-stranded form while the nicking site is also regenerated. The combined continuous repetitive action of nicking by the endonuclease and strand-displacement synthesis by the polymerase results in linear amplification of one strand of the DNA molecule. We demonstrate that DNA templates up to 5000 nucleotides can be linearly amplified using a nicking endonuclease with 7-bp recognition sequence and Sequenase version 2.0 in the presence of single-stranded DNA binding proteins. We also show that a mixture of three templates of 500, 1000, and 5000 nucleotides in length is linearly amplified with the original molar ratios of the templates preserved. Moreover, we demonstrate that a complex library of hydrodynamically sheared genomic DNA from bacteriophage lambda can be amplified linearly. Copyright © 2011 Elsevier Inc. All rights reserved.
Linear nicking endonuclease-mediated strand displacement DNA amplification

PubMed Central

Joneja, Aric; Huang, Xiaohua

2011-01-01

We describe a method for linear isothermal DNA amplification using nicking endonuclease-mediated strand displacement by a DNA polymerase. The nicking of one strand of a DNA target by the endonuclease produces a primer for the polymerase to initiate synthesis. As the polymerization proceeds, the downstream strand is displaced into a single-stranded form while the nicking site is also regenerated. The combined continuous repetitive action of nicking by the endonuclease and strand displacement synthesis by the polymerase results in linear amplification of one strand of the DNA molecule. We demonstrate that DNA templates up to five thousand nucleotides can be linearly amplified using a nicking endonuclease with seven base-pair recognition sequence and Sequenase version 2.0 in the presence of single-stranded DNA binding proteins. We also show that a mixture of three templates of 500, 1000, and 5000 nucleotides in length are linearly amplified with the original molar ratios of the templates preserved. Moreover, we demonstrate that a complex library of hydrodynamically sheared genomic DNA from bacteriophage lambda can be amplified linearly. PMID:21342654
Interstrand cross-links arising from strand breaks at true abasic sites in duplex DNA

PubMed Central

Yang, Zhiyu; Price, Nathan E.; Johnson, Kevin M.

2017-01-01

Abstract Interstrand cross-links are exceptionally bioactive DNA lesions. Endogenous generation of interstrand cross-links in genomic DNA may contribute to aging, neurodegeneration, and cancer. Abasic (Ap) sites are common lesions in genomic DNA that readily undergo spontaneous and amine-catalyzed strand cleavage reactions that generate a 2,3-didehydro-2,3-dideoxyribose sugar remnant (3’ddR5p) at the 3’-terminus of the strand break. Interestingly, this strand scission process leaves an electrophilic α,β-unsaturated aldehyde residue embedded within the resulting nicked duplex. Here we present evidence that 3’ddR5p derivatives generated by spermine-catalyzed strand cleavage at Ap sites in duplex DNA can react with adenine residues on the opposing strand to generate a complex lesion consisting of an interstrand cross-link adjacent to a strand break. The cross-link blocks DNA replication by ϕ29 DNA polymerase, a highly processive polymerase enzyme that couples synthesis with strand displacement. This suggests that 3’ddR5p-derived cross-links have the potential to block critical cellular DNA transactions that require strand separation. LC-MS/MS methods developed herein provide powerful tools for studying the occurrence and properties of these cross-links in biochemical and biological systems. PMID:28531327
The economics of stranded investment - a two-way street

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cearley, R.; McKinzie, L.

In the transition to deregulation, the risk, costs and benefits of utility assets are transferred from the customer to the investor, creating potential stranded benefits as well as stranded costs. Investors may be better or worse off depending on whether an asset`s cost is below or above market. Regulators can minimize unintended wealth transfers by compensating each potential loser in the transition. The amount of investment stranded - i.e., the portion of plant that is above market value - does seem to be a murky issue. This article sets a framework for evaluating stranded investment and traces the possible welfaremore » effects of different policies to address it. It defines {open_quote}stranded costs,{close_quote} {open_quote}stranded investment,{close_quote} and {open_quote}stranded benefits.{close_quote} It addresses their interrelationship, and shows that the redefinition of property rights during the transition to a competitive market is what leads to stranded investment. The elimination of the utility`s exclusive franchise - i.e., its obligation to serve and customers` obligation to pay - leads to the redefinition of those property rights as they pertain to the costs, benefits and risks associated with existing utility generation. Finally, the authors address the possible welfare implications from this transition.« less
Repairing the sickle cell mutation. I. Specific covalent binding of a photoreactive third strand to the mutated base pair.

PubMed

Broitman, S; Amosova, O; Dolinnaya, N G; Fresco, J R

1999-07-30

A DNA third strand with a 3'-psoralen substituent was designed to form a triplex with the sequence downstream of the T.A mutant base pair of the human sickle cell beta-globin gene. Triplex-mediated psoralen modification of the mutant T residue was sought as an approach to gene repair. The 24-nucleotide purine-rich target sequence switches from one strand to the other and has four pyrimidine interruptions. Therefore, a third strand sequence favorable to two triplex motifs was used, one parallel and the other antiparallel to it. To cope with the pyrimidine interruptions, which weaken third strand binding, 5-methylcytosine and 5-propynyluracil were used in the third strand. Further, a six residue "hook" complementary to an overhang of a linear duplex target was added to the 5'-end of the third strand via a T(4) linker. In binding to the overhang by Watson-Crick pairing, the hook facilitates triplex formation. This third strand also binds specifically to the target within a supercoiled plasmid. The psoralen moiety at the 3'-end of the third strand forms photoadducts to the targeted T with high efficiency. Such monoadducts are known to preferentially trigger reversion of the mutation by DNA repair enzymes.

Xeroderma pigmentosum complementation group C cells remove pyrimidine dimers selectively from the transcribed strand of active genes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Venema, J.; van Hoffen, A.; Karcagi, V.

1991-08-01

The authors have measured the removal of UV-induced pyrimidine dimers from DNA fragments of the adenosine deaminase (ADA) and dihydrofolate reductase (DHFR) genes in primary normal human and xeroderma pigmentosum complementation group C (XP-C) cells. Using strand-specific probes, we show that in normal cells, preferential repair of the 5{prime} part of the ADA gene is due to the rapid and efficient repair of the transcribed strand. Within 8 h after irradiation with UV at 10 J m-2, 70% of the pyrimidine dimers in this strand are removed. The nontranscribed strand is repaired at a much slower rate, with 30% dimersmore » removed after 8 h. Repair of the transcribed strand in XP-C cells occurs at a rate indistinguishable from that in normal cells, but the nontranscribed strand is not repaired significantly in these cells. Similar results were obtained for the DHFR gene. In the 3{prime} part of the ADA gene, however, both normal and XP-C cells perform fast and efficient repair of either strand, which is likely to be caused by the presence of transcription units on both strands. The factor defective in XP-C cells is apparently involved in the processing of DNA damage in inactive parts of the genome, including nontranscribed strands of active genes. These findings have important implications for the understanding of the mechanism of UV-induced excision repair and mutagenesis in mammalian cells.« less
NATO Human Resources (Manpower) Management (Gestion des ressources humaines (effectifs) de l’OTAN)

DTIC Science & Technology

2012-02-01

performances , la gestion des récompenses et du salaire, et la motivation du personnel. En conséquence, il faut que la gestion des ressources humaines...importance au fil du temps. Les ressources humaines, chargées à l’origine de l’embauche, du licenciement, de la paie et de la gestion des ...les effets des systèmes d’évaluation des performances ;
Afterrise: Deep Body Temperature Following Exercise

DTIC Science & Technology

1992-03-01

Egalement, les effets de la posture et des v~tements durant la recuperation et la temperature de la salle de recuperation furent examines. Cinq hommes se...chemise a manches courtes). Les temperatures rectales et de la peau furent mesurees A chaque minute durant les exercices et la r~cup~ration affectaient...overgarment. RESUME Cette etude fut entreprise pour documenter l’augmentation continue de la temperature rectale apres exercice dans la chaleur
Impact of Technologies on Learning in the Workplace. Final Report = L'effet des technologies d'apprentissage sur l'apprentissage a vie en milieu de travail.

ERIC Educational Resources Information Center

Dugas, Tim; Green, Lyndsay; Leckie, Norm

The use of learning technologies in the workplace and their impact on lifelong learning were examined. Data were collected from three sources: the literature on learning technologies and labor market trends affecting the adoption, implementation, and success of learning technologies in the workplace; case studies of 8 Canadian firms with 100 or…
Prevention des Toxicomanies Aupres des Filles avec des Problemes de Comportement: Effets a Court Terme (Prevention of Drug Addiction in Girls with Behavior Problems: Short-Term Effects).

ERIC Educational Resources Information Center

Vitaro, Frank; And Others

1992-01-01

This article, written in French, describes and evaluates the first phase of a program to prevent drug addiction among 110 fifth-grade girls with behavior problems in Montreal (Quebec, Canada). Evaluation of the instructional program showed positive results for student knowledge level, attitudes, and behaviors and supported program continuation…
Possibilité d'une nouvelle technologie de traitement des minerais de fer de l'Ouenza par radiométrie

NASA Astrophysics Data System (ADS)

Idres, A.; Bounouala, M.

2005-05-01

En l'absence d'une technologie fiable de traitement des haldes de minerais de fer, les caractéristiques minéralogiques et chimiques complexes et les effets néfastes des résidus miniers posent réellement un problème environnemental. A cet effet, une étude minéralogique et chimique du minerai de fer a été menée en utilisant des techniques multiples (microscopie optique, DRX, FX, MEB). En tenant compte de la nature des résidus, des échantillons représentatifs ont été testés par séparation radiométrique. Plusieurs paramètres ont été caractérisés tels que la vitesse de la bande transporteuse, le temps d'émission des rayons gamma et la granulométrie d'alimentation du procédé. Les résultats ainsi obtenus par cette méthode de séparation sont très significatifs en récupération et en teneur fer. Cependant, cette nouvelle technologie permet d'une part une meilleure valorisation des minerais de fer et d'autre part une réduction du tonnage stocké sur le carreau de la mine.
Effets tardifs d'une irradiation corporelle totale sur le métabolisme intraneuronal de la dopamine et de la sérotonine

NASA Astrophysics Data System (ADS)

Joubert, C.; Jacquet, N.; Lambert, F.; Martin, S.; Martin, C.

1998-04-01

Whole-body irradiation leads to delayed cognitive dysfunction which could result from perturbations of neurotransmission, specially the dopaminergic and the serotoninergic one. The aim of this study was to determine the concentrations of dopamine (DA), serotonin (5-HT) and their metabolites in three cerebral areas of rats, one month after (neutron-gamma) irradiation at 3.38Gy. An increase of DA, 5-HT, and their catabolites was observed. These effects are weak but observed in older rats. Au cours des mois suivant une irradiation corporell totale peuvent se manifester des troubles comportementaux qui pourraient être la conséquence d'altérations de la neuraotransmission, plus particulièrement de la transmission dopaminergique ou sérotoninergique. Nous avons recherché les variations des taux de dopamine (DA), de sérotonine (5-HT) et de leurs métabolites dans 3structures cérébrales 1 mois après une irradiation (neutron-gamma) à la dose de 3,38Gy. Les résultats préliminaires mettent en évidence une augmentation des taux de DA, de 5-HT et de leurs catabolites ; ces effets sont plus discrets mais similaires à ceux observés chez des animaux plus âgés.
Effet d'un champ magnétique uniforme sur les instabilités de Rayleigh-Bénard avec effet Soret

NASA Astrophysics Data System (ADS)

Ben Sassi, Mokhtar; Kaddeche, Slim; Abdennadher, Ali; Henry, Daniel; Hadid, Hamda Ben; Mojtabi, Abdelkader

2016-01-01

The effect of both magnitude and orientation of a uniform magnetic field on the critical transition occurring within an electrically conducting binary fluid layer, stratified in temperature and concentration, taking into account the Soret effect, is investigated numerically. For such a configuration, the results show that the critical thresholds corresponding to an arbitrary orientated magnetic field can be derived from those obtained for a vertical magnetic field and that the axes of the marginal cells are aligned with the horizontal component of the magnetic field. Moreover, an analytical study is conducted to investigate the impact of the magnetic field on long-wavelength instabilities. The effect of the magnetic field on such instabilities reveals a new phenomenon consisting in major changes of the unstable modes that lose their unicellular nature to regain their multi-roll characteristic, as it is the case without magnetic field for ψ <ψℓ0 = 131 Le / (34 - 131 Le). For a binary fluid characterized by a Lewis number Le and a separation factor ψ >ψℓ0, the value of the Hartmann number Haℓ (ψ , Le) corresponding to that transition responsible for a significant change in mass and heat transfer can be determined from the analytical relations derived in this work.
Late Quaternary slip history of the Mill Creek strand of the San Andreas fault in San Gorgonio Pass, southern California: The role of a subsidiary left-lateral fault in strand switching

USGS Publications Warehouse

Kendrick, Katherine J.; Matti, Jonathan; Mahan, Shannon

2015-01-01

The fault history of the Mill Creek strand of the San Andreas fault (SAF) in the San Gorgonio Pass region, along with the reconstructed geomorphology surrounding this fault strand, reveals the important role of the left-lateral Pinto Mountain fault in the regional fault strand switching. The Mill Creek strand has 7.1–8.7 km total slip. Following this displacement, the Pinto Mountain fault offset the Mill Creek strand 1–1.25 km, as SAF slip transferred to the San Bernardino, Banning, and Garnet Hill strands. An alluvial complex within the Mission Creek watershed can be linked to palinspastic reconstruction of drainage segments to constrain slip history of the Mill Creek strand. We investigated surface remnants through detailed geologic mapping, morphometric and stratigraphic analysis, geochronology, and pedogenic analysis. The degree of soil development constrains the duration of surface stability when correlated to other regional, independently dated pedons. This correlation indicates that the oldest surfaces are significantly older than 500 ka. Luminescence dates of 106 ka and 95 ka from (respectively) 5 and 4 m beneath a younger fan surface are consistent with age estimates based on soil-profile development. Offset of the Mill Creek strand by the Pinto Mountain fault suggests a short-term slip rate of ∼10–12.5 mm/yr for the Pinto Mountain fault, and a lower long-term slip rate. Uplift of the Yucaipa Ridge block during the period of Mill Creek strand activity is consistent with thermochronologic modeled uplift estimates.
An ultrasensitive electrochemical biosensor for polynucleotide kinase assay based on gold nanoparticle-mediated lambda exonuclease cleavage-induced signal amplification.

PubMed

Cui, Lin; Li, Yueying; Lu, Mengfei; Tang, Bo; Zhang, Chun-Yang

2018-01-15

Polynucleotide kinase (PNK) plays an essential role in cellular nucleic acid metabolism and the cellular response to DNA damage. However, conventional methods for PNK assay suffer from low sensitivity and involve multiple steps. Herein, we develop a simply electrochemical method for sensitive detection of PNK activity on the basis of Au nanoparticle (AuNP)-mediated lambda exonuclease cleavage-induced signal amplification. We use [Ru(NH 3 ) 6 ] 3+ as the electrochemically active indicator and design two DNA strands (i.e., strand 1 and strand 2) to sense PNK. The assembly of strand 2 on the AuNP surface leads to the formation of AuNP-strand 2 conjugates which can be subsequently immobilized on the gold electrode through the hybridization of strand 1 with strand 2 for the generation of a high electrochemical signal. The presence of PNK induces the phosphorylation of the strand 2-strand 1 hybrid and the subsequent cleavage of double-stranded DNA (dsDNA) by lambda exonuclease, resulting in the release of AuNP-strand 2 conjugates and [Ru(NH 3 ) 6 ] 3+ from the gold electrode surface and consequently the decrease of electrochemical signal. The PNK activity can be simply monitored by the measurement of [Ru(NH 3 ) 6 ] 3+ peak current signal. This assay is very sensitive with a detection limit of as low as 7.762 × 10 -4 UmL -1 and exhibits a large dynamic range from 0.001 to 10UmL -1 . Moreover, this method can be used to screen the PNK inhibitors, and it shows excellent performance in real sample analysis, thus holding great potential for further applications in biological researches and clinic diagnosis. Copyright © 2017 Elsevier B.V. All rights reserved.
Multiphoton near-infrared femtosecond laser pulse-induced DNA damage with and without the photosensitizer proflavine.

PubMed

Shafirovich, V; Dourandin, A; Luneva, N P; Singh, C; Kirigin, F; Geacintov, N E

1999-03-01

The excitation of pBr322 supercoiled plasmid DNA with intense near-IR 810 nm fs laser pulses by a simultaneous multiphoton absorption mechanism results in single-strand breaks after treatment of the irradiated samples with Micrococcus luteus UV endonuclease. This enzyme cleaves DNA strands at sites of cyclobutane dimers that are formed by the simultaneous absorption of three (or more) 810 nm IR photons (pulse width approximately 140 fs, 76 MHz pulse repetition, average power output focused through 10x microscope objective is approximately 1.2 MW/cm2). Direct single-strand breaks (without treatment with M. luteus) were not observed under these conditions. However, in the presence of 6 microM of the intercalator proflavine (PF), both direct single- and double-strand breaks are observed under conditions where substantial fractions of undamaged supercoiled DNA molecules are still present. The fraction of direct double-strand breaks is 30 +/- 5% of all measurable strand cleavage events, is independent of dosage (up to 6.4 GJ/cm2) and is proportional to In, where I is the average power/area of the 810 nm fs laser pulses, and n = 3 +/- 1. The nicking of two DNA strands in the immediate vicinity of the excited PF molecules gives rise to this double-strand cleavage. In contrast, excitation of the same samples under low-power, single-photon absorption conditions (approximately 400-500 nm) gives rise predominantly to single-strand breaks, but some double-strand breaks are observed at the higher dosages. Thus, single-photon excitation with 400-500 nm light and multiphoton activation of PF by near-IR fs laser pulses produces different distributions of single- and double-strand breaks. These results suggest that DNA strand cleavage originates from unrelaxed, higher excited states when PF is excited by simultaneous IR multiphoton absorption processes.
Analysis of electrical property changes of skin by oil-in-water emulsion components

PubMed Central

Jeong, CB; Han, JY; Cho, JC; Suh, KD; Nam, GW

2013-01-01

Synopsis ObjectivesAs the ‘Dry Skin Cycle’ produces continuous deterioration, cosmetic xerosis (flaky, dry skin) is one of the major concerns to most consumers. The purpose of this study was to investigate the moisturizing effect of oil-in-water (O/W) emulsion components. There are numerous types of oils, waxes, polyols and surfactants used as ingredients in skincare products. However, the moisturizing effect of each ingredient and understanding each use to make an effective moisturizing products are still not well understood. Methods To provide answers to these questions, we investigated the moisturizing effect of widely used 41 components (four different classes) in a simple O/W emulsion using capacitance methods. 106 different single oils, and combinations of oil with oil, wax, humectants, and surfactant were formulated and tested. Results In this study, we found that most of the O/W emulsion components had hydration effects on the skin. (i) The average relative water content increase (RWCI) rate of a single oil-based emulsion was 11.8 ± 5.2% (SE) and 7.9 ± 6.0% (SE) at 3 and 6 h, respectively. (ii) An oil combination emulsion showed an average RWCI rate similar to that of a single oil-based emulsion, 12.6 ± 6.0% (SE) and 12.1 ± 6.4% (SE) at 3 and 6 h, respectively (iii) A combination of waxes with oil showed an average RWCI rate of 16 ± 5.6% (SE) and 12.4 ± 4.5% (SE) at 3 and 6 h, respectively. (iv) Humectant combinations showed the highest average RWCI rate 28 ± 7.3% (SE) and 22.2 ± 7.5% (SE) at 3 and 6 h, respectively (v) Surfactant combinations had an average RWCI of 10.8 ± 4.5% (SE) and 6.0 ± 4.0% (SE) at 3 and 6 h, respectively. Conclusion Interestingly, it was difficult to find moisturizing power differences among samples in the same group. Only the humectants group showed significant differences among samples. Glycerine and urea showed significant skin hydration effects compared with other humectants. We also found a significant moisturizing effect by analysing the chemical functional groups; amide class had a higher hydration effect than betaines and disaccharides in humectants combination. Résumé Objectif Puisque le «cycle de la peau sèche” produit une détérioration continue, la xérose cosmétique (squameuse, peau sèche) est l’une des préoccupations majeures pour la plupart des consommateurs. Le but de cette étude était d’étudier l’effet hydratant des composants d’émulsions H / E. Il existe de nombreux types d’huiles, des cires, de polyols, et des tensioactifs utilisés comme ingrédients dans les produits de soins de la peau. Cependant, l’effet hydratant de chaque ingrédient et de leur utilisation dans des produits hydratants efficaces ne sont pas encore bien compris. MethodesPour apporter des réponses à ces questions, nous avons étudié l’effet hydratant des 41 éléments (4 classes différentes) largement utilisés dans une émulsion simple O/W en utilisant des méthodes de capacitance. 106 huiles individuelles différentes et des combinaisons d’huile avec de l’huile, de la cire, des humectants, et de tensioactifs ont été formulées et testées. ResultatsDans cette étude, nous avons constaté que la plupart des composants des émulsions huile-dans-eau (H/E) possédaient des effets d’hydratation de la peau. (i) Le taux moyen d’augmentation d’eau (RWCI = relative water content increase) d’une émulsion à base d’une seule huile était de 11,8 ± 5,2% (SE) et de 7,9 ± 6,0% (SE) à 3 et 6 h, respectivement. (ii) Une émulsion de combinaison d’huile montrait une RWCI similaire à celle d’une émulsion à base d’huile unique, 12,6 ± 6,0% (SE) et 12,1 ± 6,4% (SE) à 3 et 6 h, respectivement. (iii) Une combinaison des cires avec de l’huile présentait une RWCI de 16 ± 5,6% (SE) et 12,4 ± 4,5% (SE) à 3 et 6 h, respectivement. (iv) Les combinaisons d’humectant ont montré la plus forte augmentation avec +28 ± 7,3% (SE) et 22,2 ± 7,5% (SE) à 3 et 6 h, respectivement. (v) Les combinaisons de tensioactifs ont une RWCI moyenne de 10,8 ± 4,5% (SE) et de 6,0 ± 4,0% (SE) à 3 et 6 h, respectivement. ConclusionFait intéressant, il était difficile de trouver des différences de pouvoir d’hydratation entre les échantillons dans le même groupe. Seul le groupe des humectants a montré des différences significatives entre les échantillons. La glycérine et l’urée ont montré des effets significatifs sur l’hydratation de la peau par rapport aux autres humectants. Nous avons également constaté un effet hydratant important en analysant les groupes fonctionnels chimiques; la classe “amide” a eu un effet d’hydratation plus élevé que les bétaînes et disaccharides dans les combinaisons des humectants. PMID:23621673
Challenges and status of ITER conductor production

NASA Astrophysics Data System (ADS)

Devred, A.; Backbier, I.; Bessette, D.; Bevillard, G.; Gardner, M.; Jong, C.; Lillaz, F.; Mitchell, N.; Romano, G.; Vostner, A.

2014-04-01

Taking the relay of the large Hadron collider (LHC) at CERN, ITER has become the largest project in applied superconductivity. In addition to its technical complexity, ITER is also a management challenge as it relies on an unprecedented collaboration of seven partners, representing more than half of the world population, who provide 90% of the components as in-kind contributions. The ITER magnet system is one of the most sophisticated superconducting magnet systems ever designed, with an enormous stored energy of 51 GJ. It involves six of the ITER partners. The coils are wound from cable-in-conduit conductors (CICCs) made up of superconducting and copper strands assembled into a multistage cable, inserted into a conduit of butt-welded austenitic steel tubes. The conductors for the toroidal field (TF) and central solenoid (CS) coils require about 600 t of Nb3Sn strands while the poloidal field (PF) and correction coil (CC) and busbar conductors need around 275 t of Nb-Ti strands. The required amount of Nb3Sn strands far exceeds pre-existing industrial capacity and has called for a significant worldwide production scale up. The TF conductors are the first ITER components to be mass produced and are more than 50% complete. During its life time, the CS coil will have to sustain several tens of thousands of electromagnetic (EM) cycles to high current and field conditions, way beyond anything a large Nb3Sn coil has ever experienced. Following a comprehensive R&D program, a technical solution has been found for the CS conductor, which ensures stable performance versus EM and thermal cycling. Productions of PF, CC and busbar conductors are also underway. After an introduction to the ITER project and magnet system, we describe the ITER conductor procurements and the quality assurance/quality control programs that have been implemented to ensure production uniformity across numerous suppliers. Then, we provide examples of technical challenges that have been encountered and we present the status of ITER conductor production worldwide.
DNA Recombinase Proteins, their Function and Structure in the Active Form, a Computational Study

NASA Technical Reports Server (NTRS)

Carra, Claudio; Cucinotta, Francis A.

