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Sample records for potential plasmid dynamics

  1. Population dynamics model for plasmid bearing and plasmid lacking ...

    African Journals Online (AJOL)

    Streptokinase production in bioreactor is well associated to cell population dynamics. It is an established fact that two types of cell populations are found to emerge from the initial pool of recombinant cell population. This phenomenon leads to an undesired loss in yield of the product. Primary metabolites, like acetic acid etc ...

  2. Novel assay to measure the plasmid mobilizing potential of mixed microbial communities

    DEFF Research Database (Denmark)

    Klümper, Uli; Droumpali, Ariadni; Dechesne, Arnaud

    2014-01-01

    Mobilizable plasmids lack necessary genes for complete conjugation and are therefore non-self-transmissible. Instead, they rely on the conjugation system of conjugal plasmids to be horizontally transferred to new recipients. While community permissiveness, the fraction of a mixed microbial...... community that can receive self-transmissible conjugal plasmids, has been studied, the intrinsic ability of a community to mobilize plasmids that lack conjugation systems is unexplored. Here, we present a novel framework and experimental method to estimate the mobilization potential of mixed communities. We...... of the donors receiving the conjugal plasmid in the first step. Further work is needed to establish how plasmid mobilization potential varies within and across microbial communities....

  3. Insights into dynamics of mobile genetic elements in hyperthermophilic environments from five new Thermococcus plasmids.

    Directory of Open Access Journals (Sweden)

    Mart Krupovic

    Full Text Available Mobilome of hyperthermophilic archaea dwelling in deep-sea hydrothermal vents is poorly characterized. To gain insight into genetic diversity and dynamics of mobile genetic elements in these environments we have sequenced five new plasmids from different Thermococcus strains that have been isolated from geographically remote hydrothermal vents. The plasmids were ascribed to two subfamilies, pTN2-like and pEXT9a-like. Gene content and phylogenetic analyses illuminated a robust connection between pTN2-like plasmids and Pyrococcus abyssi virus 1 (PAV1, with roughly half of the viral genome being composed of genes that have homologues in plasmids. Unexpectedly, pEXT9a-like plasmids were found to be closely related to the previously sequenced plasmid pMETVU01 from Methanocaldococcus vulcanius M7. Our data suggests that the latter observation is most compatible with an unprecedented horizontal transfer of a pEXT9a-like plasmid from Thermococcales to Methanococcales. Gene content analysis revealed that thermococcal plasmids encode Hfq-like proteins and toxin-antitoxin (TA systems of two different families, VapBC and RelBE. Notably, although abundant in archaeal genomes, to our knowledge, TA and hfq-like genes have not been previously found in archaeal plasmids or viruses. Finally, the plasmids described here might prove to be useful in developing new genetic tools for hyperthermophiles.

  4. Non-additive costs and interactions alter the competitive dynamics of co-occurring ecologically distinct plasmids.

    Science.gov (United States)

    Morton, Elise R; Platt, Thomas G; Fuqua, Clay; Bever, James D

    2014-03-22

    Plasmids play an important role in shaping bacterial evolution and adaptation to heterogeneous environments. As modular genetic elements that are often conjugative, the selective pressures that act on plasmid-borne genes are distinct from those that act on the chromosome. Many bacteria are co-infected by multiple plasmids that impart niche-specific phenotypes. Thus, in addition to host-plasmid dynamics, interactions between co-infecting plasmids are likely to be important drivers of plasmid population dynamics, evolution and ecology. Agrobacterium tumefaciens is a facultative plant pathogen that commonly harbours two distinct megaplasmids. Virulence depends on the presence of the tumour-inducing (Ti) plasmid, with benefits that are primarily restricted to the disease environment. Here, we demonstrate that a second megaplasmid, the At plasmid, confers a competitive advantage in the rhizosphere. To assess the individual and interactive costs of these plasmids, we generated four isogenic derivatives: plasmidless, pAt only, pTi only and pAtpTi, and performed pairwise competitions under carbon-limiting conditions. These studies reveal a low cost to the virulence plasmid when outside of the disease environment, and a strikingly high cost to the At plasmid. In addition, the costs of pAt and pTi in the same host were significantly lower than predicted based on single plasmid costs, signifying the first demonstration of non-additivity between naturally occurring co-resident plasmids. Based on these empirically demonstrated costs and benefits, we developed a resource-consumer model to generate predictions about the frequencies of these genotypes in relevant environments, showing that non-additivity between co-residing plasmids allows for their stable coexistence across environments.

  5. Long- term manure exposure increases soil bacterial community potential for plasmid uptake

    DEFF Research Database (Denmark)

    Musovic, Sanin; Klümper, Uli; Dechesne, Arnaud

    2014-01-01

    Microbial communities derived from soils subject to different agronomic treatments were challenged with three broad host range plasmids, RP4, pIPO2tet and pRO101, via solid surface filter matings to assess their permissiveness. Approximately 1 in 10 000 soil bacterial cells could receive and main......Microbial communities derived from soils subject to different agronomic treatments were challenged with three broad host range plasmids, RP4, pIPO2tet and pRO101, via solid surface filter matings to assess their permissiveness. Approximately 1 in 10 000 soil bacterial cells could receive...... and maintain the plasmids. The community permissiveness increased up to 100% in communities derived from manured soil. While the plasmid transfer frequency was significantly influenced by both the type of plasmid and the agronomic treatment, the diversity of the transconjugal pools was purely plasmid dependent...

  6. Plasmid segregation mechanisms

    DEFF Research Database (Denmark)

    Ebersbach, G.; Gerdes, Kenn

    2005-01-01

    Bacterial plasmids encode partitioning (par) loci that ensure ordered plasmid segregation prior to cell division. par loci come in two types: those that encode actin-like ATPases and those that encode deviant Walker-type ATPases. ParM, the actin-like ATPase of plasmid R1, forms dynamic filaments...... that segregate plasmids paired at mid-cell to daughter cells. Like microtubules, ParM filaments exhibit dynamic instability (i.e., catastrophic decay) whose regulation is an important component of the DNA segregation process. The Walker box ParA ATPases are related to MinD and form highly dynamic, oscillating...... filaments that are required for the subcellular movement and positioning of plasmids. The role of the observed ATPase oscillation is not yet understood. However, we propose a simple model that couples plasmid segregation to ParA oscillation. The model is consistent with the observed movement...

  7. Dynamics in copy numbers of five plasmids of a dairy Lactococcus lactis in dairy-related conditions including near-zero growth rates.

    Science.gov (United States)

    van Mastrigt, Oscar; Lommers, Marcel M A N; de Vries, Yorick C; Abee, Tjakko; Smid, Eddy J

    2018-03-23

    Lactic acid bacteria can carry multiple plasmids affecting their performance in dairy fermentations. The expression of plasmid-encoded genes and the activity of the corresponding proteins is severely affected by changes in the number of plasmid copies. We studied the impact of growth rate on dynamics of plasmid copy numbers at high growth rates in chemostat cultures and down to near-zero growth rates in retentostat cultures. Five plasmids of the dairy strain Lactococcus lactis FM03-V1 were selected which varied in size (3 to 39 kb), in replication mechanism (theta or rolling-circle) and in putative (dairy-associated) functions. Copy numbers ranged from 1.5 to 40.5 and the copy number of theta-type replicating plasmids were negatively correlated to the plasmid size. Despite the extremely wide range of growth rates (0.0003 h -1 to 0.6 h -1 ), copy numbers of the five plasmids were stable and only slightly increased at near-zero growth rates showing that the plasmid replication rate was strictly controlled. One low-copy number plasmid, carrying a large exopolysaccharide gene cluster, was segregationally unstable during retentostat cultivations reflected in complete loss of the plasmid in one of the retentostat cultures. The copy number of the five plasmids was also hardly affected by varying the pH value, nutrient limitation or presence of citrate (maximum 2.2-fold) signifying the stability in copy number of the plasmids. Importance Lactococcus lactis is extensively used in starter cultures for dairy fermentations. Important traits for growth and survival of L. lactis in dairy fermentations are encoded by genes located on plasmids, such as genes involved in lactose and citrate metabolism, protein degradation and oligopeptide uptake and bacteriophage resistance. Because the number of plasmid copies could affect the expression of plasmid-encoded genes, it is important to know the factors that influence the plasmid copy numbers. We monitored plasmid copy numbers of L

  8. Broad-Host-Range IncP-1 plasmids and their resistance potential

    Directory of Open Access Journals (Sweden)

    Magdalena ePopowska

    2013-03-01

    Full Text Available The plasmids of the incompatibility group IncP-1, also called IncP, as extrachromosomal genetic elements can transfer and replicate virtually in all Gram-negative bacteria. They are composed of backbone genes that encode a variety of essential functions and accessory genes that have implications for human health and environmental bioremediation. Broad-host-range IncP plasmids are known to spread genes between distinct phylogenetic groups of bacteria. These genes often code for resistances to a broad spectrum of antibiotics, heavy metals and quaternary ammonium compounds used as disinfectants. The backbone of these plasmids carries modules that enable them to effectively replicate, move to a new host via conjugative transfer and to be stably maintained in bacterial cells. The adaptive, resistance and virulence genes are mainly located on mobile genetic elements integrated between the functional plasmid backbone modules. Environmental studies have demonstrated the wide distribution of IncP-like replicons in manure, soils and wastewater treatment plants. They also are present in strains of pathogenic or opportunistic bacteria, which can be a cause for concern, because they may encode multiresistance. Their broad distribution suggests that IncP plasmids play a crucial role in bacterial adaptation by utilizing horizontal gene transfer. This review summarizes the variety of genetic information and physiological functions carried by IncP plasmids, which can contribute to the spread of antibiotic and heavy metal resistance while also mediating the process of bioremediation of pollutants. Due to the location of the resistance genes on plasmids with a broad host range and the presence of transposons carrying these genes it seems that the spread of these genes would be possible and quite hazardous in infection control. Future studies are required to determine the level of risk of the spread of resistance genes located on these plasmids.

  9. Metal stressors consistently modulate bacterial conjugal plasmid uptake potential in a phylogenetically conserved manner

    DEFF Research Database (Denmark)

    Klümper, Uli; Dechesne, Arnaud; Riber, Leise

    2017-01-01

    The environmental stimulants and inhibitors of conjugal plasmid transfer in microbial communities are poorly understood. Specifically, it is not known whether exposure to stressors may cause a community to alter its plasmid uptake ability. We assessed whether metals (Cu, Cd, Ni, Zn) and one metal...... that community permissiveness is sensitive to metal(loid) stress in a manner that is both partially consistent across stressors and phylogenetically conserved.The ISME Journal advance online publication, 2 August 2016; doi:10.1038/ismej.2016.98....

  10. On quantum potential dynamics

    International Nuclear Information System (INIS)

    Goldstein, Sheldon; Struyve, Ward

    2015-01-01

    Non-relativistic de Broglie–Bohm theory describes particles moving under the guidance of the wave function. In de Broglie's original formulation, the particle dynamics is given by a first-order differential equation. In Bohm's reformulation, it is given by Newton's law of motion with an extra potential that depends on the wave function—the quantum potential—together with a constraint on the possible velocities. It was recently argued, mainly by numerical simulations, that relaxing this velocity constraint leads to a physically untenable theory. We provide further evidence for this by showing that for various wave functions the particles tend to escape the wave packet. In particular, we show that for a central classical potential and bound energy eigenstates the particle motion is often unbounded. This work seems particularly relevant for ways of simulating wave function evolution based on Bohm's formulation of the de Broglie–Bohm theory. Namely, the simulations may become unstable due to deviations from the velocity constraint. (paper)

  11. Chlamydial plasmids and bacteriophages.

    Science.gov (United States)

    Pawlikowska-Warych, Małgorzata; Śliwa-Dominiak, Joanna; Deptuła, Wiesław

    2015-01-01

    Chlamydia are absolute pathogens of humans and animals; despite being rather well recognised, they are still open for discovery. One such discovery is the occurrence of extrachromosomal carriers of genetic information. In prokaryotes, such carriers include plasmids and bacteriophages, which are present only among some Chlamydia species. Plasmids were found exclusively in Chlamydia (C.) trachomatis, C. psittaci, C. pneumoniae, C. suis, C. felis, C. muridarum and C. caviae. In prokaryotic organisms, plasmids usually code for genes that facilitate survival of the bacteria in the environment (although they are not essential). In chlamydia, their role has not been definitely recognised, apart from the fact that they participate in the synthesis of glycogen and encode proteins responsible for their virulence. Furthermore, in C. suis it was evidenced that the plasmid is integrated in a genomic island and contains the tetracycline-resistance gene. Bacteriophages specific for chlamydia (chlamydiaphages) were detected only in six species: C. psittaci, C. abortus, C. felis, C. caviae C. pecorum and C. pneumoniae. These chlamydiaphages cause inhibition of the developmental cycle, and delay transformation of reticulate bodies (RBs) into elementary bodies (EBs), thus reducing the possibility of infecting other cells in time. Plasmids and bacteriophages can be used in the diagnostics of chlamydioses; although especially in the case of plasmids, they are already used for detection of chlamydial infections. In addition, bacteriophages could be used as therapeutic agents to replace antibiotics, potentially addressing the problem of increasing antibiotic-resistance among chlamydia.

  12. Molecular potentials and relaxation dynamics

    International Nuclear Information System (INIS)

    Karo, A.M.

    1981-01-01

    The use of empirical pseudopotentials, in evaluating interatomic potentials, provides an inexpensive and convenient method for obtaining highly accurate potential curves and permits the modeling of core-valence correlation, and the inclusion of relativistic effects when these are significant. Recent calculations of the X 1 Σ + and a 3 Σ + states of LiH, NaH, KH, RbH, and CsH and the X 2 Σ + states of their anions are discussed. Pseudopotentials, including core polarization terms, have been used to replace the core electrons, and this has been coupled with the development of compact, higly-optimized basis sets for the corresponding one- and two-electron atoms. Comparisons of the neutral potential curves with experiment and other ab initio calculations show good agreement (within 1000 cm -1 over most of the potential curves) with the difference curves being considerably more accurate. In the method of computer molecular dynamics, the force acting on each particle is the resultant of all interactions with other atoms in the neighborhood and is obtained as the derivative of an effective many-body potential. Exploiting the pseudopotential approach, in obtaining the appropriate potentials may be very fruitful in the future. In the molecular dynamics example considered here, the conventional sum-of-pairwise-interatomic-potentials (SPP) approximation is used with the potentials derived either from experimental spectroscopic data or from Hartree-Fock calculations. The problem is the collisional de-excitation of vibrationally excited molecular hydrogen at an Fe surface. The calculations have been carried out for an initial vibrotational state v = 8, J = 1 and a translational temperature corresponding to a gas temperature of 500 0 K. Different angles of approach and different initial random impact points on the surface have been selected. For any given collision with the wall, the molecule may pick up or lose vibrotatonal and translational energy

  13. Black Hole Dynamic Potentials Koustubh Ajit Kabe

    Indian Academy of Sciences (India)

    Abstract. In the following paper, certain black hole dynamic potentials have been developed definitively on the lines of classical thermodynam- ics. These potentials have been refined in view of the small differences in the equations of the laws of black hole dynamics as given by Bekenstein and those of thermodynamics.

  14. Molecular potentials and relaxation dynamics

    International Nuclear Information System (INIS)

    Karo, A.M.

    1981-01-01

    The use of empirical pseudopotentials, in evaluating interatomic potentials, provides an inexpensive and convenient method for obtaining highly accurate potential curves and permits the modeling of core-valence correlation, and the inclusion of relativistic effects when these are significant. As an example, recent calculations of the chi 1 Σ + and a 3 Σ + states of LiH, NaH, KH, RbH, and CsH and the chi 2 Σ + states of their anions are discussed. Pseudopotentials, including core polarization terms, have been used to replace the core electrons, and this has been coupled with the development of compact, highly-optimized basis sets for the corresponding one- and two-electron atoms. Comparisons of the neutral potential curves with experiment and other ab initio calculations show good agreement (within 1000 cm -1 over most of the potential curves) with the difference curves being considerably more accurate

  15. Dynamical equations for the optical potential

    International Nuclear Information System (INIS)

    Kowalski, K.L.

    1981-01-01

    Dynamical equations for the optical potential are obtained starting from a wide class of N-particle equations. This is done with arbitrary multiparticle interactions to allow adaptation to few-body models of nuclear reactions and including all effects of nucleon identity. Earlier forms of the optical potential equations are obtained as special cases. Particular emphasis is placed upon obtaining dynamical equations for the optical potential from the equations of Kouri, Levin, and Tobocman including all effects of particle identity

  16. TOL plasmid transfer during bacterial conjugation in vitro and rhizoremediation of oil compounds in vivo

    International Nuclear Information System (INIS)

    Jussila, Minna M.; Zhao, Ji; Suominen, Leena; Lindstroem, Kristina

    2007-01-01

    Molecular profiling methods for horizontal transfer of aromatics-degrading plasmids were developed and applied during rhizoremediation in vivo and conjugations in vitro. pWW0 was conjugated from Pseudomonas to Rhizobium. The xylE gene was detected both in Rhizobium galegae bv. officinalis and bv. orientalis, but it was neither stably maintained in orientalis nor functional in officinalis. TOL plasmids were a major group of catabolic plasmids among the bacterial strains isolated from the oil-contaminated rhizosphere of Galega orientalis. A new finding was that some Pseudomonas migulae and Pseudomonas oryzihabitans strains harbored a TOL plasmid with both pWW0- and pDK1-type xylE gene. P. oryzihabitans 29 had received the archetypal TOL plasmid pWW0 from Pseudomonas putida PaW85. As an application for environmental biotechnology, the biodegradation potential of oil-polluted soil and the success of bioremediation could be estimated by monitoring changes not only in the type and amount but also in transfer of degradation plasmids. - Horizontal transfer of degradation plasmids in the oil-contaminated rhizosphere reveals the dynamic nature of the intrinsic biodegradation potential

  17. Potential vorticity dynamics for global scale circulations

    International Nuclear Information System (INIS)

    Lu, C.; Schubert, W.

    1994-01-01

    One of the most notable advances in extratropical dynamics this decade has been the understanding of large-scale atmospheric and oceanic processes by using potential vorticity dynamics, the so called open-quotes IPV thinking.close quotes This analysis method has also been successfully extended to some tropical atmospheric circulation systems such as hurricanes and the Hadley circulation. The fundamental idea behind such a dynamic system rests with the fact that PV is a tracer-like quantity since it is conserved (in the absence of friction and diabatic heating) following a fluid particle and carries both significant dynamic and thermodynamic information regarding fluid motion. Thus, the prediction and inversion of PV form the most succinct dynamic view of atmospheric and oceanic motions. Furthermore, PV dynamics provides access to many insightful dynamic analyses such as: Propagation of Rossby waves, barotropic and baroclinic instabilities for shear flows, and wave-mean flow interactions. All these features make IPV analysis a very attractive tool for studying geophysical fluid systems

  18. Plasmid stability in dried cells of the desert cyanobacterium Chroococcidiopsis and its potential for GFP imaging of survivors on Earth and in space.

    Science.gov (United States)

    Billi, Daniela

    2012-06-01

    Two GFP-based plasmids, namely pTTQ18-GFP-pDU1(mini) and pDUCA7-GFP, of about 7 kbp and 15 kbp respectively, able to replicate in Chroococcidiopsis sp. CCMEE 029 and CCMEE 123, were developed. Both plasmids were maintained in Chroococcidiopsis cells after 18 months of dry storage as demonstrated by colony PCR, plasmid restriction analysis, GFP imaging and colony-forming ability under selection of dried transformants; thus suggesting that strategies employed by this cyanobacterium to stabilize dried chromosomal DNA, must have protected plasmid DNA. The suitability of pDU1(mini)-plasmid for GFP tagging in Chroococcidiopsis was investigated by using the RecA homolog of Synechocystis sp. PCC 6803. After 2 months of dry storage, the presence of dried cells with a GFP-RecA(Syn) distribution resembling that of hydrated cells, supported its capability of preventing desiccation-induced genome damage, whereas the rewetted cells with filamentous GFP-RecA(Syn) structures revealed sub-lethal DNA damage. The long-term stability of plasmid DNA in dried Chroococcidiopsis has implication for space research, for example when investigating the recovery of dried cells after Martian and space simulations or when developing life support systems based on phototrophs with genetically enhanced stress tolerance and stored in the dry state for prolonged periods.

  19. Plasmid profiling of bacterial isolates from confined environments

    Science.gov (United States)

    van Houdt, Rob; Provoost, Ann; Coninx, Ilse; Leys, Natalie; Mergeay, Max

    Plasmid profiling of bacterial isolates from confined environments R. Van Houdt, I. Coninx, A. Provoost, N. Leys, and M. Mergeay Expertise group for Molecular and Cellular Biology, Institute for Environment, Health and Safety, Belgian Nuclear Research Centre (SCK•CEN), Boeretang 200, B-2400 Mol, Belgium. Human exploration of extreme and isolated hostile environments such as space requires special confined small volume habitats to protect and house the crew. However, human confinement in such small volume habitats has restrictions on waste disposal and personal hygiene and inevitably generates a particular community of microorganisms within the habitat. These microorganisms are mainly originating from the crew (skin, mucous membranes, upper respiratory tract, mouth, and gastrointestinal tract) but also include the residing environmental microorganisms. Earth-based confined habitats such as the Antarctic Research Station Concordia are used as test beds for long-duration spaceflights to study the physiologic and psychological adaptation to isolated environments. The dynamics of the environmental microbial population in such a test bed could render additional insights in assessing the potential health risks in long-duration space missions. Not only total bacterial contamination levels are important, but it is essential to identify also the predominant microbial taxa and their mobile genetic elements (MGE). These MGEs could be exchanged between bacteria by horizontal gene transfer and may alter the pathogenic potential since they often carry antibiotic resistance or more in general adaptation-enhancing traits. In this study several bacterial strains isolated in the Concordia research station were examined for their plasmid content. An optimized protocol for extraction of large plasmids showed the present of at least one plasmid in 50% of the strains. For all strains the minimal inhibitory concentration of a range of antibiotics was determined indicating resistance to

  20. Plasmid and chromosome segregation in prokaryotes

    DEFF Research Database (Denmark)

    Møller-Jensen, Jakob; Bugge Jensen, Rasmus; Gerdes, Kenn

    2000-01-01

    Recent major advances in the understanding of prokaryotic DNA segregation have been achieved by using fluorescence microscopy to visualize the localization of cellular components. Plasmids and bacterial chromosomes are partitioned in a highly dynamic fashion, suggesting the presence of a mitotic...

  1. Impact of co-carriage of IncA/C plasmids with additional plasmids on the transfer of antimicrobial resistance in Salmonella enterica isolates.

    Science.gov (United States)

    Han, Jing; Pendleton, Sean J; Deck, Joanna; Singh, Ruby; Gilbert, Jeffrey; Johnson, Timothy J; Sanad, Yasser M; Nayak, Rajesh; Foley, Steven L

    2018-04-20

    Antimicrobial resistance in Salmonella enterica is often plasmid encoded. A key resistance plasmid group is the incompatibility group (Inc) A/C plasmids that often carry multiple resistance determinants. Previous studies showed that IncA/C plasmids were often co-located with other plasmids. The current study was undertaken to evaluate the impact of plasmid co-carriage on antimicrobial resistance and plasmid transfer. A total of 1267 Salmonella isolates, representing multiple serotypes and sources were previously subjected to susceptibility testing and 251 isolates with resistance to at least 5 antimicrobial agents were identified for further study. Each isolate was subjected to PCR-based replicon typing, and those with IncA/C plasmids were selected for plasmid isolation, PCR-based mapping of IncA/C plasmid backbone genes, and conjugation assays to evaluate resistance plasmid transferability. Of the 87 identified IncA/C positive isolates, approximately 75% carried a plasmid with another identified replicon type, with the most common being I1 (39%), FIA, FIIA, FIB and HI2 (each 15%). PCR-based mapping indicated significant diversity in IncA/C backbone content, especially in regions encoding transfer-associated and hypothetical proteins. Conjugation experiments showed that nearly 68% of the isolates transferred resistance plasmids, with 90% containing additional identified plasmids or larger (>50 kb) non-typeable plasmids. The majority of IncA/C-positive strains were able to conjugally transfer antimicrobial resistance to the recipient, encoded by IncA/C and/or co-carried plasmids. These findings highlight the importance of co-located plasmids for resistance dissemination either by directly transferring resistance genes or by potentially providing the needed conjugation machinery for IncA/C plasmid transfer. Copyright © 2018. Published by Elsevier B.V.

  2. On the dynamics of gauge potential

    International Nuclear Information System (INIS)

    Tao Jiafu; Li Yuanjie; Zhang Jinru

    1992-01-01

    The gauge potential is resolved into gauge potential of strength and gauge potential of phase. The phase gauge potential can be described with an equivalent potential of inertial force. A Lagrangian density with phase gauge potential is given and some examples are discussed. The method proposed has been extended to the case of the non-Abelian group

  3. Plasmids in Gram negatives: molecular typing of resistance plasmids.

    Science.gov (United States)

    Carattoli, Alessandra

    2011-12-01

    A plasmid is defined as a double stranded, circular DNA molecule capable of autonomous replication. By definition, plasmids do not carry genes essential for the growth of host cells under non-stressed conditions but they have systems which guarantee their autonomous replication also controlling the copy number and ensuring stable inheritance during cell division. Most of the plasmids confer positively selectable phenotypes by the presence of antimicrobial resistance genes. Plasmids evolve as an integral part of the bacterial genome, providing resistance genes that can be easily exchanged among bacteria of different origin and source by conjugation. A multidisciplinary approach is currently applied to study the acquisition and spread of antimicrobial resistance in clinically relevant bacterial pathogens and the established surveillance can be implemented by replicon typing of plasmids. Particular plasmid families are more frequently detected among Enterobacteriaceae and play a major role in the diffusion of specific resistance genes. For instance, IncFII, IncA/C, IncL/M, IncN and IncI1 plasmids carrying extended-spectrum beta-lactamase genes and acquired AmpC genes are currently considered to be "epidemic resistance plasmids", being worldwide detected in Enterobacteriaceae of different origin and sources. The recognition of successful plasmids is an essential first step to design intervention strategies preventing their spread. Copyright © 2011 Elsevier GmbH. All rights reserved.

  4. Dynamic polarization potentials in heavy ion scattering

    International Nuclear Information System (INIS)

    Wolf, R.

    1984-01-01

    In this thesis the polarization potential is calculated which is caused by several collective, strongly coupled states. In the framework of the considered model space the calculation of the polarization potential was exact, i.e. no approximations were made. For this purpose the Green function of the system had to be calculated. This led to a nonlocal polarization potential. For the better interpretation possibility and for the easier use in coupled-channel or optical-model calculations from the nonlocal potentials also equivalent potentials were constructed. The properties of the local and nonlocal potentials as shape, angular momentum, and energy dependence were discussed. Furthermore parametrizations were given, how polarization effects can be regarded in a simple way in optical-model or coupled-channel calculations. The calculations were performed for the systems 12 C+ 12 C and 16 O+ 16 O. To meet as realistic results as possible, parameters for the unperturbed potential were looked for which describe as many data as possible, like angular distributions, excitation functions, and alignment of the main channels. As unperturbed potential both folding potentials and phenomenological potentials were applied in order to study the differences in the polarization potential in the application of deep and flat potentials. (orig./HSI) [de

  5. Preinflationary dynamics in loop quantum cosmology: Power-law potentials

    Science.gov (United States)

    Shahalam, M.; Sharma, Manabendra; Wu, Qiang; Wang, Anzhong

    2017-12-01

    In this paper, we study the preinflationary dynamics for the power-law potential [V (ϕ )∝ϕn] with n consideration and compare our results with the ones obtained previously for different potentials.