2007-01-01

Homologous recombination is a crucial sequence of reactions in all cells for the repair of double strand DNA (dsDNA) breaks. While it was traditionally considered as a means for generating genetic diversity, it is now known to be essential for restart of collapsed replication forks that have met a lesion on the DNA template (Cox et al., 2000). The central stage of this process requires the presence of the DNA recombinase protein, RecA in bacteria, RadA in archaea, or Rad51 in eukaryotes, which leads to an ATP-mediated DNA strand-exchange process. Despite many years of intense study, some aspects of the biochemical mechanism, and structure of the active form of recombinase proteins are not well understood. Our theoretical study is an attempt to shed light on the main structural and mechanistic issues encountered on the RecA of the e-coli, the RecA of the extremely radio resistant Deinococcus Radiodurans (promoting an inverse DNA strand-exchange repair), and the homolog human Rad51. The conformational changes are analyzed for the naked enzymes, and when they are linked to ATP and ADP. The average structures are determined over 2ns time scale of Langevian dynamics using a collision frequency of 1.0 ps(sup -1). The systems are inserted in an octahedron periodic box with a 10 Angstrom buffer of water molecules explicitly described by the TIP3P model. The corresponding binding free energies are calculated in an implicit solvent using the Poisson-Boltzmann solvent accessible surface area, MM-PBSA model. The role of the ATP is not only in stabilizing the interaction RecA-DNA, but its hydrolysis is required to allow the DNA strand-exchange to proceed. Furthermore, we extended our study, using the hybrid QM/MM method, on the mechanism of this chemical process. All the calculations were performed using the commercial code Amber 9.
Synthesis of DNA

DOEpatents

Mariella, Jr., Raymond P.

2008-11-18

A method of synthesizing a desired double-stranded DNA of a predetermined length and of a predetermined sequence. Preselected sequence segments that will complete the desired double-stranded DNA are determined. Preselected segment sequences of DNA that will be used to complete the desired double-stranded DNA are provided. The preselected segment sequences of DNA are assembled to produce the desired double-stranded DNA.
75 FR 28560 - Prestressed Concrete Steel Wire Strand From the People's Republic of China: Final Determination...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-05-21

... Wire Strand From the People's Republic of China: Final Determination of Sales at Less Than Fair Value... Steel Wire Strand From the People's Republic of China: Preliminary Determination of Sales at Less Than... Antidumping Duty Investigation of Prestressed Concrete Steel Wire Strand From the People's Republic of China...
Characterization of wood strands from young, small-diameter Douglas-fir and western hemlock trees

Treesearch

Vikram Yadama; Eini C. Lowell; Christopher E. Langum

2012-01-01

Tensile properties of strands processed from small-diameter Douglas-fir and western hemlock trees grown on the Washington coast were analyzed and effects of location within the tree on properties was examined. Reduction factors for strand properties relative to small, clear solid wood specimen properties were determined by correlating strand properties to previously...
Toxin MqsR Cleaves Single-Stranded mRNA with Various 5 Ends

DTIC Science & Technology

2016-08-24

either protein ORIGINAL RESEARCH Toxin MqsR cleaves single- stranded mRNA with various 5’ ends Nityananda Chowdhury1,*, Brian W. Kwan1,*, Louise C...in which a single 5′- GCU site was predicted to be single- stranded (ssRNA), double- stranded (dsRNA), in the loop of a stem - loop (slRNA), or in a...single- stranded 5′- GCU sites since cleavage was approximately 20- fold higher than cleavage seen with the 5′- GCU site in the stem - loop and
Failsafe multistrand tether structures for space propulsion

NASA Astrophysics Data System (ADS)

Forward, Robert L.

1992-07-01

The development of a circularly symmetric singly crosslinked multistrand space tether, named Hoytether, is reported. The Hoytether consists of a number of primary strands running the full length of the structure, with nearest neighbor primary strands crosslinked at intervals by secondary strands that are put under load only if a section of primary strand is cut by space debris. It has been demonstrated that a multistrand tether of the singly crosslinked Hoytether design can provide a long-lived failsafe multistrand replacement for a single-strand tether while imposing a minimal mass ratio penalty.
The Mechanism of Viral Replication. Structure of Replication Complexes of Encephalomyocarditis Virus

PubMed Central

Thach, Sigrid S.; Dobbertin, Darrell; Lawrence, Charles; Golini, Fred; Thach, Robert E.

1974-01-01

The structure of the purified replicative intermediate of encephalomyocarditis virus was determined by electron microscopy. Approximately 80% of the replicative intermediate complexes were characterized by a filament of double-stranded RNA of widely variable length, which had a “bush” of single-stranded RNA at one end. In many examples one or more additional single-stranded bushes were appended internally to the double-stranded RNA filament. These results support the view that before deproteinization, replicative intermediate contains little if any double-stranded RNA. Images PMID:4366773

DNA sequencing with pyrophosphatase

DOEpatents

Tabor, S.; Richardson, C.C.

1996-03-12

A kit or solution is disclosed for use in extension of an oligonucleotide primer having a first single-stranded region on a template molecule and having a second single-stranded region homologous to the first single-stranded region. The first agent is able to cause extension of the first single-stranded region of the primer on the second single-stranded region of the template in a reaction mixture. The second agent is able to reduce the amount of pyrophosphate in the reaction mixture below the amount produced during the extension in the absence of the second agent.
DNA sequencing with pyrophosphatase

DOEpatents

Tabor, Stanley; Richardson, Charles C.

1996-03-12

A kit or solution for use in extension of an oligonucleotide primer having a first single-stranded region on a template molecule having a second single-stranded region homologous to the first single-stranded region, comprising a first agent able to cause extension of the first single-stranded region of the primer on the second single-stranded region of the template in a reaction mixture, and a second agent able to reduce the amount of pyrophosphate in the reaction mixture below the amount produced during the extension in the absence of the second agent.
Modelling toehold-mediated RNA strand displacement.

PubMed

Šulc, Petr; Ouldridge, Thomas E; Romano, Flavio; Doye, Jonathan P K; Louis, Ard A

2015-03-10

We study the thermodynamics and kinetics of an RNA toehold-mediated strand displacement reaction with a recently developed coarse-grained model of RNA. Strand displacement, during which a single strand displaces a different strand previously bound to a complementary substrate strand, is an essential mechanism in active nucleic acid nanotechnology and has also been hypothesized to occur in vivo. We study the rate of displacement reactions as a function of the length of the toehold and temperature and make two experimentally testable predictions: that the displacement is faster if the toehold is placed at the 5' end of the substrate; and that the displacement slows down with increasing temperature for longer toeholds. Copyright © 2015 Biophysical Society. Published by Elsevier Inc. All rights reserved.
Evidence for a Single-Stranded Adenovirus-Associated Virus Genome: Isolation and Separation of Complementary Single Strands

PubMed Central

Berns, K. I.; Rose, J. A.

1970-01-01

Single-stranded adenovirus-associated virus type 2 deoxyribonucleic acid (AAV-2 DNA) has been isolated from the virion after enzymatic pretreatment of the particles by heating at 53 C for 1 hr in 0.015 m NaCl plus 0.0015 m sodium citrate in the presence of 1% sodium dodecyl sulfate. Double-stranded AAV-2 DNA present as a marker is not denatured by this treatment. AAV-2 single-stranded DNA is composed of two complementary species which can be separated in neutral CsCl when 5-bromodeoxyuridine has been substituted for thymidine in the DNA. The present report is the first documented instance of the separation of complementary strands of an animal virus DNA. PMID:5429749
Charge separation and charge delocalization identified in long-living states of photoexcited DNA

PubMed Central

Bucher, Dominik B.; Pilles, Bert M.; Carell, Thomas; Zinth, Wolfgang

2014-01-01

Base stacking in DNA is related to long-living excited states whose molecular nature is still under debate. To elucidate the molecular background we study well-defined oligonucleotides with natural bases, which allow selective UV excitation of one single base in the strand. IR probing in the picosecond regime enables us to dissect the contribution of different single bases to the excited state. All investigated oligonucleotides show long-living states on the 100-ps time scale, which are not observable in a mixture of single bases. The fraction of these states is well correlated with the stacking probabilities and reaches values up to 0.4. The long-living states show characteristic absorbance bands that can be assigned to charge-transfer states by comparing them to marker bands of radical cation and anion spectra. The charge separation is directed by the redox potential of the involved bases and thus controlled by the sequence. The spatial dimension of this charge separation was investigated in longer oligonucleotides, where bridging sequences separate the excited base from a sensor base with a characteristic marker band. After excitation we observe a bleach of all involved bases. The contribution of the sensor base is observable even if the bridge is composed of several bases. This result can be explained by a charge delocalization along a well-stacked domain in the strand. The presence of charged radicals in DNA strands after light absorption may cause reactions—oxidative or reductive damage—currently not considered in DNA photochemistry. PMID:24616517
Dynamics of single-stranded DNA tethered to a solid

NASA Astrophysics Data System (ADS)

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

2016-06-01

Tethering is used to deliver specific biological and industrial functions. For example, single-stranded DNA (ssDNA) is tethered to polymerases and long sequences of double-stranded DNA (dsDNA) during replication, and to solids in DNA microarrays. However, tethering ssDNA to a large object limits not only the available ssDNA conformations, but also the range of time-scales over which the mechanical responses of ssDNA are important. In this work we examine the effect of tethering by measurement of the mechanical response of ssDNA that is tethered at each end to two separate atomic force microscope cantilevers in aqueous solution. Thermal motion of the cantilevers drives the ends of the ssDNA chain at frequencies near 2 kHz. The presence of a tethered molecule makes a large difference to the asymmetric cross-correlation of two cantilevers, which enables resolution of the mechanical properties in our experiments. By analysis of the correlated motion of the cantilevers we extract the friction and stiffness of the ssDNA. We find that the measured friction is much larger than the friction that is usually associated with the unencumbered motion of ssDNA. We also find that the measured relaxation time, ∼30 μs, is much greater than prior measurements of the free-molecule relaxation time. We attribute the difference to the loss of conformational possibilities as a result of constraining the ends of the ssDNA.
3D-structured illumination microscopy reveals clustered DNA double-strand break formation in widespread γH2AX foci after high LET heavy-ion particle radiation

PubMed Central

Hagiwara, Yoshihiko; Niimi, Atsuko; Isono, Mayu; Yamauchi, Motohiro; Yasuhara, Takaaki; Limsirichaikul, Siripan; Oike, Takahiro; Sato, Hiro; Held, Kathryn D.; Nakano, Takashi; Shibata, Atsushi

2017-01-01

DNA double-strand breaks (DSBs) induced by ionising radiation are considered the major cause of genotoxic mutations and cell death. While DSBs are dispersed throughout chromatin after X-rays or γ-irradiation, multiple types of DNA damage including DSBs, single-strand breaks and base damage can be generated within 1–2 helical DNA turns, defined as a complex DNA lesion, after high Linear Energy Transfer (LET) particle irradiation. In addition to the formation of complex DNA lesions, recent evidence suggests that multiple DSBs can be closely generated along the tracks of high LET particle irradiation. Herein, by using three dimensional (3D)-structured illumination microscopy, we identified the formation of 3D widespread γH2AX foci after high LET carbon-ion irradiation. The large γH2AX foci in G2-phase cells encompassed multiple foci of replication protein A (RPA), a marker of DSBs undergoing resection during homologous recombination. Furthermore, we demonstrated by 3D analysis that the distance between two individual RPA foci within γH2AX foci was approximately 700 nm. Together, our findings suggest that high LET heavy-ion particles induce clustered DSB formation on a scale of approximately 1 μm3. These closely localised DSBs are considered to be a risk for the formation of chromosomal rearrangement after heavy-ion irradiation. PMID:29312614
PolyA Single Strand DNA Translocation Through an Alpha-Hemolysin Pore Stem

NASA Technical Reports Server (NTRS)

OKeeffe, James; Cozmuta, Ioana; Stolc, Viktor

2003-01-01

A new model for the polymer-pore interaction energy is introduced, based on an atomic-scale description of coulombic polymer-pore interaction. The enhanced drift velocity, experimentally observed for short polymers, is successfully accounted for, using this interaction energy model. For R/R(sub 0)>4 (R(sub 0)=7 angstroms) the translocation velocity approaches the free space drift velocity v(sub 0). This motivates the need to appropriately derivatize artificial nanopores, where R>R(sub 0).
Researchers use Modified CRISPR Systems to Modulate Gene Expression on a Genomic Scale | Office of Cancer Genomics

Cancer.gov

The genetic engineering system, clustered regularly interspaced short palindromic repeats (CRISPR), has conventionally been used to inactivate genes by making targeted double stranded cuts in DNA. While CRISPR is a useful tool, it can only be used to create loss-of-function modifications and often causes off-target effects due to the disruptive mechanism by which it works. CTD2 researchers at the University of California, San Francisco recently addressed these shortcomings in a publication in Cell.
Etude du champ magnetique dans les nuages moleculaires

NASA Astrophysics Data System (ADS)

Houde, Martin

2001-12-01

Ce travail est une étude du champ magnétique duns l'environnement circumstellaire des étoiles jeunes. Il a pour origine la certitude qu'avait l'auteur qu'il se devait d'être possible de détecter la présence d'un champ magnétique, et de possiblement le caractériser, par le biais d'observations de profils spectraux d'espèces moléculaires ioniques. Il en découle donc qu'un des buts principaux était de prouver que cela est effectivement possible. La thèse comporte alors des éléments théoriques et expérimentaux qui sont à la fois complémentaires et intimement liés. L'aspect théorique est basé sur l'interaction mutuelle que des particules neutres et chargées peuvent avoir l'une sur l'autre daps un plasma faiblement ionisé comme ceux existants daps les nuages moléculaires sites de formation stellaire. Il appert que la présence d'un champ magnétique a un effet direct sur le comportement des ions (via la force de Lorentz) et indirect sur les molécules neutres (via les nombreuses collisions entre les deux types de particules). Une telle interaction est, comme il est maintenant bien connu, présente dans les premières étapes de la formation dune étoile. Il s'agit bien sûr de la diffusion ambipolaire. Nous montrerons qu'il existe cependant un autre type de diffusion, jusqu'ici inconnue, qui se manifeste plus tard au tours de l'évolution des nuages moléculaires. Celle-ci peut avoir un effet dramatique sur l'apparence des profils spectraux (de rotation moléculaire) des espèces ioniques lorsque comparés à ceux qu'exhibent des espèces neutres coexistantes. Mais pour ce faire, il doit y avoir existence de mouvements organisés (des flots ou jets) de matière ou encore la présence de turbulence dans les régions considérées. Une distribution de vélocité du type maxwellienne ne révèlera pas la présence du champ magnétique. Les observations, qui ont pour but de confirmer la théorie, se situent dans le domaine des longueurs d'ondes millimétriques et sous- millimétriques. Plusieurs espèces moléculaires furent détectées dans un échantillon significatif de nuages moléculaires. L'effet prédit fut confirmé et ce peu importe si les raies observées sont opaques ou transparentes. Dans le dernier chapitre, nous considérerons une application intéressante où nous utiliserons la manifestation de cet effet (ou son manque) pour vérifier l'alignement préférentiel des flots bipolaires, qui accompagnent souvent la présence de proto- étoiles, avec le champ magnétique local.
Replication of avocado sunblotch viroid: evidence for a symmetric pathway with two rolling circles and hammerhead ribozyme processing.

PubMed Central

Daròs, J A; Marcos, J F; Hernández, C; Flores, R

1994-01-01

The structure of a series of RNAs extracted from avocado infected by the 247-nt avocado sunblotch viroid (ASBVd) was investigated. The identification of multistranded complexes containing circular ASBVd RNAs of (+) and (-) polarity suggests that replication of ASBVd proceeds through a symmetric pathway with two rolling circles where these two circular RNAs are the templates. This is in contrast to the replication of potato spindle tuber viroid and probably of most of its related viroids, which proceeds via an asymmetric pathway where circular (+)-strand and linear multimeric (-)-strand RNAs are the two templates. Linear (+) and (-) ASBVd RNAs of subgenomic length (137 nt and about 148 nt, respectively) and one linear (+)-strand ASBVd RNA of supragenomic length (383-384 nt) were also found in viroid-infected tissue. The two linear (+)-strand RNAs have the same 5'- and 3'-terminal sequences, with the supragenomic species being a fusion product of the monomeric and subgenomic (+)-strand ASBVd RNAs. The 3' termini of these two (+)-strand molecules, which at least in the subgenomic RNA has an extra nontemplate cytidylate residue, could represent sites of either premature termination of the (+)-strands or specific initiation of the (-)-strands. The 5' termini of sub- and supragenomic (+)-strand and the 5' terminus of the subgenomic (-)-strand ASBVd RNA are identical to those produced in the in vitro self-cleavage reactions of (+) and (-) dimeric ASBVd RNAs, respectively. These observations strongly suggest that the hammerhead structures which mediate the in vitro self-cleavage reactions are also operative in vivo. Images Fig. 1 Fig. 3 Fig. 4 Fig. 5 PMID:7809126
DNA Meter: Energy Tunable, Quantitative Hybridization Assay

PubMed Central

Braunlin, William; Völker, Jens; Plum, G. Eric; Breslauer, Kenneth J.

2015-01-01

We describe a novel hybridization assay that employs a unique class of energy tunable, bulge loop-containing competitor strands (C*) that hybridize to a probe strand (P). Such initial “pre-binding” of a probe strand modulates its effective “availability” for hybridizing to a target site (T). More generally, the assay described here is based on competitive binding equilibria for a common probe strand (P) between such tunable competitor strands (C*) and a target strand (T). We demonstrate that loop variable, energy tunable families of C*P complexes exhibit enhanced discrimination between targets and mismatched targets, thereby reducing false positives/negatives. We refer to a C*P complex between a C* competitor single strand and the probe strand as a “tuning fork,” since the C* strand exhibits branch points (forks) at the duplex-bulge interfaces within the complex. By varying the loop to create families of such “tuning forks,” one can construct C*P “energy ladders” capable of resolving small differences within the target that may be of biological/functional consequence. The methodology further allows quantification of target strand concentrations, a determination heretofore not readily available by conventional hybridization assays. The dual ability of this tunable assay to discriminate and quantitate targets provides the basis for developing a technology we refer to as a “DNA Meter.” Here we present data that establish proof-of-principle for an in solution version of such a DNA Meter. We envision future applications of this tunable assay that incorporate surface bound/spatially resolved DNA arrays to yield enhanced discrimination and sensitivity. PMID:23529692
Interstrand cross-links arising from strand breaks at true abasic sites in duplex DNA.

PubMed

Yang, Zhiyu; Price, Nathan E; Johnson, Kevin M; Wang, Yinsheng; Gates, Kent S

2017-06-20

Interstrand cross-links are exceptionally bioactive DNA lesions. Endogenous generation of interstrand cross-links in genomic DNA may contribute to aging, neurodegeneration, and cancer. Abasic (Ap) sites are common lesions in genomic DNA that readily undergo spontaneous and amine-catalyzed strand cleavage reactions that generate a 2,3-didehydro-2,3-dideoxyribose sugar remnant (3'ddR5p) at the 3'-terminus of the strand break. Interestingly, this strand scission process leaves an electrophilic α,β-unsaturated aldehyde residue embedded within the resulting nicked duplex. Here we present evidence that 3'ddR5p derivatives generated by spermine-catalyzed strand cleavage at Ap sites in duplex DNA can react with adenine residues on the opposing strand to generate a complex lesion consisting of an interstrand cross-link adjacent to a strand break. The cross-link blocks DNA replication by ϕ29 DNA polymerase, a highly processive polymerase enzyme that couples synthesis with strand displacement. This suggests that 3'ddR5p-derived cross-links have the potential to block critical cellular DNA transactions that require strand separation. LC-MS/MS methods developed herein provide powerful tools for studying the occurrence and properties of these cross-links in biochemical and biological systems. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.
Phosphorylation-specific status of RNAi triggers in pharmacokinetic and biodistribution analyses

PubMed Central

Trubetskoy, Vladimir S.; Griffin, Jacob B.; Nicholas, Anthony L.; Nord, Eric M.; Xu, Zhao; Peterson, Ryan M.; Wooddell, Christine I.; Rozema, David B.; Wakefield, Darren H.; Lewis, David L.

2017-01-01

Abstract The RNA interference (RNAi)-based therapeutic ARC-520 for chronic hepatitis B virus (HBV) infection consists of a melittin-derived peptide conjugated to N-acetylgalactosamine for hepatocyte targeting and endosomal escape, and cholesterol-conjugated RNAi triggers, which together result in HBV gene silencing. To characterize the kinetics of RNAi trigger delivery and 5΄-phosphorylation of guide strands correlating with gene knockdown, we employed a peptide-nucleic acid (PNA) hybridization assay. A fluorescent sense strand PNA probe binding to RNAi duplex guide strands was coupled with anion exchange high performance liquid chromatography to quantitate guide strands and metabolites. Compared to PCR- or ELISA-based methods, this assay enables separate quantitation of non-phosphorylated full-length guide strands from 5΄-phosphorylated forms that may associate with RNA-induced silencing complexes (RISC). Biodistribution studies in mice indicated that ARC-520 guide strands predominantly accumulated in liver. 5΄-phosphorylation of guide strands was observed within 5 min after ARC-520 injection, and was detected for at least 4 weeks corresponding to the duration of HBV mRNA silencing. Guide strands detected in RISC by AGO2 immuno-isolation represented 16% of total 5΄-phosphorylated guide strands in liver, correlating with a 2.7 log10 reduction of HBsAg. The PNA method enables pharmacokinetic analysis of RNAi triggers, elucidates potential metabolic processing events and defines pharmacokinetic-pharmacodynamic relationships. PMID:28180327
Regulation of yeast DNA polymerase δ-mediated strand displacement synthesis by 5′-flaps

PubMed Central

Koc, Katrina N.; Stodola, Joseph L.; Burgers, Peter M.; Galletto, Roberto

2015-01-01

The strand displacement activity of DNA polymerase δ is strongly stimulated by its interaction with proliferating cell nuclear antigen (PCNA). However, inactivation of the 3′–5′ exonuclease activity is sufficient to allow the polymerase to carry out strand displacement even in the absence of PCNA. We have examined in vitro the basic biochemical properties that allow Pol δ-exo− to carry out strand displacement synthesis and discovered that it is regulated by the 5′-flaps in the DNA strand to be displaced. Under conditions where Pol δ carries out strand displacement synthesis, the presence of long 5′-flaps or addition in trans of ssDNA suppress this activity. This suggests the presence of a secondary DNA binding site on the enzyme that is responsible for modulation of strand displacement activity. The inhibitory effect of a long 5′-flap can be suppressed by its interaction with single-stranded DNA binding proteins. However, this relief of flap-inhibition does not simply originate from binding of Replication Protein A to the flap and sequestering it. Interaction of Pol δ with PCNA eliminates flap-mediated inhibition of strand displacement synthesis by masking the secondary DNA site on the polymerase. These data suggest that in addition to enhancing the processivity of the polymerase PCNA is an allosteric modulator of other Pol δ activities. PMID:25813050
Unraveling the strands of Saturn's F ring

USGS Publications Warehouse

Murray, C.D.; Gordon, M.K.; Giuliatti, Winter S.M.

1997-01-01

Several high-resolution Voyager 2 images of Saturn's F ring show that it is composed of at least four separate, non-intersecting strands extending ~45?? in longitude. Voyager 1 images show that the two brightest strands appear to intersect, giving rise to a "braided" morphology. From a study of all available Voyager images the detectable radial structure is cataloged and reviewed. Previous indications that there is fine material interior to the orbit of the F ring are confirmed. Evidence is presented that a model of four strands with comparable eccentricities and nearly aligned perichrones is consistent with all the Voyager observations. The observed perichrone offset of the two brightest strands suggests a minimum radial separation of ~20 km, which implies intersection of these strands when their finite radial widths are taken into account. The longitude range of such an intersection includes that observed in the Voyager 1 "braid" images. The proximity of these two strands at some longitudes may account for the apparent differences in the ring between the Voyager encounters, as well as provide a source for the short-lived features detected in the Hubble Space Telescope images of the F ring. There is no evidence that the locations of the individual strands are determined by resonant perturbations with known satellites. It is proposed that the radial structure is formed by the localized action of small satellites orbiting within the strand region. ?? 1997 Academic Press.
Strand displacement activated peroxidase activity of hemin for fluorescent DNA sensing.

PubMed

Wang, Quanbo; Xu, Nan; Gui, Zhen; Lei, Jianping; Ju, Huangxian; Yan, Feng

2015-10-07

To efficiently regulate the catalytic activity of the peroxidase mimic hemin, this work designs a double-stranded DNA probe containing an intermolecular dimer of hemin, whose peroxidase activity can be activated by a DNA strand displacement reaction. The double-stranded probe is prepared by annealing two strands of hemin labelled DNA oligonucleotides. Using the fluorescent oxidation product of tyramine by H2O2 as a tracing molecule, the low peroxidase activity of the hemin dimer ensures a low fluorescence background. The strand displacement reaction of the target DNA dissociates the hemin dimer and thus significantly increases the catalytic activity of hemin to produce a large amount of dityramine for fluorescence signal readout. Based on the strand displacement regulated peroxidase activity, a simple and sensitive homogeneous fluorescent DNA sensing method is proposed. The detection can conveniently be carried out in a 96-well plate within 20 min with a detection limit of 0.18 nM. This method shows high specificity, which can effectively distinguish single-base mismatched DNA from perfectly matched target DNA. The DNA strand displacement regulated catalytic activity of hemin has promising application in the determination of various DNA analytes.
Classifying Saturn's F Ring Strands

NASA Astrophysics Data System (ADS)

Albers, Nicole; Sremcevic, M.; Esposito, L. W.; Colwell, J. E.