  6. Global transcription regulation of RK2 plasmids: a case study in the combined use of dynamical mathematical models and statistical inference for integration of experimental data and hypothesis exploration

    Directory of Open Access Journals (Sweden)

    Thomas Christopher M

    2011-07-01

    Full Text Available Abstract Background IncP-1 plasmids are broad host range plasmids that have been found in clinical and environmental bacteria. They often carry genes for antibiotic resistance or catabolic pathways. The archetypal IncP-1 plasmid RK2 is a well-characterized biological system, with a fully sequenced and annotated genome and wide range of experimental measurements. Its central control operon, encoding two global regulators KorA and KorB, is a natural example of a negatively self-regulated operon. To increase our understanding of the regulation of this operon, we have constructed a dynamical mathematical model using Ordinary Differential Equations, and employed a Bayesian inference scheme, Markov Chain Monte Carlo (MCMC using the Metropolis-Hastings algorithm, as a way of integrating experimental measurements and a priori knowledge. We also compared MCMC and Metabolic Control Analysis (MCA as approaches for determining the sensitivity of model parameters. Results We identified two distinct sets of parameter values, with different biological interpretations, that fit and explain the experimental data. This allowed us to highlight the proportion of repressor protein as dimers as a key experimental measurement defining the dynamics of the system. Analysis of joint posterior distributions led to the identification of correlations between parameters for protein synthesis and partial repression by KorA or KorB dimers, indicating the necessary use of joint posteriors for correct parameter estimation. Using MCA, we demonstrated that the system is highly sensitive to the growth rate but insensitive to repressor monomerization rates in their selected value regions; the latter outcome was also confirmed by MCMC. Finally, by examining a series of different model refinements for partial repression by KorA or KorB dimers alone, we showed that a model including partial repression by KorA and KorB was most compatible with existing experimental data. Conclusions We

  7. Puzzling with potential : dynamic testing of analogical reasoning in children

    NARCIS (Netherlands)

    Stevenson, Claire Elisabeth

    2012-01-01

    Assessment procedures are frequent in children's school careers; however, measuring potential for learning has remained a puzzle. Dynamic testing is a method to assess cognitive potential that includes training in the assessment process. The goal of this thesis project was to develop a new dynamic

  8. Puzzling with potential: dynamic testing of analogical reasoning in children

    OpenAIRE

    Stevenson, Claire Elisabeth

    2012-01-01

    Assessment procedures are frequent in children's school careers; however, measuring potential for learning has remained a puzzle. Dynamic testing is a method to assess cognitive potential that includes training in the assessment process. The goal of this thesis project was to develop a new dynamic test of analogical reasoning for school children. The main aims were to (1) investigate factors that influence children’s differences in performance and change during dynamic testing and (2) examine...

  9. Survival and evolution of a large multidrug resistance plasmid in new clinical bacterial hosts

    DEFF Research Database (Denmark)

    Porse, Andreas; Schønning, Kristian; Munck, Christian

    2016-01-01

    sequencing to show that the long-term persistence and molecular integrity of the plasmid is highly influenced by multiple factors within a 25 kb plasmid region constituting a host-dependent burden. In the E. coli hosts investigated here, improved plasmid stability readily evolves via IS26 mediated deletions...... consistently followed by all evolved E. coli lineages exposes a trade-off between horizontal and vertical transmission that may ultimately limit the dissemination potential of clinical multidrug resistance plasmids in these hosts....

  10. Dynamic properties of the Sulfolobus CRISPR/Cas and CRISPR/Cmr systems when challenged with vector-borne viral and plasmid genes and protospacers

    DEFF Research Database (Denmark)

    Guðbergsdóttir, Sóley Ruth; Deng, Ling; Chen, Zhengjun

    2011-01-01

    The adaptive immune CRISPR/Cas and CRISPR/Cmr systems of the crenarchaeal thermoacidophile Sulfolobus were challenged by a variety of viral and plasmid genes, and protospacers preceded by different dinucleotide motifs. The genes and protospacers were constructed to carry sequences matching...... individual spacers of CRISPR loci, and a range of mismatches were introduced. Constructs were cloned into vectors carrying pyrE/pyrF genes and transformed into uracil auxotrophic hosts derived from Sulfolobus solfataricus P2 or Sulfolobus islandicus REY15A. Most constructs, including those carrying different...... protospacer mismatches, yielded few viable transformants. These were shown to carry either partial deletions of CRISPR loci, covering a broad spectrum of sizes and including the matching spacer, or deletions of whole CRISPR/Cas modules. The deletions occurred independently of whether genes or protospacers...

  11. Persistence Mechanisms of Conjugative Plasmids

    DEFF Research Database (Denmark)

    Bahl, Martin Iain; Hansen, Lars H.; Sørensen, Søren Johannes

    2009-01-01

    Are plasmids selfish parasitic DNA molecules or an integrated part of the bacterial genome? This chapter reviews the current understanding of the persistence mechanisms of conjugative plasmids harbored by bacterial cells and populations. The diversity and intricacy of mechanisms affecting the suc...

  12. Explanatory chapter: how plasmid preparation kits work.

    Science.gov (United States)

    Koontz, Laura

    2013-01-01

    To isolate plasmid DNA from bacteria using a commercial plasmid miniprep kit (if interested, compare this protocol with Isolation of plasmid DNA from bacteria). Copyright © 2013 Elsevier Inc. All rights reserved.

  13. Dynamic Assessment, Potential Giftedness and Mathematics Achievement in Elementary School

    Science.gov (United States)

    Popa, Nicoleta Laura; Pauc, Ramona Loredana

    2015-01-01

    Dynamic assessment is currently discussed in educational literature as one of the most promising practices in stimulating learning among various groups of students, including gifted and potentially gifted students. The present study investigates effects of dynamic assessment on mathematics achievement among elementary school students, with…

  14. Crystal structure and pair potentials: A molecular-dynamics study

    Energy Technology Data Exchange (ETDEWEB)

    Parrinello, M.; Rahman, A.

    1980-10-06

    With use of a Lagrangian which allows for the variation of the shape and size of the periodically repeating molecular-dynamics cell, it is shown that different pair potentials lead to different crystal structures.

  15. Models in the physics: static and dynamic potentials

    International Nuclear Information System (INIS)

    Morales M, F.; Flores P, J.

    1996-01-01

    This is a brief discussion of dynamical effects on Debye screening based on the Boltzmann equation for a collisional plasma. The Debye length, the radial dependence of the interparticle potential and the electrical resistivity are quantitatively delineated

  16. In Silico Detection and Typing of Plasmids using PlasmidFinder and Plasmid Multilocus Sequence Typing

    DEFF Research Database (Denmark)

    Carattoli, Alessandra; Zankari, Ea; García-Fernández, Aurora

    2014-01-01

    In the work presented here, we designed and developed two easy-to-use Web tools for in silico detection and characterization of whole-genome sequence (WGS) and whole-plasmid sequence data from members of the family Enterobacteriaceae. These tools will facilitate bacterial typing based on draft...... genomes of multidrug-resistant Enterobacteriaceae species by the rapid detection of known plasmid types. Replicon sequences from 559 fully sequenced plasmids associated with the family Enterobacteriaceae in the NCBI nucleotide database were collected to build a consensus database for integration...... sequences identified in the 559 fully sequenced plasmids. For plasmid multilocus sequence typing (pMLST) analysis, a database that is updated weekly was generated from www.pubmlst.org and integrated into a Web tool called pMLST. Both databases were evaluated using draft genomes from a collection...

  17. On wave-packet dynamics in a decaying quadratic potential

    DEFF Research Database (Denmark)

    Møller, Klaus Braagaard; Henriksen, Niels Engholm

    1997-01-01

    We consider the time-dependent Schrodinger equation for a quadratic potential with an exponentially decaying force constant. General analytical solutions are presented and we highlight in particular, the signatures of classical mechanics in the wave packet dynamics.......We consider the time-dependent Schrodinger equation for a quadratic potential with an exponentially decaying force constant. General analytical solutions are presented and we highlight in particular, the signatures of classical mechanics in the wave packet dynamics....

  18. Extended-Spectrum-Beta-Lactamase- and Plasmid-Encoded Cephamycinase-Producing Enterobacteria in the Broiler Hatchery as a Potential Mode of Pseudo-Vertical Transmission.

    Science.gov (United States)

    Projahn, Michaela; Daehre, Katrin; Roesler, Uwe; Friese, Anika

    2017-01-01

    Antimicrobial resistance through extended-spectrum beta-lactamases (ESBLs) and transferable (plasmid-encoded) cephamycinases (pAmpCs) represents an increasing problem in human and veterinary medicine. The presence of ESBL-/pAmpC-producing commensal enterobacteria in farm animals, such as broiler chickens, is considered one possible source of food contamination and could therefore also be relevant for human colonization. Studies on transmission routes along the broiler production chain showed that 1-day-old hatchlings are already affected. In this study, ESBL-/pAmpC-positive broiler parent flocks and their corresponding eggs, as well as various environmental and air samples from the hatchery, were analyzed. The eggs were investigated concerning ESBL-/pAmpC-producing enterobacteria on the outer eggshell surface (before/after disinfection), the inner eggshell surface, and the egg content. Isolates were analyzed concerning their species, their phylogroup in the case of Escherichia coli strains, the respective resistance genes, and the phenotypical antibiotic resistance. Of the tested eggs, 0.9% (n = 560) were contaminated on their outer shell surface. Further analyses using pulsed-field gel electrophoresis showed a relationship of these strains to those isolated from the corresponding parent flocks, which demonstrates a pseudo-vertical transfer of ESBL-/pAmpC-producing enterobacteria into the hatchery. Resistant enterobacteria were also found in environmental samples from the hatchery, such as dust or surfaces which could pose as a possible contamination source for the hatchlings. All 1-day-old chicks tested negative directly after hatching. The results show a possible entry of ESBL-/pAmpC-producing enterobacteria from the parent flocks into the hatchery; however, the impact of the hatchery on colonization of the hatchlings seems to be low. ESBL-/pAmpC-producing enterobacteria occur frequently in broiler-fattening farms. Recent studies investigated the prevalence and

  19. Anisotropic Born-Mayer potential in lattice dynamics of Vanadium

    International Nuclear Information System (INIS)

    Onwuagba, B.N.

    1988-01-01

    A microscopic theory of the lattice dynamics of the transition metal vanadium is developed based on the Animalu's transition metal model potential (TMMP). The Born-Mayer potential associated with the distribution of the transition metal d-electrons is treated as anisotropic. Good agreement with experimental phonon dispersion curves longitudinal branches in the [111] direction

  20. Solitary wave dynamics in time-dependent potentials

    International Nuclear Information System (INIS)

    Abou Salem, Walid K.

    2008-01-01

    The long time dynamics of solitary wave solutions of the nonlinear Schroedinger equation in time-dependent external potentials is rigorously studied. To set the stage, the well-posedness of the Cauchy problem for a generalized nonautonomous nonlinear Schroedinger equation with time-dependent nonlinearities and potential is established. Afterward, the dynamics of NLS solitary waves in time-dependent potentials is studied. It is shown that in the space-adiabatic regime where the external potential varies slowly in space compared to the size of the soliton, the dynamics of the center of the soliton is described by Hamilton's equations, plus terms due to radiation damping. Finally, two physical applications are discussed: the first is adiabatic transportation of solitons and the second is the Mathieu instability of trapped solitons due to time-periodic perturbations

  1. Plasmid and chromosome partitioning: surprises from phylogeny

    DEFF Research Database (Denmark)

    Gerdes, Kenn; Møller-Jensen, Jakob; Bugge Jensen, Rasmus

    2000-01-01

    Plasmids encode partitioning genes (par) that are required for faithful plasmid segregation at cell division. Initially, par loci were identified on plasmids, but more recently they were also found on bacterial chromosomes. We present here a phylogenetic analysis of par loci from plasmids and chr...

  2. A survey of static and dynamic potential games

    Institute of Scientific and Technical Information of China (English)

    GONZLEZ-SNCHEZ David; HERNNDEZ-LERMA Onsimo

    2016-01-01

    Potential games are noncooperative games for which there exist auxiliary functions, called potentials,such that the maximizers of the potential are also Nash equilibria of the corresponding game. Some properties of Nash equilibria, such as existence or stability, can be derived from the potential, whenever it exists. We survey different classes of potential games in the static and dynamic cases, with a finite number of players, as well as in population games where a continuum of players is allowed. Likewise, theoretical concepts and applications are discussed by means of illustrative examples.

  3. Tunneling in a self-consistent dynamic image potential

    International Nuclear Information System (INIS)

    Rudberg, B.G.R.; Jonson, M.

    1991-01-01

    We have calculated the self-consistent effective potential for an electron tunneling through a square barrier while interacting with surface plasmons. This potential reduces to the classical image potential in the static limit. In the opposite limit, when the ''velocity'' of the tunneling electron is large, it reduces to the unperturbed square-barrier potential. For a wide variety of parameters the dynamic effects on the transmission coefficient T=|t 2 | can, for instance, be related to the Buettiker-Landauer traversal time for tunneling, given by τ BL =ℎ|d lnt/dV|

  4. Construction of Stable Fluorescent Reporter Plasmids for Use in Staphylococcus aureus

    Directory of Open Access Journals (Sweden)

    Michelle D. Rodriguez

    2017-12-01

    Full Text Available Here, the genes encoding three different fluorescent proteins were cloned into the stably maintained Staphylococcus aureus shuttle vector pKK30. The resulting plasmids were transformed into two S. aureus strains; SH1000 and RN4220. Stability assays illustrated that the three recombinant plasmids retained near 100% maintenance in vitro for 160 generations. S. aureus strain SH1000 expressing green fluorescent protein was then inoculated in an ovine model and in vivo stability for 6 days was demonstrated. In essence, these reporter plasmids represent a useful set of tools for dynamic imaging studies in S. aureus. These three reporter plasmids are available through BEI Resources.

  5. Construction of Stable Fluorescent Reporter Plasmids for Use in Staphylococcus aureus.

    Science.gov (United States)

    Rodriguez, Michelle D; Paul, Zubin; Wood, Charles E; Rice, Kelly C; Triplett, Eric W

    2017-01-01

    Here, the genes encoding three different fluorescent proteins were cloned into the stably maintained Staphylococcus aureus shuttle vector pKK30. The resulting plasmids were transformed into two S. aureus strains; SH1000 and RN4220. Stability assays illustrated that the three recombinant plasmids retained near 100% maintenance in vitro for 160 generations. S. aureus strain SH1000 expressing green fluorescent protein was then inoculated in an ovine model and in vivo stability for 6 days was demonstrated. In essence, these reporter plasmids represent a useful set of tools for dynamic imaging studies in S. aureus . These three reporter plasmids are available through BEI Resources.

  6. Dynamic of cold-atom tips in anharmonic potentials

    Science.gov (United States)

    Menold, Tobias; Federsel, Peter; Rogulj, Carola; Hölscher, Hendrik; Fortágh, József

    2016-01-01

    Background: Understanding the dynamics of ultracold quantum gases in an anharmonic potential is essential for applications in the new field of cold-atom scanning probe microscopy. Therein, cold atomic ensembles are used as sensitive probe tips to investigate nanostructured surfaces and surface-near potentials, which typically cause anharmonic tip motion. Results: Besides a theoretical description of this anharmonic tip motion, we introduce a novel method for detecting the cold-atom tip dynamics in situ and real time. In agreement with theory, the first measurements show that particle interactions and anharmonic motion have a significant impact on the tip dynamics. Conclusion: Our findings will be crucial for the realization of high-sensitivity force spectroscopy with cold-atom tips and could possibly allow for the development of advanced spectroscopic techniques such as Q-control. PMID:28144505

  7. Assessing atmospheric bias correction for dynamical consistency using potential vorticity

    International Nuclear Information System (INIS)

    Rocheta, Eytan; Sharma, Ashish; Evans, Jason P

    2014-01-01

    Correcting biases in atmospheric variables prior to impact studies or dynamical downscaling can lead to new biases as dynamical consistency between the ‘corrected’ fields is not maintained. Use of these bias corrected fields for subsequent impact studies and dynamical downscaling provides input conditions that do not appropriately represent intervariable relationships in atmospheric fields. Here we investigate the consequences of the lack of dynamical consistency in bias correction using a measure of model consistency—the potential vorticity (PV). This paper presents an assessment of the biases present in PV using two alternative correction techniques—an approach where bias correction is performed individually on each atmospheric variable, thereby ignoring the physical relationships that exists between the multiple variables that are corrected, and a second approach where bias correction is performed directly on the PV field, thereby keeping the system dynamically coherent throughout the correction process. In this paper we show that bias correcting variables independently results in increased errors above the tropopause in the mean and standard deviation of the PV field, which are improved when using the alternative proposed. Furthermore, patterns of spatial variability are improved over nearly all vertical levels when applying the alternative approach. Results point to a need for a dynamically consistent atmospheric bias correction technique which results in fields that can be used as dynamically consistent lateral boundaries in follow-up downscaling applications. (letter)

  8. Quantum-Accurate Molecular Dynamics Potential for Tungsten

    Energy Technology Data Exchange (ETDEWEB)

    Wood, Mitchell; Thompson, Aidan P.

    2017-03-01

    The purpose of this short contribution is to report on the development of a Spectral Neighbor Analysis Potential (SNAP) for tungsten. We have focused on the characterization of elastic and defect properties of the pure material in order to support molecular dynamics simulations of plasma-facing materials in fusion reactors. A parallel genetic algorithm approach was used to efficiently search for fitting parameters optimized against a large number of objective functions. In addition, we have shown that this many-body tungsten potential can be used in conjunction with a simple helium pair potential1 to produce accurate defect formation energies for the W-He binary system.

  9. Absorption dynamics and delay time in complex potentials

    Science.gov (United States)

    Villavicencio, Jorge; Romo, Roberto; Hernández-Maldonado, Alberto

    2018-05-01

    The dynamics of absorption is analyzed by using an exactly solvable model that deals with an analytical solution to Schrödinger’s equation for cutoff initial plane waves incident on a complex absorbing potential. A dynamical absorption coefficient which allows us to explore the dynamical loss of particles from the transient to the stationary regime is derived. We find that the absorption process is characterized by the emission of a series of damped periodic pulses in time domain, associated with damped Rabi-type oscillations with a characteristic frequency, ω = (E + ε)/ℏ, where E is the energy of the incident waves and ‑ε is energy of the quasidiscrete state of the system induced by the absorptive part of the Hamiltonian; the width γ of this resonance governs the amplitude of the pulses. The resemblance of the time-dependent absorption coefficient with a real decay process is discussed, in particular the transition from exponential to nonexponential regimes, a well-known feature of quantum decay. We have also analyzed the effect of the absorptive part of the potential on the dynamical delay time, which behaves differently from the one observed in attractive real delta potentials, exhibiting two regimes: time advance and time delay.

  10. Short-time quantum dynamics of sharp boundaries potentials

    Energy Technology Data Exchange (ETDEWEB)

    Granot, Er' el, E-mail: erel@ariel.ac.il; Marchewka, Avi

    2015-02-15

    Despite the high prevalence of singular potential in general, and rectangular potentials in particular, in applied scattering models, to date little is known about their short time effects. The reason is that singular potentials cause a mixture of complicated local as well as non-local effects. The object of this work is to derive a generic method to calculate analytically the short-time impact of any singular potential. In this paper it is shown that the scattering of a smooth wavefunction on a singular potential is totally equivalent, in the short-time regime, to the free propagation of a singular wavefunction. However, the latter problem was totally addressed analytically in Ref. [7]. Therefore, this equivalency can be utilized in solving analytically the short time dynamics of any smooth wavefunction at the presence of a singular potentials. In particular, with this method the short-time dynamics of any problem where a sharp boundaries potential (e.g., a rectangular barrier) is turned on instantaneously can easily be solved analytically.

  11. Short-time quantum dynamics of sharp boundaries potentials

    Science.gov (United States)

    Granot, Er'el; Marchewka, Avi

    2015-02-01

    Despite the high prevalence of singular potential in general, and rectangular potentials in particular, in applied scattering models, to date little is known about their short time effects. The reason is that singular potentials cause a mixture of complicated local as well as non-local effects. The object of this work is to derive a generic method to calculate analytically the short-time impact of any singular potential. In this paper it is shown that the scattering of a smooth wavefunction on a singular potential is totally equivalent, in the short-time regime, to the free propagation of a singular wavefunction. However, the latter problem was totally addressed analytically in Ref. [7]. Therefore, this equivalency can be utilized in solving analytically the short time dynamics of any smooth wavefunction at the presence of a singular potentials. In particular, with this method the short-time dynamics of any problem where a sharp boundaries potential (e.g., a rectangular barrier) is turned on instantaneously can easily be solved analytically.

  12. Short-time quantum dynamics of sharp boundaries potentials

    International Nuclear Information System (INIS)

    Granot, Er'el; Marchewka, Avi

    2015-01-01

    Despite the high prevalence of singular potential in general, and rectangular potentials in particular, in applied scattering models, to date little is known about their short time effects. The reason is that singular potentials cause a mixture of complicated local as well as non-local effects. The object of this work is to derive a generic method to calculate analytically the short-time impact of any singular potential. In this paper it is shown that the scattering of a smooth wavefunction on a singular potential is totally equivalent, in the short-time regime, to the free propagation of a singular wavefunction. However, the latter problem was totally addressed analytically in Ref. [7]. Therefore, this equivalency can be utilized in solving analytically the short time dynamics of any smooth wavefunction at the presence of a singular potentials. In particular, with this method the short-time dynamics of any problem where a sharp boundaries potential (e.g., a rectangular barrier) is turned on instantaneously can easily be solved analytically

  13. Determination of the static potential with dynamical fermions

    Energy Technology Data Exchange (ETDEWEB)

    Donnellan, Michael; Sommer, Rainer [Deutsches Elektronen-Synchrotron (DESY), Zeuthen (Germany). John von Neumann-Inst. fuer Computing NIC; Knechtli, Francesco [Bergische Univ. Wuppertal (Germany). Dept. of Physics; Leder, Bjoern [Bergische Univ. Wuppertal (Germany). Dept. of Mathematics

    2010-12-15

    We present in detail a technique to extract the potential between a static quark and anti-quark pair from Wilson loops measured on dynamical configurations. This technique is based on HYP smearing and leads to an exponential improvement of the noise-to-signal ratio of Wilson loops. We explain why the correct continuum potential is obtained and show numerical evidence that the cut-off effects are small. We present precise results for the non-perturbative potential. As applications, we determine the scale r{sub 0}/a and study the shape of the static potential in the range of distances around r{sub 0}, where it can be compared with phenomenological potential models. (orig.)

  14. A study of tachyon dynamics for broad classes of potentials

    Energy Technology Data Exchange (ETDEWEB)

    Quiros, Israel [Division de Ciencias e Ingenieria de la Universidad de Guanajuato, AP 150, 37150, Leon, Guanajuato (Mexico); Gonzalez, Tame [Departamento de Fisica, Universidad Central de Las Villas, 54830 Santa Clara (Cuba); Gonzalez, Dania; Napoles, Yunelsy [Departamento de Matematica, Universidad Central de Las Villas, 54830 Santa Clara (Cuba); GarcIa-Salcedo, Ricardo [Centro de Investigacion en Ciencia Aplicada y Tecnologia Avanzada-Legaria del IPN, Mexico DF (Mexico); Moreno, Claudia, E-mail: iquiros@Fisica.ugto.m, E-mail: tame@uclv.edu.c, E-mail: dgm@uclv.edu.c, E-mail: yna@uclv.edu.c, E-mail: rigarcias@ipn.m, E-mail: claudia.moreno@cucei.udg.m [Departamento de Fisica y Matematicas, Centro Universitario de Ciencias Exactas e IngenierIas, Av. Revolucion 1500 SR, Universidad de Guadalajara, 44430 Guadalajara, Jalisco (Mexico)

    2010-11-07

    We investigate in detail the asymptotic properties of tachyon cosmology for a broad class of self-interaction potentials. The present approach relies on an appropriate re-definition of the tachyon field, which, in conjunction with a method formerly applied in the bibliography in a different context allows us to generalize the dynamical systems study of tachyon cosmology to a wider class of self-interaction potentials beyond the (inverse) square-law one. It is revealed that independent of the functional form of the potential, the matter-dominated solution and the ultra-relativistic (also matter-dominated) solution are always associated with equilibrium points in the phase space of the tachyon models. The latter is always the past attractor, while the former is a saddle critical point. For inverse power-law potentials V{proportional_to}{phi}{sup -2{lambda}} the late-time attractor is always the de Sitter solution, while for sinh-like potentials V{proportional_to}sinh {sup -{alpha}}({lambda}{sup {phi}}), depending on the region of parameter space, the late-time attractor can be either the inflationary tachyon-dominated solution or the matter-scaling (also inflationary) phase. In general, for most part of known quintessential potentials, the late-time dynamics will be associated either with de Sitter inflation, or with matter-scaling, or with scalar field-dominated solutions.

  15. Solid lipid nanoparticles mediate non-viral delivery of plasmid DNA to dendritic cells

    Science.gov (United States)

    Penumarthi, Alekhya; Parashar, Deepti; Abraham, Amanda N.; Dekiwadia, Chaitali; Macreadie, Ian; Shukla, Ravi; Smooker, Peter M.

    2017-06-01

    There is an increasing demand for novel DNA vaccine delivery systems, mainly for the non-viral type as they are considered relatively safe. Therefore, solid lipid nanoparticles (SLNs) were investigated for their suitability as a non-viral DNA vaccine delivery system. SLNs were synthesised by a modified solvent-emulsification method in order to study their potential to conjugate with plasmid DNA and deliver them in vitro to dendritic cells using eGFP as the reporter plasmid. The DNA-SLN complexes were characterised by electron microscopy, gel retardation assays and dynamic light scattering. The cytotoxicity assay data supported their biocompatibility and was used to estimate safe threshold concentration resulting in high transfection rate. The transfection efficiency of these complexes in a dendritic cell line was shown to increase significantly compared to plasmid alone, and was comparable to that mediated by lipofectamine. Transmission electron microscopy studies delineated the pathway of cellular uptake. Endosomal escape was observed supporting the mechanism of transfection.

  16. The potential value of dynamic materials control in international safeguards

    International Nuclear Information System (INIS)

    Keepin, G.R.; Lovett, J.E.

    1979-01-01

    The difficulties inherent in conventional materials accountancy based on semi-annual or annual shutdown cleanout physical inventories have been recognized for many years. The increasing importance of international nuclear materials safeguards, coupled with the availability of advanced non-destructive measurement technology which could be installed on or near process lines, has led to the development of the concept of advanced or dynamic materials control. The potential benefits of dynamic materials control in terms of significantly improved detection capabilities (ranging from a few kilograms of plutonium down to perhaps a few hundred grams, even for large-scale bulk processing facilities), and even more dramatically improved detection timeliness (typically a few days, and potentially only a few hours, in advanced facilities), are reviewed. At least twelve major dynamic material control systems already in existence or in the process of being installed are noted, and some of the essential characteristics are discussed. Some currently unresolved questions are explored, and future prospects for the concept of dynamic material control in international safeguards are reviewed. (author)

  17. Antimicrobial susceptibility pattern and plasmid-mediated ...

    African Journals Online (AJOL)

    negative Staphylococci (CoNS) were isolated from clinical samples and isolates subjected to antibiotic susceptibility testing, plasmid curing and plasmid DNA isolation. Result: The highest percentages isolates were recovered from urine samples and ...

  18. Dynamics of Fermat potentials in nonperturbative gravitational lensing

    International Nuclear Information System (INIS)

    Frittelli, Simonetta; Newman, Ezra T.

    2002-01-01

    We present a framework, based on the null-surface formulation of general relativity, for discussing the dynamics of Fermat potentials for gravitational lensing in a generic situation without approximations of any kind. Additionally, we derive two lens equations: one for the case of thick compact lenses and the other one for lensing by gravitational waves. These equations in principle generalize the astrophysical scheme for lensing by removing the thin-lens approximation while retaining the weak fields

  19. Study of the dynamical potential barriers in heavy ion collisions

    International Nuclear Information System (INIS)

    Zhu, Long; Su, Jun; Xie, Wen-Jie; Zhang, Feng-Shou

    2013-01-01

    The nucleus–nucleus interaction potentials for the fusion reactions 16 O + 208 Pb, 64 Ni + 64 Ni, 58 Ni + 58 Ni and 16 O + 154 Sm are extracted from the improved isospin-dependent quantum molecular dynamics model. The shell correction effects are discussed. The negative shell correction energies lower potential barriers of a certain reaction. The incident energy dependence of the potential barrier is investigated for each system. A complex phenomenon of energy dependence is observed. It is also found that incident energy dependence of the barrier radius and barrier height shows opposite behaviors. The Coulomb potential shows weak energy dependence when distance of two colliding nuclei is lower than the touching distance. The isospin effects of the potential barrier are investigated. The orientation effects of the potential barrier is also discussed for the system 16 O + 154 Sm. The fusion cross sections that correspond to the equatorial orientation of 154 Sm are very low in sub-barrier region because of the high fusion barriers and the shallow potential pockets

  20. Origin and Evolution of Rickettsial Plasmids.

    Directory of Open Access Journals (Sweden)

    Khalid El Karkouri

    Full Text Available Rickettsia species are strictly intracellular bacteria that have undergone a reductive genomic evolution. Despite their allopatric lifestyle, almost half of the 26 currently validated Rickettsia species have plasmids. In order to study the origin, evolutionary history and putative roles of rickettsial plasmids, we investigated the evolutionary processes that have shaped 20 plasmids belonging to 11 species, using comparative genomics and phylogenetic analysis between rickettsial, microbial and non-microbial genomes.Plasmids were differentially present among Rickettsia species. The 11 species had 1 to 4 plasmid (s with a size ranging from 12 kb to 83 kb. We reconstructed pRICO, the last common ancestor of the current rickettsial plasmids. pRICO was vertically inherited mainly from Rickettsia/Orientia chromosomes and diverged vertically into a single or multiple plasmid(s in each species. These plasmids also underwent a reductive evolution by progressive gene loss, similar to that observed in rickettsial chromosomes, possibly leading to cryptic plasmids or complete plasmid loss. Moreover, rickettsial plasmids exhibited ORFans, recent gene duplications and evidence of horizontal gene transfer events with rickettsial and non-rickettsial genomes mainly from the α/γ-proteobacteria lineages. Genes related to maintenance and plasticity of plasmids, and to adaptation and resistance to stress mostly evolved under vertical and/or horizontal processes. Those involved in nucleotide/carbohydrate transport and metabolism were under the influence of vertical evolution only, whereas genes involved in cell wall/membrane/envelope biogenesis, cycle control, amino acid/lipid/coenzyme and secondary metabolites biosynthesis, transport and metabolism underwent mainly horizontal transfer events.Rickettsial plasmids had a complex evolution, starting with a vertical inheritance followed by a reductive evolution associated with increased complexity via horizontal gene

  1. Molecular dynamics simulations of solutions at constant chemical potential

    Science.gov (United States)

    Perego, C.; Salvalaglio, M.; Parrinello, M.

    2015-04-01

    Molecular dynamics studies of chemical processes in solution are of great value in a wide spectrum of applications, which range from nano-technology to pharmaceutical chemistry. However, these calculations are affected by severe finite-size effects, such as the solution being depleted as the chemical process proceeds, which influence the outcome of the simulations. To overcome these limitations, one must allow the system to exchange molecules with a macroscopic reservoir, thus sampling a grand-canonical ensemble. Despite the fact that different remedies have been proposed, this still represents a key challenge in molecular simulations. In the present work, we propose the Constant Chemical Potential Molecular Dynamics (CμMD) method, which introduces an external force that controls the environment of the chemical process of interest. This external force, drawing molecules from a finite reservoir, maintains the chemical potential constant in the region where the process takes place. We have applied the CμMD method to the paradigmatic case of urea crystallization in aqueous solution. As a result, we have been able to study crystal growth dynamics under constant supersaturation conditions and to extract growth rates and free-energy barriers.

  2. Quantum dynamics of relativistic bosons through nonminimal vector square potentials

    Energy Technology Data Exchange (ETDEWEB)

    Oliveira, Luiz P. de, E-mail: oliveira.phys@gmail.com

    2016-09-15

    The dynamics of relativistic bosons (scalar and vectorial) through nonminimal vector square (well and barrier) potentials is studied in the Duffin–Kemmer–Petiau (DKP) formalism. We show that the problem can be mapped in effective Schrödinger equations for a component of the DKP spinor. An oscillatory transmission coefficient is found and there is total reflection. Additionally, the energy spectrum of bound states is obtained and reveals the Schiff–Snyder–Weinberg effect, for specific conditions the potential lodges bound states of particles and antiparticles. - Highlights: • DKP bosons in a nonminimal vector square potential are studied. • Spin zero and spin one bosons have the same results. • The Schiff–Snyder–Weinberg effect is observed.

  3. Novel plasmids and resistance phenotypes in Yersinia pestis: unique plasmid inventory of strain Java 9 mediates high levels of arsenic resistance.

    Science.gov (United States)

    Eppinger, Mark; Radnedge, Lyndsay; Andersen, Gary; Vietri, Nicholas; Severson, Grant; Mou, Sherry; Ravel, Jacques; Worsham, Patricia L

    2012-01-01

    Growing evidence suggests that the plasmid repertoire of Yersinia pestis is not restricted to the three classical virulence plasmids. The Java 9 strain of Y. pestis is a biovar Orientalis isolate obtained from a rat in Indonesia. Although it lacks the Y. pestis-specific plasmid pMT, which encodes the F1 capsule, it retains virulence in mouse and non-human primate animal models. While comparing diverse Y. pestis strains using subtractive hybridization, we identified sequences in Java 9 that were homologous to a Y. enterocolitica strain carrying the transposon Tn2502, which is known to encode arsenic resistance. Here we demonstrate that Java 9 exhibits high levels of arsenic and arsenite resistance mediated by a novel promiscuous class II transposon, named Tn2503. Arsenic resistance was self-transmissible from Java 9 to other Y. pestis strains via conjugation. Genomic analysis of the atypical plasmid inventory of Java 9 identified pCD and pPCP plasmids of atypical size and two previously uncharacterized cryptic plasmids. Unlike the Tn2502-mediated arsenic resistance encoded on the Y. enterocolitica virulence plasmid; the resistance loci in Java 9 are found on all four indigenous plasmids, including the two novel cryptic plasmids. This unique mobilome introduces more than 105 genes into the species gene pool. The majority of these are encoded by the two entirely novel self-transmissible plasmids, which show partial homology and synteny to other enterics. In contrast to the reductive evolution in Y. pestis, this study underlines the major impact of a dynamic mobilome and lateral acquisition in the genome evolution of the plague bacterium.

  4. Novel plasmids and resistance phenotypes in Yersinia pestis: unique plasmid inventory of strain Java 9 mediates high levels of arsenic resistance.

    Directory of Open Access Journals (Sweden)

    Mark Eppinger

    Full Text Available Growing evidence suggests that the plasmid repertoire of Yersinia pestis is not restricted to the three classical virulence plasmids. The Java 9 strain of Y. pestis is a biovar Orientalis isolate obtained from a rat in Indonesia. Although it lacks the Y. pestis-specific plasmid pMT, which encodes the F1 capsule, it retains virulence in mouse and non-human primate animal models. While comparing diverse Y. pestis strains using subtractive hybridization, we identified sequences in Java 9 that were homologous to a Y. enterocolitica strain carrying the transposon Tn2502, which is known to encode arsenic resistance. Here we demonstrate that Java 9 exhibits high levels of arsenic and arsenite resistance mediated by a novel promiscuous class II transposon, named Tn2503. Arsenic resistance was self-transmissible from Java 9 to other Y. pestis strains via conjugation. Genomic analysis of the atypical plasmid inventory of Java 9 identified pCD and pPCP plasmids of atypical size and two previously uncharacterized cryptic plasmids. Unlike the Tn2502-mediated arsenic resistance encoded on the Y. enterocolitica virulence plasmid; the resistance loci in Java 9 are found on all four indigenous plasmids, including the two novel cryptic plasmids. This unique mobilome introduces more than 105 genes into the species gene pool. The majority of these are encoded by the two entirely novel self-transmissible plasmids, which show partial homology and synteny to other enterics. In contrast to the reductive evolution in Y. pestis, this study underlines the major impact of a dynamic mobilome and lateral acquisition in the genome evolution of the plague bacterium.

  5. Plasmid DNA Delivery: Nanotopography Matters.

    Science.gov (United States)

    Song, Hao; Yu, Meihua; Lu, Yao; Gu, Zhengying; Yang, Yannan; Zhang, Min; Fu, Jianye; Yu, Chengzhong

    2017-12-20

    Plasmid DNA molecules with unique loop structures have widespread bioapplications, in many cases relying heavily on delivery vehicles to introduce them into cells and achieve their functions. Herein, we demonstrate that control over delicate nanotopography of silica nanoparticles as plasmid DNA vectors has significant impact on the transfection efficacy. For silica nanoparticles with rambutan-, raspberry-, and flower-like morphologies composed of spike-, hemisphere-, and bowl-type subunit nanotopographies, respectively, the rambutan-like nanoparticles with spiky surfaces demonstrate the highest plasmid DNA binding capability and transfection efficacy of 88%, higher than those reported for silica-based nanovectors. Moreover, it is shown that the surface spikes of rambutan nanoparticles provide a continuous open space to bind DNA chains via multivalent interactions and protect the gene molecules sheltered in the spiky layer against nuclease degradation, exhibiting no significant transfection decay. This unique protection feature is in great contrast to a commercial transfection agent with similar transfection performance but poor protection capability against enzymatic cleavage. Our study provides new understandings in the rational design of nonviral vectors for efficient gene delivery.

  6. Dynamical groups of a particle in a periodic potential

    International Nuclear Information System (INIS)

    Yusuf, M.

    1992-09-01

    Solving the Schroedinger non-relativistic equation of a particle moving under the influence of the potential V(θ) = ω(1 - cosθ) leads to us to the standard Mathieu equation. Jahnke-Emde's(1938), the periodic solutions are Mathieu functions of even order. With an approximation we study two important limiting cases, a simple quantum rotator and one-dimensional linear oscillator. We show the dynamical groups of these special, and a further study of the real problem connects us an Euclidean group of 2D. An IRR of matrix elements give us the energy levels. The interface between the E 2 and Bessel Functions is showed. (author). 7 refs

  7. Degenerate primer MOB typing of multiresistant clinical isolates of E. coli uncovers new plasmid backbones.

    Science.gov (United States)

    Garcillán-Barcia, M Pilar; Ruiz del Castillo, Belén; Alvarado, Andrés; de la Cruz, Fernando; Martínez-Martínez, Luis

    2015-01-01

    Degenerate Primer MOB Typing is a PCR-based protocol for the classification of γ-proteobacterial transmissible plasmids in five phylogenetic relaxase MOB families. It was applied to a multiresistant E. coli collection, previously characterized by PCR-based replicon-typing, in order to compare both methods. Plasmids from 32 clinical isolates of multiresistant E. coli (19 extended spectrum beta-lactamase producers and 13 non producers) and their transconjugants were analyzed. A total of 95 relaxases were detected, at least one per isolate, underscoring the high potential of these strains for antibiotic-resistance transmission. MOBP12 and MOBF12 plasmids were the most abundant. Most MOB subfamilies detected were present in both subsets of the collection, indicating a shared mobilome among multiresistant E. coli. The plasmid profile obtained by both methods was compared, which provided useful data upon which decisions related to the implementation of detection methods in the clinic could be based. The phylogenetic depth at which replicon and MOB-typing classify plasmids is different. While replicon-typing aims at plasmid replication regions with non-degenerate primers, MOB-typing classifies plasmids into relaxase subfamilies using degenerate primers. As a result, MOB-typing provides a deeper phylogenetic depth than replicon-typing and new plasmid groups are uncovered. Significantly, MOB typing identified 17 plasmids and an integrative and conjugative element, which were not detected by replicon-typing. Four of these backbones were different from previously reported elements. Copyright © 2014 Elsevier Inc. All rights reserved.

  8. Dynamical analysis of Schrodinger operators with growing sparse potentials

    CERN Document Server

    Tcheremchantsev, S

    2003-01-01

    We consider Scr\\"odinger operators in l^2(Z^+) with potentials of the form V(n)=S(n)+Q(n). Here S is a sparse potential: S(n)=n^{1-\\eta \\over 2 \\eta}, 0<\\eta <1, for n=L_N and S(n)=0 else, where L_N is a very fast growing sequence. The real function Q(n) is compactly supported. We give a rather complete description of the (time-averaged) dynamics exp(-itH) \\psi for different initial states \\psi. In particular, for some \\psi we calculate explicitely the "intermittency function" \\beta_\\psi^- (p) which turns out to be nonconstant. As a particular corollary of obtained results, we show that the spectral measure restricted to (-2,2) has exact Hausdorff dimension \\eta for all boundary conditions, improving the result of Jitomirskaya and Last.

  9. Do resting brain dynamics predict oddball evoked-potential?

    Directory of Open Access Journals (Sweden)

    Lee Tien-Wen

    2011-11-01

    Full Text Available Abstract Background The oddball paradigm is widely applied to the investigation of cognitive function in neuroscience and in neuropsychiatry. Whether cortical oscillation in the resting state can predict the elicited oddball event-related potential (ERP is still not clear. This study explored the relationship between resting electroencephalography (EEG and oddball ERPs. The regional powers of 18 electrodes across delta, theta, alpha and beta frequencies were correlated with the amplitude and latency of N1, P2, N2 and P3 components of oddball ERPs. A multivariate analysis based on partial least squares (PLS was applied to further examine the spatial pattern revealed by multiple correlations. Results Higher synchronization in the resting state, especially at the alpha spectrum, is associated with higher neural responsiveness and faster neural propagation, as indicated by the higher amplitude change of N1/N2 and shorter latency of P2. None of the resting quantitative EEG indices predict P3 latency and amplitude. The PLS analysis confirms that the resting cortical dynamics which explains N1/N2 amplitude and P2 latency does not show regional specificity, indicating a global property of the brain. Conclusions This study differs from previous approaches by relating dynamics in the resting state to neural responsiveness in the activation state. Our analyses suggest that the neural characteristics carried by resting brain dynamics modulate the earlier/automatic stage of target detection.

  10. Conjugative plasmids: Vessels of the communal gene pool

    DEFF Research Database (Denmark)

    Norman, Anders; Hansen, Lars H.; Sørensen, Søren Johannes

    2009-01-01

    to the hosts and, potentially, other resident prokaryotes within specific environmental niches. Insight into the evolution of plasmid modules therefore contributes to our knowledge of gene dissemination and evolution within prokaryotic communities. This communal pool provides the prokaryotes with an important...... mechanistic framework for obtaining adaptability and functional diversity that alleviates the need for large genomes of specialized ‘private genes'....

  11. Ordering the mob: Insights into replicon and MOB typing schemes from analysis of a curated dataset of publicly available plasmids.

    Science.gov (United States)

    Orlek, Alex; Phan, Hang; Sheppard, Anna E; Doumith, Michel; Ellington, Matthew; Peto, Tim; Crook, Derrick; Walker, A Sarah; Woodford, Neil; Anjum, Muna F; Stoesser, Nicole

    2017-05-01

    Plasmid typing can provide insights into the epidemiology and transmission of plasmid-mediated antibiotic resistance. The principal plasmid typing schemes are replicon typing and MOB typing, which utilize variation in replication loci and relaxase proteins respectively. Previous studies investigating the proportion of plasmids assigned a type by these schemes ('typeability') have yielded conflicting results; moreover, thousands of plasmid sequences have been added to NCBI in recent years, without consistent annotation to indicate which sequences represent complete plasmids. Here, a curated dataset of complete Enterobacteriaceae plasmids from NCBI was compiled, and used to assess the typeability and concordance of in silico replicon and MOB typing schemes. Concordance was assessed at hierarchical replicon type resolutions, from replicon family-level to plasmid multilocus sequence type (pMLST)-level, where available. We found that 85% and 65% of the curated plasmids could be replicon and MOB typed, respectively. Overall, plasmid size and the number of resistance genes were significant independent predictors of replicon and MOB typing success. We found some degree of non-concordance between replicon families and MOB types, which was only partly resolved when partitioning plasmids into finer-resolution groups (replicon and pMLST types). In some cases, non-concordance was attributed to ambiguous boundaries between MOBP and MOBQ types; in other cases, backbone mosaicism was considered a more plausible explanation. β-lactamase resistance genes tended not to show fidelity to a particular plasmid type, though some previously reported associations were supported. Overall, replicon and MOB typing schemes are likely to continue playing an important role in plasmid analysis, but their performance is constrained by the diverse and dynamic nature of plasmid genomes. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

  12. Effect of the atmospheric pressure nonequilibrium plasmas on the conformational changes of plasmid DNA

    International Nuclear Information System (INIS)

    Yan Xu; He Guangyuan; Shi Mengjun; Gao Xuan; Li Yin; Ma Fengyun; Yu Men; Wang Changdong; Wang Yuesheng; Yang Guangxiao; Zou Fei; Lu Xinpei; Xiong Qing; Xiong Zilan

    2009-01-01

    The cold atmospheric pressure plasma, which has been widely used for biomedical applications, may potentially affect the conformation of DNA. In this letter, an atmospheric pressure plasma plume is used to investigate its effects on the conformational changes of DNA of plasmid pAHC25. It is found that the plasma plume could cause plasmid DNA topology alteration, resulting in the percentage of the supercoiled plasmid DNA form decreased while that of the open circular and linearized form of plasmid DNA increased as detected by agrose gel electrophoresis. On the other hand, further investigation by using polymerase chain reaction method shows that the atmospheric pressure plasma jet treatments under proper conditions does not affect the genes of the plasmid DNA, which may have potential application in increasing the transformation frequency by genetic engineering.

  13. Prevalence of plasmid-bearing and plasmid-free Chlamydia trachomatis infection among women who visited obstetrics and gynecology clinics in Malaysia.

    Science.gov (United States)

    Yeow, Tee Cian; Wong, Won Fen; Sabet, Negar Shafiei; Sulaiman, Sofiah; Shahhosseini, Fatemeh; Tan, Grace Min Yi; Movahed, Elaheh; Looi, Chung Yeng; Shankar, Esaki M; Gupta, Rishien; Arulanandam, Bernard P; Hassan, Jamiyah; Abu Bakar, Sazaly

    2016-03-18

    The 7.5 kb cryptic plasmid of Chlamydia trachomatis has been shown to be a virulence factor in animal models, but its significance in humans still remains unknown. The aim of this study was to investigate the prevalence and potential involvement of the C. trachomatis cryptic plasmid in causing various clinical manifestations; including infertility, reproductive tract disintegrity, menstrual disorder, and polycystic ovarian syndrome (PCOS) among genital C. trachomatis-infected patients. A total of 180 female patients of child bearing age (mean 30.9 years old, IQR:27-35) with gynecological complications and subfertility issues, who visited Obstetrics and Gynecology clinics in Kuala Lumpur, Malaysia were recruited for the study. Prevalence of genital chlamydial infection among these patients was alarmingly high at 51.1% (92/180). Of the 92 chlamydia-infected patients, 93.5% (86/92) were infected with plasmid-bearing (+) C. trachomatis while the remaining 6.5% (6/92) were caused by the plasmid-free (-) variant. Our data showed that genital C. trachomatis infection was associated with infertility issues, inflammation in the reproductive tract (mucopurulent cervicitis or endometriosis), irregular menstrual cycles and polycystic ovarian syndrome (PCOS). However, no statistical significance was detected among patients with plasmid (+) versus plasmid (-) C. trachomatis infection. Interestingly, plasmid (+) C. trachomatis was detected in all patients with PCOS, and the plasmid copy numbers were significantly higher among PCOS patients, relative to non-PCOS patients. Our findings show a high incidence of C. trachomatis infection among women with infertility or gynecological problems in Malaysia. However, due to the low number of plasmid (-) C. trachomatis cases, a significant role of the plasmid in causing virulence in human requires further investigation of a larger cohort.

  14. Dynamics of an ion chain in a harmonic potential

    International Nuclear Information System (INIS)

    Morigi, Giovanna; Fishman, Shmuel

    2004-01-01

    Cold ions in anisotropic harmonic potentials can form ion chains of various sizes. Here, the density of ions is not uniform, and thus the eigenmodes are not phononic-like waves. We study chains of N>>1 ions and evaluate analytically the long-wavelength modes and the density of states in the short-wavelength limit. These results reproduce with good approximation the dynamics of chains consisting of dozens of ions. Moreover, they allow one to determine the critical transverse frequency required for the stability of the linear structure, which is found to be in agreement with results obtained by different theoretical methods [D. H. E. Dubin, Phys. Rev. Lett. 71, 2753 (1993)] and by numerical simulations [J. P. Schiffer, Phys. Rev. Lett. 70, 818 (1993)]. We introduce and explore the thermodynamic limit for the ion chain. The thermodynamic functions are found to exhibit deviations from extensivity

  15. Nonlinear dynamics of semiclassical coherent states in periodic potentials

    International Nuclear Information System (INIS)

    Carles, Rémi; Sparber, Christof

    2012-01-01

    We consider nonlinear Schrödinger equations with either local or nonlocal nonlinearities. In addition, we include periodic potentials as used, for example, in matter wave experiments in optical lattices. By considering the corresponding semiclassical scaling regime, we construct asymptotic solutions, which are concentrated both in space and in frequency around the effective semiclassical phase-space flow induced by Bloch’s spectral problem. The dynamics of these generalized coherent states is governed by a nonlinear Schrödinger model with effective mass. In the case of nonlocal nonlinearities, we establish a novel averaging-type result in the critical case. This article is part of a special issue of Journal of Physics A: Mathematical and Theoretical devoted to ‘Coherent states: mathematical and physical aspects’. (paper)

  16. Mutation in ESBL Plasmid from Escherichia coli O104:H4 Leads Autoagglutination and Enhanced Plasmid Dissemination

    Directory of Open Access Journals (Sweden)

    Mickaël Poidevin

    2018-02-01

    Full Text Available Conjugative plasmids are one of the main driving force of wide-spreading of multidrug resistance (MDR bacteria. They are self-transmittable via conjugation as carrying the required set of genes and cis-acting DNA locus for direct cell-to-cell transfer. IncI incompatibility plasmids are nowadays often associated with extended-spectrum beta-lactamases producing Enterobacteria in clinic and environment. pESBL-EA11 was isolated from Escherichia coli O104:H4 outbreak strain in Germany in 2011. During the previous study identifying transfer genes of pESBL-EA11, it was shown that transposon insertion at certain DNA region of the plasmid, referred to as Hft, resulted in great enhancement of transfer ability. This suggested that genetic modifications can enhance dissemination of MDR plasmids. Such ‘superspreader’ mutations have attracted little attention so far despite their high potential to worsen MDR spreading. Present study aimed to gain our understanding on regulatory elements that involved pESBL transfer. While previous studies of IncI plasmids indicated that immediate downstream gene of Hft, traA, is not essential for conjugative transfer, here we showed that overexpression of TraA in host cell elevated transfer rate of pESBL-EA11. Transposon insertion or certain nucleotide substitutions in Hft led strong TraA overexpression which resulted in activation of essential regulator TraB and likely overexpression of conjugative pili. Atmospheric Scanning Electron Microscopy observation suggested that IncI pili are distinct from other types of conjugative pili (such as long filamentous F-type pili and rather expressed throughout the cell surface. High transfer efficiency in the mutant pESBL-EA11 was involved with hyperpiliation which facilitates cell-to-cell adhesion, including autoagglutination. The capability of plasmids to evolve to highly transmissible mutant is alarming, particularly it might also have adverse effect on host pathogenicity.

  17. Vortex Dynamics in Superconductors with Different Types of Pinning Potentials

    International Nuclear Information System (INIS)

    Laguna, Maria Fabiana

    2001-01-01

    In this work we study the behavior of the vortex system in the mixed state of a type II superconductor when it interacts with different kinds of pinning potentials. To do this, we perform numerical simulations in the presence of an external magnetic field, by making use of two different approaches.One corresponds to a Langevin simulation of the three dimensional XY model or Josephson-junction network, whereas the other corresponds to a Molecular dynamics simulation of two dimensional point-like vortices.We analyze the transport properties of highly anisotropic superconductors with different kinds of topological disorder in the configuration in which the external field is applied perpendicular to the CuO planes.We found that for systems with point defects the activation energy is the same for the two components of the resistivity, while in systems with columnar defects the activation energies can be different.We also study the structure, phase transitions and transport properties of the vortex system when the external magnetic field lies parallel to the planes in layered superconductors. We analyze the stability of different phases at low temperatures and show under which conditions the smectic phase is stable.Our results indicate the presence of the smectic phase in an intermediate range of temperatures.We have studied a vortex array in a periodic pinning potential with triangular and kagome geometries.We obtain the ground state vortex configurations and calculate some thermodynamic quantities for different magnetic fields.We observe several stages of lattice pinning and melting and we characterize different phases and transitions between them.Finally, simulating the Bitter pinning effect over the vortex system, we study static and dynamic properties of the vortex system in the presence of the surface Bitter pinning and the bulk pinning.We found low temperature structures similar to those obtained experimentally.We analyze the dynamics of the nucleation and growth

  18. Prevalence of plasmid-bearing and plasmid-free Chlamydia trachomatis infection among women who visited obstetrics and gynecology clinics in Malaysia

    OpenAIRE

    Yeow, Tee Cian; Wong, Won Fen; Sabet, Negar Shafiei; Sulaiman, Sofiah; Shahhosseini, Fatemeh; Tan, Grace Min Yi; Movahed, Elaheh; Looi, Chung Yeng; Shankar, Esaki M.; Gupta, Rishien; Arulanandam, Bernard P.; Hassan, Jamiyah; Abu Bakar, Sazaly

    2016-01-01

    Background The 7.5?kb cryptic plasmid of Chlamydia trachomatis has been shown to be a virulence factor in animal models, but its significance in humans still remains unknown. The aim of this study was to investigate the prevalence and potential involvement of the C. trachomatis cryptic plasmid in causing various clinical manifestations; including infertility, reproductive tract disintegrity, menstrual disorder, and polycystic ovarian syndrome (PCOS) among genital C. trachomatis?infected patie...