2009-09-01

The Cassini Ultraviolet Imaging Spectrograph (UVIS) High Speed Photometer (HSP) has recorded more than 113 stellar occultations by Saturn's F ring providing measurements with ring plane resolutions of a few dozen meters and better. Inner and outer F ring strands have been seen throughout the Cassini mission where they revealed themselves as non-continuous, azimuthally and temporally highly variable structures. In the light of a more accurate orbit description of the F ring core we find evidence for a ring that becomes dynamically more active as the system approaches anti-apse alignment with Prometheus. This is consistent with the observed increased strand activity. A recent strand that morphologically resembles the core is the strongest seen to date and points to the intricate relation between core and strands indicating the strands' violent creation. Using more than 150 identifications of various strands, we trace their kinematics and infer dynamical timescales and photometric properties. Implications for the dynamical evolution of the F ring will be discussed. This research was supported by the Cassini Project.
DNA Strand Breaks in Mitotic Germ Cells of Caenorhabditis elegans Evaluated by Comet Assay

PubMed Central

Park, Sojin; Choi, Seoyun; Ahn, Byungchan

2016-01-01

DNA damage responses are important for the maintenance of genome stability and the survival of organisms. Such responses are activated in the presence of DNA damage and lead to cell cycle arrest, apoptosis, and DNA repair. In Caenorhabditis elegans, double-strand breaks induced by DNA damaging agents have been detected indirectly by antibodies against DSB recognizing proteins. In this study we used a comet assay to detect DNA strand breaks and to measure the elimination of DNA strand breaks in mitotic germline nuclei of C. elegans. We found that C. elegans brc-1 mutants were more sensitive to ionizing radiation and camptothecin than the N2 wild-type strain and repaired DNA strand breaks less efficiently than N2. This study is the first demonstration of direct measurement of DNA strand breaks in mitotic germline nuclei of C. elegans. This newly developed assay can be applied to detect DNA strand breaks in different C. elegans mutants that are sensitive to DNA damaging agents. PMID:26903030
Effect of Subelement Spacing in Rrp Nb3Sn Deformed Strands

NASA Astrophysics Data System (ADS)

Barzi, E.; Turrioni, D.; Alsharo'a, M.; Field, M.; Hong, S.; Parrell, J.; Yamada, R.; Zhang, Y.; Zlobin, A. V.

2008-03-01

The Restacked Rod Process (RRP) is the Nb3Sn strand technology presently producing the largest critical current densities at 4.2 K and 12 T. However, when subject to transverse plastic deformation, RRP subelements (SE) merge into each other, creating larger filaments with a somewhat continuous barrier. In this case, the strand sees a larger effective filament size and its instability can dramatically increase locally leading to a cable quench. To reduce and possibly eliminate this effect, Oxford Instruments Superconducting Technology (OST) developed for FNAL a modified RRP strand design with larger Cu spacing between SE's arranged in a 60/61 array. Strand samples of this design with sizes from 0.7 to 1 mm were first evaluated for transport current properties. A comparison study was then performed between the regular 54/61 and the modified 60/61 design using 0.7 mm round and deformed strands. Finite element modeling of the deformed strands was also performed with ANSYS.

Hearing Loss in Stranded Odontocete Dolphins and Whales

PubMed Central

Mann, David; Hill-Cook, Mandy; Manire, Charles; Greenhow, Danielle; Montie, Eric; Powell, Jessica; Wells, Randall; Bauer, Gordon; Cunningham-Smith, Petra; Lingenfelser, Robert; DiGiovanni, Robert; Stone, Abigale; Brodsky, Micah; Stevens, Robert; Kieffer, George; Hoetjes, Paul

2010-01-01

The causes of dolphin and whale stranding can often be difficult to determine. Because toothed whales rely on echolocation for orientation and feeding, hearing deficits could lead to stranding. We report on the results of auditory evoked potential measurements from eight species of odontocete cetaceans that were found stranded or severely entangled in fishing gear during the period 2004 through 2009. Approximately 57% of the bottlenose dolphins and 36% of the rough-toothed dolphins had significant hearing deficits with a reduction in sensitivity equivalent to severe (70–90 dB) or profound (>90 dB) hearing loss in humans. The only stranded short-finned pilot whale examined had profound hearing loss. No impairments were detected in seven Risso's dolphins from three different stranding events, two pygmy killer whales, one Atlantic spotted dolphin, one spinner dolphin, or a juvenile Gervais' beaked whale. Hearing impairment could play a significant role in some cetacean stranding events, and the hearing of all cetaceans in rehabilitation should be tested. PMID:21072206
The Axial Velocity Distribution of a Polyethylene Strand During Extrusion: Simulation and Comparison with Measurements

NASA Astrophysics Data System (ADS)

Schneider, Christian; Schwetz, Martin; Münstedt, Helmut; Kaschta, Joachim

2004-09-01

The velocity distribution along the axis of a low-density polyethylene (LDPE) melt strand extruded through an axisymmetric capillary and drawn by various forces is simulated using an integral constitutive equation with a PSM damping function (Papanastasiou, Scriven, Macosko, Journal of Rheology, 27: 381 410, 1983). The simulations are performed for different drawdown forces of the strand. The numerical results are compared with experimental data obtained by velocity measurements using the laser-Doppler velocimetry. The strand is drawn by rotating wheels as used in a Rheotens™ testing device. At drawdown forces greater than zero the investigations show that the strand velocity does not increase linearly with increasing distance from the die exit. Instead, it is observed that the acceleration of the strand increases monotonically. Except in the next vicinity of the die exit there is a good agreement between simulation and experiment. However, near to the die the simulation predicts a higher strand velocity.
Hearing loss in stranded odontocete dolphins and whales.

PubMed

Mann, David; Hill-Cook, Mandy; Manire, Charles; Greenhow, Danielle; Montie, Eric; Powell, Jessica; Wells, Randall; Bauer, Gordon; Cunningham-Smith, Petra; Lingenfelser, Robert; DiGiovanni, Robert; Stone, Abigale; Brodsky, Micah; Stevens, Robert; Kieffer, George; Hoetjes, Paul

2010-11-03

The causes of dolphin and whale stranding can often be difficult to determine. Because toothed whales rely on echolocation for orientation and feeding, hearing deficits could lead to stranding. We report on the results of auditory evoked potential measurements from eight species of odontocete cetaceans that were found stranded or severely entangled in fishing gear during the period 2004 through 2009. Approximately 57% of the bottlenose dolphins and 36% of the rough-toothed dolphins had significant hearing deficits with a reduction in sensitivity equivalent to severe (70-90 dB) or profound (>90 dB) hearing loss in humans. The only stranded short-finned pilot whale examined had profound hearing loss. No impairments were detected in seven Risso's dolphins from three different stranding events, two pygmy killer whales, one Atlantic spotted dolphin, one spinner dolphin, or a juvenile Gervais' beaked whale. Hearing impairment could play a significant role in some cetacean stranding events, and the hearing of all cetaceans in rehabilitation should be tested.
Deposition of organic matter on a high-energy sand beach by a mass stranding of the cnidarian Velella velella (L.)

NASA Astrophysics Data System (ADS)

Kemp, Paul F.

1986-10-01

Strandings of cnidaria occur commonly on exposed shorelines. In some years, large numbers of the chondrophoran Velella velella (L.) are stranded on Pacific beaches of North America. The quantity of organic material deposited on an Oregon beach by one of three mass strandings in 1984 was measured. An average of 2573 g ash-free dry weight (AFDW) was deposited per meter of shoreline, representing 1223 g m -1 of carbon and 347 g m -1 of nitrogen. No significant reduction in AFDW m -1 of the decomposing material was observed in the first three days. The drying mat of stranded material was broken apart by wave action after nine days and most of the material was absent after twelve days. Measurement of microbial and primary production in the period following a stranding may help to determine how long nutrients derived from the stranded material are retained in the beach and surf system.
The Reduction of the Critical Currents in Nb3Sn Cables under Transverse Loads

DOE Office of Scientific and Technical Information (OSTI.GOV)

Van Oort, J.M.; Scanlan, R.M.; Weijers, H.W.

1992-08-01

The degradation of the critical current of impregnated Rutherford type Nb{sub 3}Sn cables is investigated as a function of the applied transverse load and magnetic field. The cable is made of TWCA modified jelly-roll type strand material and has a keystone angle of 1.0 degree. The voltage-current characteristics are determined for the magnetic field ranging from 2 to 11 tesla and transverse pressure up to 250 MPa on the cable surface. It is found that the 48-strand cable, made of strands with 6 elements in the matrix, shows a larger critical current degradation than the 26-strand cable with 36 elementsmore » per strand. The global degradation of the 48-strand cable is 63% at 150 MPa, and 40% at 150 MPa for the 26-strand cable. Micro-analysis of the cross-section shows permanent damage to the sharp edge of the cable. The influence of the keystone angle on the critical-current degradation is currently under investigation.« less
The immortal strand hypothesis: still non-randomly segregating opinions.

PubMed

Wakeman, Jane A; Hmadcha, Abdelkrim; Soria, Bernat; McFarlane, Ramsay J

2012-06-01

Abstract Cairns first suggested a mechanism for protecting the genomes of stem cells (SCs) from replicative errors some 40 years ago when he proposed the immortal strand hypothesis, which argued for the inheritance of a so-called immortal strand by an SC following asymmetric SC divisions. To date, the existence of immortal strands remains contentious with published evidence arguing in favour of and against the retention of an immortal strand by asymmetrically dividing SCs. The conflicting evidence is derived from a diverse array of studies on adult SC types and is predominantly based on following the fate of labelled DNA strands during asymmetric cell division events. Here, we review current data, highlighting limitations of such labelling techniques, and suggest how interpretation of such data may be improved in the future.
A Study of Stranding of Juvenile Salmon by Ship Wakes Along the Lower Columbia River Using a Before-and-After Design: Before-Phase Results

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pearson, Walter H.; Skalski, J R.; Sobocinski, Kathryn L.

2006-02-01

Ship wakes produced by deep-draft vessels transiting the lower Columbia River have been observed to cause stranding of juvenile salmon. Proposed deepening of the Columbia River navigation channel has raised concerns about the potential impact of the deepening project on juvenile salmon stranding. The Portland District of the U.S. Army Corps of Engineers requested that the Pacific Northwest National Laboratory design and conduct a study to assess stranding impacts that may be associated with channel deepening. The basic study design was a multivariate analysis of covariance of field observations and measurements under a statistical design for a before and aftermore » impact comparison. We have summarized field activities and statistical analyses for the ?before? component of the study here. Stranding occurred at all three sampling sites and during all three sampling seasons (Summer 2004, Winter 2005, and Spring 2005), for a total of 46 stranding events during 126 observed vessel passages. The highest occurrence of stranding occurred at Barlow Point, WA, where 53% of the observed events resulted in stranding. Other sites included Sauvie Island, OR (37%) and County Line Park, WA (15%). To develop an appropriate impact assessment model that accounted for relevant covariates, regression analyses were conducted to determine the relationships between stranding probability and other factors. Nineteen independent variables were considered as potential factors affecting the incidence of juvenile salmon stranding, including tidal stage, tidal height, river flow, current velocity, ship type, ship direction, ship condition (loaded/unloaded), ship speed, ship size, and a proxy variable for ship kinetic energy. In addition to the ambient and ship characteristics listed above, site, season, and fish density were also considered. Although no single factor appears as the primary factor for stranding, statistical analyses of the covariates resulted in the following equations: (1) Stranding Probability {approx} Location + Kinetic Energy Proxy + Tidal Height + Salmonid Density + Kinetic energy proxy ? Tidal Height + Tidal Height x Salmonid Density. (2) Stranding Probability {approx} Location + Total Wave Distance + Salmonid Density Index. (3) Log(Total Wave Height) {approx} Ship Block + Tidal Height + Location + Ship Speed. (4) Log(Total Wave Excursion Across the Beach) {approx} Location + Kinetic Energy Proxy + Tidal Height The above equations form the basis for a conceptual model of the factors leading to salmon stranding. The equations also form the basis for an approach for assessing impacts of dredging under the before/after study design.« less
Oriented-strand-board- the wave of the future- for the building trade

Treesearch

Linda Ashton

1984-01-01

Move over, plywood. Oriented-strand board is here. It's less expensive. It's as durable. It has as many uses. And it is the wave of the future. "Oriented-strand board is a direct substitute for plywood" said Jerry Buckner, plant manager for the Martco oriented-strand board plant in Lemoyen. OSB, as it is commonly called, is a structural panel made...
Role of CREB in CML

DTIC Science & Technology

2007-02-01

antisense RNA for suppressing gene expression in nematode worms (Caenorhabditis elegans) 2. This was followed by the introduction of dsRNA into worms...When single-stranded antisense RNA and double stranded RNA was introduced into worms, they found that dsRNA was more effective than either strand...RISC ( RNA -induced silencing complex), which contains helicase activity that unwinds the two strands 3 of RNA molecules, allowing the antisense
Motion Cues in Flight Simulation and Simulator Induced Sickness

DTIC Science & Technology

1988-06-01

asseusod in a driving simulator by means of a response surface methodology central-composite design . The most salient finding of the study was that visual...across treatment conditions. For an orthogonal response surface methodology (IBM) design with only tro independent variables. it can be readily shown that...J.E.Fowikes 8 SESSION III - ETIOLOGICAL FACTORS IN SIMULATOR-INDUCED AFTER EFFETS THE USE OF VE& IIBULAR MODELS FOR DESIGN AND EVALUATION OF FLIGHT
Engineering Aerodynamics

DTIC Science & Technology

1986-12-01

effective Reynolds Number5 to include the effet Of turbulence, which was supported in a convincing manner by the same ratio of 2.4 betwveen the Reynolds...iLIFT DEVICIS 143 methods incorl)orating various forms of flas) are shown on Figure 59. The other two methods, Boundary Layer Control and the Magnus ...Class Airship Hlull with Varying Lengths of Cylindric Midships," N.A.CA. Technical Report No. 138 (1922). 276 ENGINEERING AERODYNAMICS [Ch. 9 -- - - 2.0
Environmental Exposure and Design Criteria for Offshore Oil and Gas Structures

DTIC Science & Technology

1980-05-01

reliability ar_alysis. Because there are no clear lines of demarcation between them, these methods are often used in varying combinations. Sound ...cludes that OCSEA-P not now effe.tively contribute...to the accrual of sound scientific information adequate for OCS management." One reason for such a...procedures for resolving differences need to be developed. Sound and timely assessments of environmental exposure risks will require: 1) adequate levels of
A Snowball's Chance? Communities and Families Working To Prevent Youth Crime = Effet de boule de neige? Les communautes et les familles collaborent a la prevention de la criminalite chez les jeunes.

ERIC Educational Resources Information Center

Theilheimer, Ish, Ed.; Eisner, Kathy, Ed.

1996-01-01

This issue of the Canadian quarterly "Transitions," in French and English language versions, examines the prevention of youth crime, with a specific focus on activities, trends, and research dealing with Canadian families. Major articles in this issue are: (1) "A Snowball's Chance? Communities and Families Working to Prevent Youth…
Superomniphobic Surfaces for Military Applications: Nano- and Micro-Fabrication Methods. Chapter 1: Lithographic Fabrication of Surfaces with Different Microgeometries and Investigation of Their Wetting Behaviour

DTIC Science & Technology

2011-01-01

plus important, comparativement à une échelle plus large. Les résultats indiquent qu’un effet de cette nature est attribuable à des facteurs...par un angle de contact à l’avancement plus petit et un angle de contact au retrait plus important, comparativement à une échelle plus large. Les...Methods ............................................................................................................ 10 3.1 Experimental Design
Recherche universitaire et priorites nationales: l'effet du financement public sur la recherche energie solaire au Canada (University Research and National Priorities: The Effect of Public Financing on Solar Energy Research in Canada).

ERIC Educational Resources Information Center

Dalpe, Robert; Gingras, Yves

1990-01-01

The role of two main sources of university research financing in solar energy is examined to assess whether they oriented research in the direction of government programs. The strongest relationship appears to be in journal publication patterns. This scientific community has acquired the capacity to tap varying sources. (Author/MSE)
Survey of stranded gas and delivered costs to Europe of selected gas resources

USGS Publications Warehouse

Attanasi, E.D.; Freeman, P.A.

2011-01-01

Two important trends affecting the expected growth of global gas markets are (1) the shift by many industrialized countries from coal-fired electricity generation to the use of natural gas to generate electricity and (2) the industrialization of the heavily populated Asian countries of India and China. This paper surveys discovered gas in stranded conventional gas accumulations and presents estimates of the cost of developing and producing stranded gas in selected countries. Stranded gas is natural gas in discovered or identified fields that is not currently commercially producible for either physical or economic reasons. Published reserves of gas at the global level do not distinguish between volumes of gas in producing fields and volumes in nonproducing fields. Data on stranded gas reported here-that is the volumes, geographical distribution, and size distributions of stranded gas fields at the country and regional level-are based on the examination of individual-field data and represent a significant improvement in information available to industry and government decision makers. Globally, stranded gas is pervasive, but large volumes in large accumulations are concentrated in only a few areas. The cost component of the paper focuses on stranded conventional gas accumulations in Africa and South America that have the potential to augment supplies to Europe. The methods described for the computation of extraction and transport costs are innovative in that they use information on the sizes and geographical distribution of the identified stranded gas fields. The costs are based on industry data specific to the country and geologic basin where the stranded gas is located. Gas supplies to Europe can be increased significantly at competitive costs by the development of stranded gas. Net extraction costs of producing the identified gas depend critically on the natural-gas-liquids (NGLs) content, the prevailing prices of liquids, the size of the gas accumulation, and the deposit's location. The diversity of the distribution of stranded gas is one obstacle to the exercise of market power by the Gas Exporting Countries Forum (GECF). Copyright ?? 2011 Society of Petroleum Engineers.
Gauging the influence of increased search effort on reporting rates of bottlenose dolphin (Tursiops truncatus) strandings following the deepwater horizon oil spill.

PubMed

Pitchford, Jonathan L; Garcia, Michael; Pulis, Eric E; Ambert, Ashley Millan; Heaton, Andrew J; Solangi, Moby

2018-01-01

The co-occurrence of the Deepwater Horizon oil spill and the northern Gulf of Mexico cetacean Unusual Mortality Event have raised questions about the stability of inshore bottlenose dolphin (Tursiops truncatus) populations throughout the region. Several factors could have contributed to the ongoing event, but little attention has been paid to the potential effects of increased search effort and reporting of strandings associated with oil spill response activities, which were widespread for an extended period. This study quantified the influence of increased search effort by estimating the number of bottlenose dolphin strandings reported by oil spill responders and comparing monthly stranding rates with and without response-related records. Results showed that response teams reported an estimated 58% of strandings during the Active Response period within the study area. Comparison of Poisson rates tests showed that when responder-influenced stranding records were removed, the monthly stranding rates from the Active Response period (May 2010 -April 2014) were similar to the Post-Removal Actions Deemed Complete period (May 2013 -March 2015) (e.g., p = 0.83 for remote areas in Louisiana). Further, analyses using the Getis-Ord Gi* spatial statistic showed that when response-related stranding reports were removed from the Active Response period, significant spatial clustering of strandings (p < 0.05) was reduced by 48% in coastal Louisiana. Collectively, these results suggest that increased search effort resulting from the Deepwater Horizon oil spill response throughout remote portions of the Unusual Mortality Event geographic region had the capacity to increase reporting and recovery of marine mammal strandings to unusually high levels. To better understand how stranding data relates to actual mortality, more work is needed to quantify dolphin population size, population trends, and carcass detection rates including the role of search effort. This is vital for understanding the status of a protected species within the northern Gulf of Mexico.
The role of cytosine methylation on charge transport through a DNA strand

DOE Office of Scientific and Technical Information (OSTI.GOV)

Qi, Jianqing, E-mail: jqqi@uw.edu; Anantram, M. P., E-mail: anantmp@uw.edu; Govind, Niranjan, E-mail: niri.govind@pnnl.gov

Cytosine methylation has been found to play a crucial role in various biological processes, including a number of human diseases. The detection of this small modification remains challenging. In this work, we computationally explore the possibility of detecting methylated DNA strands through direct electrical conductance measurements. Using density functional theory and the Landauer-Büttiker method, we study the electronic properties and charge transport through an eight base-pair methylated DNA strand and its native counterpart. We first analyze the effect of cytosine methylation on the tight-binding parameters of two DNA strands and then model the transmission of the electrons and conductance throughmore » the strands both with and without decoherence. We find that the main difference of the tight-binding parameters between the native DNA and the methylated DNA lies in the on-site energies of (methylated) cytosine bases. The intra- and inter-strand hopping integrals between two nearest neighboring guanine base and (methylated) cytosine base also change with the addition of the methyl groups. Our calculations show that in the phase-coherent limit, the transmission of the methylated strand is close to the native strand when the energy is nearby the highest occupied molecular orbital level and larger than the native strand by 5 times in the bandgap. The trend in transmission also holds in the presence of the decoherence with the same rate. The lower conductance for the methylated strand in the experiment is suggested to be caused by the more stable structure due to the introduction of the methyl groups. We also study the role of the exchange-correlation functional and the effect of contact coupling by choosing coupling strengths ranging from weak to strong coupling limit.« less
A Sensor-Type PC Strand with an Embedded FBG Sensor for Monitoring Prestress Forces

PubMed Central

Kim, Sung Tae; Park, YoungHwan; Park, Sung Yong; Cho, Keunhee; Cho, Jeong-Rae

2015-01-01

Prestressed Concrete Wire and Strand (PC) strands are the most used materials to introduce prestress in a Pre-Stressed Concrete (PSC) structure. However, it is difficult to evaluate the final prestress force of the PC strand after prestressing or its residual prestress force after completion of the structure on site. This impossibility to assess eventual loss of prestress of the PC strand has resulted in a number of serious accidents and even in the collapse of several structures. This situation stresses the necessity to maintain the prestress force residual or after prestressing for the evaluation of the health of the concrete structure throughout its lifespan. Recently, several researchers have studied methods enabling one to verify the prestress force by inserting an optical fiber sensor inside the strand but failed to provide simple techniques for the fabrication of these devices to fulfill measurement performance from the design prestress to failure. Moreover, these methods require the additional installation of electrical resistance strain gages, displacement sensors and load cells on the outer surface of the structure for long-term precise measurement. This paper proposes a method enabling one to evaluate precisely and effectively the prestress force of the PC strand and intends to verify the applicability of the proposed method on actual concrete structures. To that end, an innovative PC strand is developed by embedding a Fiber Bragg Grating (FBG) sensor in the core wire of the PC strand so as to enable short term as well as long term monitoring. The measurement performance of the developed strand is then evaluated experimentally and the reliability of the monitoring data is assessed. PMID:25580903
A sensor-type PC strand with an embedded FBG sensor for monitoring prestress forces.

PubMed

Kim, Sung Tae; Park, YoungHwan; Park, Sung Yong; Cho, Keunhee; Cho, Jeong-Rae

2015-01-08

Prestressed Concrete Wire and Strand (PC) strands are the most used materials to introduce prestress in a Pre-Stressed Concrete (PSC) structure. However, it is difficult to evaluate the final prestress force of the PC strand after prestressing or its residual prestress force after completion of the structure on site. This impossibility to assess eventual loss of prestress of the PC strand has resulted in a number of serious accidents and even in the collapse of several structures. This situation stresses the necessity to maintain the prestress force residual or after prestressing for the evaluation of the health of the concrete structure throughout its lifespan. Recently, several researchers have studied methods enabling one to verify the prestress force by inserting an optical fiber sensor inside the strand but failed to provide simple techniques for the fabrication of these devices to fulfill measurement performance from the design prestress to failure. Moreover, these methods require the additional installation of electrical resistance strain gages, displacement sensors and load cells on the outer surface of the structure for long-term precise measurement. This paper proposes a method enabling one to evaluate precisely and effectively the prestress force of the PC strand and intends to verify the applicability of the proposed method on actual concrete structures. To that end, an innovative PC strand is developed by embedding a Fiber Bragg Grating (FBG) sensor in the core wire of the PC strand so as to enable short term as well as long term monitoring. The measurement performance of the developed strand is then evaluated experimentally and the reliability of the monitoring data is assessed.

The role of cytosine methylation on charge transport through a DNA strand

NASA Astrophysics Data System (ADS)

Qi, Jianqing; Govind, Niranjan; Anantram, M. P.

2015-09-01

Cytosine methylation has been found to play a crucial role in various biological processes, including a number of human diseases. The detection of this small modification remains challenging. In this work, we computationally explore the possibility of detecting methylated DNA strands through direct electrical conductance measurements. Using density functional theory and the Landauer-Büttiker method, we study the electronic properties and charge transport through an eight base-pair methylated DNA strand and its native counterpart. We first analyze the effect of cytosine methylation on the tight-binding parameters of two DNA strands and then model the transmission of the electrons and conductance through the strands both with and without decoherence. We find that the main difference of the tight-binding parameters between the native DNA and the methylated DNA lies in the on-site energies of (methylated) cytosine bases. The intra- and inter-strand hopping integrals between two nearest neighboring guanine base and (methylated) cytosine base also change with the addition of the methyl groups. Our calculations show that in the phase-coherent limit, the transmission of the methylated strand is close to the native strand when the energy is nearby the highest occupied molecular orbital level and larger than the native strand by 5 times in the bandgap. The trend in transmission also holds in the presence of the decoherence with the same rate. The lower conductance for the methylated strand in the experiment is suggested to be caused by the more stable structure due to the introduction of the methyl groups. We also study the role of the exchange-correlation functional and the effect of contact coupling by choosing coupling strengths ranging from weak to strong coupling limit.
Programming Self-Assembly of DNA Origami Honeycomb Two-Dimensional Lattices and Plasmonic Metamaterials.