  19. Large-scale preparation of plasmid DNA.

    Science.gov (United States)

    Heilig, J S; Elbing, K L; Brent, R

    2001-05-01

    Although the need for large quantities of plasmid DNA has diminished as techniques for manipulating small quantities of DNA have improved, occasionally large amounts of high-quality plasmid DNA are desired. This unit describes the preparation of milligram quantities of highly purified plasmid DNA. The first part of the unit describes three methods for preparing crude lysates enriched in plasmid DNA from bacterial cells grown in liquid culture: alkaline lysis, boiling, and Triton lysis. The second part describes four methods for purifying plasmid DNA in such lysates away from contaminating RNA and protein: CsCl/ethidium bromide density gradient centrifugation, polyethylene glycol (PEG) precipitation, anion-exchange chromatography, and size-exclusion chromatography.

  20. Development of molecular dynamics potential for uranium silicide fuels

    Energy Technology Data Exchange (ETDEWEB)

    Yu, Jianguo; Zhang, Yongfeng; Hales, Jason D.

    2016-09-01

    Use of uranium–silicide (U-Si) in place of uranium dioxide (UO2) is one of the promising concepts being proposed to increase the accident tolerance of nuclear fuels. This is due to a higher thermal conductivity than UO2 that results in lower centerline temperatures. U-Si also has a higher fissile density, which may enable some new cladding concepts that would otherwise require increased enrichment limits to compensate for their neutronic penalty. However, many critical material properties for U-Si have not been determined experimentally. For example, silicide compounds (U3Si2 and U3Si) are known to become amorphous under irradiation. There was clear independent experimental evidence to support a crystalline to amorphous transformation in those compounds. However, it is still not well understood how the amorphous transformation will affect on fuel behavior. It is anticipated that modeling and simulation may deliver guidance on the importance of various properties and help prioritize experimental work. In order to develop knowledge-based models for use at the engineering scale with a minimum of empirical parameters and increase the predictive capabilities of the developed model, inputs from atomistic simulations are essential. First-principles based density functional theory (DFT) calculations will provide the most reliable information. However, it is probably not possible to obtain kinetic information such as amorphization under irradiation directly from DFT simulations due to size and time limitations. Thus, a more feasible way may be to employ molecular dynamics (MD) simulation. Unfortunately, so far no MD potential is available for U-Si to discover the underlying mechanisms. Here, we will present our recent progress in developing a U-Si potential from ab initio data. This work is supported by the Nuclear Energy Advanced Modeling and Simulation (NEAMS) program funded by the U.S. Department of Energy, Office of Nuclear Energy.

  1. Comparative Sequence Analysis of Multidrug-Resistant IncA/C Plasmids from Salmonella enterica.

    Science.gov (United States)

    Hoffmann, Maria; Pettengill, James B; Gonzalez-Escalona, Narjol; Miller, John; Ayers, Sherry L; Zhao, Shaohua; Allard, Marc W; McDermott, Patrick F; Brown, Eric W; Monday, Steven R

    2017-01-01

    Determinants of multidrug resistance (MDR) are often encoded on mobile elements, such as plasmids, transposons, and integrons, which have the potential to transfer among foodborne pathogens, as well as to other virulent pathogens, increasing the threats these traits pose to human and veterinary health. Our understanding of MDR among Salmonella has been limited by the lack of closed plasmid genomes for comparisons across resistance phenotypes, due to difficulties in effectively separating the DNA of these high-molecular weight, low-copy-number plasmids from chromosomal DNA. To resolve this problem, we demonstrate an efficient protocol for isolating, sequencing and closing IncA/C plasmids from Salmonella sp. using single molecule real-time sequencing on a Pacific Biosciences (Pacbio) RS II Sequencer. We obtained six Salmonella enterica isolates from poultry, representing six different serovars, each exhibiting the MDR-Ampc resistance profile. Salmonella plasmids were obtained using a modified mini preparation and transformed with Escherichia coli DH10Br. A Qiagen Large-Construct kit™ was used to recover highly concentrated and purified plasmid DNA that was sequenced using PacBio technology. These six closed IncA/C plasmids ranged in size from 104 to 191 kb and shared a stable, conserved backbone containing 98 core genes, with only six differences among those core genes. The plasmids encoded a number of antimicrobial resistance genes, including those for quaternary ammonium compounds and mercury. We then compared our six IncA/C plasmid sequences: first with 14 IncA/C plasmids derived from S. enterica available at the National Center for Biotechnology Information (NCBI), and then with an additional 38 IncA/C plasmids derived from different taxa. These comparisons allowed us to build an evolutionary picture of how antimicrobial resistance may be mediated by this common plasmid backbone. Our project provides detailed genetic information about resistance genes in

  2. Comparative Sequence Analysis of Multidrug-Resistant IncA/C Plasmids from Salmonella enterica

    Directory of Open Access Journals (Sweden)

    Maria Hoffmann

    2017-08-01

    Full Text Available Determinants of multidrug resistance (MDR are often encoded on mobile elements, such as plasmids, transposons, and integrons, which have the potential to transfer among foodborne pathogens, as well as to other virulent pathogens, increasing the threats these traits pose to human and veterinary health. Our understanding of MDR among Salmonella has been limited by the lack of closed plasmid genomes for comparisons across resistance phenotypes, due to difficulties in effectively separating the DNA of these high-molecular weight, low-copy-number plasmids from chromosomal DNA. To resolve this problem, we demonstrate an efficient protocol for isolating, sequencing and closing IncA/C plasmids from Salmonella sp. using single molecule real-time sequencing on a Pacific Biosciences (Pacbio RS II Sequencer. We obtained six Salmonella enterica isolates from poultry, representing six different serovars, each exhibiting the MDR-Ampc resistance profile. Salmonella plasmids were obtained using a modified mini preparation and transformed with Escherichia coli DH10Br. A Qiagen Large-Construct kit™ was used to recover highly concentrated and purified plasmid DNA that was sequenced using PacBio technology. These six closed IncA/C plasmids ranged in size from 104 to 191 kb and shared a stable, conserved backbone containing 98 core genes, with only six differences among those core genes. The plasmids encoded a number of antimicrobial resistance genes, including those for quaternary ammonium compounds and mercury. We then compared our six IncA/C plasmid sequences: first with 14 IncA/C plasmids derived from S. enterica available at the National Center for Biotechnology Information (NCBI, and then with an additional 38 IncA/C plasmids derived from different taxa. These comparisons allowed us to build an evolutionary picture of how antimicrobial resistance may be mediated by this common plasmid backbone. Our project provides detailed genetic information about

  3. Exploring the Potential of Dynamic Perspective Taking on Business Processes

    Directory of Open Access Journals (Sweden)

    Florian Krenn

    2016-10-01

    Full Text Available Although many organizations have started to work with business process models in their operational practice, they have not explored the entire potential of intertwining business process modeling with organizational development. Process specifications contain workflows that require execution, in order to achieve business objectives and support business operation effectively. With the advent of Subject-oriented and Social Business Process Management, communication and stakeholder interaction have become novel perspectives on how to design and implement processes. They go beyond formal responsibilities encoded in functional roles, and are not very common across organizational hierarchies. However, stakeholders, including organizational developers and IT specialists, can be supported looking at processes and their execution from either perspective, namely, from a traditional one, focusing on functions and task accomplishment, and from an interactional perspective, focusing on communication among stakeholders and system interactions. The introduced dual-mode workflow execution engine UeberFlow allows considering both perspectives during process runtime, thus, checking operational completeness from either perspective. Stakeholders can start modeling with a perspective they are familiar with and subsequently proceed with the another one by switching dynamically to an alternate mode of execution. The presented meta-model and architecture of such a dual mode support tool enables coupling business process management directly with organizational development.

  4. POTENTIALS OF IMAGE BASED ACTIVE RANGING TO CAPTURE DYNAMIC SCENES

    Directory of Open Access Journals (Sweden)

    B. Jutzi

    2012-09-01

    Full Text Available Obtaining a 3D description of man-made and natural environments is a basic task in Computer Vision and Remote Sensing. To this end, laser scanning is currently one of the dominating techniques to gather reliable 3D information. The scanning principle inherently needs a certain time interval to acquire the 3D point cloud. On the other hand, new active sensors provide the possibility of capturing range information by images with a single measurement. With this new technique image-based active ranging is possible which allows capturing dynamic scenes, e.g. like walking pedestrians in a yard or moving vehicles. Unfortunately most of these range imaging sensors have strong technical limitations and are not yet sufficient for airborne data acquisition. It can be seen from the recent development of highly specialized (far-range imaging sensors – so called flash-light lasers – that most of the limitations could be alleviated soon, so that future systems will be equipped with improved image size and potentially expanded operating range. The presented work is a first step towards the development of methods capable for application of range images in outdoor environments. To this end, an experimental setup was set up for investigating these proposed possibilities. With the experimental setup a measurement campaign was carried out and first results will be presented within this paper.

  5. Potential vorticity dynamics in the Canadian Climate Centre GCM

    International Nuclear Information System (INIS)

    Koshyk, J.N.; McFarlane, N.

    1994-01-01

    The global distribution of Ertel potential vorticity (PV), simulated by the Canadian Climate Centre general circulation model (CCC GCM) is examined. An expression for PV in terms of an arbitrary vertical coordinate is formulated. This expression is used to calculate temporally averaged PV from the model temperature and wind fields. It is shown that a good approximation to the temporally averaged PV can be obtained from temporally averaged temperature and wind fields. An equation governing the time evolution of PV in the model vertical coordinate system is also derived. This equation is written in flux form and the associated flux is examined in a lower stratographic region of enhanced gravity-wave drag, above the Tibetan plateau. In this region, the southward transport of PV effected by gravity-wave drag is balanced to a large degree by the advection of PV northward. Finally, results from a recent experimental version of the CCC GCM, with an uppermost level at 1 mb, are used to examine PV dynamics associated with a spontaneous model stratospheric sudden warming. The warming is preceded by 2 successive large amplitude wavenumber 1 disturbances in the lower stratosphere. The second of these leads to splitting of the mid-stratospheric vortex into a double vortex pattern, as is clearly evident on maps of the 850K PV field during the warming period

  6. [Replication of Streptomyces plasmids: the DNA nucleotide sequence of plasmid pSB 24.2].

    Science.gov (United States)

    Bolotin, A P; Sorokin, A V; Aleksandrov, N N; Danilenko, V N; Kozlov, Iu I

    1985-11-01

    The nucleotide sequence of DNA in plasmid pSB 24.2, a natural deletion derivative of plasmid pSB 24.1 isolated from S. cyanogenus was studied. The plasmid amounted by its size to 3706 nucleotide pairs. The G-C composition was equal to 73 per cent. The analysis of the DNA structure in plasmid pSB 24.2 revealed the protein-encoding sequence of DNA, the continuity of which was significant for replication of the plasmid containing more than 1300 nucleotide pairs. The analysis also revealed two A-T-rich areas of DNA, the G-C composition of which was less than 55 per cent and a DNA area with a branched pin structure. The results may be of value in investigation of plasmid replication in actinomycetes and experimental cloning of DNA with this plasmid as a vector.

  7. Potential of dynamic spectrum allocation in LTE macro networks

    Science.gov (United States)

    Hoffmann, H.; Ramachandra, P.; Kovács, I. Z.; Jorguseski, L.; Gunnarsson, F.; Kürner, T.

    2015-11-01

    In recent years Mobile Network Operators (MNOs) worldwide are extensively deploying LTE networks in different spectrum bands and utilising different bandwidth configurations. Initially, the deployment is coverage oriented with macro cells using the lower LTE spectrum bands. As the offered traffic (i.e. the requested traffic from the users) increases the LTE deployment evolves with macro cells expanded with additional capacity boosting LTE carriers in higher frequency bands complemented with micro or small cells in traffic hotspot areas. For MNOs it is crucial to use the LTE spectrum assets, as well as the installed network infrastructure, in the most cost efficient way. The dynamic spectrum allocation (DSA) aims at (de)activating the available LTE frequency carriers according to the temporal and spatial traffic variations in order to increase the overall LTE system performance in terms of total network capacity by reducing the interference. This paper evaluates the DSA potential of achieving the envisaged performance improvement and identifying in which system and traffic conditions the DSA should be deployed. A self-optimised network (SON) DSA algorithm is also proposed and evaluated. The evaluations have been carried out in a hexagonal and a realistic site-specific urban macro layout assuming a central traffic hotspot area surrounded with an area of lower traffic with a total size of approximately 8 × 8 km2. The results show that up to 47 % and up to 40 % possible DSA gains are achievable with regards to the carried system load (i.e. used resources) for homogenous traffic distribution with hexagonal layout and for realistic site-specific urban macro layout, respectively. The SON DSA algorithm evaluation in a realistic site-specific urban macro cell deployment scenario including realistic non-uniform spatial traffic distribution shows insignificant cell throughput (i.e. served traffic) performance gains. Nevertheless, in the SON DSA investigations, a gain of up

  8. Characterization of new plasmids from methylotrophic bacteria.

    Science.gov (United States)

    Brenner, V; Holubová, I; Benada, O; Hubácek, J

    1991-07-01

    Several tens of methanol-utilizing bacterial strains isolated from soil were screened for the presence of plasmids. From the obligate methylotroph Methylomonas sp. strain R103a plasmid pIH36 (36 kb) was isolated and its restriction map was constructed. In pink-pigmented facultative methylotrophs (PPFM), belonging to the genus Methylobacterium four plasmids were detected: plasmids pIB200 (200 kb) and pIB14 (14 kb) in the strain R15d and plasmids pWU14 (14 kb) and pWU7 (7.8 kb) in the strain M17. Because of the small size and the presence of several unique REN sites (HindIII, EcoRI, NcoI), plasmid pWU7 was chosen for the construction of a vector for cloning in methylotrophs. Cointegrates pKWU7A and pKWU7B were formed between pWU7 and the E. coli plasmid pK19 Kmr, which were checked for conjugative transfer from E. coli into the methylotrophic host.

  9. Study on fusion potential barrier in heavy ion reactions based on the dynamical model

    International Nuclear Information System (INIS)

    Tian Junlong; Wu Xizhen; Li Zhuxia; Wang Ning; Liu Fuhu

    2004-01-01

    Based on an improved quantum molecular dynamics model the static and dynamic potential in the entrance channel of synthesis of superheavy nuclei are studied. The dependence of the static potential (and driving potential) on mass-asymmetry is obtained. From this study authors find out that the mass-symmetric system seems to be difficult to fuse and the fusing system with the largest driving potential could be the optimal choice of the projectile-target combination. By comparing the static potential barrier with the dynamic one authors find that the latter one is lower than former one obviously, and that the dynamical potential barrier is entrance energy dependent. The maximum and minimum of dynamic potential barriers approach to the diabatic (sudden approximation) and the adiabatic static potential barriers, respectively

  10. A binary plasmid system for shuffling combinatorial antibody libraries.

    OpenAIRE

    Collet, T A; Roben, P; O'Kennedy, R; Barbas, C F; Burton, D R; Lerner, R A

    1992-01-01

    We have used a binary system of replicon-compatible plasmids to test the potential for promiscuous recombination of heavy and light chains within sets of human Fab fragments isolated from combinatorial antibody libraries. Antibody molecules showed a surprising amount of promiscuity in that a particular heavy chain could recombine with multiple light chains with retention of binding to a protein antigen. The degree to which a given heavy chain productively paired with any light chain to bind a...

  11. Comparative symbiotic plasmid analysis indicates that symbiosis gene ancestor type affects plasmid genetic evolution.

    Science.gov (United States)

    Wang, X; Zhao, L; Zhang, L; Wu, Y; Chou, M; Wei, G

    2018-07-01

    Rhizobial symbiotic plasmids play vital roles in mutualistic symbiosis with legume plants by executing the functions of nodulation and nitrogen fixation. To explore the gene composition and genetic constitution of rhizobial symbiotic plasmids, comparison analyses of 24 rhizobial symbiotic plasmids derived from four rhizobial genera was carried out. Results illustrated that rhizobial symbiotic plasmids had higher proportion of functional genes participating in amino acid transport and metabolism, replication; recombination and repair; carbohydrate transport and metabolism; energy production and conversion and transcription. Mesorhizobium amorphae CCNWGS0123 symbiotic plasmid - pM0123d had similar gene composition with pR899b and pSNGR234a. All symbiotic plasmids shared 13 orthologous genes, including five nod and eight nif/fix genes which participate in the rhizobia-legume symbiosis process. These plasmids contained nod genes from four ancestors and fix genes from six ancestors. The ancestral type of pM0123d nod genes was similar with that of Rhizobium etli plasmids, while the ancestral type of pM0123d fix genes was same as that of pM7653Rb. The phylogenetic trees constructed based on nodCIJ and fixABC displayed different topological structures mainly due to nodCIJ and fixABC ancestral type discordance. The study presents valuable insights into mosaic structures and the evolution of rhizobial symbiotic plasmids. This study compared 24 rhizobial symbiotic plasmids that included four genera and 11 species, illuminating the functional gene composition and symbiosis gene ancestor types of symbiotic plasmids from higher taxonomy. It provides valuable insights into mosaic structures and the evolution of symbiotic plasmids. © 2018 The Society for Applied Microbiology.

  12. Analysis of plasmid profiling as a method for rapid differentiation of food-associated Clostridium perfringens strains.

    Science.gov (United States)

    Jones, M K; Iwanejko, L A; Longden, M S

    1989-09-01

    Plasmid analysis of over 120 strains of Clostridium perfringens, isolated during food-poisoning incidents and from animal carcasses and food constituents with no association with food poisoning, showed the potential of plasmid profiling as a means of differentiating epidemiologically related strains. On average 65% of freshly isolated strains contained one or more plasmids which could be used in the analysis. Comparison of profiles of strains from unrelated sources or unrelated strains from the same source showed a particularly wide variety of plasmid profiles. Thus the possibility that epidemiologically-unrelated strains might possess similar profiles appears to be very low in this organism. Analysis of serologically-related strains from the same source revealed similar plasmid profiles in all the plasmid-bearing strains examined. A high proportion (71%) of fresh and well-characterized food-poisoning strains possessed plasmids of 6.2 kb in size (compared with 19% of non-food-poisoning strains). The possible role of these plasmids is discussed, since the structural gene encoding the enterotoxin type A was not present on any of the plasmids in the food-poisoning strains tested.

  13. Plasmid fermentation process for DNA immunization applications.

    Science.gov (United States)

    Carnes, Aaron E; Williams, James A

    2014-01-01

    Plasmid DNA for immunization applications must be of the highest purity and quality. The ability of downstream purification to efficiently produce a pure final product is directly influenced by the performance of the upstream fermentation process. While several clinical manufacturing facilities already have validated fermentation processes in place to manufacture plasmid DNA for use in humans, a simple and inexpensive laboratory-scale fermentation process can be valuable for in-house production of plasmid DNA for use in animal efficacy studies. This chapter describes a simple fed-batch fermentation process for producing bacterial cell paste enriched with high-quality plasmid DNA. A constant feeding strategy results in a medium cell density culture with continuously increasing plasmid amplification towards the end of the process. Cell banking and seed culture preparation protocols, which can dramatically influence final product yield and quality, are also described. These protocols are suitable for production of research-grade plasmid DNA at the 100 mg-to-1.5 g scale from a typical 10 L laboratory benchtop fermentor.

  14. Plasmid-mediated mineralization of 4-chlorobiphenyl

    International Nuclear Information System (INIS)

    Shields, M.S.; Hooper, S.W.; Sayler, G.S.

    1985-01-01

    Strains of Alcaligenes and Acinetobacter spp. were isolated from a mixed culture already proven to be proficient at complete mineralization of monohalogenated biphenyls. These strains were shown to harbor a 35 x 10(6)-dalton plasmid mediating a complete pathway for 4-chlorobiphenyl (4CB) oxidation. Subsequent plasmid curing of these bacteria resulted in the abolishment of the 4CB mineralization phenotype and loss of even early 4CB metabolism by Acinetobacter spp. Reestablishment of the Alcaligenes plasmid, denoted pSS50, in the cured Acinetobacter spp. via filter surface mating resulted in the restoration of 4CB mineralization abilities. 4CB mineralization, however, proved to be an unstable characteristic in some subcultured strains. Such loss was not found to coincide with any detectable alteration in plasmid size. Cultures capable of complete mineralization, as well as those limited to partial metabolism of 4CB, produced 4-chlorobenzoate as a metabolite. Demonstration of mineralization of a purified 14 C-labeled chlorobenzoate showed it to be a true intermediate in 4CB mineralization. Unlike the mineralization capability, the ability to produce a metabolite has proven to be stable on subculture. These results indicate the occurrence of a novel plasmid, or evolved catabolic plasmid, that mediates the complete mineralization of 4CB

  15. The grounds for time dependent market potentials from dealers' dynamics

    Science.gov (United States)

    Yamada, K.; Takayasu, H.; Takayasu, M.

    2008-06-01

    We apply the potential force estimation method to artificial time series of market price produced by a deterministic dealer model. We find that dealers’ feedback of linear prediction of market price based on the latest mean price changes plays the central role in the market’s potential force. When markets are dominated by dealers with positive feedback the resulting potential force is repulsive, while the effect of negative feedback enhances the attractive potential force.

  16. Velocity Potential in Engineering Hydraulics versus Force Potential in Groundwater Dynamics

    Science.gov (United States)

    Weyer, K.

    2013-12-01

    required to overcome the resistance to downward flow in penetrated rocks. As one of the consequences, the engineering hydraulics concept of buoyancy forces does not comply with physics. In general the vectorial forces within gravitationally-driven flow systems are ignored when using engineering hydraulics. Scheidegger (1974, p. 79) states, however, verbatim and unequivocally: 'It is thus a force potential and not a velocity potential which governs flow through porous media' (emphasis added). This presentation will outline the proper forces for groundwater flow and their calculations based on Hubbert's force potential and additional physical insights by Weyer (1978). REFERENCES Bear, J. 1972. Dynamics of Fluids in Porous Media. American Elsevier Publishing Company, Inc., New York, NY, USA. de Marsily, G. 1986. Quantitative Hydrogeology: Groundwater Hydrology for Engineers. Academic Press, San Diego, California, USA. Hubbert, M.K. 1940. The theory of groundwater motion. Journal of Geology 48(8): 785-944. Muskat, Morris, 1937. The flow of homogeneous fluids through porous media. McGraw-Hill Book Company Inc., New York, NY, USA Scheidegger. A.E., 1974. The physics of flow through permeable media. Third Edition. University of Toronto Press, Toronto, Ontario, Canada Weyer, K.U., 1978. Hydraulic forces in permeable media. Bulletin du B.R.G.M., Vol. 91, pp. 286-297, Orléans, France.

  17. Behavior of IncQ Plasmids in Agrobacterium tumefaciens

    NARCIS (Netherlands)

    Hille, Jacques; Schilperoort, Rob

    1981-01-01

    Inc-Q plasmids were introduced into Agrobacterium tumefuciens, by mobilization from Escherichia coli with an Inc-P plasmid, or by transformation with purified plasmid DNA. It was found that they were stably maintained. The presence of an Inc-Q plasmid did not influence tumorigenicity. These results

  18. Potential Originality and Effectiveness: The Dynamic Definition of Creativity

    Science.gov (United States)

    Corazza, Giovanni Emanuele

    2016-01-01

    Given the central role of creativity in the future post-information society, a call for a pragmatist approach to the study of creativity is advocated, that brings as a consequence the recognition of the dynamic nature of this phenomenon. At the foundation of the proposed new theoretical framework lies the definition of creativity itself, which is…

  19. Complex dynamical invariants for two-dimensional complex potentials

    Indian Academy of Sciences (India)

    Abstract. Complex dynamical invariants are searched out for two-dimensional complex poten- tials using rationalization method within the framework of an extended complex phase space characterized by x = x1 + ip3, y = x2 + ip4, px = p1 + ix3, py = p2 + ix4. It is found that the cubic oscillator and shifted harmonic oscillator ...

  20. Analytical formulation for φ4 field potential dynamics

    International Nuclear Information System (INIS)

    Javidan, Kurosh; Ghahraman, Arash

    2011-01-01

    An analytical model for adding a space dependent potential to the φ 4 field equation of motion is presented, by constructing a collective coordinate system for the solitary solutions of this model. The interaction of φ 4 solitons with a delta function potential barrier and also delta function potential well is investigated. Most of the characters of interaction are derived analytically while they are calculated by other models numerically. We will find that the behaviour of a solitary solution is like a point particle which is moved under the influence of a complicated effective potential. The effective potential is a function of the field initial conditions and also of parameters of the added potential. (author)

  1. Estimating the Transfer Range of Plasmids Encoding Antimicrobial Resistance in a Wastewater Treatment Plant Microbial Community

    DEFF Research Database (Denmark)

    Li, Liguan; Dechesne, Arnaud; He, Zhiming

    2018-01-01

    sludge microbial community was challenged in standardized filter matings with one of three multidrug resistance plasmids (pKJK5, pB10, and RP4) harbored by Escherichia coli or Pseudomonas putida. Different donor–plasmid combinations had distinct transfer frequencies, ranging from 3 to 50 conjugation...... events per 100000 cells of the WWTP microbial community. In addition, transfer was observed to a broad phylogenetic range of 13 bacterial phyla with several taxa containing potentially pathogenic species. Preferential transfer to taxa belonging to the predicted evolutionary host range of the plasmids...... ARG transmission. However, the contribution of microbial communities in WWTPs to ARG dissemination remains poorly understood. Here, we examined for the first time plasmid permissiveness of an activated sludge microbial community by utilizing an established fluorescent bioreporter system. The activated...

  2. Dynamic Artificial Potential Fields for Autonomous Camera Control

    DEFF Research Database (Denmark)

    Burelli, Paolo; Jhala, Arnav Harish

    2009-01-01

    the implementation and evaluation of Artificial Potential Fields for automatic camera placement. We first describe the re- casting of the frame composition problem as a solution to a two particles suspended in an Artificial Potential Field. We demonstrate the application of this technique to control both camera...

  3. Dynamical Aperture Control in Accelerator Lattices With Multipole Potentials

    CERN Document Server

    Morozov, I

    2017-01-01

    We develop tools for symbolic representation of a non-linear accelerator model and analytical methods for description of non-linear dynamics. Information relevant to the dynamic aperture (DA) is then obtained from this model and can be used for indirect DA control or as a complement to direct numerical optimization. We apply two analytical methods and use multipole magnets to satisfy derived analytical constraints. The accelerator model is represented as a product of unperturbed and perturbed exponential operators with the exponent of the perturbed operator given as a power series in the perturbation parameter. Normal forms can be applied to this representation and the lattice parameters are used to control the normal form Hamiltonian and normal form transformation. Hamiltonian control is used to compute a control term or controlled operator. Lattice parameters are then fitted to satisfy the imposed control constraints. Theoretical results, as well as illustrative examples, are presented.

  4. Population dynamics of potentially harmful algal blooms in Bizerte ...

    African Journals Online (AJOL)

    These were numerically dominated by potentially toxic species of the diatom genus Pseudo-nitzschia, which were present year-round at all stations. ... Canonical correspondence analyses revealed significant relationships between the harmful phytoplankton species monitored and the environmental conditions.