PubMed

Wang, Pengfei; Gaitanaros, Stavros; Lee, Seungwoo; Bathe, Mark; Shih, William M; Ke, Yonggang

2016-06-22

Scaffolded DNA origami has proven to be a versatile method for generating functional nanostructures with prescribed sub-100 nm shapes. Programming DNA-origami tiles to form large-scale 2D lattices that span hundreds of nanometers to the micrometer scale could provide an enabling platform for diverse applications ranging from metamaterials to surface-based biophysical assays. Toward this end, here we design a family of hexagonal DNA-origami tiles using computer-aided design and demonstrate successful self-assembly of micrometer-scale 2D honeycomb lattices and tubes by controlling their geometric and mechanical properties including their interconnecting strands. Our results offer insight into programmed self-assembly of low-defect supra-molecular DNA-origami 2D lattices and tubes. In addition, we demonstrate that these DNA-origami hexagon tiles and honeycomb lattices are versatile platforms for assembling optical metamaterials via programmable spatial arrangement of gold nanoparticles (AuNPs) into cluster and superlattice geometries.
Double-stranded RNA virus in the human pathogenic fungus Blastomyces dermatitidis.

PubMed Central

Kohno, S; Fujimura, T; Rulong, S; Kwon-Chung, K J

1994-01-01

Double-stranded RNA viruses were detected in a strain of Blastomyces dermatitidis isolated from a patient in Uganda. The viral particles are spherical (mostly 44 to 50 nm in diameter) and consist of about 25% double-stranded RNA (5 kb) and 75% protein (90 kDa). The virus contains transcriptional RNA polymerase activity; it synthesized single-stranded RNA in vitro in a conservative manner. The newly synthesized single-stranded RNA was a full-length strand, and the rate of chain elongation was approximately 170 nucleotides per min. The virus-containing strain shows no morphological difference from virus-free strains in the mycelial phase. Although the association with the presence of the virus is unclear, the virus-infected strain converts to the yeast form at 37 degrees C, but the yeast cells fail to multiply at that temperature. Images PMID:7933142
Enzyme-free colorimetric detection systems based on the DNA strand displacement competition reaction

NASA Astrophysics Data System (ADS)

Zhang, Z.; Birkedal, V.; Gothelf, K. V.

2016-05-01

The strand displacement competition assay is based on the dynamic equilibrium of the competitive hybridization of two oligonucleotides (A and B) to a third oligonucleotide (S). In the presence of an analyte that binds to a specific affinity-moiety conjugated to strand B, the equilibrium shifts, which can be detected by a shift in the fluorescence resonance energy transfer signal between dyes attached to the DNA strands. In the present study we have integrated an ATP aptamer in the strand B and demonstrated the optical detection of ATP. Furthermore we explore a new readout method using a split G-quadruplex DNAzyme for colorimetric readout of the detection of streptavidin by the naked eye. Finally, we integrate the whole G-quadruplex DNAzyme system in a single DNA strand and show that it is applicable to colorimetric detection.
Isolation and characterization of naturally occurring hairpin structures in single-stranded DNA of coliphage M13

DOE Office of Scientific and Technical Information (OSTI.GOV)

Niyogi, S.K.; Mitra, S.

With precise conditions of digestion with single-strand-specific nucleases, namely, endonuclease S1 of Aspergillus oryzae and exonuclease I of Escherichia coli, nuclease-resistant DNA cores can be obtained reproducibly from single-stranded M13 DNA. The DNA cores are composed almost exclusively of two sizes (60 and 44 nucleotides long). These have high (G + C)-contents relative to that of intact M13 DNA, and arise from restricted regions of the M13 genome. The resistance of these fragments to single-strand-specific nucleases and their nondenaturability strongly suggest the presence of double-stranded segments in these core pieces. That the core pieces are only partially double-stranded is shownmore » by their lack of complete base complementarity and their pattern of elution from hydroxyapatite.« less
Cryptic MCAT enhancer regulation in fibroblasts and smooth muscle cells. Suppression of TEF-1 mediated activation by the single-stranded DNA-binding proteins, Pur alpha, Pur beta, and MSY1.

PubMed

Carlini, Leslie E; Getz, Michael J; Strauch, Arthur R; Kelm, Robert J

2002-03-08

An asymmetric polypurine-polypyrimidine cis-element located in the 5' region of the mouse vascular smooth muscle alpha-actin gene serves as a binding site for multiple proteins with specific affinity for either single- or double-stranded DNA. Here, we test the hypothesis that single-stranded DNA-binding proteins are responsible for preventing a cryptic MCAT enhancer centered within this element from cooperating with a nearby serum response factor-interacting CArG motif to trans-activate the minimal promoter in fibroblasts and smooth muscle cells. DNA binding studies revealed that the core MCAT sequence mediates binding of transcription enhancer factor-1 to the double-stranded polypurine-polypyrimidine element while flanking nucleotides account for interaction of Pur alpha and Pur beta with the purine-rich strand and MSY1 with the complementary pyrimidine-rich strand. Mutations that selectively impaired high affinity single-stranded DNA binding by fibroblast or smooth muscle cell-derived Pur alpha, Pur beta, and MSY1 in vitro, released the cryptic MCAT enhancer from repression in transfected cells. Additional experiments indicated that Pur alpha, Pur beta, and MSY1 also interact specifically, albeit weakly, with double-stranded DNA and with transcription enhancer factor-1. These results are consistent with two plausible models of cryptic MCAT enhancer regulation by Pur alpha, Pur beta, and MSY1 involving either competitive single-stranded DNA binding or masking of MCAT-bound transcription enhancer factor-1.
Gold nanoparticle enhanced fluorescence anisotropy for the assay of single nucleotide polymorphisms (SNPs) based on toehold-mediated strand-displacement reaction.

PubMed

Wang, Xinyi; Zou, Mingjian; Huang, Hongduan; Ren, Yuqian; Li, Limei; Yang, Xiaoda; Li, Na

2013-03-15

We developed a highly differentiating, homogeneous gold nanoparticle (AuNP) enhanced fluorescence anisotropic method for single nucleotide polymorphism (SNP) detection at nanomolar level using toehold-mediated strand-displacement reaction. The template strand, containing a toehold domain with an allele-specific site, was immobilized on the surface of AuNPs, and the solution fluorescence anisotropy was markedly enhanced when the fluorescein-labeled blocking DNA was attached to the AuNP via hybridization. Strand-displacement by the target ssDNA strand resulted in detachment of fluorescein-labeled DNA from AuNPs, and thus decreased fluorescence anisotropy. The drastic kinetic difference in strand-displacement from toehold design was used to distinguish between the perfectly matched and the single-base mismatched strands. Free energy changes were calculated to elucidate the dependence of the differentiation ability on the mutation site in the toehold region. A solid negative signal change can be obtained for single-base mismatched strand in the dynamic range of the calibration curve, and a more than 10-fold signal difference can still be observed in a mixed solution containing 100 times the single-base mismatched strand, indicating the good specificity of the method. This proposed method can be performed with a standard spectrofluorimeter in a homogeneous and cost-effective manner, and has the potential to be extended to the application of fluorescence anisotropy method of SNP detection. Copyright © 2012 Elsevier B.V. All rights reserved.
Ca2+ improves organization of single-stranded DNA bases in human Rad51 filament, explaining stimulatory effect on gene recombination.

PubMed

Fornander, Louise H; Frykholm, Karolin; Reymer, Anna; Renodon-Cornière, Axelle; Takahashi, Masayuki; Nordén, Bengt

2012-06-01

Human RAD51 protein (HsRad51) catalyses the DNA strand exchange reaction for homologous recombination. To clarify the molecular mechanism of the reaction in vitro being more effective in the presence of Ca(2+) than of Mg(2+), we have investigated the effect of these ions on the structure of HsRad51 filament complexes with single- and double-stranded DNA, the reaction intermediates. Flow linear dichroism spectroscopy shows that the two ionic conditions induce significantly different structures in the HsRad51/single-stranded DNA complex, while the HsRad51/double-stranded DNA complex does not demonstrate this ionic dependence. In the HsRad51/single-stranded DNA filament, the primary intermediate of the strand exchange reaction, ATP/Ca(2+) induces an ordered conformation of DNA, with preferentially perpendicular orientation of nucleobases relative to the filament axis, while the presence of ATP/Mg(2+), ADP/Mg(2+) or ADP/Ca(2+) does not. A high strand exchange activity is observed for the filament formed with ATP/Ca(2+), whereas the other filaments exhibit lower activity. Molecular modelling suggests that the structural variation is caused by the divalent cation interfering with the L2 loop close to the DNA-binding site. It is proposed that the larger Ca(2+) stabilizes the loop conformation and thereby the protein-DNA interaction. A tight binding of DNA, with bases perpendicularly oriented, could facilitate strand exchange.
Stress and Friction Distribution around Slab Corner in Continuous Casting Mold with Different Corner Structures

NASA Astrophysics Data System (ADS)

Yu, Sheng; Long, Mujun; Chen, Huabiao; Chen, Dengfu; Liu, Tao; Duan, Huamei; Cao, Junsheng

2018-06-01

The non-uniform friction and thermal stress in the mold are important as causes of the transverse cracks around strand corner. To analyze the stress distribution features around strand corner, a three-dimensional thermo-elastoplastic finite-element mold model with different corner structures (right-angle, big-chamfer, multi-chamfer, and fillet) was established. The temperature field in the mold was indirectly coupled through a three-dimensional fluid flow and heat transfer model. In addition, the non-uniform mold friction stress loaded on the strand surface was calculated through a friction model. The results show that the stress distribution on the shell is similar to the temperature distribution. The stress concentration appears in the strand corner and the lower part of wide face. The friction stress enhances the corner stress around the edge of the air-gap. For chamfered molds, the stress around the corner between the wide face and chamfer face is larger than that between the narrow face and chamfer face. Around the corner region, both the stress peak and the area of the large stress zone of the right-angle strand are the largest, while those of big-chamfered, multi-chamfered, and fillet strands decrease in that order. The stress peak position of the chamfered strands is closer to the mold exit than that of the right-angle strand. Compared with the use of the right-angle mold, the application of chamfered molds is able to reduce the stress concentration around the strand corner.
Stress and Friction Distribution around Slab Corner in Continuous Casting Mold with Different Corner Structures

NASA Astrophysics Data System (ADS)

Yu, Sheng; Long, Mujun; Chen, Huabiao; Chen, Dengfu; Liu, Tao; Duan, Huamei; Cao, Junsheng

2018-02-01

The non-uniform friction and thermal stress in the mold are important as causes of the transverse cracks around strand corner. To analyze the stress distribution features around strand corner, a three-dimensional thermo-elastoplastic finite-element mold model with different corner structures (right-angle, big-chamfer, multi-chamfer, and fillet) was established. The temperature field in the mold was indirectly coupled through a three-dimensional fluid flow and heat transfer model. In addition, the non-uniform mold friction stress loaded on the strand surface was calculated through a friction model. The results show that the stress distribution on the shell is similar to the temperature distribution. The stress concentration appears in the strand corner and the lower part of wide face. The friction stress enhances the corner stress around the edge of the air-gap. For chamfered molds, the stress around the corner between the wide face and chamfer face is larger than that between the narrow face and chamfer face. Around the corner region, both the stress peak and the area of the large stress zone of the right-angle strand are the largest, while those of big-chamfered, multi-chamfered, and fillet strands decrease in that order. The stress peak position of the chamfered strands is closer to the mold exit than that of the right-angle strand. Compared with the use of the right-angle mold, the application of chamfered molds is able to reduce the stress concentration around the strand corner.
Markers of Decompression Stress of Mass Stranded/Live Caught and Released vs. Single Stranded Marine Mammals

DTIC Science & Technology

2014-09-30

Caught and Released vs. Single Stranded Marine Mammals Michael Moore Biology Department Woods Hole Oceanographic Institution Woods Hole, MA 02543...analyze blood samples from captive, wild-caught, and stranded marine mammals in order to compare concentrations of Microparticles (MPs). If confirmed...military sonar or during seismic exploration, may harm marine animals. It has been suggested that alteration in physiology or diving behavior may
The binding efficiency of RPA to telomeric G-strands folded into contiguous G-quadruplexes is independent of the number of G4 units.

PubMed

Lancrey, Astrid; Safa, Layal; Chatain, Jean; Delagoutte, Emmanuelle; Riou, Jean-François; Alberti, Patrizia; Saintomé, Carole

2018-03-01

Replication protein A (RPA) is a single-stranded DNA binding protein involved in replication and in telomere maintenance. During telomere replication, G-quadruplexes (G4) can accumulate on the lagging strand template and need to be resolved. It has been shown that human RPA is able to unfold a single G4. Nevertheless, the G-strand of human telomeres is prone to fold into higher-order structures formed by contiguous G-quadruplexes. To understand how RPA deals with these structures, we studied its interaction with telomeric G-strands folding into an increasing number of contiguous G4s. The aim of this study was to determine whether the efficiency of binding/unfolding of hRPA to telomeric G-strands depends on the number of G4 units. Our data show that the number n of contiguous G4 units (n ≥ 2) does not affect the efficiency of hRPA to coat transiently exposed single-stranded telomeric G-strands. This feature may be essential in preventing instability due to G4 structures during telomere replication. Copyright © 2017 Elsevier B.V. and Société Française de Biochimie et Biologie Moléculaire (SFBBM). All rights reserved.
Observed mechanism for the breakup of small bundles of cellulose Iα and Iβ in ionic liquids from molecular dynamics simulations.

PubMed

Rabideau, Brooks D; Agarwal, Animesh; Ismail, Ahmed E

2013-04-04

Explicit, all-atom molecular dynamics simulations are used to study the breakup of small bundles of cellulose Iα and Iβ in the ionic liquids [BMIM]Cl, [EMIM]Ac, and [DMIM]DMP. In all cases, significant breakup of the bundles is observed with the initial breakup following a common underlying mechanism. Anions bind strongly to the hydroxyl groups of the exterior strands of the bundle, forming negatively charged complexes. Binding also weakens the intrastrand hydrogen bonds present in the cellulose strands, providing greater strand flexibility. Cations then intercalate between the individual strands, likely due to charge imbalances, providing the bulk to push the individual moieties apart and initiating the separation. The peeling of an individual strand from the main bundle is observed in [EMIM]Ac with an analysis of its hydrogen bonds with other strands showing that the chain detaches glucan by glucan from the main bundle in discrete, rapid events. Further analysis shows that the intrastrand hydrogen bonds of each glucan tend to break for a sustained period of time before the interstrand hydrogen bonds break and strand detachment occurs. Examination of similar nonpeeling strands shows that, without this intrastrand hydrogen bond breakage, the structural rigidity of the individual unit can hinder its peeling despite interstrand hydrogen bond breakage.
Heat transfer characteristics of an emergent strand

NASA Technical Reports Server (NTRS)

Simon, W. E.; Witte, L. C.; Hedgcoxe, P. G.

1974-01-01

A mathematical model was developed to describe the heat transfer characteristics of a hot strand emerging into a surrounding coolant. A stable strand of constant efflux velocity is analyzed, with a constant (average) heat transfer coefficient on the sides and leading surface of the strand. After developing a suitable governing equation to provide an adequate description of the physical system, the dimensionless governing equation is solved with Laplace transform methods. The solution yields the temperature within the strand as a function of axial distance and time. Generalized results for a wide range of parameters are presented, and the relationship of the results and experimental observations is discussed.
Cosegregation of chromosomes containing immortal DNA strands in cells that cycle with asymmetric stem cell kinetics.

PubMed

Merok, Joshua R; Lansita, Janice A; Tunstead, James R; Sherley, James L

2002-12-01

A long-standing intriguing hypothesis in cancer biology is that adult stem cells avoid mutations from DNA replication errors by a unique pattern of chromosome segregation. At each asymmetric cell division, adult stem cells have been postulated to selectively retain a set of chromosomes that contain old template DNA strands (i.e., "immortal DNA strands"). Using cultured cells that cycle with asymmetric cell kinetics, we confirmed both the existence of immortal DNA strands and the cosegregation of chromosomes that bear them. Our findings also lead us to propose a role for immortal DNA strands in tissue aging as well as cancer.
Vegetation controls on the maximum size of coastal dunes.

PubMed

Durán, Orencio; Moore, Laura J

2013-10-22

Coastal dunes, in particular foredunes, support a resilient ecosystem and reduce coastal vulnerability to storms. In contrast to dry desert dunes, coastal dunes arise from interactions between biological and physical processes. Ecologists have traditionally addressed coastal ecosystems by assuming that they adapt to preexisting dune topography, whereas geomorphologists have studied the properties of foredunes primarily in connection to physical, not biological, factors. Here, we study foredune development using an ecomorphodynamic model that resolves the coevolution of topography and vegetation in response to both physical and ecological factors. We find that foredune growth is eventually limited by a negative feedback between wind flow and topography. As a consequence, steady-state foredunes are scale invariant, which allows us to derive scaling relations for maximum foredune height and formation time. These relations suggest that plant zonation (in particular for strand "dune-building" species) is the primary factor controlling the maximum size of foredunes and therefore the amount of sand stored in a coastal dune system. We also find that aeolian sand supply to the dunes determines the timescale of foredune formation. These results offer a potential explanation for the empirical relation between beach type and foredune size, in which large (small) foredunes are found on dissipative (reflective) beaches. Higher waves associated with dissipative beaches increase the disturbance of strand species, which shifts foredune formation landward and thus leads to larger foredunes. In this scenario, plants play a much more active role in modifying their habitat and altering coastal vulnerability than previously thought.
Corrosion characteristics of post-tensioning strands in ungrouted ducts : summary.

DOT National Transportation Integrated Search

2011-01-01

To prevent corrosion of post-tensioning strands, FDOT construction specifications currently require post-tensioning ducts to be grouted within seven calendar days of strand installation. This period challenges construction schedules on large projects...
Bubbles in live-stranded dolphins.

PubMed

Dennison, S; Moore, M J; Fahlman, A; Moore, K; Sharp, S; Harry, C T; Hoppe, J; Niemeyer, M; Lentell, B; Wells, R S

2012-04-07

Bubbles in supersaturated tissues and blood occur in beaked whales stranded near sonar exercises, and post-mortem in dolphins bycaught at depth and then hauled to the surface. To evaluate live dolphins for bubbles, liver, kidneys, eyes and blubber-muscle interface of live-stranded and capture-release dolphins were scanned with B-mode ultrasound. Gas was identified in kidneys of 21 of 22 live-stranded dolphins and in the hepatic portal vasculature of 2 of 22. Nine then died or were euthanized and bubble presence corroborated by computer tomography and necropsy, 13 were released of which all but two did not re-strand. Bubbles were not detected in 20 live wild dolphins examined during health assessments in shallow water. Off-gassing of supersaturated blood and tissues was the most probable origin for the gas bubbles. In contrast to marine mammals repeatedly diving in the wild, stranded animals are unable to recompress by diving, and thus may retain bubbles. Since the majority of beached dolphins released did not re-strand it also suggests that minor bubble formation is tolerated and will not lead to clinically significant decompression sickness.
DNA interrogation by the CRISPR RNA-guided endonuclease Cas9.

PubMed

Sternberg, Samuel H; Redding, Sy; Jinek, Martin; Greene, Eric C; Doudna, Jennifer A

2014-03-06

The clustered regularly interspaced short palindromic repeats (CRISPR)-associated enzyme Cas9 is an RNA-guided endonuclease that uses RNA-DNA base-pairing to target foreign DNA in bacteria. Cas9-guide RNA complexes are also effective genome engineering agents in animals and plants. Here we use single-molecule and bulk biochemical experiments to determine how Cas9-RNA interrogates DNA to find specific cleavage sites. We show that both binding and cleavage of DNA by Cas9-RNA require recognition of a short trinucleotide protospacer adjacent motif (PAM). Non-target DNA binding affinity scales with PAM density, and sequences fully complementary to the guide RNA but lacking a nearby PAM are ignored by Cas9-RNA. Competition assays provide evidence that DNA strand separation and RNA-DNA heteroduplex formation initiate at the PAM and proceed directionally towards the distal end of the target sequence. Furthermore, PAM interactions trigger Cas9 catalytic activity. These results reveal how Cas9 uses PAM recognition to quickly identify potential target sites while scanning large DNA molecules, and to regulate scission of double-stranded DNA.
Phosphate steering by Flap Endonuclease 1 promotes 5'-flap specificity and incision to prevent genome instability

DOE PAGES

Tsutakawa, Susan E.; Thompson, Mark J.; Arvai, Andrew S.; ...

2017-06-27

DNA replication and repair enzyme Flap Endonuclease 1 (FEN1) is vital for genome integrity, and FEN1 mutations arise in multiple cancers. FEN1 precisely cleaves single-stranded (ss) 5'-flaps one nucleotide into duplex (ds) DNA. Yet, how FEN1 selects for but does not incise the ss 5'-flap was enigmatic. Here we combine crystallographic, biochemical and genetic analyses to show that two dsDNA binding sites set the 5'polarity and to reveal unexpected control of the DNA phosphodiester backbone by electrostatic interactions. Via phosphate steering', basic residues energetically steer an inverted ss 5'-flap through a gateway over FEN1's active site and shift dsDNA formore » catalysis. Mutations of these residues cause an 18,000-fold reduction in catalytic rate in vitro and large-scale trinucleotide (GAA) n repeat expansions in vivo, implying failed phosphate-steering promotes an unanticipated lagging-strand template-switch mechanism during replication. Thus, phosphate steering is an unappreciated FEN1 function that enforces 5'-flap specificity and catalysis, preventing genomic instability.« less

DNA interrogation by the CRISPR RNA-guided endonuclease Cas9

NASA Astrophysics Data System (ADS)

Sternberg, Samuel H.; Redding, Sy; Jinek, Martin; Greene, Eric C.; Doudna, Jennifer A.

2014-03-01

The clustered regularly interspaced short palindromic repeats (CRISPR)-associated enzyme Cas9 is an RNA-guided endonuclease that uses RNA-DNA base-pairing to target foreign DNA in bacteria. Cas9-guide RNA complexes are also effective genome engineering agents in animals and plants. Here we use single-molecule and bulk biochemical experiments to determine how Cas9-RNA interrogates DNA to find specific cleavage sites. We show that both binding and cleavage of DNA by Cas9-RNA require recognition of a short trinucleotide protospacer adjacent motif (PAM). Non-target DNA binding affinity scales with PAM density, and sequences fully complementary to the guide RNA but lacking a nearby PAM are ignored by Cas9-RNA. Competition assays provide evidence that DNA strand separation and RNA-DNA heteroduplex formation initiate at the PAM and proceed directionally towards the distal end of the target sequence. Furthermore, PAM interactions trigger Cas9 catalytic activity. These results reveal how Cas9 uses PAM recognition to quickly identify potential target sites while scanning large DNA molecules, and to regulate scission of double-stranded DNA.
Structure and DNA-binding of meiosis-specific protein Hop2

NASA Astrophysics Data System (ADS)

Zhou, Donghua; Moktan, Hem; Pezza, Roberto

2014-03-01

Here we report structure elucidation of the DNA binding domain of homologous pairing protein 2 (Hop2), which is important to gene diversity when sperms and eggs are produced. Together with another protein Mnd1, Hop2 enhances the strand invasion activity of recombinase Dmc1 by over 30 times, facilitating proper synapsis of homologous chromosomes. However, the structural and biochemical bases for the function of Hop2 and Mnd1 have not been well understood. As a first step toward such understanding, we recently solved the structure for the N-terminus of Hop2 (1-84) using solution NMR. This fragment shows a typical winged-head conformation with recognized DNA binding activity. DNA interacting sites were then investigated by chemical shift perturbations in a titration experiment. Information of these sites was used to guide protein-DNA docking with MD simulation, revealing that helix 3 is stably lodged in the DNA major groove and that wing 1 (connecting strands 2 and 3) transiently comes in contact with the minor groove in nanosecond time scale. Mutagenesis analysis further confirmed the DNA binding sites in this fragment of the protein.
Phosphate steering by Flap Endonuclease 1 promotes 5'-flap specificity and incision to prevent genome instability

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tsutakawa, Susan E.; Thompson, Mark J.; Arvai, Andrew S.

DNA replication and repair enzyme Flap Endonuclease 1 (FEN1) is vital for genome integrity, and FEN1 mutations arise in multiple cancers. FEN1 precisely cleaves single-stranded (ss) 5'-flaps one nucleotide into duplex (ds) DNA. Yet, how FEN1 selects for but does not incise the ss 5'-flap was enigmatic. Here we combine crystallographic, biochemical and genetic analyses to show that two dsDNA binding sites set the 5'polarity and to reveal unexpected control of the DNA phosphodiester backbone by electrostatic interactions. Via phosphate steering', basic residues energetically steer an inverted ss 5'-flap through a gateway over FEN1's active site and shift dsDNA formore » catalysis. Mutations of these residues cause an 18,000-fold reduction in catalytic rate in vitro and large-scale trinucleotide (GAA) n repeat expansions in vivo, implying failed phosphate-steering promotes an unanticipated lagging-strand template-switch mechanism during replication. Thus, phosphate steering is an unappreciated FEN1 function that enforces 5'-flap specificity and catalysis, preventing genomic instability.« less
In vitro molecular machine learning algorithm via symmetric internal loops of DNA.

PubMed

Lee, Ji-Hoon; Lee, Seung Hwan; Baek, Christina; Chun, Hyosun; Ryu, Je-Hwan; Kim, Jin-Woo; Deaton, Russell; Zhang, Byoung-Tak

2017-08-01

Programmable biomolecules, such as DNA strands, deoxyribozymes, and restriction enzymes, have been used to solve computational problems, construct large-scale logic circuits, and program simple molecular games. Although studies have shown the potential of molecular computing, the capability of computational learning with DNA molecules, i.e., molecular machine learning, has yet to be experimentally verified. Here, we present a novel molecular learning in vitro model in which symmetric internal loops of double-stranded DNA are exploited to measure the differences between training instances, thus enabling the molecules to learn from small errors. The model was evaluated on a data set of twenty dialogue sentences obtained from the television shows Friends and Prison Break. The wet DNA-computing experiments confirmed that the molecular learning machine was able to generalize the dialogue patterns of each show and successfully identify the show from which the sentences originated. The molecular machine learning model described here opens the way for solving machine learning problems in computer science and biology using in vitro molecular computing with the data encoded in DNA molecules. Copyright © 2017. Published by Elsevier B.V.
Etude experimentale des excitations topologiques de l'effet Hall quantique a nu = 1 dans les heterostructures semiconductrices a double puits quantique

NASA Astrophysics Data System (ADS)

Charlebois, Serge

De nombreux travaux theoriques et experimentaux ont ete publies sur les excitations topologiques de gaz electroniques bidimensionnels (GE2D), appellees skyrmions, dans le regime de l'effet Hall quantique a remplissage unitaire. On attend des excitations semblables appellees bimerons dans les systemes formes de deux GE2D couples. Contrairement au cas des GE2D simples, aucune experience n'a, a notre connaissance, presente la mesure d'une propriete specifique aux bimerons. Nous presentons dans cette these des travaux experimentaux ayant pour objectif l'etude d'excitations topologiques dans les heterostructures a double puits quantique. Une manifestation attendue (les bimerons est la presence d'une anisotropie dans la conductivite a travers une constriction. Nous avons concu un dispositif original a point de contact a trois grilles non-coplanaires. Ce dispositif a trois grilles a la particularite de permettre la creation d'une constriction etroite dans le double GE2D tout en permettant l'equilibrage de la densite electronique entre les deux puits dans l'etroit canal de conduction. Nous avons fabrique ce dispositif de taille submicronique par electrolithographie sur des heterostructures a double puits. Les dispositifs ainsi fabriques ont ete etudies a basse temperature (0.3K) et ont montre un fonctionnement conforme aux attentes. Les travaux n'ont pas permis de mettre en evidence une anisotropie de transport revelatrice de l'existence de bimerons. Cette these est a notre connaissance la premiere etude experimentale visant la realisation de l'experience d'anisotropie de transport et est ainsi une contribution significative a l'avancement des connaissances dans ce domaine. Les travaux theoriques que nous presentons ont permis de montrer l'effet des excitations topologiques sur la capacite grille-GE2D du systeme. Ces travaux ouvrent la voie de la detection des bimerons par l'intermediaire de la mesure de la capacite grille-GE2D ou encore de la susceptibilite electrique du GE2D. Poursuivant cet objectif, nous avons concu, realise et teste un dispositif de mesure in situ de la capacite grille-GE2D d'une heterostructure. Nous avons egalement suggere d'autres methodes experimentales pour la mise en evidence des bimerons par le couplage de la texture de pseudospin a la capacite du GE2D.
Stranded investment, prices and privacy factor in FERC rulings

DOE Office of Scientific and Technical Information (OSTI.GOV)

O`Driscoll, M.

The Federal Energy Regulatory Commission upheld its rejection of United Illuminating Co.`s bid to recover stranded investment costs. Since UI has no wholesale customers, it is a matter best left to state regulators, FERC said. UI`s stranded investment recovery plan was part of the company`s transmission access tariff, which provides for open access transmission service at cost-based rates. FERC ordered UI to delete the stranded investment provisions, saying UI was trying to recover in its wholesale transmission rates the costs of generation facility investments that were incurred to provide service to retail customers that leave its system, reasoning that UImore » was seeking protection from what may be legitimate retail franchise competition, which is a state matter. UI, however, said deleting the stranded investment provision would preclude it from arguing in an individual rate filling under the transmission tariff that stranded investment costs should be borne by the wheeling customer.« less
A label-free fluorescent aptamer sensor based on regulation of malachite green fluorescence

PubMed Central

Xu, Weichen; Lu, Yi

2009-01-01

We report a label-free fluorescent aptamer sensor for adenosine based on the regulation of malachite green (MG) fluorescence, with comparable sensitivity and selectivity to other labeled adenosine aptamer-based sensors. The sensor consists of free MG, an aptamer strand containing an adenosine aptamer next to an MG aptamer, and a bridging strand that partially hybridizes to the aptamer strand. Such a hybridization prevents MG from binding to MG aptamer, resulting in low fluorescence of MG in the absence of adenosine. Addition of adenosine causes the adenosine aptamer to bind adenosine, weakening the hybridization of the aptamer strand with the bridging strand, making it possible for MG to bind to the aptamer strand and exhibits high fluorescence intensity. Since this design is based purely on nucleic acid hybridization, it can be generally applied to other aptamers for the label-free detection of a broad range of analytes. PMID:20017558
Enhanced Strain Measurement Range of an FBG Sensor Embedded in Seven-Wire Steel Strands.

PubMed

Kim, Jae-Min; Kim, Chul-Min; Choi, Song-Yi; Lee, Bang Yeon

2017-07-18

FBG sensors offer many advantages, such as a lack of sensitivity to electromagnetic waves, small size, high durability, and high sensitivity. However, their maximum strain measurement range is lower than the yield strain range (about 1.0%) of steel strands when embedded in steel strands. This study proposes a new FBG sensing technique in which an FBG sensor is recoated with polyimide and protected by a polyimide tube in an effort to enhance the maximum strain measurement range of FBG sensors embedded in strands. The validation test results showed that the proposed FBG sensing technique has a maximum strain measurement range of 1.73% on average, which is 1.73 times higher than the yield strain of the strands. It was confirmed that recoating the FBG sensor with polyimide and protecting the FBG sensor using a polyimide tube could effectively enhance the maximum strain measurement range of FBG sensors embedded in strands.
Dynamic DNA nanotechnology using strand-displacement reactions

NASA Astrophysics Data System (ADS)

Zhang, David Yu; Seelig, Georg

2011-02-01

The specificity and predictability of Watson-Crick base pairing make DNA a powerful and versatile material for engineering at the nanoscale. This has enabled the construction of a diverse and rapidly growing set of DNA nanostructures and nanodevices through the programmed hybridization of complementary strands. Although it had initially focused on the self-assembly of static structures, DNA nanotechnology is now also becoming increasingly attractive for engineering systems with interesting dynamic properties. Various devices, including circuits, catalytic amplifiers, autonomous molecular motors and reconfigurable nanostructures, have recently been rationally designed to use DNA strand-displacement reactions, in which two strands with partial or full complementarity hybridize, displacing in the process one or more pre-hybridized strands. This mechanism allows for the kinetic control of reaction pathways. Here, we review DNA strand-displacement-based devices, and look at how this relatively simple mechanism can lead to a surprising diversity of dynamic behaviour.
Control of DNA strand displacement kinetics using toehold exchange.

PubMed

Zhang, David Yu; Winfree, Erik

2009-12-02

DNA is increasingly being used as the engineering material of choice for the construction of nanoscale circuits, structures, and motors. Many of these enzyme-free constructions function by DNA strand displacement reactions. The kinetics of strand displacement can be modulated by toeholds, short single-stranded segments of DNA that colocalize reactant DNA molecules. Recently, the toehold exchange process was introduced as a method for designing fast and reversible strand displacement reactions. Here, we characterize the kinetics of DNA toehold exchange and model it as a three-step process. This model is simple and quantitatively predicts the kinetics of 85 different strand displacement reactions from the DNA sequences. Furthermore, we use toehold exchange to construct a simple catalytic reaction. This work improves the understanding of the kinetics of nucleic acid reactions and will be useful in the rational design of dynamic DNA and RNA circuits and nanodevices.
Nuclear Proximity of Mtr4 with RNA exosome restricts DNA mutational asymmetry

PubMed Central

Lim, Junghyun; Giri, Pankaj Kumar; Kazadi, David; Laffleur, Brice; Zhang, Wanwei; Grinstein, Veronika; Pefanis, Evangelos; Brown, Lewis M.; Ladewig, Erik; Martin, Ophélie; Chen, Yuling; Rabadan, Raul; Boyer, François; Rothschild, Gerson; Cogné, Michel; Pinaud, Eric; Deng, Haiteng; Basu, Uttiya

2017-01-01

SUMMARY The distribution of sense and antisense strand DNA mutations on transcribed duplex DNA contributes to the development of immune and neural systems along with the progression of cancer. Because developmentally matured B cells undergo biologically programmed strand-specific DNA mutagenesis at focal DNA/RNA hybrid structures, they make a convenient system to investigate strand-specific mutagenesis mechanisms. We demonstrate that the sense and antisense strand DNA mutagenesis at the immunoglobulin heavy chain locus and some other regions of the B cell genome depends upon localized RNA processing protein complex formation in the nucleus. Both the physical proximity and coupled activities of RNA helicase Mtr4 (and Senataxin) with the noncoding RNA processing function of RNA exosome determine the strand specific distribution of DNA mutations. Our study suggests that strand-specific DNA mutagenesis-associated mechanisms will play major roles in other undiscovered aspects of organismic development. PMID:28431250
Current-voltage characteristics of double stranded versus single stranded DNA molecules

NASA Astrophysics Data System (ADS)

Hartzell, B.; Chen, Hong; Heremans, J. J.; McCord, B.; Soghomonian, V.

2004-03-01

Investigation of DNA conductivity has focused on the native, duplex structure, with controversial results. Here, we present the influence of the double-helical structure on charge transport through lambda DNA molecules. The current-voltage (I-V) characteristics of both disulfide-labeled double stranded DNA (dsDNA) and disulfide-labeled single stranded DNA (ssDNA) were measured. The ssDNA was formed from the dsDNA using two different methods for comparison purposes: a thermal/chemical denaturation and enzymatic digestion utilizing lambda exonuclease. Resulting I-V characteristics of both the double stranded and single stranded samples were close-to-linear when measured at room temperature. However, the ssDNA samples consistently gave conductivity values about two orders of magnitude smaller in amplitude. Our results suggest an integral relationship between the native structure of DNA with its stacked base pairs and the molecule's ability to support charge transport.(NSF NIRT 0103034)
Mammalian DNA single-strand break repair: an X-ra(y)ted affair.

PubMed

Caldecott, K W

2001-05-01

The genetic stability of living cells is continuously threatened by the presence of endogenous reactive oxygen species and other genotoxic molecules. Of particular threat are the thousands of DNA single-strand breaks that arise in each cell, each day, both directly from disintegration of damaged sugars and indirectly from the excision repair of damaged bases. If un-repaired, single-strand breaks can be converted into double-strand breaks during DNA replication, potentially resulting in chromosomal rearrangement and genetic deletion. Consequently, cells have adopted multiple pathways to ensure the rapid and efficient removal of single-strand breaks. A general feature of these pathways appears to be the extensive employment of protein-protein interactions to stimulate both the individual component steps and the overall repair reaction. Our current understanding of DNA single-strand break repair is discussed, and testable models for the architectural coordination of this important process are presented. Copyright 2001 John Wiley & Sons, Inc.
Tolerance of DNA Mismatches in Dmc1 Recombinase-mediated DNA Strand Exchange.

PubMed

Borgogno, María V; Monti, Mariela R; Zhao, Weixing; Sung, Patrick; Argaraña, Carlos E; Pezza, Roberto J

2016-03-04

Recombination between homologous chromosomes is required for the faithful meiotic segregation of chromosomes and leads to the generation of genetic diversity. The conserved meiosis-specific Dmc1 recombinase catalyzes homologous recombination triggered by DNA double strand breaks through the exchange of parental DNA sequences. Although providing an efficient rate of DNA strand exchange between polymorphic alleles, Dmc1 must also guard against recombination between divergent sequences. How DNA mismatches affect Dmc1-mediated DNA strand exchange is not understood. We have used fluorescence resonance energy transfer to study the mechanism of Dmc1-mediated strand exchange between DNA oligonucleotides with different degrees of heterology. The efficiency of strand exchange is highly sensitive to the location, type, and distribution of mismatches. Mismatches near the 3' end of the initiating DNA strand have a small effect, whereas most mismatches near the 5' end impede strand exchange dramatically. The Hop2-Mnd1 protein complex stimulates Dmc1-catalyzed strand exchange on homologous DNA or containing a single mismatch. We observed that Dmc1 can reject divergent DNA sequences while bypassing a few mismatches in the DNA sequence. Our findings have important implications in understanding meiotic recombination. First, Dmc1 acts as an initial barrier for heterologous recombination, with the mismatch repair system providing a second level of proofreading, to ensure that ectopic sequences are not recombined. Second, Dmc1 stepping over infrequent mismatches is likely critical for allowing recombination between the polymorphic sequences of homologous chromosomes, thus contributing to gene conversion and genetic diversity. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.
Tolerance of DNA Mismatches in Dmc1 Recombinase-mediated DNA Strand Exchange*

PubMed Central

Borgogno, María V.; Monti, Mariela R.; Zhao, Weixing; Sung, Patrick; Argaraña, Carlos E.; Pezza, Roberto J.

2016-01-01

Recombination between homologous chromosomes is required for the faithful meiotic segregation of chromosomes and leads to the generation of genetic diversity. The conserved meiosis-specific Dmc1 recombinase catalyzes homologous recombination triggered by DNA double strand breaks through the exchange of parental DNA sequences. Although providing an efficient rate of DNA strand exchange between polymorphic alleles, Dmc1 must also guard against recombination between divergent sequences. How DNA mismatches affect Dmc1-mediated DNA strand exchange is not understood. We have used fluorescence resonance energy transfer to study the mechanism of Dmc1-mediated strand exchange between DNA oligonucleotides with different degrees of heterology. The efficiency of strand exchange is highly sensitive to the location, type, and distribution of mismatches. Mismatches near the 3′ end of the initiating DNA strand have a small effect, whereas most mismatches near the 5′ end impede strand exchange dramatically. The Hop2-Mnd1 protein complex stimulates Dmc1-catalyzed strand exchange on homologous DNA or containing a single mismatch. We observed that Dmc1 can reject divergent DNA sequences while bypassing a few mismatches in the DNA sequence. Our findings have important implications in understanding meiotic recombination. First, Dmc1 acts as an initial barrier for heterologous recombination, with the mismatch repair system providing a second level of proofreading, to ensure that ectopic sequences are not recombined. Second, Dmc1 stepping over infrequent mismatches is likely critical for allowing recombination between the polymorphic sequences of homologous chromosomes, thus contributing to gene conversion and genetic diversity. PMID:26709229
DNA unwinding by ring-shaped T4 helicase gp41 is hindered by tension on the occluded strand.

PubMed

Ribeck, Noah; Saleh, Omar A

2013-01-01

The replicative helicase for bacteriophage T4 is gp41, which is a ring-shaped hexameric motor protein that achieves unwinding of dsDNA by translocating along one strand of ssDNA while forcing the opposite strand to the outside of the ring. While much study has been dedicated to the mechanism of binding and translocation along the ssDNA strand encircled by ring-shaped helicases, relatively little is known about the nature of the interaction with the opposite, 'occluded' strand. Here, we investigate the interplay between the bacteriophage T4 helicase gp41 and the ss/dsDNA fork by measuring, at the single-molecule level, DNA unwinding events on stretched DNA tethers in multiple geometries. We find that gp41 activity is significantly dependent on the geometry and tension of the occluded strand, suggesting an interaction between gp41 and the occluded strand that stimulates the helicase. However, the geometry dependence of gp41 activity is the opposite of that found previously for the E. coli hexameric helicase DnaB. Namely, tension applied between the occluded strand and dsDNA stem inhibits unwinding activity by gp41, while tension pulling apart the two ssDNA tails does not hinder its activity. This implies a distinct variation in helicase-occluded strand interactions among superfamily IV helicases, and we propose a speculative model for this interaction that is consistent with both the data presented here on gp41 and the data that had been previously reported for DnaB.
Protein stabilization by introduction of cross-strand disulfides.

PubMed

Chakraborty, Kausik; Thakurela, Sudhir; Prajapati, Ravindra Singh; Indu, S; Ali, P Shaik Syed; Ramakrishnan, C; Varadarajan, Raghavan

2005-11-08

Disulfides cross-link residues in a protein that are separated in primary sequence and stabilize the protein through entropic destabilization of the unfolded state. While the removal of naturally occurring disulfides leads to protein destabilization, introduction of engineered disulfides does not always lead to significant stabilization of a protein. We have analyzed naturally occurring disulfides that span adjacent antiparallel strands of beta sheets (cross-strand disulfides). Cross-strand disulfides have recently been implicated as redox-based conformational switches in proteins such as gp120 and CD4. The propensity of these disulfides to act as conformational switches was postulated on the basis of the hypothesis that this class of disulfide is conformationally strained. In the present analysis, there was no evidence to suggest that cross-strand disulfides are more strained compared to other disulfides as assessed by their torsional energy. It was also observed that these disulfides occur solely at non-hydrogen-bonded (NHB) registered pairs of adjacent antiparallel strands and not at hydrogen-bonded (HB) positions as suggested previously. One of the half-cystines involved in cross-strand disulfide formation often occurs at an edge strand. Experimental confirmation of the stabilizing effects of such disulfides was carried out in Escherichia coli thioredoxin. Four pairs of cross-strand cysteines were introduced, two at HB and two at NHB pairs. Disulfides were formed in all four cases. However, as predicted from our analysis, disulfides at NHB positions resulted in an increase in melting temperature of 7-10 degrees C, while at HB positions there was a corresponding decrease of -7 degrees C. The reduced state of all proteins had similar stability.
Assembling of G-strands into novel tetra-molecular parallel G4-DNA nanostructures using avidin-biotin recognition.

PubMed

Borovok, Natalia; Iram, Natalie; Zikich, Dragoslav; Ghabboun, Jamal; Livshits, Gideon I; Porath, Danny; Kotlyar, Alexander B

2008-09-01

We describe a method for the preparation of novel long (hundreds of nanometers), uniform, inter-molecular G4-DNA molecules composed of four parallel G-strands. The only long continuous G4-DNA reported so far are intra-molecular structures made of a single G-strand. To enable a tetra-molecular assembly of the G-strands we developed a novel approach based on avidin-biotin biological recognition. The steps of the G4-DNA production include: (i) Enzymatic synthesis of long poly(dG)-poly(dC) molecules with biotinylated poly(dG)-strand; (ii) Formation of a complex between avidin-tetramer and four biotinylated poly(dG)-poly(dC) molecules; (iii) Separation of the poly(dC) strands from the poly(dG)-strands, which are connected to the avidin; (iv) Assembly of the four G-strands attached to the avidin into tetra-molecular G4-DNA. The average contour length of the formed structures, as measured by AFM, is equal to that of the initial poly(dG)-poly(dC) molecules, suggesting a tetra-molecular mechanism of the G-strands assembly. The height of tetra-molecular G4-nanostructures is larger than that of mono-molecular G4-DNA molecules having similar contour length. The CD spectra of the tetra- and mono-molecular G4-DNA are markedly different, suggesting different structural organization of these two types of molecules. The tetra-molecular G4-DNA nanostructures showed clear electrical polarizability. This suggests that they may be useful for molecular electronics.
Corrosion characteristics of unprotected post-tensioning strands under stress.

DOT National Transportation Integrated Search

2014-05-01

An investigation was conducted to determine the effect of stress condition : and environmental exposure on corrosion of post-tensioned strands during ungrouted periods. : Exposures for periods of up to 4 weeks of stressed, as-received strand placed i...
Examining a DNA Replication Requirement for Bacteriophage λ Red- and Rac Prophage RecET-Promoted Recombination in Escherichia coli.

PubMed

Thomason, Lynn C; Costantino, Nina; Court, Donald L

2016-09-13

Recombineering, in vivo genetic engineering with bacteriophage homologous recombination systems, is a powerful technique for making genetic modifications in bacteria. Two systems widely used in Escherichia coli are the Red system from phage λ and RecET from the defective Rac prophage. We investigated the in vivo dependence of recombineering on DNA replication of the recombining substrate using plasmid targets. For λ Red recombination, when DNA replication of a circular target plasmid is prevented, recombination with single-stranded DNA oligonucleotides is greatly reduced compared to that under replicating conditions. For RecET recombination, when DNA replication of the targeted plasmid is prevented, the recombination frequency is also reduced, to a level identical to that seen for the Red system in the absence of replication. The very low level of oligonucleotide recombination observed in the absence of any phage recombination functions is the same in the presence or absence of DNA replication. In contrast, both the Red and RecET systems recombine a nonreplicating linear dimer plasmid with high efficiency to yield a circular monomer. Therefore, the DNA replication requirement is substrate dependent. Our data are consistent with recombination by both the Red and RecET systems occurring predominately by single-strand annealing rather than by strand invasion. Bacteriophage homologous recombination systems are widely used for in vivo genetic engineering in bacteria. Single- or double-stranded linear DNA substrates containing short flanking homologies to chromosome targets are used to generate precise and accurate genetic modifications when introduced into bacteria expressing phage recombinases. Understanding the molecular mechanism of these recombination systems will facilitate improvements in the technology. Here, two phage-specific systems are shown to require exposure of complementary single-strand homologous targets for efficient recombination; these single-strand regions may be created during DNA replication or by single-strand exonuclease digestion of linear duplex DNA. Previously, in vitro studies reported that these recombinases promote the single-strand annealing of two complementary DNAs and also strand invasion of a single DNA strand into duplex DNA to create a three-stranded region. Here, in vivo experiments show that recombinase-mediated annealing of complementary single-stranded DNA is the predominant recombination pathway in E. coli. Copyright © 2016 Thomason et al.

Report of the Working Group on Aerodynamics of Aircraft Afterbody.

DTIC Science & Technology

1986-06-01

14 I 21 2.1.71 Addy A.L. Experimeftal-Theoretical Correlation of Supersonic Jet-on Base Pressure for Cylindrical Afterbodies. J. Aircraft, Vol. 7, No...An Improved Experimental-Theoretical Base Pressure Cor- Addy A.L. relation for Conical and Cylindrical Afterbodies with Agrell J. Centered Propulsive...2.1.92 Carri~re P. Effet d’une Injection de Fluide dans l’Eau-Morte sur les Conditions de Recollement d’un Ecoulement Plan Supersonique. Comptes
Wind Tunnel Wall Corrections (la Correction des effets de paroi en soufflerie)

DTIC Science & Technology

1998-10-01

round holes drilled either normal to the wall surface or at a fixed angle to the normal. Variable porosity features have been implemented in several...walls (holes drilled at 60 deg from the normal), including variable porosity configurations and the effects of screens and splitter plates for edge-tone...Figure 5.68 Schematic of slender wing and the indicated gauge func- tions in anticipation of matching. As detailed in Malmuth and Cole [122], the problems
Quel effet de l’euro sur le commerce europeen des produits forestiers? Académie d’Agriculture de France, Notes Académiques

Treesearch

Joseph Buongiorno

2015-01-01

The objective of this study was to determine the effect of the monetary union on the trade of forest products between euro-using countries. A differential gravity model of bilateral trade flows was developed and estimated with data for the bilateral trade between 12 euro countries from 1988 to 2013, for commodity groups HS44 (wood and articles of wood), HS47 (pulp of...
Africa Civic Action Planning and Implementation Guide

DTIC Science & Technology

1988-03-17

transfert du titre de propriet4 ou. que les d~fectuosit~s provenant de la conception sont... transfert du * .~.titre prendra effet normalement. au point de chargement chez le * fabricant; et pour ].es articles de de’fense fournis sur les stocks...dition avant l~e transfert . du Ititre de proprie’t4. Si l~e "lieu de livraison" d~sign4 est autre que le point initial d’expe’d’tion, l~e
Flow cytomeric measurement of DNA and incorporated nucleoside analogs

DOEpatents

Dolbeare, Frank A.; Gray, Joe W.

1989-01-01

A method is provided for simultaneously measuring total cellular DNA and incorporated nucleoside analog. The method entails altering the cellular DNA of cells grown in the presence of a nucleoside analog so that single stranded and double stranded portions are present. Separate stains are used against the two portions. An immunochemical stain is used against the single stranded portion to provide a measure of incorporated nucleoside analog, and a double strand DNA-specific stain is used against the double stranded portion to simultaneously provide a measure of total cellular DNA. The method permits rapid flow cytometric analysis of cell populations, rapid identification of cycling and noncycling subpopulations, and determination of the efficacy of S phase cytotoxic anticancer agents.
Bioprinting Using Mechanically Robust Core-Shell Cell-Laden Hydrogel Strands.