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

    International Nuclear Information System (INIS)

    Devi, O Babynanda; Singh, C Amuba

    2014-01-01

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

  6. Soil weed seedbank dynamic and allelopathic potential of Tithonia ...

    African Journals Online (AJOL)

    The phenomenon of allelopathy is receiving increased attention as a possible alternative weed control method that is environment-friendly when compared with the use of herbicides with a wide range of toxic side effects which pose potential hazards to the environment. This study was designed to estimate the distribution of ...

  7. Charge density glass dynamics - Soft potentials and soft modes

    Energy Technology Data Exchange (ETDEWEB)

    Biljakovic, K., E-mail: katica@ifs.hr [Institute of Physics, HR-10001, Zagreb, P.O. Box 304 (Croatia); Staresinic, D., E-mail: damirs@ifs.hr [Institute of Physics, HR-10001, Zagreb, P.O. Box 304 (Croatia); Lasjaunias, J.C., E-mail: jean-claude.lasjaunias@pop3.grenoble.cnrs.fr [Institut Neel, CNRS, BP 166, F-38042, Grenoble, Cedex 9 (France); Remenyi, G., E-mail: Gyorgy.Remenyi@grenoble.cnrs.fr [Institut Neel, CNRS, BP 166, F-38042, Grenoble, Cedex 9 (France); Melin, R., E-mail: Regis.Melin@grenoble.cnrs.fr [Institut Neel, CNRS, BP 166, F-38042, Grenoble, Cedex 9 (France); Monceau, P., E-mail: pierre.monceau@grenoble.cnrs.fr [Institut Neel, CNRS, BP 166, F-38042, Grenoble, Cedex 9 (France); Sahling, S., E-mail: sven.olaf@gmail.com [Institut fuer Festkoerperphysik, Universitaet Dresden, D-01062, Dresden (Germany)

    2012-06-01

    An universal fingerprint of glasses has been found in low-temperature thermodynamic properties of charge/spin density wave (C/SDW) systems. Deviations from the well-known Debye, elastic continuum prediction for specific heat (flat C{sub p}/T{sup 3} plot) appear as two anomalies; the upturn below 1 K and a broad bump at T{approx}10 K (named Boson peak in glasses). The first one, inherent of localized two level systems within the shalow corrugated phase space, exhibits slow relaxation with the complex dynamics. The second one, 'Boson peak-like peak' was attributed to the pinned mode and incomplete softening of CDW superstructural mode. We discuss similar C{sub p}(T) features found also in incommensurate dielectrics with well documented soft-mode anomalies.

  8. Repair promoted by plasmid pKM101 is different from SOS repair

    International Nuclear Information System (INIS)

    Goze, A.; Devoret, R.

    1979-01-01

    In E. coli K12 bacteria carrying plasmid pKM101, prophage lambda was induced at UV doses higher than in plasmid-less parental bacteria. UV-induced reactivation per se was less effective. Bacteria with pKM101 showed no alteration in their division cycle. Plasmid PKM101 coded for a constitutive error-prone repair different from the inducible error-prone repair called SOS repair. Plasmid pKM101 protected E. coli bacteria from UV damage but slightly sensitized them to X-ray lesions. Protection against UV damage was effective in mutant bacteria deficient in DNA excision-repair provided that the recA, lexA and uvrE genes were functional. Survival of phages lambda and S13 after UV irradiation was enhanced in bacteria carrying plasmid pKM101; phage lambda mutagenesis was also increased. Plasmid pKM101 repaired potentially lethal DNA lesions, although Wild-type DNA sequences may not necessarily be restored; hence the mutations observed are the traces of the original DNA lesions. (Auth.)

  9. Comparative metagenomic analysis of plasmid encoded functions in the human gut microbiome

    Directory of Open Access Journals (Sweden)

    Marchesi Julian R

    2010-01-01

    particular the increased relative abundance and broad phylogenetic distribution was identified for a putative RelBE toxin/antitoxin addiction module, a putative phosphohydrolase/phosphoesterase, and an ORF of unknown function. Our analysis also indicates that some plasmids or plasmid families are present in the gut microbiomes of geographically isolated human hosts with a broad global distribution (America, Japan and Europe, and are potentially unique to the human gut microbiome. Further investigation of the plasmid population associated with the human gut is likely to provide important insights into the development, functioning and evolution of the human gut microbiota.

  10. Evaluation of the effect of non-B DNA structures on plasmid integrity via accelerated stability studies.

    Science.gov (United States)

    Ribeiro, S C; Monteiro, G A; Prazeres, D M F

    2009-04-01

    Plasmid biopharmaceuticals are a new class of medicines with an enormous potential. Attempts to increase the physical stability of highly purified supercoiled (SC) plasmid DNA in pharmaceutical aqueous solutions have relied on: (i) changing the DNA sequence, (ii) improving manufacturing to reduce deleterious impurities and initial DNA damage, and (iii) controlling the storage medium characteristics. In this work we analyzed the role of secondary structures on the degradation of plasmid molecules. Accelerated stability experiments were performed with SC, open circular (OC) and linear (L) isoforms of three plasmids which differed only in the "single-strandlike" content of their polyadenylation (poly A) signals. We have proved that the presence of more altered or interrupted (non-B) DNA secondary structures did not directly translate into an easier strand scission of the SC isoforms. Rather, those unusual structures imposed a lower degree of SC in the plasmids, leading to an increase in their resistance to thermal degradation. However, this behavior was reversed when the relaxed or L isoforms were tested, in which case the absence of SC rendered the plasmids essentially double-stranded. Overall, this work suggests that plasmid DNA sequence and secondary structures should be taken into account in future investigations of plasmid stability during prolonged storage.

  11. Eulerian velocity reconstruction in ideal atmospheric dynamics using potential vorticity and potential temperature

    Science.gov (United States)

    Blender, R.

    2009-04-01

    An approach for the reconstruction of atmospheric flow is presented which uses space- and time-dependent fields of density ?, potential vorticity Q and potential temperature Î& cedil;[J. Phys. A, 38, 6419 (2005)]. The method is based on the fundamental equations without approximation. The basic idea is to consider the time-dependent continuity equation as a condition for zero divergence of momentum in four dimensions (time and space, with unit velocity in time). This continuity equation is solved by an ansatz for the four-dimensional momentum using three conserved stream functions, the potential vorticity, potential temperature and a third field, denoted as ?-potential. In zonal flows, the ?-potential identifies the initial longitude of particles, whereas potential vorticity and potential temperature identify mainly meridional and vertical positions. Since the Lagrangian tracers Q, Î&,cedil; and ? determine the Eulerian velocity field, the reconstruction combines the Eulerian and the Lagrangian view of hydrodynamics. In stationary flows, the ?-potential is related to the Bernoulli function. The approach requires that the gradients of the potential vorticity and potential temperature do not vanish when the velocity remains finite. This behavior indicates a possible interrelation with stability conditions. Examples with analytical solutions are presented for a Rossby wave and zonal and rotational shear flows.

  12. Electric Potential and Electric Field Imaging with Dynamic Applications & Extensions

    Science.gov (United States)

    Generazio, Ed

    2017-01-01

    The technology and methods for remote quantitative imaging of electrostatic potentials and electrostatic fields in and around objects and in free space is presented. Electric field imaging (EFI) technology may be applied to characterize intrinsic or existing electric potentials and electric fields, or an externally generated electrostatic field made be used for volumes to be inspected with EFI. The baseline sensor technology (e-Sensor) and its construction, optional electric field generation (quasi-static generator), and current e- Sensor enhancements (ephemeral e-Sensor) are discussed. Critical design elements of current linear and real-time two-dimensional (2D) measurement systems are highlighted, and the development of a three dimensional (3D) EFI system is presented. Demonstrations for structural, electronic, human, and memory applications are shown. Recent work demonstrates that phonons may be used to create and annihilate electric dipoles within structures. Phonon induced dipoles are ephemeral and their polarization, strength, and location may be quantitatively characterized by EFI providing a new subsurface Phonon-EFI imaging technology. Results from real-time imaging of combustion and ion flow, and their measurement complications, will be discussed. Extensions to environment, Space and subterranean applications will be presented, and initial results for quantitative characterizing material properties are shown. A wearable EFI system has been developed by using fundamental EFI concepts. These new EFI capabilities are demonstrated to characterize electric charge distribution creating a new field of study embracing areas of interest including electrostatic discharge (ESD) mitigation, manufacturing quality control, crime scene forensics, design and materials selection for advanced sensors, combustion science, on-orbit space potential, container inspection, remote characterization of electronic circuits and level of activation, dielectric morphology of

  13. Processing of Nonconjugative Resistance Plasmids by Conjugation Nicking Enzyme of Staphylococci

    Energy Technology Data Exchange (ETDEWEB)

    Pollet, Rebecca M.; Ingle, James D.; Hymes, Jeff P.; Eakes, Thomas C.; Eto, Karina Yui; Kwong, Stephen M.; Ramsay, Joshua P.; Firth, Neville; Redinbo, Matthew R. (Curtin U.); (Sydney); (UNC)

    2016-01-04

    Antimicrobial resistance inStaphylococcus aureuspresents an increasing threat to human health. This resistance is often encoded on mobile plasmids, such as pSK41; however, the mechanism of transfer of these plasmids is not well understood. In this study, we first examine key protein-DNA interactions formed by the relaxase enzyme, NES, which initiates and terminates the transfer of the multidrug resistance plasmid pSK41. Two loops on the NES protein, hairpin loops 1 and 2, form extensive contacts with the DNA hairpin formed at theoriTregion of pSK41, and here we establish that these contacts are essential for proper DNA cleavage and religation by the full 665-residue NES proteinin vitro. Second, pSK156 and pCA347 are nonconjugativeStaphylococcus aureusplasmids that contain sequences similar to theoriTregion of pSK41 but differ in the sequence predicted to form a DNA hairpin. We show that pSK41-encoded NES is able to bind, cleave, and religate theoriTsequences of these nonconjugative plasmidsin vitro. Although pSK41 could mobilize a coresident plasmid harboring its cognateoriT, it was unable to mobilize plasmids containing the pSK156 and pCA347 variantoriTmimics, suggesting that an accessory protein like that previously shown to confer specificity in the pWBG749 system may also be involved in transmission of plasmids containing a pSK41-likeoriT. These data indicate that the conjugative relaxase intransmechanism recently described for the pWBG749 family of plasmids also applies to the pSK41 family of plasmids, further heightening the potential significance of this mechanism in the horizontal transfer of staphylococcal plasmids.

    IMPORTANCEUnderstanding the

  14. Potential energy landscape signatures of slow dynamics in glass forming liquids

    DEFF Research Database (Denmark)

    Sastry, S.; Debenedetti, P. G.; Stillinger, F. H.

    1999-01-01

    We study the properties of local potential energy minima (‘inherent structures’) sampled by liquids at low temperatures as an approach to elucidating the mechanisms of the observed dynamical slowing down observed as the glass transition temperature is approached. This onset of slow dynamics...

  15. Identifying High Academic Potential in Australian Aboriginal Children Using Dynamic Testing

    Science.gov (United States)

    Chaffey, Graham W.; Bailey, Stan B.; Vine, Ken W.

    2015-01-01

    The primary purpose of this study was to determine the effectiveness of dynamic testing as a method for identifying high academic potential in Australian Aboriginal children. The 79 participating Aboriginal children were drawn from Years 3-5 in rural schools in northern New South Wales. The dynamic testing method used in this study involved a…

  16. Phase-dependent dynamic potential of magnetically coupled two-degree-of-freedom bistable energy harvester.

    Science.gov (United States)

    Kim, Pilkee; Nguyen, Minh Sang; Kwon, Ojin; Kim, Young-Jin; Yoon, Yong-Jin

    2016-09-28

    A system of magnetically coupled oscillators has been recently considered as a promising compact structure to integrate multiple bistable energy harvesters (BEHs), but its design is not straightforward owing to its varying potential energy pattern, which has not been understood completely yet. This study introduces the concept of phase-dependent dynamic potential in a magnetically coupled BEH system with two degrees of freedom (DOFs) to explain the underlying principle of the complicated dynamics of the system. Through theoretical simulations and analyses, two distinct dynamic regimes, called the out-of-phase and in-phase mode regimes in this report, are found to exist in the frequency regions of the 1 st and 2 nd primary intrawell resonances. For the out-of-phase mode regime, the frequency displacement (and output power) responses of the 2-DOF BEH system exhibit typical double-well dynamics, whereas for the in-phase mode regime, only single-well dynamics is observed though the system is statically bistable. These dynamic regimes are also revealed to be caused by the difference in the dynamic potential energy trajectories propagating on a high-dimensional potential energy surface. The present approach to the dynamics of the 2-DOF BEH system can be extended and applied to higher-DOF systems, which sheds light on compact and efficient designs of magnetically coupled BEH chain structures.

  17. Quantum Nuclear Extension of Electron Nuclear Dynamics on Folded Effective-Potential Surfaces

    DEFF Research Database (Denmark)

    Hall, B.; Deumens, E.; Ohrn, Y.

    2014-01-01

    A perennial problem in quantum scattering calculations is accurate theoretical treatment of low energy collisions. We propose a method of extracting a folded, nonadiabatic, effective potential energy surface from electron nuclear dynamics (END) trajectories; we then perform nuclear wave packet...

  18. Classical and quantum dynamics in an inverse square potential

    International Nuclear Information System (INIS)

    Guillaumín-España, Elisa; Núñez-Yépez, H. N.; Salas-Brito, A. L.

    2014-01-01

    The classical motion of a particle in a 3D inverse square potential with negative energy, E, is shown to be geodesic, i.e., equivalent to the particle's free motion on a non-compact phase space manifold irrespective of the sign of the coupling constant. We thus establish that all its classical orbits with E < 0 are unbounded. To analyse the corresponding quantum problem, the Schrödinger equation is solved in momentum space. No discrete energy levels exist in the unrenormalized case and the system shows a complete “fall-to-the-center” with an energy spectrum unbounded by below. Such behavior corresponds to the non-existence of bound classical orbits. The symmetry of the problem is SO(3) × SO(2, 1) corroborating previously obtained results

  19. Classical and quantum dynamics in an inverse square potential

    Energy Technology Data Exchange (ETDEWEB)

    Guillaumín-España, Elisa, E-mail: ege@correo.azc.uam.mx [Laboratorio de Sistemas Dinámicos, Departamento de Ciencias Básicas, Universidad Autónoma Metropolitana, Unidad Azcapotzalco, Azcapotzalco CP 02200 D. F. (Mexico); Núñez-Yépez, H. N., E-mail: nyhn@xanum.uam.mx [Departamento de Física, Universidad Autónoma Metropolitana, Unidad Iztapalapa, Apartado Postal 55-534, Iztapalapa CP 09340 D. F. (Mexico); Salas-Brito, A. L., E-mail: asb@correo.azc.uam.mx [Instituto de Ciencias Nucleares, Universidad Nacional Autónoma de México (ICN-UNAM), Apartado Postal 70-543, 04510 México D F (Mexico)

    2014-10-15

    The classical motion of a particle in a 3D inverse square potential with negative energy, E, is shown to be geodesic, i.e., equivalent to the particle's free motion on a non-compact phase space manifold irrespective of the sign of the coupling constant. We thus establish that all its classical orbits with E < 0 are unbounded. To analyse the corresponding quantum problem, the Schrödinger equation is solved in momentum space. No discrete energy levels exist in the unrenormalized case and the system shows a complete “fall-to-the-center” with an energy spectrum unbounded by below. Such behavior corresponds to the non-existence of bound classical orbits. The symmetry of the problem is SO(3) × SO(2, 1) corroborating previously obtained results.

  20. In Vivo Transfer and Microevolution of Avian Native IncA/C2blaNDM-1-Carrying Plasmid pRH-1238 during a Broiler Chicken Infection Study.

    Science.gov (United States)

    Hadziabdic, Sead; Fischer, Jennie; Malorny, Burkhard; Borowiak, Maria; Guerra, Beatriz; Kaesbohrer, Annemarie; Gonzalez-Zorn, Bruno; Szabo, Istvan

    2018-04-01

    The emergence and spread of carbapenemase-producing Enterobacteriaceae (CPE) in wildlife and livestock animals pose an important safety concern for public health. With our in vivo broiler chicken infection study, we investigated the transfer and experimental microevolution of the bla NDM-1 -carrying IncA/C 2 plasmid (pRH-1238) introduced by avian native Salmonella enterica subsp. enterica serovar Corvallis without inducing antibiotic selection pressure. We evaluated the dependency of the time point of inoculation on donor ( S Corvallis [12-SA01738]) and plasmid-free Salmonella recipient [d-tartrate-fermenting (d-Ta + ) S Paratyphi B (13-SA01617), referred to here as S Paratyphi B (d-Ta + )] excretion by quantifying their excretion dynamics. Using plasmid profiling by S1 nuclease-restricted pulsed-field gel electrophoresis, we gained insight into the variability of the native plasmid content among S Corvallis reisolates as well as plasmid acquisition in S Paratyphi B (d-Ta + ) and the enterobacterial gut microflora. Whole-genome sequencing enabled us to gain an in-depth insight into the microevolution of plasmid pRH-1238 in S Corvallis and enterobacterial recipient isolates. Our study revealed that the fecal excretion of avian native carbapenemase-producing S Corvallis is significantly higher than that of S Paratyphi (d-Ta + ) and is not hampered by S Paratyphi (d-Ta + ). Acquisition of pRH-1238 in other Enterobacteriaceae and several events of plasmid pRH-1238 transfer to different Escherichia coli sequence types and Klebsiella pneumoniae demonstrated an interspecies broad host range. Regardless of the microevolutionary structural deletions in pRH-1238, the single carbapenem resistance marker bla NDM-1 was maintained on pRH-1238 throughout the trial. Furthermore, we showed the importance of the gut E. coli population as a vector of pRH-1238. In a potential scenario of the introduction of NDM-1-producing S Corvallis into a broiler flock, the pRH-1238 plasmid could

  1. Plasmid transfer by conjugation in Xylella fastidiosa.

    Science.gov (United States)

    Recombination and horizontal gene transfer have been implicated in the adaption of Xylella fastidiosa (Xf) to infect a wide variety of different plant species. There is evidence that certain strains of Xf carry native plasmids equipped with transfer and mobilization genes, suggesting conjugation as ...

  2. Standardized Cloning and Curing of Plasmids

    DEFF Research Database (Denmark)

    Lauritsen, Ida; Kim, Se Hyeuk; Porse, Andreas

    2018-01-01

    and exchange of genetic parts in the Standard European Vectors Architecture (SEVA) vector system. Additionally, to facilitate rapid testing and iterative bioengineering using different vector designs, we provide a one-step protocol for a universal CRISPR-Cas9-based plasmid curing system (pFREE) and demonstrate...

  3. Optimization of plasmid electrotransformation into Escherichia coli ...

    African Journals Online (AJOL)

    In order to improve electroporation, optical density of bacteria, recovery time and electrical parameter (field strength and capacitance) were optimized using the Taguchi statistical method. ANOVA of obtained data indicated that the optimal conditions of electrotransformation of pET-28a (+) plasmid into Escherichia coli ...

  4. Plasmid mediated quinolone resistance in Enterobacteriaceae

    NARCIS (Netherlands)

    Veldman, K.T.; LS Klinisch Onderzoek Wagenaar

    2014-01-01

    This thesis describes the occurrence of Plasmid Mediated Quinolone Resistance (PMQR) in Salmonella and E. coli from The Netherlands and other European countries. Furthermore, the genetic background of these genes was characterized. Fluoroquinolones are widely used antibiotics in both human and

  5. Antimicrobial resistance and plasmid profiles of Aeromonas ...

    African Journals Online (AJOL)

    The purpose of this study was to investigate the presence of Aeromonas hydrophila at commonly used water collection points on the River Njoro and to determine the in-vitro antimicrobial susceptibility and plasmid profiles of isolates. In total, 126 samples were collected and 36.5% of them were positive for A. hydrophila.

  6. Antimicrobial resistance patterns and plasmid profiles of ...

    African Journals Online (AJOL)

    Objectives: To determine the frequency of resistance of Staphylococcus aureus to various antimicrobial agents, and the relationship between antimicrobial resistance of the isolates and carriage of plasmids. Design: A random sampling of milk and meat samples was carried out. Setting: Milk was collected from various dairy ...

  7. Simple method for identification of plasmid-coded proteins

    International Nuclear Information System (INIS)

    Sancar, A.; Hack, A.M.; Rupp, W.D.

    1979-01-01

    Proteins encoded by plasmid DNA are specifically labeled in uv-irradiated cells of Escherichia coli carrying recA and uvrA mutations because extensive degradation of the chromosome DNA occurs concurrently with amplification of plasmid DNA

  8. Dynamics of the inward rectifier K+ current during the action potential of guinea pig ventricular myocytes

    OpenAIRE

    Ibarra, J.; Morley, G.E.; Delmar, M.

    1991-01-01

    The potassium selective, inward rectifier current (IK1) is known to be responsible for maintaining the resting membrane potential of quiescent ventricular myocytes. However, the contribution of this current to the different phases of the cardiac action potential has not been adequately established. In the present study, we have used the action potential clamp (APC) technique to characterize the dynamic changes of a cesium-sensitive (i.e., Ik1) current which occur during the action potential. ...

  9. The Salmonella genomic island 1 is specifically mobilized in trans by the IncA/C multidrug resistance plasmid family.

    Science.gov (United States)

    Douard, Gregory; Praud, Karine; Cloeckaert, Axel; Doublet, Benoît

    2010-12-20

    The Salmonella genomic island 1 (SGI1) is a Salmonella enterica-derived integrative mobilizable element (IME) containing various complex multiple resistance integrons identified in several S. enterica serovars and in Proteus mirabilis. Previous studies have shown that SGI1 transfers horizontally by in trans mobilization in the presence of the IncA/C conjugative helper plasmid pR55. Here, we report the ability of different prevalent multidrug resistance (MDR) plasmids including extended-spectrum β-lactamase (ESBL) gene-carrying plasmids to mobilize the multidrug resistance genomic island SGI1. Through conjugation experiments, none of the 24 conjugative plasmids tested of the IncFI, FII, HI2, I1, L/M, N, P incompatibility groups were able to mobilize SGI1 at a detectable level (transfer frequency IncA/C incompatibility group. Several conjugative IncA/C MDR plasmids as well as the sequenced IncA/C reference plasmid pRA1 of 143,963 bp were shown to mobilize in trans SGI1 from a S. enterica donor to the Escherichia coli recipient strain. Depending on the IncA/C plasmid used, the conjugative transfer of SGI1 occurred at frequencies ranging from 10(-3) to 10(-6) transconjugants per donor. Of particular concern, some large IncA/C MDR plasmids carrying the extended-spectrum cephalosporinase bla(CMY-2) gene were shown to mobilize in trans SGI1. The ability of the IncA/C MDR plasmid family to mobilize SGI1 could contribute to its spread by horizontal transfer among enteric pathogens. Moreover, the increasing prevalence of IncA/C plasmids in MDR S. enterica isolates worldwide has potential implications for the epidemic success of the antibiotic resistance genomic island SGI1 and its close derivatives.

  10. Bending localization of nitrous oxide under anharmonicity and Fermi coupling: the dynamical potential approach

    International Nuclear Information System (INIS)

    Zhang Chi; Wu Guo-Zhen; Fang Chao

    2010-01-01

    This paper studies the vibrational nonlinear dynamics of nitrous oxide with Fermi coupling between the symmetric stretching and bending coordinates by classical dynamical potential approach. This is a global approach in the sense that the overall dynamics is evidenced by the classical nonlinear variables such as the fixed points and the focus are on a set of levels instead of individual ones. The dynamics of nitrous oxide is demonstrated to be not so much dependent on the excitation energy. Moreover, the localized bending mode is shown to be ubiquitous in all the energy range studied

  11. Analysis of plasmid genes by phylogenetic profiling and visualization of homology relationships using Blast2Network

    Directory of Open Access Journals (Sweden)

    Bazzicalupo Marco

    2008-12-01

    Full Text Available Abstract Background Phylogenetic methods are well-established bioinformatic tools for sequence analysis, allowing to describe the non-independencies of sequences because of their common ancestor. However, the evolutionary profiles of bacterial genes are often complicated by hidden paralogy and extensive and/or (multiple horizontal gene transfer (HGT events which make bifurcating trees often inappropriate. In this context, plasmid sequences are paradigms of network-like relationships characterizing the evolution of prokaryotes. Actually, they can be transferred among different organisms allowing the dissemination of novel functions, thus playing a pivotal role in prokaryotic evolution. However, the study of their evolutionary dynamics is complicated by the absence of universally shared genes, a prerequisite for phylogenetic analyses. Results To overcome such limitations we developed a bioinformatic package, named Blast2Network (B2N, allowing the automatic phylogenetic profiling and the visualization of homology relationships in a large number of plasmid sequences. The software was applied to the study of 47 completely sequenced plasmids coming from Escherichia, Salmonella and Shigella spps. Conclusion The tools implemented by B2N allow to describe and visualize in a new way some of the evolutionary features of plasmid molecules of Enterobacteriaceae; in particular it helped to shed some light on the complex history of Escherichia, Salmonella and Shigella plasmids and to focus on possible roles of unannotated proteins. The proposed methodology is general enough to be used for comparative genomic analyses of bacteria.

  12. Structures of actin-like ParM filaments show architecture of plasmid-segregating spindles.

    Science.gov (United States)

    Bharat, Tanmay A M; Murshudov, Garib N; Sachse, Carsten; Löwe, Jan

    2015-07-02

    Active segregation of Escherichia coli low-copy-number plasmid R1 involves formation of a bipolar spindle made of left-handed double-helical actin-like ParM filaments. ParR links the filaments with centromeric parC plasmid DNA, while facilitating the addition of subunits to ParM filaments. Growing ParMRC spindles push sister plasmids to the cell poles. Here, using modern electron cryomicroscopy methods, we investigate the structures and arrangements of ParM filaments in vitro and in cells, revealing at near-atomic resolution how subunits and filaments come together to produce the simplest known mitotic machinery. To understand the mechanism of dynamic instability, we determine structures of ParM filaments in different nucleotide states. The structure of filaments bound to the ATP analogue AMPPNP is determined at 4.3 Å resolution and refined. The ParM filament structure shows strong longitudinal interfaces and weaker lateral interactions. Also using electron cryomicroscopy, we reconstruct ParM doublets forming antiparallel spindles. Finally, with whole-cell electron cryotomography, we show that doublets are abundant in bacterial cells containing low-copy-number plasmids with the ParMRC locus, leading to an asynchronous model of R1 plasmid segregation.

  13. Dynamics of Bose-Einstein condensates in novel optical potentials

    Energy Technology Data Exchange (ETDEWEB)

    Kueber, Johannes

    2014-07-21

    Matter wave interferometry offers a novel approach for high precision measurements, such as the determination of physical constants like the local gravity constant g or the fine-structure constant. Since its early demonstration, it has become an important tool in the fields of fundamental and applied physics. The present work covers the implementation of matter wave interferometers as well as the creation of novel guiding potentials for ultra-cold ensembles of atoms and Bose-Einstein condensates for this purpose. In addition, novel techniques for the manipulation of atoms with Bragg lattices are presented, serving as elements for interferometry. The measurements in this work are performed with a Bose-Einstein condensate of 25000 {sup 87}rubidium atoms created in a crossed optical dipole trap. The crossed optical dipole trap is loaded from a magneto-optical trap and allows a measurement every 25 s. This work introduces the novel technique of double Bragg diffraction as a tool for atom optics for the first time experimentally. The creation of beamsplitters and mirrors for advanced interferometric measurements is characterized. An in depth discussion on the momentum distribution of atomic clouds and its influence on double Bragg diffraction is given. Additionally experimental results for higher-order Bragg diffraction are explained and double Bragg diffraction is used to implement a full Ramsey-type interferometer. A second central result of this work is the implementation of novel guiding structures for ultra-cold atoms. These structures are created with conical refraction, an effect that occurs when light is guided along one of the optical axis of a bi-axial crystal. The conical refraction crystal used to operate the novel trapping geometries is a KGd(WO{sub 4}){sub 2} crystal that has been specifically cut orthogonal to one of the optical axis. Two regimes are discussed in detail: the creation of a toroidal matter wave guide and the implementation of a three

  14. Electron injection dynamics in high-potential porphyrin photoanodes.

    Science.gov (United States)

    Milot, Rebecca L; Schmuttenmaer, Charles A

    2015-05-19

    There is a growing need to utilize carbon neutral energy sources, and it is well known that solar energy can easily satisfy all of humanity's requirements. In order to make solar energy a viable alternative to fossil fuels, the problem of intermittency must be solved. Batteries and supercapacitors are an area of active research, but they currently have relatively low energy-to-mass storage capacity. An alternative and very promising possibility is to store energy in chemical bonds, or make a solar fuel. The process of making solar fuel is not new, since photosynthesis has been occurring on earth for about 3 billion years. In order to produce any fuel, protons and electrons must be harvested from a species in its oxidized form. Photosynthesis uses the only viable source of electrons and protons on the scale needed for global energy demands: water. Because artificial photosynthesis is a lofty goal, water oxidation, which is a crucial step in the process, has been the initial focus. This Account provides an overview of how terahertz spectroscopy is used to study electron injection, highlights trends from previously published reports, and concludes with a future outlook. It begins by exploring similarities and differences between dye-sensitized solar cells (DSSCs) for producing electricity and a putative device for splitting water and producing a solar fuel. It then identifies two important problems encountered when adapting DSSC technology to water oxidation-improper energy matching between sensitizer energy levels with the potential for water oxidation and the instability of common anchoring groups in water-and discusses steps to address them. Emphasis is placed on electron injection from sensitizers to metal oxides because this process is the initial step in charge transport. Both the rate and efficiency of electron injection are analyzed on a sub-picosecond time scale using time-resolved terahertz spectroscopy (TRTS). Bio-inspired pentafluorophenyl porphyrins are

  15. Conjugal properties of the Sinorhizobium meliloti plasmid mobilome.

    Science.gov (United States)

    Pistorio, Mariano; Giusti, María A; Del Papa, María F; Draghi, Walter O; Lozano, Mauricio J; Tejerizo, Gonzalo Torres; Lagares, Antonio

    2008-09-01

    The biology and biochemistry of plasmid transfer in soil bacteria is currently under active investigation because of its central role in prokaryote adaptation and evolution. In this work, we examined the conjugal properties of the cryptic plasmids present in a collection of the N(2)-fixing legume-symbiont Sinorhizobium meliloti. The study was performed on 65 S. meliloti isolates recovered from 25 humic soils of Argentina, which were grouped into 22 plasmid-profile types [i.e. plasmid operational taxonomic units (OTUs)]. The cumulative Shannon index calculated for the observed plasmid profiles showed a clear saturation plateau, thus indicating an adequate representation of the S. meliloti plasmid-profile types in the isolates studied. The results show that isolates of nearly 14% of the plasmid OTUs hosted transmissible plasmids and that isolates of 29% of the plasmid OTUs were able to retransfer the previously characterized mobilizable-cryptic plasmid pSmeLPU88b to a third recipient strain. It is noteworthy that isolates belonging to 14% of the plasmid OTUs proved to be refractory to the entrance of the model plasmid pSmeLPU88b, suggesting either the presence of surface exclusion phenomena or the occurrence of restriction incompatibility with the incoming replicon. Incompatibility for replication between resident plasmids and plasmid pSmeLPU88b was observed in c. 20% of the OTUs. The results reported here reveal a widespread compatibility among the conjugal functions of the cryptic plasmids in S. meliloti, and this fact, together with the observed high proportion of existing donor genotypes, points to the extrachromosomal compartment of the species as being an extremely active plasmid mobilome.

  16. Dynamic fracture testing of ferritic steels using direct current potential drop method

    International Nuclear Information System (INIS)

    Oh, Y. J.; Kim, J. H.; Hwang, I. S.; Park, Y. W.

    2000-01-01

    To apply leak-before-break (LBB) concept to nuclear pipes, the dynamic strain aging of low carbon steel materials has to be considered. For this goal, the J-R tests are needed over a range of temperatures and loading rates, including rapid dynamic loading conditions. In dynamic J-R tests, the unloading compliance method can not be applied and usually the direct current potential drop (DCPD) method has been used. But, even the DCPD method was known to have the problem in defining the crack initiation point due to a potential peak arising in early part of loading of ferromagnetic materials. In this study, potential peaks characteristics were investigated for SA106Gr.C piping steels, and the definition of crack initiation point was made by back tracking from final physical crack length, and it was proposed that this technique could be applied to DCPD method in dynamic loading J-R test

  17. Plasmid mediated enhancement of uv resistance in Streptococcus faecalis

    International Nuclear Information System (INIS)

    Miehl, R.; Miller, M.; Yasbin, R.E.

    1980-01-01

    A 38.5-Mdal plasmid of Streptococcus faecalis subdp. zymogenes has been shown to enhance survival following uv irradiation. In addition, the presence of this plasmid increases the mutation frequencies following uv irradiation and enhanced W-reactivation. The data presented indicate that S. faecalis has an inducible error-prone repair system and that the plasmid enhances these repair functions

  18. Quantum dynamics on potential energy surfaces. Simpler states and simpler dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Keller, Johannes Friedrich

    2015-09-25

    In this dissertation we analyze and simplify wave functions and observables in the context of quantum molecular dynamics. The two main topics we discuss are the structure of Hagedorn wave packets in position and phase space, and semiclassical approximations for the propagation of quantum expectations with nonnegative phase space densities. We provide algorithmic discretizations for these approximations and illustrate their validity and applicability by means of numerical experiments.

  19. Fluorescence quenching studies of potential-dependent DNA reorientation dynamics at glassy carbon electrode surfaces.

    Science.gov (United States)

    Li, Qin; Cui, Chenchen; Higgins, Daniel A; Li, Jun

    2012-09-05

    The potential-dependent reorientation dynamics of double-stranded DNA (ds-DNA) attached to planar glassy carbon electrode (GCE) surfaces were investigated. The orientation state of surface-bound ds-DNA was followed by monitoring the fluorescence from a 6-carboxyfluorescein (FAM6) fluorophore covalently linked to the distal end of the DNA. Positive potentials (i.e., +0.2 V vs open circuit potential, OCP) caused the ds-DNA to align parallel to the electrode surface, resulting in strong dipole-electrode quenching of FAM6 fluorescence. Switching of the GCE potential to negative values (i.e., -0.2 V vs OCP) caused the ds-DNA to reorient perpendicular to the electrode surface, with a concomitant increase in FAM6 fluorescence. In addition to the very fast (submilliseconds) dynamics of the initial reorientation process, slow (0.1-0.9 s) relaxation of FAM6 fluorescence to intermediate levels was also observed after potential switching. These dynamics have not been previously described in the literature. They are too slow to be explained by double layer charging, and chronoamperometry data showed no evidence of such effects. Both the amplitude and rate of the dynamics were found to depend upon buffer concentration, and ds-DNA length, demonstrating a dependence on the double layer field. The dynamics are concluded to arise from previously undetected complexities in the mechanism of potential-dependent ds-DNA reorientation. The possible origins of these dynamics are discussed. A better understanding of these dynamics will lead to improved models for potential-dependent ds-DNA reorientation at electrode surfaces and will facilitate the development of advanced electrochemical devices for detection of target DNAs.

  20. Construction of Biologically Functional Bacterial Plasmids In Vitro

    Science.gov (United States)

    Cohen, Stanley N.; Chang, Annie C. Y.; Boyer, Herbert W.; Helling, Robert B.

    1973-01-01

    The construction of new plasmid DNA species by in vitro joining of restriction endonuclease-generated fragments of separate plasmids is described. Newly constructed plasmids that are inserted into Escherichia coli by transformation are shown to be biologically functional replicons that possess genetic properties and nucleotide base sequences from both of the parent DNA molecules. Functional plasmids can be obtained by reassociation of endonuclease-generated fragments of larger replicons, as well as by joining of plasmid DNA molecules of entirely different origins. Images PMID:4594039

  1. Plasmid Flux in Escherichia coli ST131 Sublineages, Analyzed by Plasmid Constellation Network (PLACNET), a New Method for Plasmid Reconstruction from Whole Genome Sequences

    Science.gov (United States)

    Garcillán-Barcia, M. Pilar; Mora, Azucena; Blanco, Jorge; Coque, Teresa M.; de la Cruz, Fernando

    2014-01-01

    Bacterial whole genome sequence (WGS) methods are rapidly overtaking classical sequence analysis. Many bacterial sequencing projects focus on mobilome changes, since macroevolutionary events, such as the acquisition or loss of mobile genetic elements, mainly plasmids, play essential roles in adaptive evolution. Existing WGS analysis protocols do not assort contigs between plasmids and the main chromosome, thus hampering full analysis of plasmid sequences. We developed a method (called plasmid constellation networks or PLACNET) that identifies, visualizes and analyzes plasmids in WGS projects by creating a network of contig interactions, thus allowing comprehensive plasmid analysis within WGS datasets. The workflow of the method is based on three types of data: assembly information (including scaffold links and coverage), comparison to reference sequences and plasmid-diagnostic sequence features. The resulting network is pruned by expert analysis, to eliminate confounding data, and implemented in a Cytoscape-based graphic representation. To demonstrate PLACNET sensitivity and efficacy, the plasmidome of the Escherichia coli lineage ST131 was analyzed. ST131 is a globally spread clonal group of extraintestinal pathogenic E. coli (ExPEC), comprising different sublineages with ability to acquire and spread antibiotic resistance and virulence genes via plasmids. Results show that plasmids flux in the evolution of this lineage, which is wide open for plasmid exchange. MOBF12/IncF plasmids were pervasive, adding just by themselves more than 350 protein families to the ST131 pangenome. Nearly 50% of the most frequent γ–proteobacterial plasmid groups were found to be present in our limited sample of ten analyzed ST131 genomes, which represent the main ST131 sublineages. PMID:25522143

  2. Plasmid flux in Escherichia coli ST131 sublineages, analyzed by plasmid constellation network (PLACNET), a new method for plasmid reconstruction from whole genome sequences.

    Science.gov (United States)

    Lanza, Val F; de Toro, María; Garcillán-Barcia, M Pilar; Mora, Azucena; Blanco, Jorge; Coque, Teresa M; de la Cruz, Fernando

    2014-12-01

    Bacterial whole genome sequence (WGS) methods are rapidly overtaking classical sequence analysis. Many bacterial sequencing projects focus on mobilome changes, since macroevolutionary events, such as the acquisition or loss of mobile genetic elements, mainly plasmids, play essential roles in adaptive evolution. Existing WGS analysis protocols do not assort contigs between plasmids and the main chromosome, thus hampering full analysis of plasmid sequences. We developed a method (called plasmid constellation networks or PLACNET) that identifies, visualizes and analyzes plasmids in WGS projects by creating a network of contig interactions, thus allowing comprehensive plasmid analysis within WGS datasets. The workflow of the method is based on three types of data: assembly information (including scaffold links and coverage), comparison to reference sequences and plasmid-diagnostic sequence features. The resulting network is pruned by expert analysis, to eliminate confounding data, and implemented in a Cytoscape-based graphic representation. To demonstrate PLACNET sensitivity and efficacy, the plasmidome of the Escherichia coli lineage ST131 was analyzed. ST131 is a globally spread clonal group of extraintestinal pathogenic E. coli (ExPEC), comprising different sublineages with ability to acquire and spread antibiotic resistance and virulence genes via plasmids. Results show that plasmids flux in the evolution of this lineage, which is wide open for plasmid exchange. MOBF12/IncF plasmids were pervasive, adding just by themselves more than 350 protein families to the ST131 pangenome. Nearly 50% of the most frequent γ-proteobacterial plasmid groups were found to be present in our limited sample of ten analyzed ST131 genomes, which represent the main ST131 sublineages.

  3. Plasmid flux in Escherichia coli ST131 sublineages, analyzed by plasmid constellation network (PLACNET, a new method for plasmid reconstruction from whole genome sequences.

    Directory of Open Access Journals (Sweden)

    Val F Lanza

    2014-12-01

    Full Text Available Bacterial whole genome sequence (WGS methods are rapidly overtaking classical sequence analysis. Many bacterial sequencing projects focus on mobilome changes, since macroevolutionary events, such as the acquisition or loss of mobile genetic elements, mainly plasmids, play essential roles in adaptive evolution. Existing WGS analysis protocols do not assort contigs between plasmids and the main chromosome, thus hampering full analysis of plasmid sequences. We developed a method (called plasmid constellation networks or PLACNET that identifies, visualizes and analyzes plasmids in WGS projects by creating a network of contig interactions, thus allowing comprehensive plasmid analysis within WGS datasets. The workflow of the method is based on three types of data: assembly information (including scaffold links and coverage, comparison to reference sequences and plasmid-diagnostic sequence features. The resulting network is pruned by expert analysis, to eliminate confounding data, and implemented in a Cytoscape-based graphic representation. To demonstrate PLACNET sensitivity and efficacy, the plasmidome of the Escherichia coli lineage ST131 was analyzed. ST131 is a globally spread clonal group of extraintestinal pathogenic E. coli (ExPEC, comprising different sublineages with ability to acquire and spread antibiotic resistance and virulence genes via plasmids. Results show that plasmids flux in the evolution of this lineage, which is wide open for plasmid exchange. MOBF12/IncF plasmids were pervasive, adding just by themselves more than 350 protein families to the ST131 pangenome. Nearly 50% of the most frequent γ-proteobacterial plasmid groups were found to be present in our limited sample of ten analyzed ST131 genomes, which represent the main ST131 sublineages.

  4. The porcine circovirus type 1 capsid gene promoter improves antigen expression and immunogenicity in a HIV-1 plasmid vaccine

    Directory of Open Access Journals (Sweden)

    Burger Marieta

    2011-02-01

    Full Text Available Abstract Background One of the promising avenues for development of vaccines against Human immunodeficiency virus type 1 (HIV-1 and other human pathogens is the use of plasmid-based DNA vaccines. However, relatively large doses of plasmid must be injected for a relatively weak response. We investigated whether genome elements from Porcine circovirus type 1 (PCV-1, an apathogenic small ssDNA-containing virus, had useful expression-enhancing properties that could allow dose-sparing in a plasmid vaccine. Results The linearised PCV-1 genome inserted 5' of the CMV promoter in the well-characterised HIV-1 plasmid vaccine pTHgrttnC increased expression of the polyantigen up to 2-fold, and elicited 3-fold higher CTL responses in mice at 10-fold lower doses than unmodified pTHgrttnC. The PCV-1 capsid gene promoter (Pcap alone was equally effective. Enhancing activity was traced to a putative composite host transcription factor binding site and a "Conserved Late Element" transcription-enhancing sequence previously unidentified in circoviruses. Conclusions We identified a novel PCV-1 genome-derived enhancer sequence that significantly increased antigen expression from plasmids in in vitro assays, and improved immunogenicity in mice of the HIV-1 subtype C vaccine plasmid, pTHgrttnC. This should allow significant dose sparing of, or increased responses to, this and other plasmid-based vaccines. We also report investigations of the potential of other circovirus-derived sequences to be similarly used.

  5. Combining a reactive potential with a harmonic approximation for molecular dynamics simulation of failure: construction of a reduced potential

    Science.gov (United States)

    Tejada, I. G.; Brochard, L.; Stoltz, G.; Legoll, F.; Lelièvre, T.; Cancès, E.

    2015-01-01

    Molecular dynamics is a simulation technique that can be used to study failure in solids, provided the inter-atomic potential energy is able to account for the complex mechanisms at failure. Reactive potentials fitted on ab initio results or on experimental values have the ability to adapt to any complex atomic arrangement and, therefore, are suited to simulate failure. But the complexity of these potentials, together with the size of the systems considered, make simulations computationally expensive. In order to improve the efficiency of numerical simulations, simpler harmonic potentials can be used instead of complex reactive potentials in the regions where the system is close to its ground state and a harmonic approximation reasonably fits the actual reactive potential. However the validity and precision of such an approach has not been investigated in detail yet. We present here a methodology for constructing a reduced potential and combining it with the reactive one. We also report some important features of crack propagation that may be affected by the coupling of reactive and reduced potentials. As an illustrative case, we model a crystalline two-dimensional material (graphene) with a reactive empirical bond-order potential (REBO) or with harmonic potentials made of bond and angle springs that are designed to reproduce the second order approximation of REBO in the ground state. We analyze the consistency of this approximation by comparing the mechanical behavior and the phonon spectra of systems modeled with these potentials. These tests reveal when the anharmonicity effects appear. As anharmonic effects originate from strain, stress or temperature, the latter quantities are the basis for establishing coupling criteria for on the fly substitution in large simulations.

  6. Ecological and genetic determinants of plasmid distribution in Escherichia coli.

    Science.gov (United States)

    Medaney, Frances; Ellis, Richard J; Raymond, Ben

    2016-11-01

    Bacterial plasmids are important carriers of virulence and antibiotic resistance genes. Nevertheless, little is known of the determinants of plasmid distribution in bacterial populations. Here the factors affecting the diversity and distribution of the large plasmids of Escherichia coli were explored in cattle grazing on semi-natural grassland, a set of populations with low frequencies of antibiotic resistance genes. Critically, the population genetic structure of bacterial hosts was chararacterized. This revealed structured E. coli populations with high diversity between sites and individuals but low diversity within cattle hosts. Plasmid profiles, however, varied considerably within the same E. coli genotype. Both ecological and genetic factors affected plasmid distribution: plasmid profiles were affected by site, E. coli diversity, E. coli genotype and the presence of other large plasmids. Notably 3/26 E. coli serotypes accounted for half the observed plasmid-free isolates indicating that within species variation can substantially affect carriage of the major conjugative plasmids. The observed population structure suggest that most of the opportunities for within species plasmid transfer occur between different individuals of the same genotype and support recent experimental work indicating that plasmid-host coevolution, and epistatic interactions on fitness costs are likely to be important in determining occupancy. © 2016 The Authors. Environmental Microbiology published by Society for Applied Microbiology and John Wiley & Sons Ltd.

  7. Charge-transfer modified embedded atom method dynamic charge potential for Li-Co-O system.

    Science.gov (United States)

    Kong, Fantai; Longo, Roberto C; Liang, Chaoping; Nie, Yifan; Zheng, Yongping; Zhang, Chenxi; Cho, Kyeongjae

    2017-11-29

    To overcome the limitation of conventional fixed charge potential methods for the study of Li-ion battery cathode materials, a dynamic charge potential method, charge-transfer modified embedded atom method (CT-MEAM), has been developed and applied to the Li-Co-O ternary system. The accuracy of the potential has been tested and validated by reproducing a variety of structural and electrochemical properties of LiCoO 2 . A detailed analysis on the local charge distribution confirmed the capability of this potential for dynamic charge modeling. The transferability of the potential is also demonstrated by its reliability in describing Li-rich Li 2 CoO 2 and Li-deficient LiCo 2 O 4 compounds, including their phase stability, equilibrium volume, charge states and cathode voltages. These results demonstrate that the CT-MEAM dynamic charge potential could help to overcome the challenge of modeling complex ternary transition metal oxides. This work can promote molecular dynamics studies of Li ion cathode materials and other important transition metal oxides systems that involve complex electrochemical and catalytic reactions.

  8. Dynamical Symmetries of Two-Dimensional Dirac Equation with Screened Coulomb and Isotropic Harmonic Oscillator Potentials

    International Nuclear Information System (INIS)

    Wang Qing; Hou Yu-Long; Jing Jian; Long Zheng-Wen

    2014-01-01

    In this paper, we study symmetrical properties of two-dimensional (2D) screened Dirac Hydrogen atom and isotropic harmonic oscillator with scalar and vector potentials of equal magnitude (SVPEM). We find that it is possible for both cases to preserve so(3) and su(2) dynamical symmetries provided certain conditions are satisfied. Interestingly, the conditions for preserving these dynamical symmetries are exactly the same as non-relativistic screened Hydrogen atom and screened isotropic oscillator preserving their dynamical symmetries. Some intuitive explanations are proposed. (general)

  9. Crossover to potential energy landscape dominated dynamics in a model glass-forming liquid

    DEFF Research Database (Denmark)

    Schrøder, Thomas; Sastry, S.; Dyre, Jeppe

    2000-01-01

    An equilibrated model glass-forming liquid is studied by mapping successive configurations produced by molecular dynamics simulation onto a time series of inherent structures (local minima in the potential energy). Using this "inherent dynamics" approach we find direct numerical evidence for the ......An equilibrated model glass-forming liquid is studied by mapping successive configurations produced by molecular dynamics simulation onto a time series of inherent structures (local minima in the potential energy). Using this "inherent dynamics" approach we find direct numerical evidence...... for the long held view that below a crossover temperature, Tx, the liquid's dynamics can be separated into (i) vibrations around inherent structures and (ii) transitions between inherent structures [M. Goldstein, J. Chem. Phys. 51, 3728 (1969)], i.e., the dynamics become "dominated" by the potential energy...... landscape. In agreement with previous proposals, we find that Tx is within the vicinity of the mode-coupling critical temperature Tc. We further find that near Tx, transitions between inherent structures occur via cooperative, stringlike rearrangements of groups of particles moving distances substantially...

  10. Comparative genomics of multidrug resistance-encoding IncA/C plasmids from commensal and pathogenic Escherichia coli from multiple animal sources.

    Science.gov (United States)

    Fernández-Alarcón, Claudia; Singer, Randall S; Johnson, Timothy J

    2011-01-01

    Incompatibility group A/C (IncA/C) plasmids have received recent attention for their broad host range and ability to confer resistance to multiple antimicrobial agents. Due to the potential spread of multidrug resistance (MDR) phenotypes from foodborne pathogens to human pathogens, the dissemination of these plasmids represents a public health risk. In this study, four animal-source IncA/C plasmids isolated from Escherichia coli were sequenced and analyzed, including isolates from commercial dairy cows, pigs and turkeys in the U.S. and Chile. These plasmids were initially selected because they either contained the floR and tetA genes encoding for florfenicol and tetracycline resistance, respectively, and/or the bla(CMY-2) gene encoding for extended spectrum β-lactamase resistance. Overall, sequence analysis revealed that each of the four plasmids retained a remarkably stable and conserved backbone sequence, with differences observed primarily within their accessory regions, which presumably have evolved via horizontal gene transfer events involving multiple modules. Comparison of these plasmids with other available IncA/C plasmid sequences further defined the core and accessory elements of these plasmids in E. coli and Salmonella. Our results suggest that the bla(CMY-2) plasmid lineage appears to have derived from an ancestral IncA/C plasmid type harboring floR-tetAR-strAB and Tn21-like accessory modules. Evidence is mounting that IncA/C plasmids are widespread among enteric bacteria of production animals and these emergent plasmids have flexibility in their acquisition of MDR-encoding modules, necessitating further study to understand the evolutionary mechanisms involved in their dissemination and stability in bacterial populations.

  11. Comparative genomics of multidrug resistance-encoding IncA/C plasmids from commensal and pathogenic Escherichia coli from multiple animal sources.

    Directory of Open Access Journals (Sweden)

    Claudia Fernández-Alarcón

    Full Text Available Incompatibility group A/C (IncA/C plasmids have received recent attention for their broad host range and ability to confer resistance to multiple antimicrobial agents. Due to the potential spread of multidrug resistance (MDR phenotypes from foodborne pathogens to human pathogens, the dissemination of these plasmids represents a public health risk. In this study, four animal-source IncA/C plasmids isolated from Escherichia coli were sequenced and analyzed, including isolates from commercial dairy cows, pigs and turkeys in the U.S. and Chile. These plasmids were initially selected because they either contained the floR and tetA genes encoding for florfenicol and tetracycline resistance, respectively, and/or the bla(CMY-2 gene encoding for extended spectrum β-lactamase resistance. Overall, sequence analysis revealed that each of the four plasmids retained a remarkably stable and conserved backbone sequence, with differences observed primarily within their accessory regions, which presumably have evolved via horizontal gene transfer events involving multiple modules. Comparison of these plasmids with other available IncA/C plasmid sequences further defined the core and accessory elements of these plasmids in E. coli and Salmonella. Our results suggest that the bla(CMY-2 plasmid lineage appears to have derived from an ancestral IncA/C plasmid type harboring floR-tetAR-strAB and Tn21-like accessory modules. Evidence is mounting that IncA/C plasmids are widespread among enteric bacteria of production animals and these emergent plasmids have flexibility in their acquisition of MDR-encoding modules, necessitating further study to understand the evolutionary mechanisms involved in their dissemination and stability in bacterial populations.

  12. An interatomic potential model for molecular dynamics simulation of silicon etching by Br+-containing plasmas

    International Nuclear Information System (INIS)

    Ohta, H.; Iwakawa, A.; Eriguchi, K.; Ono, K.

    2008-01-01

    An interatomic potential model for Si-Br systems has been developed for performing classical molecular dynamics (MD) simulations. This model enables us to simulate atomic-scale reaction dynamics during Si etching processes by Br + -containing plasmas such as HBr and Br 2 plasmas, which are frequently utilized in state-of-the-art techniques for the fabrication of semiconductor devices. Our potential form is based on the well-known Stillinger-Weber potential function, and the model parameters were systematically determined from a database of potential energies obtained from ab initio quantum-chemical calculations using GAUSSIAN03. For parameter fitting, we propose an improved linear scheme that does not require any complicated nonlinear fitting as that in previous studies [H. Ohta and S. Hamaguchi, J. Chem. Phys. 115, 6679 (2001)]. In this paper, we present the potential derivation and simulation results of bombardment of a Si(100) surface using a monoenergetic Br + beam

  13. Nonlinear dynamics in a trapped atomic Bose-Einstein condensate induced by an oscillating Gaussian potential

    International Nuclear Information System (INIS)

    Fujimoto, Kazuya; Tsubota, Makoto

    2011-01-01

    We consider a trapped atomic Bose-Einstein condensate penetrated by a repulsive Gaussian potential and theoretically investigate the dynamics induced by oscillating the Gaussian potential. Our study is based on the numerical calculation of the two-dimensional Gross-Pitaevskii equation. Our calculation reveals the dependence of the characteristic behavior of the condensate on the amplitude and frequency of the oscillating potential. These dynamics are deeply related to the nucleation and dynamics of quantized vortices and solitons. When the potential oscillates with a large amplitude, it nucleates many vortex pairs that move away from the potential. When the amplitude of the oscillation is small, it nucleates solitons through an annihilation of vortex pairs. We discuss three issues concerning the nucleation of vortices. The first is the phase diagram for the nucleation of vortices and solitons near the oscillating potential. The second is the mechanism and critical velocity of the nucleation. The critical velocity of the nucleation is an important issue in quantum fluids, and we propose an expression for the velocity containing both the coherence length and the size of the potential. The third is the divergence of the nucleation time, which is the time it takes for the potential to nucleate vortices, near the critical parameters for vortex nucleation.