PubMed

Mistry, Pritesh; Aied, Ahmed; Alexander, Morgan; Shakesheff, Kevin; Bennett, Andrew; Yang, Jing

2017-06-01

The strand material in extrusion-based bioprinting determines the microenvironments of the embedded cells and the initial mechanical properties of the constructs. One unmet challenge is the combination of optimal biological and mechanical properties in bioprinted constructs. Here, a novel bioprinting method that utilizes core-shell cell-laden strands with a mechanically robust shell and an extracellular matrix-like core has been developed. Cells encapsulated in the strands demonstrate high cell viability and tissue-like functions during cultivation. This process of bioprinting using core-shell strands with optimal biochemical and biomechanical properties represents a new strategy for fabricating functional human tissues and organs. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
Dependence of the Contact Resistance on the Design of Stranded Conductors

PubMed Central

Zeroukhi, Youcef; Napieralska-Juszczak, Ewa; Vega, Guillaume; Komeza, Krzysztof; Morganti, Fabrice; Wiak, Slawomir

2014-01-01

During the manufacturing process multi-strand conductors are subject to compressive force and rotation moments. The current distribution in the multi-strand conductors is not uniform and is controlled by the transverse resistivity. This is mainly determined by the contact resistance at the strand crossovers and inter-strand contact resistance. The surface layer properties, and in particular the crystalline structure and degree of oxidation, are key parameters in determining the transverse resistivity. The experimental set-ups made it possible to find the dependence of contact resistivity as a function of continuous working stresses and cable design. A study based on measurements and numerical simulation is made to identify the contact resistivity functions. PMID:25196112
Pharmacogénétique: qu'en est-il au Maroc?

PubMed Central

Idrissi, Meryem Janati; Ouldim, Karim; Amarti, Afaf; El Hassouni, Mohamed; Khabbal, Youssef

2013-01-01

La pharmacogénétique est l’étude de l'influence des variations génétiques interindividuelles sur la réponse aux médicaments, avec le but d'améliorer la prise en charge des patients en visant une médecine personnalisée. Au fait le génome de deux personnes ne diffère que par 0.1% des 3.2 milliards de paires de bases, ce qui implique les effets indésirables des médicaments, qui ont un très important impact sur le plan clinique que sur le plan économique. Or cette dernière décennie ces effets indésirables ont pu être évités grâce aux tests pharmacogénétiques. Au Maroc, la recherche en pharmacogénétique commence à susciter l'intérêt des chercheurs avec quelques études. Une toute première étude en 1986, sur l'acétylation de l'isoniazide chez la population marocaine, suivie par deux autres en 2011 se focalisant sur le métabolisme du tacrolimus et des anti-vitamines K. Ainsi l'espoir maintenant est d'identifier les majoritaires polymorphismes génétiques affectant les patients marocains, afin de leur fournir une prise en charge adaptée. PMID:23785548
Kerr effect in the isotropic phase of a side-chain polymeric liquid crystal

NASA Astrophysics Data System (ADS)

Reys, V.; Dormoy, Y.; Collin, D.; Keller, P.; Martinoty, P.

1992-02-01

The birefringence induced by a pulsed electrical field was used to study the pretransitional effects associated with the isotropic phase of a side-chain polysiloxane. The results obtained show that these effects are characterised by a conventional value of the static exponent and an abnormal value of the dynamic exponent, which shows that the dynamic theory of low molecular weight liquid crystals does not apply. The results also reveal competition between the dipolar moments induced by the electrical field and the permanent moments of the mesogenic molecules. La biréfringence induite par un champ électrique impulsionnel a été utilisée pour étudier les effets prétransitionnels associés à la phase isotrope d'un polysiloxane à chaînes latérales. Les résultats obtenus montrent que ces effets sont caractérisés par une valeur classique de l'exposant statique et une valeur anormale de l'exposant dynamique. Ce dernier résultat montre que la théorie dynamique des cristaux liquides de bas poids moléculaire n'est pas applicable au cas présent. Les expériences mettent également en évidence une compétition entre les moments dipolaires induits par le champ électrique et les moments permanents des molécules mésogènes.
Excitations Élémentaires au Voisinage de la Surface de Séparation d'un Métal Normal et d'un Métal Supraconducteur

NASA Astrophysics Data System (ADS)

Saint-James, Par D.

On étudie le spectre d'excitation pour une couche de métal normal déposée sur un supraconducteur. On montre que si l'interaction attractive électron-électron est négligeable dans le métal normal, il n'y a pas de gap d'énergie dans le spectre d'excitation, même si l'épaisseur de la couche normale est petite. Une étude analogue, conduisant à une conclusion similaire, est menée pour deux supraconducteurs accolés et pour des sphères de métal normal baignant dans un supraconducteur. L'effet prévu pourrait expliquer quelques résultats particuliers observés dans des mesures d'effet tunnel dans des supraconducteurs durs. The excitation spectrum of a layer of normal metal (N) deposited on a superconducting substrate (S) is discussed. It is shown that if the electron-electron attractive interaction is negligibly small in (N) there is no energy gap in the excitation spectrum even if the thickness of the layer (N) is small. A similar study, with equivalent conclusions, has been carried out for two superconductors and for normal metal spheres embedded in a superconductor. The effect may possibly explain some peculiar results of tunnelling experiments on hard superconductors.
Genomic differentiation among wild cyanophages despite widespread horizontal gene transfer

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gregory, Ann C.; Solonenko, Sergei A.; Ignacio-Espinoza, J. Cesar

Genetic recombination is a driving force in genome evolution. Among viruses it has a dual role. For genomes with higher fitness, it maintains genome integrity in the face of high mutation rates. Conversely, for genomes with lower fitness, it provides immediate access to sequence space that cannot be reached by mutation alone. Understanding how recombination impacts the cohesion and dissolution of individual whole genomes within viral sequence space is poorly understood across double-stranded DNA bacteriophages (a.k.a phages) due to the challenges of obtaining appropriately scaled genomic datasets. Here in this study we explore the role of recombination in both maintainingmore » and differentiating whole genomes of 142 wild double-stranded DNA marine cyanophages. Phylogenomic analysis across the 51 core genes revealed ten lineages, six of which were well represented. These phylogenomic lineages represent discrete genotypic populations based on comparisons of intra- and inter- lineage shared gene content, genome-wide average nucleotide identity, as well as detected gaps in the distribution of pairwise differences between genomes. McDonald-Kreitman selection tests identified putative niche-differentiating genes under positive selection that differed across the six well-represented genotypic populations and that may have driven initial divergence. Concurrent with patterns of recombination of discrete populations, recombination analyses of both genic and intergenic regions largely revealed decreased genetic exchange across individual genomes between relative to within populations. Lastly, these findings suggest that discrete double-stranded DNA marine cyanophage populations occur in nature and are maintained by patterns of recombination akin to those observed in bacteria, archaea and in sexual eukaryotes.« less
Comparison of the effect of NaOH and TE buffer on 25 to 100 eV electron induced damage to ΦX174 dsDNA

NASA Astrophysics Data System (ADS)

Kumar, S. V. K.; Murali, Megha; Kushwaha, Preksha

2015-09-01

In this article we report the usage of (1) ΦX174 dsDNA as a model for electron - DNA interaction studies, (2) semiconductor grade 100 silicon wafer, gold on chrome on glass, and tantalum foil substrates, drying process and effect of temperature, on the DNA film formation and its stability, (3) stability of DNA films formed from DNA suspended in nano pure water and with additives like NaOH and TE buffer, and (4) effect of 0.001 mM NaOH and TE buffer (at pH 7.5) additives on DNA damage induced by 25 to 100 eV electrons. The results show that when tantalum foils are used as a substrate, it results in films, which have DNA distributed fairly uniformly and is also stable against strand breaks affected due to the stress of the drying. Electron irradiation of DNA suspended in TE buffer result in the formation of only relaxed form. When the DNA is suspended in 0.001 mM NaOH and irradiated similarly, linear form and cross links are also formed, in addition to relaxed form. This could be likely due to the secondary electrons interacting with Na+ ions that are bound to the DNA causing a second strand break in the opposite strand. Contribution to the Topical Issue "COST Action Nano-IBCT: Nano-scale Processes Behind Ion-Beam Cancer Therapy", edited by Andrey Solov'yov, Nigel Mason, Gustavo García, Eugene Surdutovich.
Genomic differentiation among wild cyanophages despite widespread horizontal gene transfer

DOE PAGES

Gregory, Ann C.; Solonenko, Sergei A.; Ignacio-Espinoza, J. Cesar; ...

2016-11-16

Genetic recombination is a driving force in genome evolution. Among viruses it has a dual role. For genomes with higher fitness, it maintains genome integrity in the face of high mutation rates. Conversely, for genomes with lower fitness, it provides immediate access to sequence space that cannot be reached by mutation alone. Understanding how recombination impacts the cohesion and dissolution of individual whole genomes within viral sequence space is poorly understood across double-stranded DNA bacteriophages (a.k.a phages) due to the challenges of obtaining appropriately scaled genomic datasets. Here in this study we explore the role of recombination in both maintainingmore » and differentiating whole genomes of 142 wild double-stranded DNA marine cyanophages. Phylogenomic analysis across the 51 core genes revealed ten lineages, six of which were well represented. These phylogenomic lineages represent discrete genotypic populations based on comparisons of intra- and inter- lineage shared gene content, genome-wide average nucleotide identity, as well as detected gaps in the distribution of pairwise differences between genomes. McDonald-Kreitman selection tests identified putative niche-differentiating genes under positive selection that differed across the six well-represented genotypic populations and that may have driven initial divergence. Concurrent with patterns of recombination of discrete populations, recombination analyses of both genic and intergenic regions largely revealed decreased genetic exchange across individual genomes between relative to within populations. Lastly, these findings suggest that discrete double-stranded DNA marine cyanophage populations occur in nature and are maintained by patterns of recombination akin to those observed in bacteria, archaea and in sexual eukaryotes.« less
Lumped-Element Dynamic Electro-Thermal model of a superconducting magnet

NASA Astrophysics Data System (ADS)

Ravaioli, E.; Auchmann, B.; Maciejewski, M.; ten Kate, H. H. J.; Verweij, A. P.

2016-12-01

Modeling accurately electro-thermal transients occurring in a superconducting magnet is challenging. The behavior of the magnet is the result of complex phenomena occurring in distinct physical domains (electrical, magnetic and thermal) at very different spatial and time scales. Combined multi-domain effects significantly affect the dynamic behavior of the system and are to be taken into account in a coherent and consistent model. A new methodology for developing a Lumped-Element Dynamic Electro-Thermal (LEDET) model of a superconducting magnet is presented. This model includes non-linear dynamic effects such as the dependence of the magnet's differential self-inductance on the presence of inter-filament and inter-strand coupling currents in the conductor. These effects are usually not taken into account because superconducting magnets are primarily operated in stationary conditions. However, they often have significant impact on magnet performance, particularly when the magnet is subject to high ramp rates. Following the LEDET method, the complex interdependence between the electro-magnetic and thermal domains can be modeled with three sub-networks of lumped-elements, reproducing the electrical transient in the main magnet circuit, the thermal transient in the coil cross-section, and the electro-magnetic transient of the inter-filament and inter-strand coupling currents in the superconductor. The same simulation environment can simultaneously model macroscopic electrical transients and phenomena at the level of superconducting strands. The model developed is a very useful tool for reproducing and predicting the performance of conventional quench protection systems based on energy extraction and quench heaters, and of the innovative CLIQ protection system as well.
Diversity and distribution of single-stranded DNA phages in the North Atlantic Ocean

PubMed Central

Tucker, Kimberly P; Parsons, Rachel; Symonds, Erin M; Breitbart, Mya

2011-01-01

Knowledge of marine phages is highly biased toward double-stranded DNA (dsDNA) phages; however, recent metagenomic surveys have also identified single-stranded DNA (ssDNA) phages in the oceans. Here, we describe two complete ssDNA phage genomes that were reconstructed from a viral metagenome from 80 m depth at the Bermuda Atlantic Time-series Study (BATS) site in the northwestern Sargasso Sea and examine their spatial and temporal distributions. Both genomes (SARssφ1 and SARssφ2) exhibited similarity to known phages of the Microviridae family in terms of size, GC content, genome organization and protein sequence. PCR amplification of the replication initiation protein (Rep) gene revealed narrow and distinct depth distributions for the newly described ssDNA phages within the upper 200 m of the water column at the BATS site. Comparison of Rep gene sequences obtained from the BATS site over time revealed changes in the diversity of ssDNA phages over monthly time scales, although some nearly identical sequences were recovered from samples collected 4 years apart. Examination of ssDNA phage diversity along transects through the North Atlantic Ocean revealed a positive correlation between genetic distance and geographic distance between sampling sites. Together, the data suggest fundamental differences between the distribution of these ssDNA phages and the distribution of known marine dsDNA phages, possibly because of differences in host range, host distribution, virion stability, or viral evolution mechanisms and rates. Future work needs to elucidate the host ranges for oceanic ssDNA phages and determine their ecological roles in the marine ecosystem. PMID:21124487
Colonic stem cell data are consistent with the immortal model of stem cell division under non-random strand segregation.

PubMed

Walters, K

2009-06-01

Colonic stem cells are thought to reside towards the base of crypts of the colon, but their numbers and proliferation mechanisms are not well characterized. A defining property of stem cells is that they are able to divide asymmetrically, but it is not known whether they always divide asymmetrically (immortal model) or whether there are occasional symmetrical divisions (stochastic model). By measuring diversity of methylation patterns in colon crypt samples, a recent study found evidence in favour of the stochastic model, assuming random segregation of stem cell DNA strands during cell division. Here, the effect of preferential segregation of the template strand is considered to be consistent with the 'immortal strand hypothesis', and explore the effect on conclusions of previously published results. For a sample of crypts, it is shown how, under the immortal model, to calculate mean and variance of the number of unique methylation patterns allowing for non-random strand segregation and compare them with those observed. The calculated mean and variance are consistent with an immortal model that incorporates non-random strand segregation for a range of stem cell numbers and levels of preferential strand segregation. Allowing for preferential strand segregation considerably alters previously published conclusions relating to stem cell numbers and turnover mechanisms. Evidence in favour of the stochastic model may not be as strong as previously thought.
Combining image processing and modeling to generate traces of beta-strands from cryo-EM density images of beta-barrels.

PubMed

Si, Dong; He, Jing

2014-01-01

Electron cryo-microscopy (Cryo-EM) technique produces 3-dimensional (3D) density images of proteins. When resolution of the images is not high enough to resolve the molecular details, it is challenging for image processing methods to enhance the molecular features. β-barrel is a particular structure feature that is formed by multiple β-strands in a barrel shape. There is no existing method to derive β-strands from the 3D image of a β-barrel at medium resolutions. We propose a new method, StrandRoller, to generate a small set of possible β-traces from the density images at medium resolutions of 5-10Å. StrandRoller has been tested using eleven β-barrel images simulated to 10Å resolution and one image isolated from the experimentally derived cryo-EM density image at 6.7Å resolution. StrandRoller was able to detect 81.84% of the β-strands with an overall 1.5Å 2-way distance between the detected and the observed β-traces, if the best of fifteen detections is considered. Our results suggest that it is possible to derive a small set of possible β-traces from the β-barrel cryo-EM image at medium resolutions even when no separation of the β-strands is visible in the images.
Homologous Recombination Repair Signaling in Chemical Carcinogenesis: Prolonged Particulate Hexavalent Chromium Exposure Suppresses the Rad51 Response in Human Lung Cells

PubMed Central

Qin, Qin; Xie, Hong; Wise, Sandra S.; Browning, Cynthia L.; Thompson, Kelsey N.; Holmes, Amie L.; Wise, John Pierce

2014-01-01

The aim of this study was to focus on hexavalent chromium, [Cr(VI)], a chemical carcinogen and major public health concern, and consider its ability to impact DNA double strand break repair. We further focused on particulate Cr(VI), because it is the more potent carcinogenic form of Cr(VI). DNA double strand break repair serves to protect cells against the detrimental effects of DNA double strand breaks. For particulate Cr(VI), data show DNA double strand break repair must be overcome for neoplastic transformation to occur. Acute Cr(VI) exposures reveal a robust DNA double strand break repair response, however, longer exposures have not been considered. Using the comet assay, we found longer exposures to particulate zinc chromate induced concentration-dependent increases in DNA double strand breaks indicating breaks were occurring throughout the exposure time. Acute (24 h) exposure induced DNA double strand break repair signaling by inducing Mre11 foci formation, ATM phosphorylation and phosphorylated ATM foci formation, Rad51 protein levels and Rad51 foci formation. However, longer exposures reduced the Rad51 response. These data indicate a major chemical carcinogen can simultaneously induce DNA double strand breaks and alter their repair and describe a new and important aspect of the carcinogenic mechanism for Cr(VI). PMID:25173789
High incidence of non-random template strand segregation and asymmetric fate determination in dividing stem cells and their progeny.

PubMed

Conboy, Michael J; Karasov, Ariela O; Rando, Thomas A

2007-05-01

Decades ago, the "immortal strand hypothesis" was proposed as a means by which stem cells might limit acquiring mutations that could give rise to cancer, while continuing to proliferate for the life of an organism. Originally based on observations in embryonic cells, and later studied in terms of stem cell self-renewal, this hypothesis has remained largely unaccepted because of few additional reports, the rarity of the cells displaying template strand segregation, and alternative interpretations of experiments involving single labels or different types of labels to follow template strands. Using sequential pulses of halogenated thymidine analogs (bromodeoxyuridine [BrdU], chlorodeoxyuridine [CldU], and iododeoxyuridine [IdU]), and analyzing stem cell progeny during induced regeneration in vivo, we observed extraordinarily high frequencies of segregation of older and younger template strands during a period of proliferative expansion of muscle stem cells. Furthermore, template strand co-segregation was strongly associated with asymmetric cell divisions yielding daughters with divergent fates. Daughter cells inheriting the older templates retained the more immature phenotype, whereas daughters inheriting the newer templates acquired a more differentiated phenotype. These data provide compelling evidence of template strand co-segregation based on template age and associated with cell fate determination, suggest that template strand age is monitored during stem cell lineage progression, and raise important caveats for the interpretation of label-retaining cells.
[Investigation of RNA viral genome amplification by multiple displacement amplification technique].

PubMed

Pang, Zheng; Li, Jian-Dong; Li, Chuan; Liang, Mi-Fang; Li, De-Xin

2013-06-01

In order to facilitate the detection of newly emerging or rare viral infectious diseases, a negative-strand RNA virus-severe fever with thrombocytopenia syndrome bunyavirus, and a positive-strand RNA virus-dengue virus, were used to investigate RNA viral genome unspecific amplification by multiple displacement amplification technique from clinical samples. Series of 10-fold diluted purified viral RNA were utilized as analog samples with different pathogen loads, after a series of reactions were sequentially processed, single-strand cDNA, double-strand cDNA, double-strand cDNA treated with ligation without or with supplemental RNA were generated, then a Phi29 DNA polymerase depended isothermal amplification was employed, and finally the target gene copies were detected by real time PCR assays to evaluate the amplification efficiencies of various methods. The results showed that multiple displacement amplification effects of single-strand or double-strand cDNA templates were limited, while the fold increases of double-strand cDNA templates treated with ligation could be up to 6 X 10(3), even 2 X 10(5) when supplemental RNA existed, and better results were obtained when viral RNA loads were lower. A RNA viral genome amplification system using multiple displacement amplification technique was established in this study and effective amplification of RNA viral genome with low load was achieved, which could provide a tool to synthesize adequate viral genome for multiplex pathogens detection.

Bacillus subtilis DNA polymerases, PolC and DnaE, are required for both leading and lagging strand synthesis in SPP1 origin-dependent DNA replication

PubMed Central

Seco, Elena M.

2017-01-01

Abstract Firmicutes have two distinct replicative DNA polymerases, the PolC leading strand polymerase, and PolC and DnaE synthesizing the lagging strand. We have reconstituted in vitro Bacillus subtilis bacteriophage SPP1 θ-type DNA replication, which initiates unidirectionally at oriL. With this system we show that DnaE is not only restricted to lagging strand synthesis as previously suggested. DnaG primase and DnaE polymerase are required for initiation of DNA replication on both strands. DnaE and DnaG synthesize in concert a hybrid RNA/DNA ‘initiation primer’ on both leading and lagging strands at the SPP1 oriL region, as it does the eukaryotic Pol α complex. DnaE, as a RNA-primed DNA polymerase, extends this initial primer in a reaction modulated by DnaG and one single-strand binding protein (SSB, SsbA or G36P), and hands off the initiation primer to PolC, a DNA-primed DNA polymerase. Then, PolC, stimulated by DnaG and the SSBs, performs the bulk of DNA chain elongation at both leading and lagging strands. Overall, these modulations by the SSBs and DnaG may contribute to the mechanism of polymerase switch at Firmicutes replisomes. PMID:28575448
Importance of length and sequence order on magnesium binding to surface-bound oligonucleotides studied by second harmonic generation and atomic force microscopy.

PubMed

Holland, Joseph G; Geiger, Franz M

2012-06-07

The binding of magnesium ions to surface-bound single-stranded oligonucleotides was studied under aqueous conditions using second harmonic generation (SHG) and atomic force microscopy (AFM). The effect of strand length on the number of Mg(II) ions bound and their free binding energy was examined for 5-, 10-, 15-, and 20-mers of adenine and guanine at pH 7, 298 K, and 10 mM NaCl. The binding free energies for adenine and guanine sequences were calculated to be -32.1(4) and -35.6(2) kJ/mol, respectively, and invariant with strand length. Furthermore, the ion density for adenine oligonucleotides did not change as strand length increased, with an average value of 2(1) ions/strand. In sharp contrast, guanine oligonucleotides displayed a linear relationship between strand length and ion density, suggesting that cooperativity is important. This data gives predictive capabilities for mixed strands of various lengths, which we exploit for 20-mers of adenines and guanines. In addition, the role sequence order plays in strands of hetero-oligonucleotides was examined for 5'-A(10)G(10)-3', 5'-(AG)(10)-3', and 5'-G(10)A(10)-3' (here the -3' end is chemically modified to bind to the surface). Although the free energy of binding is the same for these three strands (averaged to be -33.3(4) kJ/mol), the total ion density increases when several guanine residues are close to the 3' end (and thus close to the solid support substrate). To further understand these results, we analyzed the height profiles of the functionalized surfaces with tapping-mode atomic force microscopy (AFM). When comparing the average surface height profiles of the oligonucleotide surfaces pre- and post- Mg(II) binding, a positive correlation was found between ion density and the subsequent height decrease following Mg(II) binding, which we attribute to reductions in Coulomb repulsion and strand collapse once a critical number of Mg(II) ions are bound to the strand.
Grade 300 prestressing strand and the effect of vertical casting position.

DOT National Transportation Integrated Search

2009-01-01

The purpose of this investigation was (1) to compare the differences in the transfer length, development length, and flexural strength among Grade 300 strand, the traditional Grade 270 strand, and the predictions of these properties obtained using cu...
Structural analysis of viral replicative intermediates isolated from adenovirus type 2-infected HeLa cell nuclei.

PubMed Central

Kedinger, C; Brison, O; Perrin, F; Wilhelm, J

1978-01-01

Deoxyribonucleoprotein complexes released 17 h postinfection from adenovirus type 1 (Ad2)-infected HeLa cell nuclei were shown by electron microscopy to contain filaments much thicker (about 200 A [20 nm]) than double-stranded DNA (about 20 A [2 nm]). The complexes were partially purified through a linear sucrose gradient, concentrated, and further purified in a metrizamide gradient. The major protein present in the complexes was identified as the 72,000-dalton (72K), adenovirus-coded single-stranded DNA-binding protein (72K DBP). Three types of complexes have been visualized by electron microscopy. Some linear complexes were uniformly thick, and their length corresponded roughly to that of the adenovirus genome. Other linear genome-length complexes appeared to consist of a thick filament connected to a thinner filament with the diameter of double-stranded DNA. Forked complexes consisting of one thick filament connected to a genome-length, thinner double-stranded DNA filament were also visualized. Both thick and thin filaments were sensitive to DNase and not to RNase, but only the thick filaments were digested by the single-strand-specific Neurospora crassa nuclease, indicating that they correspond to a complex of 72K DBP and Ad2 single-stranded DNA. Experiments with anti-72K DBP immunoglobulins indicated that these nucleoprotein complexes, containing the 72K DBP, correspond to replicative intermediates. Both strands of the Ad2 genome were found associated to the 72K DBP. Altogether, our results establish the in vivo association of the 72K DBP with adenovirus single-stranded DNA, as previously suggested from in vitro studies, and support a strand displacement mechanism for Ad2 DNA replication, in which both strands can be displaced. In addition, our results indicate that, late in infection, histones are not bound to adenovirus DNA in the form of a nucleosomal chromatine-like structure. Images PMID:207893
Structural analysis of viral replicative intermediates isolated from adenovirus type 2-infected HeLa cell nuclei.