  14. Improvement of in vivo transfer of plasmid DNA in muscle : Comparison of electroporation versus ultrasound

    NARCIS (Netherlands)

    Kusumanto, Yoka H.; Mulder, Nanno H.; Dam, Wendy A.; Losen, Mario H.; Meijer, Coby; Hospers, Geke A. P.

    Plasmid-based gene delivery to muscle is a treatment strategy for many diseases with potential advantages above viral-based gene delivery methods, however, with a relative low transfection efficiency. We compared two physical methods-electroporation and ultrasound-that facilitate DNA uptake into

  15. Overcoming potential energy distortions in constrained internal coordinate molecular dynamics simulations

    Energy Technology Data Exchange (ETDEWEB)

    Kandel, Saugat; Salomon-Ferrer, Romelia; Larsen, Adrien B.; Vaidehi, Nagarajan, E-mail: nvaidehi@coh.org [Division of Immunology, Beckman Research Institute of the City of Hope, Duarte, California 91010 (United States); Jain, Abhinandan, E-mail: Abhi.Jain@jpl.nasa.gov [Jet Propulsion Laboratory, California Institute of Technology, 4800 Oak Grove Drive, Pasadena, California 91109 (United States)

    2016-01-28

    The Internal Coordinate Molecular Dynamics (ICMD) method is an attractive molecular dynamics (MD) method for studying the dynamics of bonded systems such as proteins and polymers. It offers a simple venue for coarsening the dynamics model of a system at multiple hierarchical levels. For example, large scale protein dynamics can be studied using torsional dynamics, where large domains or helical structures can be treated as rigid bodies and the loops connecting them as flexible torsions. ICMD with such a dynamic model of the protein, combined with enhanced conformational sampling method such as temperature replica exchange, allows the sampling of large scale domain motion involving high energy barrier transitions. Once these large scale conformational transitions are sampled, all-torsion, or even all-atom, MD simulations can be carried out for the low energy conformations sampled via coarse grained ICMD to calculate the energetics of distinct conformations. Such hierarchical MD simulations can be carried out with standard all-atom forcefields without the need for compromising on the accuracy of the forces. Using constraints to treat bond lengths and bond angles as rigid can, however, distort the potential energy landscape of the system and reduce the number of dihedral transitions as well as conformational sampling. We present here a two-part solution to overcome such distortions of the potential energy landscape with ICMD models. To alleviate the intrinsic distortion that stems from the reduced phase space in torsional MD, we use the Fixman compensating potential. To additionally alleviate the extrinsic distortion that arises from the coupling between the dihedral angles and bond angles within a force field, we propose a hybrid ICMD method that allows the selective relaxing of bond angles. This hybrid ICMD method bridges the gap between all-atom MD and torsional MD. We demonstrate with examples that these methods together offer a solution to eliminate the potential

  16. A study on dynamic model of steady-state visual evoked potentials.

    Science.gov (United States)

    Zhang, Shangen; Han, Xu; Chen, Xiaogang; Wang, Yijun; Gao, Shangkai; Gao, Xiaorong

    2018-04-04

    Significant progress has been made in the past two decades to considerably improve the performance of steady-state visual evoked potential (SSVEP)-based brain-computer interface (BCI). However, there are still some unsolved problems that may help us to improve BCI performance, one of which is that our understanding of the dynamic process of SSVEP is still superficial, especially for the transient-state response. This study introduced an antiphase stimulation method (antiphase: phase 0/π), which can simultaneously separate and extract SSVEP and event-related potential (ERP) signals from EEG, and eliminate the interference of ERP to SSVEP. Based on the SSVEP signals obtained by the antiphase stimulation method, the envelope of SSVEP was extracted by the Hilbert transform, and the dynamic model of SSVEP was quantitatively studied by mathematical modeling. The step response of a second-order linear system was used to fit the envelope of SSVEP, and its characteristics were represented by four parameters with physical and physiological meanings: one was amplitude related, one was latency related and two were frequency related. This study attempted to use pre-stimulation paradigms to modulate the dynamic model parameters, and quantitatively analyze the results by applying the dynamic model to further explore the pre-stimulation methods that had the potential to improve BCI performance. The results showed that the dynamic model had good fitting effect with SSVEP under three pre-stimulation paradigms. The test results revealed that the parameters of SSVEP dynamic models could be modulated by the pre-stimulation baseline luminance, and the gray baseline luminance pre-stimulation obtained the highest performance. This study proposed a dynamic model which was helpful to understand and utilize the transient characteristics of SSVEP. This study also found that pre-stimulation could be used to adjust the parameters of SSVEP model, and had the potential to improve the performance

  17. CARTOGRAPHIE DU PLASMIDE pSU100, PLASMIDE CRYPTIQUE DE LACTOBACILLUS CASEI

    Directory of Open Access Journals (Sweden)

    F BENSALAH

    2003-06-01

    Ce plasmide appelé pSU100 a été cloné dans le vecteur de transformation pUC18 au site EcoRI chez E. coli JM103. Les profils électrophorétiques de restriction obtenus par des digestions simples, doubles et triples sous l’action de 33 endonucléases, ont contribué à l’élaboration d’une carte de restriction de ce plasmide. Cinq sites uniques ont été identifiés, ainsi que d’autres sites doubles et multiples. Une étude préliminaire du rôle physiologique de ce plasmide a permis de déceler une résistance à la kanamycine.

  18. Calculation of the electrostatic potential of lipid bilayers from molecular dynamics simulations: methodological issues

    DEFF Research Database (Denmark)

    Gurtovenko, Andrey A; Vattulainen, Ilpo

    2009-01-01

    of the electrostatic potential from atomic-scale molecular dynamics simulations of lipid bilayers. We discuss two slightly different forms of Poisson equation that are normally used to calculate the membrane potential: (i) a classical form when the potential and the electric field are chosen to be zero on one...... systems). For symmetric bilayers we demonstrate that both approaches give essentially the same potential profiles, provided that simulations are long enough (a production run of at least 100 ns is required) and that fluctuations of the center of mass of a bilayer are properly accounted for. In contrast...

  19. Characteristics of plasmids in multi-drug-resistant Enterobacteriaceae isolated during prospective surveillance of a newly opened hospital in Iraq.

    Directory of Open Access Journals (Sweden)

    Xiao-Zhe Huang

    relationship with other parts of world. The large plasmids, carrying resistance genes and transfer-associated genes, may be potential factors for regional dissemination of antibiotic resistance.

  20. Yeast transformation mediated by Agrobacterium strains harboring an Ri plasmid: comparative study between GALLS of an Ri plasmid and virE of a Ti plasmid.

    Science.gov (United States)

    Kiyokawa, Kazuya; Yamamoto, Shinji; Sato, Yukari; Momota, Naoto; Tanaka, Katsuyuki; Moriguchi, Kazuki; Suzuki, Katsunori

    2012-07-01

    Agrobacterium strains containing a Ti plasmid can transfer T-DNA not only to plants but also to fungi, including the yeast Saccharomyces cerevisiae. However, no Agrobacterium strain harboring an Ri plasmid has been evaluated in fungal transformation. Some Ri plasmids have GALLS , instead of virE1 and virE2. GALLS protein can functionally substitute in plant transformation for a structurally different protein VirE2. In this study, we compared the yeast transformation ability among Agrobacterium donors: a strain containing a Ti plasmid, strains harboring either an agropine-type or a mikimopine-type Ri plasmid, and a strain having a modified Ri plasmid supplemented with a Ti plasmid type virE operon. Agrobacterium strains possessing GALLS transformed yeast cells far less efficiently than the strain containing virE operon. Production of GALLS in recipient yeast cells improved the yeast transformation mediated by an Agrobacterium strain lacking neither GALLS nor virE operon. A reporter assay to detect mobilization of the proteins fused with Cre recombinase revealed that VirE2 protein is much more abundant in yeast cells than GALLS. Based on these results, we concluded that the low yeast transformability mediated by Agrobacterium strains having the Ri plasmid is because of low amount of mobilized GALLS in yeast cells. © 2012 The Authors Journal compilation © 2012 by the Molecular Biology Society of Japan/Blackwell Publishing Ltd.

  1. Dynamics of action potential initiation in the GABAergic thalamic reticular nucleus in vivo.

    Science.gov (United States)

    Muñoz, Fabián; Fuentealba, Pablo

    2012-01-01

    Understanding the neural mechanisms of action potential generation is critical to establish the way neural circuits generate and coordinate activity. Accordingly, we investigated the dynamics of action potential initiation in the GABAergic thalamic reticular nucleus (TRN) using in vivo intracellular recordings in cats in order to preserve anatomically-intact axo-dendritic distributions and naturally-occurring spatiotemporal patterns of synaptic activity in this structure that regulates the thalamic relay to neocortex. We found a wide operational range of voltage thresholds for action potentials, mostly due to intrinsic voltage-gated conductances and not synaptic activity driven by network oscillations. Varying levels of synchronous synaptic inputs produced fast rates of membrane potential depolarization preceding the action potential onset that were associated with lower thresholds and increased excitability, consistent with TRN neurons performing as coincidence detectors. On the other hand the presence of action potentials preceding any given spike was associated with more depolarized thresholds. The phase-plane trajectory of the action potential showed somato-dendritic propagation, but no obvious axon initial segment component, prominent in other neuronal classes and allegedly responsible for the high onset speed. Overall, our results suggest that TRN neurons could flexibly integrate synaptic inputs to discharge action potentials over wide voltage ranges, and perform as coincidence detectors and temporal integrators, supported by a dynamic action potential threshold.

  2. The two dynamical states in sinusoidal potentials: An analog simulation experiment

    Science.gov (United States)

    Sawkmie, Ivan Skhem; Mahato, Mangal C.

    2018-04-01

    The phenomenon of stochastic resonance (SR) is usually found to occur theoretically as well as experimentally in bi-stable systems [1]. Recently, it was numerically shown that SR is found to occur in underdamped (friction coefficient γ) sinusoidal potentials also. The occurrence of SR is explained in terms of two competing dynamical states of trajectories as a response to the external periodic drive. We setup an analog simulation experiment similar to the analog simulation work done earlier to study stochastic nonlinear dynamics [2], to verify the existence of the two dynamical states and to investigate the occurrence of SR in sinusoidal potentials obtained earlier [3]. We discuss our experimental setup and the results obtained in detail.

  3. Wave packet dynamics and photofragmentation in time-dependent quadratic potentials

    DEFF Research Database (Denmark)

    Møller, Klaus Braagaard; Henriksen, Niels Engholm

    1996-01-01

    We study the dynamics of generalized harmonic oscillator states in time-dependent quadratic potentials and derive analytical expressions for the momentum space and the Wigner phase space representation of these wave packets. Using these results we consider a model for the rotational excitation...

  4. Eikonal form of the dynamic polarization potential and its application to the scattering of exotic nuclei

    Energy Technology Data Exchange (ETDEWEB)

    Canto, L F; Donangelo, R [Universidade Federal do Rio de Janeiro, RJ (Brazil). Inst. de Fisica; Hussein, M S [Sao Paulo Univ. (Brazil). Inst. de Fisica

    1991-07-01

    The eikonal theory of the dynamic polarization potential (DDP) is developed. Application to the scattering of loosely bound exotic nuclei is made. In particular, the effect of our DPP on the scattering of {sup 11}Li+{sup 12}C at 85 AxMeV is discussed. (orig.).

  5. Dynamic Airline Scheduling: An Analysis of the Potentials of Refleeting and Retiming

    DEFF Research Database (Denmark)

    Warburg, Valdemar; Hansen, Troels G.; Larsen, Allan

    2008-01-01

    We present a Dynamic Airline Scheduling (DAS) technique which is able to change departure times and reassign aircraft types during the booking process to meet fluctuating passenger demands. The procedure is tested on several different days before departure, resulting in a significant profit...... increase for a major European airline. The results also indicate that applying DAS close to departure yields the largest potential....

  6. Dynamic Airline Scheduling: An Analysis of the Potentials of Refleeting and Retiming

    DEFF Research Database (Denmark)

    Warburg, Valdemar; Hansen, Troels G.; Larsen, Allan

    We present a Dynamic Airline Scheduling (DAS) technique which is able to change departure times and reassign aircraft types during the booking process to meet fluctuating passenger demands. The procedure is tested on several different days before departure, resulting in a significant profit...... increase for a major European airline. The results also indicate that applying DAS close to departure yields the largest potential....

  7. Protection from ischemic heart injury by a vigilant heme oxygenase-1 plasmid system.

    Science.gov (United States)

    Tang, Yao Liang; Tang, Yi; Zhang, Y Clare; Qian, Keping; Shen, Leping; Phillips, M Ian

    2004-04-01

    Although human heme oxygenase-1 (hHO-1) could provide a useful approach for cellular protection in the ischemic heart, constitutive overexpression of hHO-1 may lead to unwanted side effects. To avoid this, we designed a hypoxia-regulated hHO-1 gene therapy system that can be switched on and off. This vigilant plasmid system is composed of myosin light chain-2v promoter and a gene switch that is based on an oxygen-dependent degradation domain from the hypoxia inducible factor-1-alpha. The vector can sense ischemia and switch on the hHO-1 gene system, specifically in the heart. In an in vivo experiment, the vigilant hHO-1 plasmid or saline was injected intramyocardially into myocardial infarction mice or sham operation mice. After gene transfer, expression of hHO-1 was only detected in the ischemic heart treated with vigilant hHO-1 plasmids. Masson trichrome staining showed significantly fewer fibrotic areas in vigilant hHO-1 plasmids-treated mice compared with saline control (43.0%+/-4.8% versus 62.5%+/-3.3%, PhHO-1 expression in peri-infarct border areas, concomitant with higher Bcl-2 levels and lower Bax, Bak, and caspase 3 levels in the ischemic myocardium compared with saline control. By use of a cardiac catheter, heart from vigilant hHO-1 plasmids-treated mice showed improved recovery of contractile and diastolic performance after myocardial infarction compared with saline control. This study documents the beneficial regulation and therapeutic potential of vigilant plasmid-mediated hHO-1 gene transfer. This novel gene transfer strategy can provide cardiac-specific protection from future repeated bouts of ischemic injury.

  8. The effect of interatomic potential in molecular dynamics simulation of low energy ion implantation

    International Nuclear Information System (INIS)

    Chan, H.Y.; Nordlund, K.; Peltola, J.; Gossmann, H.-J.L.; Ma, N.L.; Srinivasan, M.P.; Benistant, F.; Chan, Lap

    2005-01-01

    Being able to accurately predict dopant profiles at sub-keV implant energies is critical for the microelectronic industry. Molecular Dynamics (MD), with its capability to account for multiple interactions as energy lowers, is an increasingly popular simulation method. We report our work on sub-keV implantation using MD and investigate the effect of different interatomic potentials on the range profiles. As an approximation, only pair potentials are considered in this work. Density Functional Theory (DFT) is used to calculate the pair potentials for a wide range of dopants (B, C, N, F, Si, P, Ga, Ge, As, In and Sb) in single crystalline silicon. A commonly used repulsive potential is also included in the study. Importance of the repulsive and attractive regions of the potential has been investigated with different elements and we show that a potential depicting the right attractive forces is especially important for heavy elements at low energies

  9. Drug resistance plasmids in Lactobacillus acidophilus and Lactobacillus reuteri.

    OpenAIRE

    Vescovo, M; Morelli, L; Bottazzi, V

    1982-01-01

    Sixteen strains of Lactobacillus reuteri and 20 strains of Lactobacillus acidophilus were tested for resistance to 22 antibiotics by using commercially available sensitivity disks. Evidence suggesting linkage of these resistances to plasmids was obtained by "curing" experiments with acridine dyes and high growth temperatures. Examination of plasmid patterns of agarose gel electrophoresis provided further evidence of loss in plasmid DNA under curing conditions in some of the strains examined.

  10. Dynamics in the quantum/classical limit based on selective use of the quantum potential

    International Nuclear Information System (INIS)

    Garashchuk, Sophya; Dell’Angelo, David; Rassolov, Vitaly A.

    2014-01-01

    A classical limit of quantum dynamics can be defined by compensation of the quantum potential in the time-dependent Schrödinger equation. The quantum potential is a non-local quantity, defined in the trajectory-based form of the Schrödinger equation, due to Madelung, de Broglie, and Bohm, which formally generates the quantum-mechanical features in dynamics. Selective inclusion of the quantum potential for the degrees of freedom deemed “quantum,” defines a hybrid quantum/classical dynamics, appropriate for molecular systems comprised of light and heavy nuclei. The wavefunction is associated with all of the nuclei, and the Ehrenfest, or mean-field, averaging of the force acting on the classical degrees of freedom, typical of the mixed quantum/classical methods, is avoided. The hybrid approach is used to examine evolution of light/heavy systems in the harmonic and double-well potentials, using conventional grid-based and approximate quantum-trajectory time propagation. The approximate quantum force is defined on spatial domains, which removes unphysical coupling of the wavefunction fragments corresponding to distinct classical channels or configurations. The quantum potential, associated with the quantum particle, generates forces acting on both quantum and classical particles to describe the backreaction

  11. Dynamics in the quantum/classical limit based on selective use of the quantum potential

    Energy Technology Data Exchange (ETDEWEB)

    Garashchuk, Sophya, E-mail: garashchuk@sc.edu; Dell’Angelo, David; Rassolov, Vitaly A. [Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208 (United States)

    2014-12-21

    A classical limit of quantum dynamics can be defined by compensation of the quantum potential in the time-dependent Schrödinger equation. The quantum potential is a non-local quantity, defined in the trajectory-based form of the Schrödinger equation, due to Madelung, de Broglie, and Bohm, which formally generates the quantum-mechanical features in dynamics. Selective inclusion of the quantum potential for the degrees of freedom deemed “quantum,” defines a hybrid quantum/classical dynamics, appropriate for molecular systems comprised of light and heavy nuclei. The wavefunction is associated with all of the nuclei, and the Ehrenfest, or mean-field, averaging of the force acting on the classical degrees of freedom, typical of the mixed quantum/classical methods, is avoided. The hybrid approach is used to examine evolution of light/heavy systems in the harmonic and double-well potentials, using conventional grid-based and approximate quantum-trajectory time propagation. The approximate quantum force is defined on spatial domains, which removes unphysical coupling of the wavefunction fragments corresponding to distinct classical channels or configurations. The quantum potential, associated with the quantum particle, generates forces acting on both quantum and classical particles to describe the backreaction.

  12. Vortex dynamics in two-dimensional Josephson junction arrays with asymmetrically bimodulated potential

    International Nuclear Information System (INIS)

    Nie, Qing-Miao; Zhang, Sha-Sha; Chen, Qing-Hu; Zhou, Wei

    2012-01-01

    On the basis of resistively-shunted junction dynamics, we study vortex dynamics in two-dimensional Josephson junction arrays with asymmetrically single and bimodulated periodic pinning potential for the full range of vortex density f. The ratchet effect occurring at a certain range of temperature, current, and f, is observed in our simulation. We explain the microscopic behavior behind this effect by analyzing the vortex distribution and interaction. The reversal of the ratchet effect can be observed at several f values for a small driven current. This effect is stronger when the asymmetric potential is simultaneously introduced in two directions. -- Highlights: ► The ratchet effect in Josephson junction arrays strongly depends on vortex density. ► The reversed ratchet effect can be observed at several f for a small current. ► The interaction between vortices can explain the reversed ratchet effect. ► The ratchet effect is enhanced by injecting the bimodulated asymmetric potential.

  13. Onset Dynamics of Action Potentials in Rat Neocortical Neurons and Identified Snail Neurons: Quantification of the Difference

    OpenAIRE

    Volgushev, Maxim; Malyshev, Aleksey; Balaban, Pavel; Chistiakova, Marina; Volgushev, Stanislav; Wolf, Fred

    2008-01-01

    The generation of action potentials (APs) is a key process in the operation of nerve cells and the communication between neurons. Action potentials in mammalian central neurons are characterized by an exceptionally fast onset dynamics, which differs from the typically slow and gradual onset dynamics seen in identified snail neurons. Here we describe a novel method of analysis which provides a quantitative measure of the onset dynamics of action potentials. This method captures the...

  14. Plasmid P1 replication: negative control by repeated DNA sequences.

    OpenAIRE

    Chattoraj, D; Cordes, K; Abeles, A

    1984-01-01

    The incompatibility locus, incA, of the unit-copy plasmid P1 is contained within a fragment that is essentially a set of nine 19-base-pair repeats. One or more copies of the fragment destabilizes the plasmid when present in trans. Here we show that extra copies of incA interfere with plasmid DNA replication and that a deletion of most of incA increases plasmid copy number. Thus, incA is not essential for replication but is required for its control. When cloned in a high-copy-number vector, pi...

  15. Plasmids foster diversification and adaptation of bacterial populations in soil.

    Science.gov (United States)

    Heuer, Holger; Smalla, Kornelia

    2012-11-01

    It is increasingly being recognized that the transfer of conjugative plasmids across species boundaries plays a vital role in the adaptability of bacterial populations in soil. There are specific driving forces and constraints of plasmid transfer within bacterial communities in soils. Plasmid-mediated genetic variation allows bacteria to respond rapidly with adaptive responses to challenges such as irregular antibiotic or metal concentrations, or opportunities such as the utilization of xenobiotic compounds. Cultivation-independent detection and capture of plasmids from soil bacteria, and complete sequencing have provided new insights into the role and ecology of plasmids. Broad host range plasmids such as those belonging to IncP-1 transfer a wealth of accessory functions which are carried by similar plasmid backbones. Plasmids with a narrower host range can be more specifically adapted to particular species and often transfer genes which complement chromosomally encoded functions. Plasmids seem to be an ancient and successful strategy to ensure survival of a soil population in spatial and temporal heterogeneous conditions with various environmental stresses or opportunities that occur irregularly or as a novel challenge in soil. © 2012 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

  16. Permissiveness of soil microbial communities towards broad host range plasmids

    DEFF Research Database (Denmark)

    Klümper, Uli

    . Plasmids are implicated in the rapid spread of antibiotic resistance and the emergence of multi-resistant pathogenic bacteria, making it crucial to be able to quantify, understand, and, ideally, control plasmid transfer in mixed microbial communities. The fate of plasmids in microbial communities...... of microbial communities may be directly interconnected through transfer of BHR plasmids at a so far unrecognized level. The developed method furthermore enabled me to explore how agronomic practices may affect gene transfer in soil microbial communities. I compared bacterial communities extracted from plots...

  17. Cosmological dynamics with non-minimally coupled scalar field and a constant potential function

    International Nuclear Information System (INIS)

    Hrycyna, Orest; Szydłowski, Marek

    2015-01-01

    Dynamical systems methods are used to investigate global behaviour of the spatially flat Friedmann-Robertson-Walker cosmological model in gravitational theory with a non-minimally coupled scalar field and a constant potential function. We show that the system can be reduced to an autonomous three-dimensional dynamical system and additionally is equipped with an invariant manifold corresponding to an accelerated expansion of the universe. Using this invariant manifold we find an exact solution of the reduced dynamics. We investigate all solutions for all admissible initial conditions using theory of dynamical systems to obtain a classification of all evolutional paths. The right-hand sides of the dynamical system depend crucially on the value of the non-minimal coupling constant therefore we study bifurcation values of this parameter under which the structure of the phase space changes qualitatively. We found a special bifurcation value of the non-minimal coupling constant which is distinguished by dynamics of the model and may suggest some additional symmetry in matter sector of the theory

  18. Cosmological dynamics with non-minimally coupled scalar field and a constant potential function

    Energy Technology Data Exchange (ETDEWEB)

    Hrycyna, Orest [Theoretical Physics Division, National Centre for Nuclear Research, Hoża 69, 00-681 Warszawa (Poland); Szydłowski, Marek, E-mail: orest.hrycyna@ncbj.gov.pl, E-mail: marek.szydlowski@uj.edu.pl [Astronomical Observatory, Jagiellonian University, Orla 171, 30-244 Kraków (Poland)

    2015-11-01

    Dynamical systems methods are used to investigate global behaviour of the spatially flat Friedmann-Robertson-Walker cosmological model in gravitational theory with a non-minimally coupled scalar field and a constant potential function. We show that the system can be reduced to an autonomous three-dimensional dynamical system and additionally is equipped with an invariant manifold corresponding to an accelerated expansion of the universe. Using this invariant manifold we find an exact solution of the reduced dynamics. We investigate all solutions for all admissible initial conditions using theory of dynamical systems to obtain a classification of all evolutional paths. The right-hand sides of the dynamical system depend crucially on the value of the non-minimal coupling constant therefore we study bifurcation values of this parameter under which the structure of the phase space changes qualitatively. We found a special bifurcation value of the non-minimal coupling constant which is distinguished by dynamics of the model and may suggest some additional symmetry in matter sector of the theory.

  19. Influence of the interatomic potentials on molecular dynamics simulations of displacement cascades

    CERN Document Server

    Becquart, C S; Legris, A; Van Duysen, J C

    2000-01-01

    Molecular dynamics (MD) is a powerful tool to study the displacement cascades initiated by the neutrons when they interact with matter. Key components of this technique are the interatomic potentials which model the binding of the different constitutive atoms. There exist many interatomic potentials dedicated to alpha-Fe and we have tested three of them for the study of radiation damage. We have found that the primary damage is potential sensitive. From our study, it appears that some characteristics of the potentials, not always considered, can be correlated to the type of damage produced by displacement cascades. The repulsive part of the potential has a strong influence on the cascade morphology. Moreover, equilibrium properties such as the atoms mean square displacements, the vacancy migration and vacancy-vacancy binding energies also appear to have some influence and should be investigated carefully when simulating radiation damage. It is therefore very important to use extreme care when trying to obtain...

  20. The Plasmid Mobilome of the Model Plant-Symbiont Sinorhizobium meliloti: Coming up with New Questions and Answers.

    Science.gov (United States)

    Lagares, Antonio; Sanjuán, Juan; Pistorio, Mariano

    2014-10-01

    Rhizobia are Gram-negative Alpha- and Betaproteobacteria living in the underground which have the ability to associate with legumes for the establishment of nitrogen-fixing symbioses. Sinorhizobium meliloti in particular-the symbiont of Medicago, Melilotus, and Trigonella spp.-has for the past decades served as a model organism for investigating, at the molecular level, the biology, biochemistry, and genetics of a free-living and symbiotic soil bacterium of agricultural relevance. To date, the genomes of seven different S. meliloti strains have been fully sequenced and annotated, and several other draft genomic sequences are also available. The vast amount of plasmid DNA that S. meliloti frequently bears (up to 45% of its total genome), the conjugative ability of some of those plasmids, and the extent of the plasmid diversity has provided researchers with an extraordinary system to investigate functional and structural plasmid molecular biology within the evolutionary context surrounding a plant-associated model bacterium. Current evidence indicates that the plasmid mobilome in S. meliloti is composed of replicons varying greatly in size and having diverse conjugative systems and properties along with different evolutionary stabilities and biological roles. While plasmids carrying symbiotic functions (pSyms) are known to have high structural stability (approaching that of chromosomes), the remaining plasmid mobilome (referred to as the non-pSym, functionally cryptic, or accessory compartment) has been shown to possess remarkable diversity and to be highly active in conjugation. In light of the modern genomic and current biochemical data on the plasmids of S. meliloti, the current article revises their main structural components, their transfer and regulatory mechanisms, and their potential as vehicles in shaping the evolution of the rhizobial genome.