PubMed

Kedinger, C; Brison, O; Perrin, F; Wilhelm, J

1978-05-01

Deoxyribonucleoprotein complexes released 17 h postinfection from adenovirus type 1 (Ad2)-infected HeLa cell nuclei were shown by electron microscopy to contain filaments much thicker (about 200 A [20 nm]) than double-stranded DNA (about 20 A [2 nm]). The complexes were partially purified through a linear sucrose gradient, concentrated, and further purified in a metrizamide gradient. The major protein present in the complexes was identified as the 72,000-dalton (72K), adenovirus-coded single-stranded DNA-binding protein (72K DBP). Three types of complexes have been visualized by electron microscopy. Some linear complexes were uniformly thick, and their length corresponded roughly to that of the adenovirus genome. Other linear genome-length complexes appeared to consist of a thick filament connected to a thinner filament with the diameter of double-stranded DNA. Forked complexes consisting of one thick filament connected to a genome-length, thinner double-stranded DNA filament were also visualized. Both thick and thin filaments were sensitive to DNase and not to RNase, but only the thick filaments were digested by the single-strand-specific Neurospora crassa nuclease, indicating that they correspond to a complex of 72K DBP and Ad2 single-stranded DNA. Experiments with anti-72K DBP immunoglobulins indicated that these nucleoprotein complexes, containing the 72K DBP, correspond to replicative intermediates. Both strands of the Ad2 genome were found associated to the 72K DBP. Altogether, our results establish the in vivo association of the 72K DBP with adenovirus single-stranded DNA, as previously suggested from in vitro studies, and support a strand displacement mechanism for Ad2 DNA replication, in which both strands can be displaced. In addition, our results indicate that, late in infection, histones are not bound to adenovirus DNA in the form of a nucleosomal chromatine-like structure.
Repair of DNA Strand Breaks in a Minichromosome In Vivo: Kinetics, Modeling, and Effects of Inhibitors

PubMed Central

Kumala, Slawomir; Fujarewicz, Krzysztof; Jayaraju, Dheekollu; Rzeszowska-Wolny, Joanna; Hancock, Ronald

2013-01-01

To obtain an overall picture of the repair of DNA single and double strand breaks in a defined region of chromatin in vivo, we studied their repair in a ∼170 kb circular minichromosome whose length and topology are analogous to those of the closed loops in genomic chromatin. The rate of repair of single strand breaks in cells irradiated with γ photons was quantitated by determining the sensitivity of the minichromosome DNA to nuclease S1, and that of double strand breaks by assaying the reformation of supercoiled DNA using pulsed field electrophoresis. Reformation of supercoiled DNA, which requires that all single strand breaks have been repaired, was not slowed detectably by the inhibitors of poly(ADP-ribose) polymerase-1 NU1025 or 1,5-IQD. Repair of double strand breaks was slowed by 20–30% when homologous recombination was supressed by KU55933, caffeine, or siRNA-mediated depletion of Rad51 but was completely arrested by the inhibitors of nonhomologous end-joining wortmannin or NU7441, responses interpreted as reflecting competition between these repair pathways similar to that seen in genomic DNA. The reformation of supercoiled DNA was unaffected when topoisomerases I or II, whose participation in repair of strand breaks has been controversial, were inhibited by the catalytic inhibitors ICRF-193 or F11782. Modeling of the kinetics of repair provided rate constants and showed that repair of single strand breaks in minichromosome DNA proceeded independently of repair of double strand breaks. The simplicity of quantitating strand breaks in this minichromosome provides a usefull system for testing the efficiency of new inhibitors of their repair, and since the sequence and structural features of its DNA and its transcription pattern have been studied extensively it offers a good model for examining other aspects of DNA breakage and repair. PMID:23382828
The biomechanical evaluation of a novel 3-strand docking technique for ulnar collateral ligament reconstruction in the elbow.

PubMed

Williams, Phillip N; McGarry, Michelle H; Ihn, Hansel; Schulz, Brian M; Limpisvasti, Orr; ElAttrache, Neal S; Lee, Thay Q

2018-05-07

The original 2-strand docking technique for elbow ulnar collateral ligament reconstruction has recently been modified to use a 3-strand graft. To date, no biomechanical study has compared the 2 techniques. We hypothesized that the 3-strand docking technique would restore valgus laxity to its native state, with comparable load-to-failure characteristics to the 2-strand docking technique. Sixteen fresh cadaveric elbows were matched to the corresponding contralateral side from the same individual to create 8 matched pairs and were then randomized to undergo ulnar collateral ligament reconstruction using either the 2- or 3-strand technique. Valgus laxity and rotation measurements were quantified using a MicroScribe 3DLX digitizer at various flexion angles for the native state, transected state, and 1 of the 2 tested reconstructed ligaments. Each reconstruction was then tested to failure. Valgus laxity for the intact state at elbow flexion angles of 30°, 60°, 90°, and 120° was 7° ± 2°, 7° ± 2°, 6° ± 1°, and 5° ± 2°, respectively. These values were similar to those of both reconstruction techniques. On load-to-failure testing, there was no significant difference in any parameter recorded. Yield torques for the 3- and 2-strand reconstructions were 13.4 ± 4.80 N/m and 11.8 ± 4.76 N/m, respectively (P = .486). The ultimate torques were 15.7 ± 6.10 N/m and 14.4 ± 5.58 N/m for the 3- and 2-strand techniques, respectively (P = .582). The 3-strand docking technique was able to restore valgus laxity to the native state, with similar load-to-failure characteristics to the 2-strand docking technique. Copyright © 2018 Journal of Shoulder and Elbow Surgery Board of Trustees. All rights reserved.
Factors affecting harp seal (Pagophilus groenlandicus) strandings in the Northwest Atlantic.

PubMed

Soulen, Brianne K; Cammen, Kristina; Schultz, Thomas F; Johnston, David W

2013-01-01

The effects of climate change on high latitude regions are becoming increasingly evident, particularly in the rapid decline of sea ice cover in the Arctic. Many high latitude species dependent on sea ice are being forced to adapt to changing habitats. Harp seals (Pagophilus groenlandicus) are an indicator species for changing high-latitude ecosystems. This study analyzed multiple factors including ice cover, demographics, and genetic diversity, which could affect harp seal stranding rates along the eastern coast of the United States. Ice cover assessments were conducted for the month of February in the Gulf of St. Lawrence whelping region from 1991-2010 using remote sensing data, and harp seal stranding data were collected over the same time period. Genetic diversity, which may affect how quickly species can adapt to changing climates, was assessed using ten microsatellite markers to determine mean d (2) in a subset of stranded and by-caught (presumably healthy) seals sampled along the northeast U.S. coast. Our study found a strong negative correlation (R (2) = 0.49) between ice cover in the Gulf of St. Lawrence and yearling harp seal strandings, but found no relationship between sea ice conditions and adult strandings. Our analysis revealed that male seals stranded more frequently than females during the study period and that this relationship was strongest during light ice years. In contrast, we found no significant difference in mean d (2) between stranded and by-caught harp seals. The results demonstrate that sea ice cover and demographic factors have a greater influence on harp seal stranding rates than genetic diversity, with only a little of the variance in mean d (2) among stranded seals explained by ice cover. Any changes in these factors could have major implications for harp seals, and these findings should be considered in the development of future management plans for the Arctic that incorporate climate variability.
Factors Affecting Harp Seal (Pagophilus groenlandicus) Strandings in the Northwest Atlantic

PubMed Central

Schultz, Thomas F.; Johnston, David W.

2013-01-01

The effects of climate change on high latitude regions are becoming increasingly evident, particularly in the rapid decline of sea ice cover in the Arctic. Many high latitude species dependent on sea ice are being forced to adapt to changing habitats. Harp seals (Pagophilus groenlandicus) are an indicator species for changing high-latitude ecosystems. This study analyzed multiple factors including ice cover, demographics, and genetic diversity, which could affect harp seal stranding rates along the eastern coast of the United States. Ice cover assessments were conducted for the month of February in the Gulf of St. Lawrence whelping region from 1991–2010 using remote sensing data, and harp seal stranding data were collected over the same time period. Genetic diversity, which may affect how quickly species can adapt to changing climates, was assessed using ten microsatellite markers to determine mean d 2 in a subset of stranded and by-caught (presumably healthy) seals sampled along the northeast U.S. coast. Our study found a strong negative correlation (R 2 = 0.49) between ice cover in the Gulf of St. Lawrence and yearling harp seal strandings, but found no relationship between sea ice conditions and adult strandings. Our analysis revealed that male seals stranded more frequently than females during the study period and that this relationship was strongest during light ice years. In contrast, we found no significant difference in mean d 2 between stranded and by-caught harp seals. The results demonstrate that sea ice cover and demographic factors have a greater influence on harp seal stranding rates than genetic diversity, with only a little of the variance in mean d 2 among stranded seals explained by ice cover. Any changes in these factors could have major implications for harp seals, and these findings should be considered in the development of future management plans for the Arctic that incorporate climate variability. PMID:23874759
Force-induced rupture of double-stranded DNA in the absence and presence of covalently bonded anti-tumor drugs: Insights from molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Upadhyaya, Anurag; Nath, Shesh; Kumar, Sanjay

2018-06-01

DNA intra-strand cross-link (ICL) agents are widely used in the treatment of cancer. ICLs are thought to form a link between the same strand (intra-strand) or complimentary strand (inter-strand) and thereby increase the stability of DNA, which forbids the processes like replication and transcription. As a result, cell death occurs. In this work, we have studied the enhanced stability of a double stranded DNA in the presence of ICLs and compared our findings with the results obtained in the absence of these links. Using atomistic simulations with explicit solvent, a force is applied along and perpendicular to the direction of the helix and we measured the rupture force and the unzipping force of DNA-ICL complexes. Our results show that the rupture and the unzipping forces increase significantly in the presence of these links. The ICLs bind to the minor groove of DNA, which enhance the DNA stabilisation. Such information may be used to design alternative drugs that can stall replication and transcription that are critical to a growing number of anticancer drug discovery efforts.
Modelling the effects of stranding on the Atlantic salmon population in the Dale River, Norway.

PubMed

Sauterleute, Julian F; Hedger, Richard D; Hauer, Christoph; Pulg, Ulrich; Skoglund, Helge; Sundt-Hansen, Line E; Bakken, Tor Haakon; Ugedal, Ola

2016-12-15

Rapid dewatering in rivers as a consequence of hydropower operations may cause stranding of juvenile fish and have a negative impact on fish populations. We implemented stranding into an Atlantic salmon population model in order to evaluate long-term effects on the population in the Dale River, Western Norway. Furthermore, we assessed the sensitivity of the stranding model to dewatered area in comparison to biological parameters, and compared different methods for calculating wetted area, the main abiotic input parameter to the population model. Five scenarios were simulated dependent on fish life-stage, season and light level. Our simulation results showed largest negative effect on the population abundance for hydropeaking during winter daylight. Salmon smolt production had highest sensitivity to the stranding mortality of older juvenile fish, suggesting that stranding of fish at these life-stages is likely to have greater population impacts than that of earlier life-stages. Downstream retention effects on the ramping velocity were found to be negligible in the stranding model, but are suggested to be important in the context of mitigation measure design. Copyright Â© 2016 Elsevier B.V. All rights reserved.
Design and Characterization of DNA Strand-Displacement Circuits in Serum-Supplemented Cell Medium.

PubMed

Fern, Joshua; Schulman, Rebecca

2017-09-15

The functional stability and lifetimes of synthetic molecular circuits in biological environments are important for long-term, stable sensors or controllers of cell or tissue behavior. DNA-based molecular circuits, in particular DNA strand-displacement circuits, provide simple and effective biocompatible control mechanisms and sensors, but are vulnerable to digestion by nucleases present in living tissues and serum-supplemented cell culture. The stability of double-stranded and single-stranded DNA circuit components in serum-supplemented cell medium and the corresponding effect of nuclease-mediated degradation on circuit performance were characterized to determine the major routes of degradation and DNA strand-displacement circuit failure. Simple circuit design choices, such as the use of 5' toeholds within the DNA complexes used as reactants in the strand-displacement reactions and the termination of single-stranded components with DNA hairpin domains at the 3' termini, significantly increase the functional lifetime of the circuit components in the presence of nucleases. Simulations of multireaction circuits, guided by the experimentally measured operation of single-reaction circuits, enable predictive realization of multilayer and competitive-reaction circuit behavior. Together, these results provide a basic route to increased DNA circuit stability in cell culture environments.
In trans paired nicking triggers seamless genome editing without double-stranded DNA cutting.

PubMed

Chen, Xiaoyu; Janssen, Josephine M; Liu, Jin; Maggio, Ignazio; 't Jong, Anke E J; Mikkers, Harald M M; Gonçalves, Manuel A F V

2017-09-22

Precise genome editing involves homologous recombination between donor DNA and chromosomal sequences subjected to double-stranded DNA breaks made by programmable nucleases. Ideally, genome editing should be efficient, specific, and accurate. However, besides constituting potential translocation-initiating lesions, double-stranded DNA breaks (targeted or otherwise) are mostly repaired through unpredictable and mutagenic non-homologous recombination processes. Here, we report that the coordinated formation of paired single-stranded DNA breaks, or nicks, at donor plasmids and chromosomal target sites by RNA-guided nucleases based on CRISPR-Cas9 components, triggers seamless homology-directed gene targeting of large genetic payloads in human cells, including pluripotent stem cells. Importantly, in addition to significantly reducing the mutagenicity of the genome modification procedure, this in trans paired nicking strategy achieves multiplexed, single-step, gene targeting, and yields higher frequencies of accurately edited cells when compared to the standard double-stranded DNA break-dependent approach.CRISPR-Cas9-based gene editing involves double-strand breaks at target sequences, which are often repaired by mutagenic non-homologous end-joining. Here the authors use Cas9 nickases to generate coordinated single-strand breaks in donor and target DNA for precise homology-directed gene editing.
Design and Characterization of DNA Strand-Displacement Circuits in Serum-Supplemented Cell Medium

DOE PAGES

Fern, Joshua; Schulman, Rebecca

2017-05-30

The functional stability and lifetimes of synthetic molecular circuits in biological environments are important for long-term, stable sensors or controllers of cell or tissue behavior. DNA-based molecular circuits, particularly DNA strand-displacement circuits, provide simple and effective biocompatible control mechanisms and sensors, but are vulnerable to digestion by nucleases present in living tissues and serum-supplemented cell culture. The stability of double-stranded and single-stranded DNA circuit components in serum-supplemented cell medium and the corresponding effect of nuclease-mediated degradation on circuit performance were characterized to determine the major routes of degradation and DNA strand-displacement circuit failure. Simple circuit design choices, such as themore » use of 5' toeholds within the DNA complexes used as reactants in the strand-displacement reactions and the termination of single-stranded components with DNA hairpin domains at the 3' termini, significantly increase the functional lifetime of the circuit components in the presence of nucleases. Furthermore, simulations of multireaction circuits, guided by the experimentally measured operation of single-reaction circuits, enable predictive realization of multilayer and competitive-reaction circuit behavior. Altogether, these results provide a basic route to increased DNA circuit stability in cell culture environments.« less
Design and Characterization of DNA Strand-Displacement Circuits in Serum-Supplemented Cell Medium

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fern, Joshua; Schulman, Rebecca

The functional stability and lifetimes of synthetic molecular circuits in biological environments are important for long-term, stable sensors or controllers of cell or tissue behavior. DNA-based molecular circuits, particularly DNA strand-displacement circuits, provide simple and effective biocompatible control mechanisms and sensors, but are vulnerable to digestion by nucleases present in living tissues and serum-supplemented cell culture. The stability of double-stranded and single-stranded DNA circuit components in serum-supplemented cell medium and the corresponding effect of nuclease-mediated degradation on circuit performance were characterized to determine the major routes of degradation and DNA strand-displacement circuit failure. Simple circuit design choices, such as themore » use of 5' toeholds within the DNA complexes used as reactants in the strand-displacement reactions and the termination of single-stranded components with DNA hairpin domains at the 3' termini, significantly increase the functional lifetime of the circuit components in the presence of nucleases. Furthermore, simulations of multireaction circuits, guided by the experimentally measured operation of single-reaction circuits, enable predictive realization of multilayer and competitive-reaction circuit behavior. Altogether, these results provide a basic route to increased DNA circuit stability in cell culture environments.« less
Analysis of strand transfer and template switching mechanisms of DNA gap repair by homologous recombination in Escherichia coli: predominance of strand transfer.

PubMed

Izhar, Lior; Goldsmith, Moshe; Dahan, Ronny; Geacintov, Nicholas; Lloyd, Robert G; Livneh, Zvi

2008-09-12

Daughter strand gaps formed upon interruption of replication at DNA lesions in Escherichia coli can be repaired by either translesion DNA synthesis or homologous recombination (HR) repair. Using a plasmid-based assay system that enables discrimination between strand transfer and template switching (information copying) modes of HR gap repair, we found that approximately 80% of strand gaps were repaired by physical strand transfer from the donor, whereas approximately 20% appear to be repaired by template switching. HR gap repair operated on both small and bulky lesions and largely depended on RecA and RecF but not on the RecBCD nuclease. In addition, we found that HR was mildly reduced in cells lacking the RuvABC and RecG proteins involved in resolution of Holliday junctions. These results, obtained for the first time under conditions that detect the two HR gap repair mechanisms, provide in vivo high-resolution molecular evidence for the predominance of the strand transfer mechanism in HR gap repair. A small but significant portion of HR gap repair appears to occur via a template switching mechanism.
Functional RNA structures throughout the Hepatitis C Virus genome.

PubMed

Adams, Rebecca L; Pirakitikulr, Nathan; Pyle, Anna Marie

2017-06-01

The single-stranded Hepatitis C Virus (HCV) genome adopts a set of elaborate RNA structures that are involved in every stage of the viral lifecycle. Recent advances in chemical probing, sequencing, and structural biology have facilitated analysis of RNA folding on a genome-wide scale, revealing novel structures and networks of interactions. These studies have underscored the active role played by RNA in every function of HCV and they open the door to new types of RNA-targeted therapeutics. Copyright © 2017 Elsevier B.V. All rights reserved.
78 FR 54867 - Proposed Information Collection; Comment Request; Marine Mammal Health and Stranding Response...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-09-06

... DEPARTMENT OF COMMERCE National Oceanic and Atmospheric Administration Proposed Information Collection; Comment Request; Marine Mammal Health and Stranding Response Program, Level A Stranding and Rehabilitation Disposition Data Sheet AGENCY: National Oceanic and Atmospheric Administration, Commerce. ACTION...
Repairing/strengthening of bridges with post-tensioned FRP strands and performance evaluation.

DOT National Transportation Integrated Search

2008-06-01

The proposed project is to take advantage of some new developments in bridge engineering to apply fiber reinforced polymers (FRP) post-tensioning strands on a selected structure. The use of externally post-tensioned FRP strands to repair/strengthen b...
Porcine circovirus: transcription and rolling-circle DNA replication

USDA-ARS?s Scientific Manuscript database

This review summarizes the molecular studies pertaining to porcine circovirus (PCV) transcription and DNA replication. The genome of PCV is circular, single-stranded DNA and contains 1759-1768 nucleotides. Both the genome-strand (packaged in the virus particle) and the complementary-strand (synthesi...

Implementation of 0.7 in. diameter strands in prestressed concrete girders.

DOT National Transportation Integrated Search

2013-03-01

For several years, 0.7 in. diameter strands have been successfully used in cable bridges and for mining applications. Using these large diameter strands at 2 in. by 2 in. spacing in pretensioned concrete girders results in approximately 35% increase ...
Normalized cDNA libraries

DOEpatents

Soares, Marcelo B.; Efstratiadis, Argiris

1997-01-01

This invention provides a method to normalize a directional cDNA library constructed in a vector that allows propagation in single-stranded circle form comprising: (a) propagating the directional cDNA library in single-stranded circles; (b) generating fragments complementary to the 3' noncoding sequence of the single-stranded circles in the library to produce partial duplexes; (c) purifying the partial duplexes; (d) melting and reassociating the purified partial duplexes to moderate Cot; and (e) purifying the unassociated single-stranded circles, thereby generating a normalized cDNA library.
Normalized cDNA libraries

DOEpatents

Soares, M.B.; Efstratiadis, A.

1997-06-10

This invention provides a method to normalize a directional cDNA library constructed in a vector that allows propagation in single-stranded circle form comprising: (a) propagating the directional cDNA library in single-stranded circles; (b) generating fragments complementary to the 3{prime} noncoding sequence of the single-stranded circles in the library to produce partial duplexes; (c) purifying the partial duplexes; (d) melting and reassociating the purified partial duplexes to moderate Cot; and (e) purifying the unassociated single-stranded circles, thereby generating a normalized cDNA library. 4 figs.
Modality effect in false recognition: evidence from Chinese characters.

PubMed

Mao, Wei Bin; Yang, Zhi Liang; Wang, Lin Song

2010-02-01

Using the Deese/Roediger-McDermott (DRM) false memory method, Smith and Hunt ( 1998 ) first reported the modality effect on false memory and showed that false recall from DRM lists was lower following visual study than following auditory study, which led to numerous studies on the mechanism of modality effect on false memory and provided many competing explanations. In the present experiment, the authors tested the modality effect in false recognition by using a blocked presentation condition and a random presentation condition. The present experiment found a modality effect different from the results of the previous research; namely, false recognition was shown to be greater following visual study than following auditory study, especially in the blocked presentation condition rather than in the random presentation condition. The authors argued that this reversed modality effect may be due to different encoding and processing characteristics between Chinese characters and English words. Compared with English words, visual graphemes of critical lures in Chinese lists are likely to be activated and encoded in participants' minds, thus it is more difficult for participants to discriminate later inner graphemes from those items presented in visual modality. Hence visual presentation could lead to more false recognition than auditory presentation in Chinese lists. The results in the present experiment demonstrated that semantic activation occurring during the encoding and retrieve phases played an important role in modality effect in false recognition, and our findings might be explained by the activation-monitoring account. Utilisant la méthode de fausse mémoire de Deese/Roediger-McDermott (DRM), Smith et Hunt ( 1998 ) ont d'abord rendu compte de l'effet de modalité sur la fausse mémoire et ils ont montré que le faux rappel à partir des listes de DRM était plus faible suivant une étude visuelle plutôt qu'une étude auditive. Ceci a mené à plusieurs études sur le mécanisme de l'effet de modalité sur la fausse mémoire, lesquelles ont fourni plusieurs explications concurrentes. Dans la présente expérience, les auteurs ont testé l'effet de modalité dans la fausse reconnaissance en utilisant une condition de présentation fixe et une condition de présentation aléatoire. Cette expérience a révélé un effet de modalité différent des résultats obtenus dans les recherches antérieures. En effet, la fausse reconnaissance était plus élevée suivant une étude visuelle plutôt qu'une étude auditive, spécialement dans la condition de présentation fixe. Les auteurs suggèrent que cet effet de modalité inverse peut être dû à des caractéristiques d'encodage et de processus différentes entre les caractères chinois et les mots anglais. Comparativement aux mots anglais, les graphèmes visuels des leurres critiques dans les listes chinoises sont susceptibles d'être activés et encodés dans l'esprit des participants, rendant plus difficile de discriminer les graphèmes intériorisés plus tard de ces items présentés dans la modalité visuelle. Ainsi, la présentation visuelle pourrait mener à davantage de fausse reconnaissance que la présentation auditive dans les listes chinoises. Les résultats de la présente expérience ont démontré que l'activation sémantique se produisait durant l'encodage et que la phase de retrait jouait un rôle important dans l'effet de modalité dans la fausse reconnaissance. Nos résultats peuvent être expliqués par la théorie activation-contrôle. Utilizando el método de Deese/Roediger-McDermott (DRM) de falsa mamoria, Smith y Hunt ( 1998 ) fueron los primeros en encontrar el efecto de modalidad en la falsa memoria y demostraron que los falsos recuerdos del listado DRM fueron más bajos después de un estudio visual que después de un estudio auditivo lo cual llevó a varios estudios sobre el mecanismo del efecto de la modalidad sobre falsos recuerdos y proporcionó varias explicaciones que compiten entre sí. En el presente trabajo, los autores estudiaron el efecto de la modalidad en el falso reconocimiento utilizando una condición de presentación en bloques y otra condición de presentación de forma aleatoria. El presente experimento encontró un efecto de la modalidad diferente de los resultados de los estudios anteriores. En concreto, el reconocimiento falso ha resultado ser mayor después del estudio visual que después del estudio auditivo, especialmente en caso de la presentación en bloques en comparación con la condición de presentación aleatoria. Los autores argumentan que este efecto inverso de la modalidad puede ser causado por diferentes características de codificación y procesamiento entre caracteres chinos y palabras inglesas. En comparación con las palabras inglesas, los grafemas visuales de las palabras críticas en chino tienen probabilidad de ser activadas y codificadas en las mentes de los participantes, por tanto, es más difícil discriminar posteriores grafemas internos de los que fueron presentados en la modalidad visual. Por tanto, la presentación visual podría conducir a más falsos reconocimientos que la presentación auditiva en los listados de palabras chinas. Los resultados del presente experimento demostraron que la activación semántica durante las fases de codificación y recuperación jugó un rol importante en el efecto de falso reconocimiento según modalidad y que nuestros resultados se pueden explicar teniendo en cuenta la activación y la vigilancia.
Pharmacothérapie de la dépression chez les aînés

PubMed Central

Frank, Christopher

2014-01-01

Résumé Objectif Discuter du traitement pharmacologique de la dépression chez les personnes âgées, y compris le choix des antidépresseurs, le titrage de la dose, la surveillance de la réponse et des effets secondaires et le traitement des cas réfractaires. Sources des données Les lignes directrices de 2006 de la Canadian Coalition for Seniors’ Mental Health sur l’évaluation et le traitement de la dépression ont servi comme source principale. Pour recenser les articles publiés après les lignes directrices, on a procédé à une recherche documentaire dans MEDLINE de 2007 à 2012 à l’aide des expressions en anglais depression, treatment, drug therapy et elderly. Message principal Le but du traitement devrait être la rémission des symptômes. L’amélioration des symptômes peut être surveillée en fonction des objectifs du patient qu’on a identifiés ou en se servant d’outils cliniques comme le Patient Health Questionnaire–9. On devrait envisager le traitement en 3 étapes: l’étape du traitement aigu pour obtenir la rémission des symptômes, une étape de continuation pour prévenir la récurrence d’un même épisode de la maladie (rechute) et une étape de maintien (prophylaxie) pour prévenir de futurs épisodes (récurrence). Le dosage initial devrait être la moitié de la dose de départ habituelle chez l’adulte et il devrait être titré régulièrement jusqu’à ce que le patient réponde, jusqu’à ce que la dose maximale soit atteinte ou encore que les effets secondaires en limitent l’augmentation. Parmi les effets secondaires fréquents, on peut mentionner les chutes, la nausée, les étourdissements, les céphalées et, moins communément, l’hyponatrémie et des changements dans l’intervalle QT. Des stratégies pour changer ou augmenter les antidépresseurs sont présentées. Les patients plus âgés devraient être traités pendant au moins un an à compter de l’observation d’une amélioration clinique et ceux qui ont une dépression récurrente ou des symptômes sévères devraient continuer le traitement indéfiniment. La prise en charge de situations particulières comme une dépression profonde ou une dépression avec psychose est discutée, y compris le recours à une thérapie électroconvulsive. Les critères pour demander une consultation en psychiatrie gériatrique sont indiqués; par ailleurs, de nombreux médecins de famille n’ont pas aisément accès à une telle ressource ou à d’autres stratégies cliniques non pharmacologiques. Conclusion L’efficacité de la pharmacothérapie de la dépression n’est pas considérablement influencée par l’âge. L’identification de la dépression, le choix du traitement approprié, le tritrage des médicaments, la surveillance des effets secondaires et la durée suffisante du traitement amélioreront les résultats pour les patients plus âgés.
Developpement et validation d'un outil base sur l'acoustique geometrique pour le diagnostic du bruit de nacelle

NASA Astrophysics Data System (ADS)

Minard, Benoit

De nos jours, la problématique du bruit généré par les avions est devenue un point de développement important dans le domaine de l'aéronautique. C'est ainsi que de nombreuses études sont faites dans le domaine et une première approche consiste à modéliser de façon numérique ce bruit de manière à réduire de façon conséquente les coûts lors de la conception. C'est dans ce contexte qu'un motoriste a demandé à l'université de Sherbrooke, et plus particulièrement au groupe d'acoustique de l'Université de Sherbrooke (GAUS), de développer un outil de calcul de la propagation des ondes acoustiques dans les nacelles mais aussi pour l'étude des effets d'installation. Cet outil de prédiction leur permet de réaliser des études afin d'optimiser les traitements acoustiques (« liners »), la géométrie de ces nacelles pour des études portant sur l'intérieur de la nacelle et des études de positionnement des moteurs et de design pour les effets d'installation. L'objectif de ce projet de maîtrise était donc de poursuivre le travail réalisé par [gousset, 2011] sur l'utilisation d'une méthode de lancer de rayons pour l'étude des effets d'installation des moteurs d'avion. L'amélioration du code, sa rapidité, sa fiabilité et sa généralité étaient les objectifs principaux. Le code peut être utilisé avec des traitements acoustiques de surfaces («liners») et peut prendre en compte le phénomène de la diffraction par les arêtes et enfin peut être utilisé pour réaliser des études dans des environnements complexes tels que les nacelles d'avion. Le code développé fonctionne en 3D et procéde en 3 étapes : (1) Calcul des faisceaux initiaux (division d'une sphère, demi-sphère, maillage des surfaces de la géométrie) (2) Propagation des faisceaux dans l'environnement d'étude : calcul de toutes les caractéristiques des rayons convergents (amplitude, phase, nombre de réflexions, ...) (3) Reconstruction du champ de pression en un ou plusieurs points de l'espace à partir de rayons convergents (sommation des contributions de chaque rayon) : sommation cohérente. Le code (GA3DP) permet de prendre en compte les traitements de surface des parois, la directivité de la source, l'atténuation atmosphérique et la diffraction d'ordre 1. Le code a été validé en utilisant différentes méthodes telles que la méthode des sources-images, la méthode d'analyse modale ou encore la méthode des éléments finis de frontière. Un module Matlab a été créé spécialement pour l'étude des effets d'installation et intégré au code existant chez Pratt & Whitney Canada. Mots-clés : Acoustique géométrique - Ray-Tracing - Lancer de faisceaux - Diffraction - Sommation Cohérente - Niveau de Pression.
The impact of environmental factors on marine turtle stranding rates

PubMed Central

Flint, Mark; Limpus, Colin J.; Mills, Paul C.

2017-01-01

Globally, tropical and subtropical regions have experienced an increased frequency and intensity in extreme weather events, ranging from severe drought to protracted rain depressions and cyclones, these coincided with an increased number of marine turtles subsequently reported stranded. This study investigated the relationship between environmental variables and marine turtle stranding. The environmental variables examined in this study, in descending order of importance, were freshwater discharge, monthly mean maximum and minimum air temperatures, monthly average daily diurnal air temperature difference and rainfall for the latitudinal hotspots (-27°, -25°, -23°, -19°) along the Queensland coast as well as for major embayments within these blocks. This study found that marine turtle strandings can be linked to these environmental variables at different lag times (3–12 months), and that cumulative (months added together for maximum lag) and non-cumulative (single month only) effects cause different responses. Different latitudes also showed different responses of marine turtle strandings, both in response direction and timing.Cumulative effects of freshwater discharge in all latitudes resulted in increased strandings 10–12 months later. For latitudes -27°, -25° and -23° non-cumulative effects for discharge resulted in increased strandings 7–12 months later. Latitude -19° had different results for the non-cumulative bay with strandings reported earlier (3–6 months). Monthly mean maximum and minimum air temperatures, monthly average daily diurnal air temperature difference and rainfall had varying results for each examined latitude. This study will allow first responders and resource managers to be better equipped to deal with increased marine turtle stranding rates following extreme weather events. PMID:28771635
Evolutionary dynamics of adult stem cells: comparison of random and immortal-strand segregation mechanisms.

PubMed

Tannenbaum, Emmanuel; Sherley, James L; Shakhnovich, Eugene I

2005-04-01

This paper develops a point-mutation model describing the evolutionary dynamics of a population of adult stem cells. Such a model may prove useful for quantitative studies of tissue aging and the emergence of cancer. We consider two modes of chromosome segregation: (1) random segregation, where the daughter chromosomes of a given parent chromosome segregate randomly into the stem cell and its differentiating sister cell and (2) "immortal DNA strand" co-segregation, for which the stem cell retains the daughter chromosomes with the oldest parent strands. Immortal strand co-segregation is a mechanism, originally proposed by [Cairns Nature (London) 255, 197 (1975)], by which stem cells preserve the integrity of their genomes. For random segregation, we develop an ordered strand pair formulation of the dynamics, analogous to the ordered strand pair formalism developed for quasispecies dynamics involving semiconservative replication with imperfect lesion repair (in this context, lesion repair is taken to mean repair of postreplication base-pair mismatches). Interestingly, a similar formulation is possible with immortal strand co-segregation, despite the fact that this segregation mechanism is age dependent. From our model we are able to mathematically show that, when lesion repair is imperfect, then immortal strand co-segregation leads to better preservation of the stem cell lineage than random chromosome segregation. Furthermore, our model allows us to estimate the optimal lesion repair efficiency for preserving an adult stem cell population for a given period of time. For human stem cells, we obtain that mispaired bases still present after replication and cell division should be left untouched, to avoid potentially fixing a mutation in both DNA strands.
Low concentration of arsenite exacerbates UVR-induced DNA strand breaks by inhibiting PARP-1 activity

DOE Office of Scientific and Technical Information (OSTI.GOV)

Qin Xujun; Department of Toxicology, Fourth Military Medical University, Xi'an, Shaanxi, 710032; Hudson, Laurie G.

2008-10-01

Epidemiological studies have associated arsenic exposure with many types of human cancers. Arsenic has also been shown to act as a co-carcinogen even at low concentrations. However, the precise mechanism of its co-carcinogenic action is unknown. Recent studies indicate that arsenic can interfere with DNA-repair processes. Poly(ADP-ribose) polymerase (PARP)-1 is a zinc-finger DNA-repair protein, which can promptly sense DNA strand breaks and initiate DNA-repair pathways. In the present study, we tested the hypothesis that low concentrations of arsenic could inhibit PAPR-1 activity and so exacerbate levels of ultraviolet radiation (UVR)-induced DNA strand breaks. HaCat cells were treated with arsenite and/ormore » UVR, and then DNA strand breaks were assessed by comet assay. Low concentrations of arsenite ({<=} 2 {mu}M) alone did not induce significant DNA strand breaks, but greatly enhanced the DNA strand breaks induced by UVR. Further studies showed that 2 {mu}M arsenite effectively inhibited PARP-1 activity. Zinc supplementation of arsenite-treated cells restored PARP-1 activity and significantly diminished the exacerbating effect of arsenite on UVR-induced DNA strand breaks. Importantly, neither arsenite treatment, nor zinc supplementation changed UVR-triggered reactive oxygen species (ROS) formation, suggesting that their effects upon UVR-induced DNA strand breaks are not through a direct free radical mechanism. Combination treatments of arsenite with PARP-1 inhibitor 3-aminobenzamide or PARP-1 siRNA demonstrate that PARP-1 is the target of arsenite. Together, these findings show that arsenite at low concentration exacerbates UVR-induced DNA strand breaks by inhibiting PARP-1 activity, which may represent an important mechanism underlying the co-carcinogenicity of arsenic.« less
Design of a Sensitive and Selective Electrochemical Aptasensor for the Determination of the Complementary cDNA of miRNA-145 Based on the Intercalation and Electrochemical Reduction of Doxorubicin.

PubMed

Mohamadi, Maryam; Mostafavi, Ali; Torkzadeh-Mahani, Masoud

2017-11-01

The aim of this research was the determination of a microRNA (miRNA) using a DNA electrochemical aptasensor. In this biosensor, the complementary complementary DNA (cDNA) of miRNA-145 (a sense RNA transcript) was the target strand and the cDNA of miRNA-145 was the probe strand. Both cDNAs can be the product of the reverse transcriptase-polymerase chain reaction of miRNA. The proposed aptasensor's function was based on the hybridization of target strands with probes immobilized on the surface of a working electrode and the subsequent intercalation of doxorubicin (DOX) molecules functioning as the electroactive indicators of any double strands that formed. Electrochemical transduction was performed by measuring the cathodic current resulting from the electrochemical reduction of the intercalated molecules at the electrode surface. In the experiment, because many DOX molecules accumulated on each target strand on the electrode surface, amplification was inherently easy, without a need for enzymatic or complicated amplification strategies. The proposed aptasensor also had the excellent ability to regenerate as a result of the melting of the DNA duplex. Moreover, the use of DNA probe strands obviated the challenges of working with an RNA probe, such as sensitivity to RNase enzyme. In addition to the linear relationship between the electrochemical signal and the concentration of the target strands that ranged from 2.0 to 80.0 nM with an LOD of 0.27 nM, the proposed biosensor was clearly capable of distinguishing between complementary (target strand) and noncomplementary sequences. The presented biosensor was successfully applied for the quantification of DNA strands corresponding to miRNA-145 in human serum samples.
Sak4 of Phage HK620 Is a RecA Remote Homolog With Single-Strand Annealing Activity Stimulated by Its Cognate SSB Protein.

PubMed

Hutinet, Geoffrey; Besle, Arthur; Son, Olivier; McGovern, Stephen; Guerois, Raphaël; Petit, Marie-Agnès; Ochsenbein, Françoise; Lecointe, François

2018-01-01

Bacteriophages are remarkable for the wide diversity of proteins they encode to perform DNA replication and homologous recombination. Looking back at these ancestral forms of life may help understanding how similar proteins work in more sophisticated organisms. For instance, the Sak4 family is composed of proteins similar to the archaeal RadB protein, a Rad51 paralog. We have previously shown that Sak4 allowed single-strand annealing in vivo , but only weakly compared to the phage λ Redβ protein, highlighting putatively that Sak4 requires partners to be efficient. Here, we report that the purified Sak4 of phage HK620 infecting Escherichia coli is a poorly efficient annealase on its own. A distant homolog of SSB, which gene is usually next to the sak4 gene in various species of phages, highly stimulates its recombineering activity in vivo. In vitro , Sak4 binds single-stranded DNA and performs single-strand annealing in an ATP-dependent way. Remarkably, the single-strand annealing activity of Sak4 is stimulated by its cognate SSB. The last six C-terminal amino acids of this SSB are essential for the binding of Sak4 to SSB-covered single-stranded DNA, as well as for the stimulation of its annealase activity. Finally, expression of sak4 and ssb from HK620 can promote low-level of recombination in vivo , though Sak4 and its SSB are unable to promote strand exchange in vitro . Regarding its homology with RecA, Sak4 could represent a link between two previously distinct types of recombinases, i.e., annealases that help strand exchange proteins and strand exchange proteins themselves.
Artificial and Solar UV Radiation Induces Strand Breaks and Cyclobutane Pyrimidine Dimers in Bacillus subtilis Spore DNA

PubMed Central

Slieman, Tony A.; Nicholson, Wayne L.

2000-01-01

The loss of stratospheric ozone and the accompanying increase in solar UV flux have led to concerns regarding decreases in global microbial productivity. Central to understanding this process is determining the types and amounts of DNA damage in microbes caused by solar UV irradiation. While UV irradiation of dormant Bacillus subtilis endospores results mainly in formation of the “spore photoproduct” 5-thyminyl-5,6-dihydrothymine, genetic evidence indicates that an additional DNA photoproduct(s) may be formed in spores exposed to solar UV-B and UV-A radiation (Y. Xue and W. L. Nicholson, Appl. Environ. Microbiol. 62:2221–2227, 1996). We examined the occurrence of double-strand breaks, single-strand breaks, cyclobutane pyrimidine dimers, and apurinic-apyrimidinic sites in spore DNA under several UV irradiation conditions by using enzymatic probes and neutral or alkaline agarose gel electrophoresis. DNA from spores irradiated with artificial 254-nm UV-C radiation accumulated single-strand breaks, double-strand breaks, and cyclobutane pyrimidine dimers, while DNA from spores exposed to artificial UV-B radiation (wavelengths, 290 to 310 nm) accumulated only cyclobutane pyrimidine dimers. DNA from spores exposed to full-spectrum sunlight (UV-B and UV-A radiation) accumulated single-strand breaks, double-strand breaks, and cyclobutane pyrimidine dimers, whereas DNA from spores exposed to sunlight from which the UV-B component had been removed with a filter (“UV-A sunlight”) accumulated only single-strand breaks and double-strand breaks. Apurinic-apyrimidinic sites were not detected in spore DNA under any of the irradiation conditions used. Our data indicate that there is a complex spectrum of UV photoproducts in DNA of bacterial spores exposed to solar UV irradiation in the environment. PMID:10618224
Fecal bacterial communities of wild-captured and stranded green turtles (Chelonia mydas) on the Great Barrier Reef.

PubMed

Ahasan, Md Shamim; Waltzek, Thomas B; Huerlimann, Roger; Ariel, Ellen

2017-12-01

Green turtles (Chelonia mydas) are endangered marine herbivores that break down food particles, primarily sea grasses, through microbial fermentation. However, the microbial community and its role in health and disease is still largely unexplored. In this study, we investigated and compared the fecal bacterial communities of eight wild-captured green turtles to four stranded turtles in the central Great Barrier Reef regions that include Bowen and Townsville. We used high-throughput sequencing analysis targeting the hypervariable V1-V3 regions of the bacterial 16S rRNA gene. At the phylum level, Firmicutes predominated among wild-captured green turtles, followed by Bacteroidetes and Proteobacteria. In contrast, Proteobacteria (Gammaproteobacteria) was the most significantly dominant phylum among all stranded turtles, followed by Bacteroidetes and Firmicutes. In addition, Fusobacteria was also significantly abundant in stranded turtles. No significant differences were found between the wild-captured turtles in Bowen and Townsville. At the family level, the core bacterial community consisted of 25 families that were identified in both the wild-captured and stranded green turtles, while two unique sets of 14 families each were only found in stranded or wild-captured turtles. The predominance of Bacteroides in all groups indicates the importance of these bacteria in turtle gut health. In terms of bacterial diversity and richness, wild-captured green turtles showed a higher bacterial diversity and richness compared with stranded turtles. The marked differences in the bacterial communities between wild-captured and stranded turtles suggest the possible dysbiosis in stranded turtles in addition to potential causal agents. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.
Sak4 of Phage HK620 Is a RecA Remote Homolog With Single-Strand Annealing Activity Stimulated by Its Cognate SSB Protein

PubMed Central

Hutinet, Geoffrey; Besle, Arthur; Son, Olivier; McGovern, Stephen; Guerois, Raphaël; Petit, Marie-Agnès; Ochsenbein, Françoise; Lecointe, François

2018-01-01

Bacteriophages are remarkable for the wide diversity of proteins they encode to perform DNA replication and homologous recombination. Looking back at these ancestral forms of life may help understanding how similar proteins work in more sophisticated organisms. For instance, the Sak4 family is composed of proteins similar to the archaeal RadB protein, a Rad51 paralog. We have previously shown that Sak4 allowed single-strand annealing in vivo, but only weakly compared to the phage λ Redβ protein, highlighting putatively that Sak4 requires partners to be efficient. Here, we report that the purified Sak4 of phage HK620 infecting Escherichia coli is a poorly efficient annealase on its own. A distant homolog of SSB, which gene is usually next to the sak4 gene in various species of phages, highly stimulates its recombineering activity in vivo. In vitro, Sak4 binds single-stranded DNA and performs single-strand annealing in an ATP-dependent way. Remarkably, the single-strand annealing activity of Sak4 is stimulated by its cognate SSB. The last six C-terminal amino acids of this SSB are essential for the binding of Sak4 to SSB-covered single-stranded DNA, as well as for the stimulation of its annealase activity. Finally, expression of sak4 and ssb from HK620 can promote low-level of recombination in vivo, though Sak4 and its SSB are unable to promote strand exchange in vitro. Regarding its homology with RecA, Sak4 could represent a link between two previously distinct types of recombinases, i.e., annealases that help strand exchange proteins and strand exchange proteins themselves. PMID:29740405
The N-terminal strand modulates immunoglobulin light chain fibrillogenesis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pozo-Yauner, Luis del, E-mail: ldelpozo@inmegen.gob.mx; Wall, Jonathan S.; González Andrade, Martín

2014-01-10

Highlights: •We evaluated the impact of mutations in the N-terminal strand of 6aJL2 protein. •Mutations destabilized the protein in a position-dependent manner. •Destabilizing mutations accelerated the fibrillogenesis by shortening the lag time. •The effect on the kinetic of fibril elongation by seeding was of different nature. •The N-terminal strand is buried in the fibrillar state of 6aJL2 protein. -- Abstract: It has been suggested that the N-terminal strand of the light chain variable domain (V{sub L}) protects the molecule from aggregation by hindering spurious intermolecular contacts. We evaluated the impact of mutations in the N-terminal strand on the thermodynamic stabilitymore » and kinetic of fibrillogenesis of the V{sub L} protein 6aJL2. Mutations in this strand destabilized the protein in a position-dependent manner, accelerating the fibrillogenesis by shortening the lag time; an effect that correlated with the extent of destabilization. In contrast, the effect on the kinetics of fibril elongation, as assessed in seeding experiments was of different nature, as it was not directly dependant on the degree of destabilization. This finding suggests different factors drive the nucleation-dependent and elongation phases of light chain fibrillogenesis. Finally, taking advantage of the dependence of the Trp fluorescence upon environment, four single Trp substitutions were made in the N-terminal strand, and changes in solvent exposure during aggregation were evaluated by acrylamide-quenching. The results suggest that the N-terminal strand is buried in the fibrillar state of 6aJL2 protein. This finding suggest a possible explanation for the modulating effect exerted by the mutations in this strand on the aggregation behavior of 6aJL2 protein.« less
Multistrand superconductor cable

DOEpatents

Borden, A.R.

1984-03-08

Improved multistrand Rutherford-type superconductor cable is produced by using strands which are preformed, prior to being wound into the cable, so that each strand has a variable cross section, with successive portions having a substantially round cross section, a transitional oval cross section, a rectangular cross section, a transitional oval cross section, a round cross section and so forth, in repetitive cycles along the length of the strand. The cable is wound and flattened so that the portions of rectangular cross section extend across the two flat sides of the cable at the strand angle. The portions of round cross section are bent at the edges of the flattened cable, so as to extend between the two flat sides. The rectangular portions of the strands slide easil
The occurrence of antibodies against single-stranded DNA in the sera of patients with acute and chronic leukaemia.

PubMed Central

Izui, S; Lambert, P H; Carpentier, N; Miescher, P A

1976-01-01

One hundred and seventy-five sera from thirty-three patients with acute myeloid leukaemia, forty-two patients with chronic myeloid leukaemia and twelve patients with acute lymphatic leukaemia were examined by a radioimmunological technique for the presence of antibodies against single-stranded and double-stranded DNA. The levels of single-stranded DNA binding activity was significantly higher in all three types of leukaemia compared to those of healthy controls. In contrast, none of these sera exhibited a positive reaction with double-stranded DNA. In some cases the level of serum anti-DNA antibodies increased after the decrease of the leucocyte count. The presence of anti-DNA antibodies in leukaemic patients may have some biological significance. PMID:780020
Enhanced Strain Measurement Range of an FBG Sensor Embedded in Seven-Wire Steel Strands

PubMed Central

Kim, Jae-Min; Kim, Chul-Min; Choi, Song-Yi

2017-01-01

FBG sensors offer many advantages, such as a lack of sensitivity to electromagnetic waves, small size, high durability, and high sensitivity. However, their maximum strain measurement range is lower than the yield strain range (about 1.0%) of steel strands when embedded in steel strands. This study proposes a new FBG sensing technique in which an FBG sensor is recoated with polyimide and protected by a polyimide tube in an effort to enhance the maximum strain measurement range of FBG sensors embedded in strands. The validation test results showed that the proposed FBG sensing technique has a maximum strain measurement range of 1.73% on average, which is 1.73 times higher than the yield strain of the strands. It was confirmed that recoating the FBG sensor with polyimide and protecting the FBG sensor using a polyimide tube could effectively enhance the maximum strain measurement range of FBG sensors embedded in strands. PMID:28718826
Mass stranding of wedge-tailed shearwater chicks in Hawaii

USGS Publications Warehouse

Work, Thierry M.; Rameyer, Robert

1999-01-01

Unusual numbers of wedge-tailed shearwater (Puffinus pacificus) chicks stranded on Oahu (Hawaii, USA) in 1994. Compared to healthy wedge-tailed shearwater (WTSW) chicks, stranded chicks were underweight, dehydrated, leukopenic, lymphopenic, eosinopenic, and heterophilic; some birds were toxemic and septic. Stranded chicks also were hypoglycemic and had elevated aspartate amino transferase levels. Most chicks apparently died from emaciation, dehydration, or bacteremia. Because many birds with bacteremia also had severe necrosis of the gastrointestinal (GI) mucosa associated with bacteria, we suspect the GI tract to be the source of disseminated bacterial infection. The identity of the bacteria was not confirmed. The daily number of chicks stranded was significantly related to average wind speeds, and the mortality coincided with the fledging period for WTSW. Strong southeasterly winds were a distinguishing meteorologic factor in 1994 and contributed to the distribution of stranded chicks on Oahu. More objective data on WTSW demographics would enhance future efforts to determine predisposing causes of WTSW wrecks and their effects on seabird colonies.
Reconstitution of a eukaryotic replisome reveals suppression mechanisms that define leading/lagging strand operation

PubMed Central

Georgescu, Roxana E; Schauer, Grant D; Yao, Nina Y; Langston, Lance D; Yurieva, Olga; Zhang, Dan; Finkelstein, Jeff; O'Donnell, Mike E

2015-01-01

We have reconstituted a eukaryotic leading/lagging strand replisome comprising 31 distinct polypeptides. This study identifies a process unprecedented in bacterial replisomes. While bacteria and phage simply recruit polymerases to the fork, we find that suppression mechanisms are used to position the distinct eukaryotic polymerases on their respective strands. Hence, Pol ε is active with CMG on the leading strand, but it is unable to function on the lagging strand, even when Pol δ is not present. Conversely, Pol δ-PCNA is the only enzyme capable of extending Okazaki fragments in the presence of Pols ε and α. We have shown earlier that Pol δ-PCNA is suppressed on the leading strand with CMG (Georgescu et al., 2014). We propose that CMG, the 11-subunit helicase, is responsible for one or both of these suppression mechanisms that spatially control polymerase occupancy at the fork. DOI: http://dx.doi.org/10.7554/eLife.04988.001 PMID:25871847

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