  1. Evidence on dynamic effects in the water content – water potential relation of building materials

    DEFF Research Database (Denmark)

    Scheffler, Gregor Albrecht; Plagge, Rudolf

    2008-01-01

    static and dynamic moisture storage data and the more pronounced was the corresponding dynamic hysteresis. The paper thus provides clear experimental evidence on dynamic effects in the water content – water potential relation of building materials. By that, data published by previous authors as Topp et......Hygrothermal simulation has become a widely applied tool for the design and assessment of building structures under possible indoor and outdoor climatic conditions. One of the most important prerequisites of such simulations is reliable material data. Different approaches exist here to derive...... the required material functions, i.e. the moisture storage characteristic and the liquid water conductivity, from measured basic properties. The current state of the art in material modelling as well as the corresponding transport theory implies that the moisture transport function is unique...

  2. Broad host range plasmids can invade an unexpectedly diverse fraction of a soil bacterial community

    DEFF Research Database (Denmark)

    Klümper, Uli; Riber, Leise; Dechesne, Arnaud

    2014-01-01

    and Actinobacteria suggests that inter-Gram plasmid transfer of IncP-1 and IncPromA-type plasmids is a frequent phenomenon. While the plasmid receiving fractions of the community were both plasmid- and donor- dependent, we identified a core super-permissive fraction that could take up different plasmids from diverse...

  3. Parametrization of complex absorbing potentials for time-dependent quantum dynamics

    International Nuclear Information System (INIS)

    Vibok, A.; Balint-Kurti, G.G.

    1992-01-01

    Five different forms of complex absorbing potentials are examined and compared. Such potentials are needed to absorb wavepackets near the edges of grids in time-dependent quantum dynamical calculations. The extent to which the different potentials transmit or reflect an incident wavepacket is quantified, and optimal potential parameters to minimize both the reflection and transmission for each type of potential are derived. A rigorously derived scaling procedure, which permits the derivation of optimal potential parameters for use with any chosen mass or kinetic energy from those optimized for different conditions, is described. Tables are also presented which permit the immediate selection of the parameters for an absorbing potential of a particular form so as to allow a preselected (very small) degree of transmitted plus reflected probability to be attained. It is always desirable to devote a minimal region to the absorbing potential, while at the same time effectively absorbing all of the wavepacket and neither transmitting nor reflecting any of it. The tables presented here enable the use to easily select the potential parameters he will require to attain these goals. 23 refs., 7 figs., 4 tabs

  4. Ionization-potential depression and dynamical structure factor in dense plasmas

    Science.gov (United States)

    Lin, Chengliang; Röpke, Gerd; Kraeft, Wolf-Dietrich; Reinholz, Heidi

    2017-07-01

    The properties of a bound electron system immersed in a plasma environment are strongly modified by the surrounding plasma. The modification of an essential quantity, the ionization energy, is described by the electronic and ionic self-energies, including dynamical screening within the framework of the quantum statistical theory. Introducing the ionic dynamical structure factor as the indicator for the ionic microfield, we demonstrate that ionic correlations and fluctuations play a critical role in determining the ionization potential depression. This is, in particular, true for mixtures of different ions with large mass and charge asymmetry. The ionization potential depression is calculated for dense aluminum plasmas as well as for a CH plasma and compared to the experimental data and more phenomenological approaches used so far.

  5. Geometric and potential dynamics interpretation of the optic ring resonator bistability

    Science.gov (United States)

    Chiangga, S.; Chittha, T.; Frank, T. D.

    2015-07-01

    The optical bistability is a fundamental nonlinear feature of the ring resonator. A geometric and potential dynamics interpretation of the bistability is given. Accordingly, the bistability of the nonlinear system is shown to be a consequence of geometric laws of vector calculus describing the resonator ring. In contrast, the so-called transcendental relations that have been obtained in the literature in order to describe the optical wave are interpreted in terms of potential dynamical systems. The proposed novel interpretation provides new insights into the nature of the ring resonator optical bistability. The fundamental work by Rukhlenko, Premaratne and Agrawal (2010) as well as a more recent study by Chiangga, Pitakwongsaporn, Frank and Yupapin (2013) are considered.

  6. Dynamics of one-dimensional domain walls interacting with disorder potential

    International Nuclear Information System (INIS)

    Krusin-Elbaum, L.; Shibauchi, T.; Argyle, B.; Gignac, L.; Zabel, T.; Weller, D.

    2001-01-01

    Dynamics of 1D perpendicular-anisotropy domain walls in a few monolayer-thin Co films is imaged by polar Kerr microscopy. When domain walls, driven by a square-pulsed magnetic fields, travel through a random disordered potential landscape, they display Gaussian-distributed roughness characteristic of this landscape. Average velocity of the domain wall driven by a constant magnetic field strongly depends on a strain field which modifies (increases) the elastic energy of the wall and reduces the wall velocity

  7. Engineered Potentials and Dynamics of Ultracold Quantum Gases Under the Microscope

    Science.gov (United States)

    2014-05-09

    CONTRACT OR GRANT NUMBER: DESCRIPTION OF MATERIAL INSTITUTION: PRINCIPAL INVESTIGATOR: Paola Cappellaro TYPE REPORT: Ph.D. Dissertation PERIOD...CONTRACT NUMBER Engineered potentials and dynamics of ulu·acold quantum gases W911NF-11-1-0400 under the microscope Sb. GRANT NUMBER Sc. PROGRAM...Schnorrberger, M. Moreno- Cardoner , S. Fölling, and I. Bloch, “Counting atoms using interaction blockade in an optical superlat- tice,” Phys. Rev. Lett

  8. Exact time-dependent exchange-correlation potentials for strong-field electron dynamics

    International Nuclear Information System (INIS)

    Lein, Manfred; Kuemmel, Stephan

    2005-01-01

    By solving the time-dependent Schroedinger equation and inverting the time-dependent Kohn-Sham scheme we obtain the exact time-dependent exchange-correlation potential of density-functional theory for the strong-field dynamics of a correlated system. We demonstrate that essential features of the exact exchange-correlation potential can be related to derivative discontinuities in stationary density-functional theory. Incorporating the discontinuity in a time-dependent density-functional calculation greatly improves the description of the ionization process

  9. Numerical computation of soliton dynamics for NLS equations in a driving potential

    Directory of Open Access Journals (Sweden)

    Marco Caliari

    2010-06-01

    Full Text Available We provide numerical computations for the soliton dynamics of the nonlinear Schrodinger equation with an external potential. After computing the ground state solution r of a related elliptic equation we show that, in the semi-classical regime, the center of mass of the solution with initial datum built upon r is driven by the solution to $ddot x=- abla V(x$. Finally, we provide examples and analyze the numerical errors in the two dimensional case when V is a harmonic potential.

  10. Coherent wave packet dynamics in a double-well potential in cavity

    Science.gov (United States)

    Zheng, Li; Li, Gang; Ding, Ming-Song; Wang, Yong-Liang; Zhang, Yun-Cui

    2018-02-01

    We investigate the coherent wave packet dynamics of a two-level atom trapped in a symmetric double-well potential in a near-resonance cavity. Prepared on one side of the double-well potential, the atom wave packet oscillates between the left and right wells, while recoil induced by the emitted photon from the atom entangles the atomic internal and external degrees of freedom. The collapse and revival of the tunneling occurs. Adjusting the width of the wave packets, one can modify the tunneling frequency and suppress the tunneling.

  11. Detailed balance method for chemical potential determination in Monte Carlo and molecular dynamics simulations

    International Nuclear Information System (INIS)

    Fay, P.J.; Ray, J.R.; Wolf, R.J.

    1994-01-01

    We present a new, nondestructive, method for determining chemical potentials in Monte Carlo and molecular dynamics simulations. The method estimates a value for the chemical potential such that one has a balance between fictitious successful creation and destruction trials in which the Monte Carlo method is used to determine success or failure of the creation/destruction attempts; we thus call the method a detailed balance method. The method allows one to obtain estimates of the chemical potential for a given species in any closed ensemble simulation; the closed ensemble is paired with a ''natural'' open ensemble for the purpose of obtaining creation and destruction probabilities. We present results for the Lennard-Jones system and also for an embedded atom model of liquid palladium, and compare to previous results in the literature for these two systems. We are able to obtain an accurate estimate of the chemical potential for the Lennard-Jones system at higher densities than reported in the literature

  12. Calculation of surface potentials at the silica–water interface using molecular dynamics: Challenges and opportunities

    Science.gov (United States)

    Lowe, Benjamin M.; Skylaris, Chris-Kriton; Green, Nicolas G.; Shibuta, Yasushi; Sakata, Toshiya

    2018-04-01

    Continuum-based methods are important in calculating electrostatic properties of interfacial systems such as the electric field and surface potential but are incapable of providing sufficient insight into a range of fundamentally and technologically important phenomena which occur at atomistic length-scales. In this work a molecular dynamics methodology is presented for interfacial electric field and potential calculations. The silica–water interface was chosen as an example system, which is highly relevant for understanding the response of field-effect transistors sensors (FET sensors). Detailed validation work is presented, followed by the simulated surface charge/surface potential relationship. This showed good agreement with experiment at low surface charge density but at high surface charge density the results highlighted challenges presented by an atomistic definition of the surface potential. This methodology will be used to investigate the effect of surface morphology and biomolecule addition; both factors which are challenging using conventional continuum models.

  13. Characterization of the glass transition of water predicted by molecular dynamics simulations using nonpolarizable intermolecular potentials.

    Science.gov (United States)

    Kreck, Cara A; Mancera, Ricardo L

    2014-02-20

    Molecular dynamics simulations allow detailed study of the experimentally inaccessible liquid state of supercooled water below its homogeneous nucleation temperature and the characterization of the glass transition. Simple, nonpolarizable intermolecular potentials are commonly used in classical molecular dynamics simulations of water and aqueous systems due to their lower computational cost and their ability to reproduce a wide range of properties. Because the quality of these predictions varies between the potentials, the predicted glass transition of water is likely to be influenced by the choice of potential. We have thus conducted an extensive comparative investigation of various three-, four-, five-, and six-point water potentials in both the NPT and NVT ensembles. The T(g) predicted from NPT simulations is strongly correlated with the temperature of minimum density, whereas the maximum in the heat capacity plot corresponds to the minimum in the thermal expansion coefficient. In the NVT ensemble, these points are instead related to the maximum in the internal pressure and the minimum of its derivative, respectively. A detailed analysis of the hydrogen-bonding properties at the glass transition reveals that the extent of hydrogen-bonds lost upon the melting of the glassy state is related to the height of the heat capacity peak and varies between water potentials.

  14. Dynamical ion transfer between coupled Coulomb crystals in a double-well potential.

    Science.gov (United States)

    Klumpp, Andrea; Zampetaki, Alexandra; Schmelcher, Peter

    2017-09-01

    We investigate the nonequilibrium dynamics of coupled Coulomb crystals of different sizes trapped in a double well potential. The dynamics is induced by an instantaneous quench of the potential barrier separating the two crystals. Due to the intra- and intercrystal Coulomb interactions and the asymmetric population of the potential wells, we observe a complex reordering of ions within the two crystals as well as ion transfer processes from one well to the other. The study and analysis of the latter processes constitutes the main focus of this work. In particular, we examine the dependence of the observed ion transfers on the quench amplitude performing an analysis for different crystalline configurations ranging from one-dimensional ion chains via two-dimensional zigzag chains and ring structures to three-dimensional spherical structures. Such an analysis provides us with the means to extract the general principles governing the ion transfer dynamics and we gain some insight on the structural disorder caused by the quench of the barrier height.

  15. Plasmid Conjugation in E. coli and Drug Resistance | Igwe ...

    African Journals Online (AJOL)

    This study aimed at determining the antibiotics susceptibility pattern of E. coli isolates claimed to be multidrug resistance using disc diffusion method. It also determined the presence of transferable resistance plasmids through conjugation and evaluated the medical significance of plasmid encoding E. coli and drug ...

  16. Resistant plasmid profile analysis of multidrug resistant Escherichia ...

    African Journals Online (AJOL)

    Multiple drug resistance isolates causing UTI has seri- ous implications for the empiric therapy against patho- genic isolates and for the possible co-selection of antimicrobial resistant mediated by multi drug resistant plasmids21,22. E. coli from clinical isolates are known to harbour plasmids of different molecular sizes23.

  17. Plasmid-Mediated Antimicrobial Resistance in Staphylococci and Other Firmicutes.

    Science.gov (United States)

    Schwarz, Stefan; Shen, Jianzhong; Wendlandt, Sarah; Fessler, Andrea T; Wang, Yang; Kadlec, Kristina; Wu, Cong-Ming

    2014-12-01

    In staphylococci and other Firmicutes, resistance to numerous classes of antimicrobial agents, which are commonly used in human and veterinary medicine, is mediated by genes that are associated with mobile genetic elements. The gene products of some of these antimicrobial resistance genes confer resistance to only specific members of a certain class of antimicrobial agents, whereas others confer resistance to the entire class or even to members of different classes of antimicrobial agents. The resistance mechanisms specified by the resistance genes fall into any of three major categories: active efflux, enzymatic inactivation, and modification/replacement/protection of the target sites of the antimicrobial agents. Among the mobile genetic elements that carry such resistance genes, plasmids play an important role as carriers of primarily plasmid-borne resistance genes, but also as vectors for nonconjugative and conjugative transposons that harbor resistance genes. Plasmids can be exchanged by horizontal gene transfer between members of the same species but also between bacteria belonging to different species and genera. Plasmids are highly flexible elements, and various mechanisms exist by which plasmids can recombine, form cointegrates, or become integrated in part or in toto into the chromosomal DNA or into other plasmids. As such, plasmids play a key role in the dissemination of antimicrobial resistance genes within the gene pool to which staphylococci and other Firmicutes have access. This chapter is intended to provide an overview of the current knowledge of plasmid-mediated antimicrobial resistance in staphylococci and other Firmicutes.

  18. Application of methylation in improving plasmid transformation into Helicobacter pylori.

    Science.gov (United States)

    Zhao, Huilin; Xu, Linlin; Rong, Qianyu; Xu, Zheng; Ding, Yunfei; Zhang, Ying; Wu, Yulong; Li, Boqing; Ji, Xiaofei

    2018-05-23

    Helicobacter pylori is an important gastrointestinal pathogen. Its strains possess different levels of powerful restriction modification systems, which are significant barriers to genetic tools used for studying the role of functional genes in its pathogenesis. Methylating vectors in vitro was reported as an alternative to overcome this barrier in several bacteria. In this study we used two H. pylori-E. coli shuttle plasmids and several single/double-crossover homologous recombination gene-targeting plasmids, to test the role of methylation in H. pylori transformation. According to our results, transformants could be obtained only after shuttle plasmids were methylated before transformation. It is helpful in gene complementation and over-expression although at a low frequency. The frequency of gene-targeting transformation was also increased after methylation, especially for the single-crossover recombination plasmids, the transformants of which could only be obtained after methylation. For the double-crossover recombination targeting plasmids, the initial yield of transformants was 0.3-0.8 × 10 2 CFUs per microgram plasmid DNA. With the help of methylation, the yield was increased to 0.4-1.3 × 10 2 CFUs per microgram plasmid DNA. These results suggest that in vitro methylation can improve H. pylori transformation by different plasmids, which will benefit the pathogenic mechanism research. Copyright © 2018. Published by Elsevier B.V.

  19. Functional analysis of three plasmids from Lactobacillus plantarum

    NARCIS (Netherlands)

    Kranenburg, R. van; Golic, N.; Bongers, R.; Leer, R.J.; Vos, W.M. de; Siezen, R.J.; Kleerebezem, M.

    2005-01-01

    Lactobacillus plantarum WCFS1 harbors three plasmids, pWCFS101, pWCFS102, and pWCFS103, with sizes of 1,917, 2,365, and 36,069 bp, respectively. The two smaller plasmids are of unknown function and contain replication genes that are likely to function via the rolling-circle replication mechanism.

  20. Production and pharmaceutical formulation of plasmid DNA vaccines

    NARCIS (Netherlands)

    van der Heijden, I.

    2013-01-01

    Research leading to the thesis ‘Production and pharmaceutical formulation of plasmid DNA vaccines‘ can be divided into two parts. The first part describes the development of a Good Manufacturing Practice (GMP) compliant plasmid DNA production process of pDNA vaccines for the treatment of Human

  1. Transfer of conjugative plasmids among bacteria under environmentally relevant conditions

    DEFF Research Database (Denmark)

    Musovic, Sanin

    Mobile genetiske elementer (f.eks. plasmider), der ofte bærer ekstra funktioner såsom antibiotikaresistens, eller kataboliske- og xenobiotiske nedbrydnings gener, antages at have en meget vigtigt evolutionær rolle for bakterier. I denne PhD afhandling undersøgte jeg størrelsen af plasmid overførs...

  2. Two novel conjugative plasmids from a single strain of Sulfolobus

    NARCIS (Netherlands)

    Erauso, G.; Stedman, K.M.; Werken, van de H.J.G.; Zillig, W.; Oost, van der J.

    2006-01-01

    Two conjugative plasmids (CPs) were isolated and characterized from the same 'Sulfolobus islandicus' strain, SOG2/4, The plasmids were separated from each other and transferred into Sulfolobus soltataricus. One has a high copy number and is not stable (pSOG1) whereas the other has a low copy number

  3. The technology of large-scale pharmaceutical plasmid purification ...

    African Journals Online (AJOL)

    Further test demonstrated that the pcDNAlacZ purified with CTAB and authoritative endotoxin-free plasmid Kit had the similar transfection efficiency in vivo and in vitro. CTAB can be used for plasmid purification; the main advantages of the DNAs purified with CTAB include the avoidance of animal-derived enzymes, toxic ...

  4. Quantifying and resolving multiple vector transformants in S. cerevisiae plasmid libraries.

    Science.gov (United States)

    Scanlon, Thomas C; Gray, Elizabeth C; Griswold, Karl E

    2009-11-20

    In addition to providing the molecular machinery for transcription and translation, recombinant microbial expression hosts maintain the critical genotype-phenotype link that is essential for high throughput screening and recovery of proteins encoded by plasmid libraries. It is known that Escherichia coli cells can be simultaneously transformed with multiple unique plasmids and thusly complicate recombinant library screening experiments. As a result of their potential to yield misleading results, bacterial multiple vector transformants have been thoroughly characterized in previous model studies. In contrast to bacterial systems, there is little quantitative information available regarding multiple vector transformants in yeast. Saccharomyces cerevisiae is the most widely used eukaryotic platform for cell surface display, combinatorial protein engineering, and other recombinant library screens. In order to characterize the extent and nature of multiple vector transformants in this important host, plasmid-born gene libraries constructed by yeast homologous recombination were analyzed by DNA sequencing. It was found that up to 90% of clones in yeast homologous recombination libraries may be multiple vector transformants, that on average these clones bear four or more unique mutant genes, and that these multiple vector cells persist as a significant proportion of library populations for greater than 24 hours during liquid outgrowth. Both vector concentration and vector to insert ratio influenced the library proportion of multiple vector transformants, but their population frequency was independent of transformation efficiency. Interestingly, the average number of plasmids born by multiple vector transformants did not vary with their library population proportion. These results highlight the potential for multiple vector transformants to dominate yeast libraries constructed by homologous recombination. The previously unrecognized prevalence and persistence of multiply

  5. Quantifying and resolving multiple vector transformants in S. cerevisiae plasmid libraries

    Directory of Open Access Journals (Sweden)

    Gray Elizabeth C

    2009-11-01

    Full Text Available Abstract Background In addition to providing the molecular machinery for transcription and translation, recombinant microbial expression hosts maintain the critical genotype-phenotype link that is essential for high throughput screening and recovery of proteins encoded by plasmid libraries. It is known that Escherichia coli cells can be simultaneously transformed with multiple unique plasmids and thusly complicate recombinant library screening experiments. As a result of their potential to yield misleading results, bacterial multiple vector transformants have been thoroughly characterized in previous model studies. In contrast to bacterial systems, there is little quantitative information available regarding multiple vector transformants in yeast. Saccharomyces cerevisiae is the most widely used eukaryotic platform for cell surface display, combinatorial protein engineering, and other recombinant library screens. In order to characterize the extent and nature of multiple vector transformants in this important host, plasmid-born gene libraries constructed by yeast homologous recombination were analyzed by DNA sequencing. Results It was found that up to 90% of clones in yeast homologous recombination libraries may be multiple vector transformants, that on average these clones bear four or more unique mutant genes, and that these multiple vector cells persist as a significant proportion of library populations for greater than 24 hours during liquid outgrowth. Both vector concentration and vector to insert ratio influenced the library proportion of multiple vector transformants, but their population frequency was independent of transformation efficiency. Interestingly, the average number of plasmids born by multiple vector transformants did not vary with their library population proportion. Conclusion These results highlight the potential for multiple vector transformants to dominate yeast libraries constructed by homologous recombination. The

  6. Identification of IncA/C Plasmid Replication and Maintenance Genes and Development of a Plasmid Multilocus Sequence Typing Scheme.

    Science.gov (United States)

    Hancock, Steven J; Phan, Minh-Duy; Peters, Kate M; Forde, Brian M; Chong, Teik Min; Yin, Wai-Fong; Chan, Kok-Gan; Paterson, David L; Walsh, Timothy R; Beatson, Scott A; Schembri, Mark A

    2017-02-01

    Plasmids of incompatibility group A/C (IncA/C) are becoming increasingly prevalent within pathogenic Enterobacteriaceae They are associated with the dissemination of multiple clinically relevant resistance genes, including bla CMY and bla NDM Current typing methods for IncA/C plasmids offer limited resolution. In this study, we present the complete sequence of a bla NDM-1 -positive IncA/C plasmid, pMS6198A, isolated from a multidrug-resistant uropathogenic Escherichia coli strain. Hypersaturated transposon mutagenesis, coupled with transposon-directed insertion site sequencing (TraDIS), was employed to identify conserved genetic elements required for replication and maintenance of pMS6198A. Our analysis of TraDIS data identified roles for the replicon, including repA, a toxin-antitoxin system; two putative partitioning genes, parAB; and a putative gene, 053 Construction of mini-IncA/C plasmids and examination of their stability within E. coli confirmed that the region encompassing 053 contributes to the stable maintenance of IncA/C plasmids. Subsequently, the four major maintenance genes (repA, parAB, and 053) were used to construct a new plasmid multilocus sequence typing (PMLST) scheme for IncA/C plasmids. Application of this scheme to a database of 82 IncA/C plasmids identified 11 unique sequence types (STs), with two dominant STs. The majority of bla NDM -positive plasmids examined (15/17; 88%) fall into ST1, suggesting acquisition and subsequent expansion of this bla NDM -containing plasmid lineage. The IncA/C PMLST scheme represents a standardized tool to identify, track, and analyze the dissemination of important IncA/C plasmid lineages, particularly in the context of epidemiological studies. Copyright © 2017 American Society for Microbiology.

  7. Expansion of the IncX plasmid family for improved identification and typing of novel plasmids in drug-resistant Enterobacteriaceae

    DEFF Research Database (Denmark)

    Johnson, Timothy J.; Bielak, Eliza Maria; Fortini, Daniela

    2012-01-01

    and biofilm formation. Previous plasmid-based replicon typing procedures have indicated that the prevalence of IncX plasmids is low among members of the Enterobacteriaceae. However, examination of a number of IncX-like plasmid sequences and their occurrence in various organisms suggests that IncX plasmid...

  8. Deciphering conjugative plasmid permissiveness in wastewater microbiomes

    DEFF Research Database (Denmark)

    Jacquiod, Samuel Jehan Auguste; Brejnrod, Asker Daniel; Milani, Stefan Morberg

    2017-01-01

    Wastewater treatment plants (WWTPs) are designed to robustly treat polluted water. They are characterized by ceaseless flows of organic, chemical and microbial matter, followed by treatment steps before environmental release. WWTPs are hotspots of horizontal gene transfer between bacteria via...... still remains largely uncharted. Furthermore, current in vitro methods used to assess conjugation in complex microbiomes do not include in situ behaviours of recipient cells, resulting in partial understanding of transfers. We investigated the in vitro conjugation capacities of WWTP microbiomes from...... inlet sewage and outlet treated water using the broad-host range IncP-1 conjugative plasmid, pKJK5. A thorough molecular approach coupling metagenomes to 16S rRNA DNA/cDNA amplicon sequencing was established to characterize microbiomes using the ecological concept of functional response groups. A broad...

  9. Plasmid-mediated UV-protection in Streptococcus lactis

    Energy Technology Data Exchange (ETDEWEB)

    Chopin, M.C.; Rouault, A. (Institut National de la Recherche Agronomique, Rennes (France). Lab. de Recherches de Technologie Laitiere); Moillo-Batt, A. (Institut National de la Sante et de la Recherche Medicale (INSERM), Hopital de Pontchaillon, 35 - Rennes (France))

    1985-02-01

    Streptococcus lactis strain IL594 contains 9 plasmids, designated pIL1 to pIL9. On the basis of protoplast-induced curing experiments the authors showed that derivatives containing pIL7 were resistant to UV-irradiation while derivatives lacking pIL7 were sensitive. The pIL7-determined UV-protection was confirmed by co-transfer of the plasmid and of the character into a plasmid-free derivative of S. lactis IL594. Moreover, prophage induction required higher UV-fluence in this derivative carrying pIL7 than in the plasmid-free strain. This is the first report of a plasmid-mediated UV-protection in group N streptococci.

  10. Plasmid-mediated UV-protection in Streptococcus lactis

    International Nuclear Information System (INIS)

    Chopin, M.-C.; Rouault, A.

    1985-01-01

    Streptococcus lactis strain IL594 contains 9 plasmids, designated pIL1 to pIL9. On the basis of protoplast-induced curing experiments the authors showed that derivatives containing pIL7 were resistant to UV-irradiation while derivatives lacking pIL7 were sensitive. The pIL7-determined UV-protection was confirmed by cotransfer of the plasmid and of the character into a plasmid-free derivative of S. lactis IL594. Moreover, prophage induction required higher UV-fluence in this derivative carrying pIL7 than in the plasmid-free strain. This is the first report of a plasmid-mediated UV-protection in group N streptococci. (orig.)

  11. Restriction Fragment Length Polymorphisms of Virulence Plasmids in Rhodococcus equi

    Science.gov (United States)

    Takai, Shinji; Shoda, Masato; Sasaki, Yukako; Tsubaki, Shiro; Fortier, Guillaume; Pronost, Stephane; Rahal, Karim; Becu, Teotimo; Begg, Angela; Browning, Glenn; Nicholson, Vivian M.; Prescott, John F.

    1999-01-01

    Virulent Rhodococcus equi, which is a well-known cause of pyogranulomatous pneumonia in foals, possesses a large plasmid encoding virulence-associated 15- to 17-kDa antigens. Foal and soil isolates from five countries—Argentina, Australia, Canada, France, and Japan—were investigated for the presence of 15- to 17-kDa antigens by colony blotting, using the monoclonal antibody 10G5, and the gene coding for 15- to 17-kDa antigens by PCR. Plasmid DNAs extracted from positive isolates were digested with restriction endonucleases BamHI, EcoRI, EcoT22I, and HindIII, and the digestion patterns that resulted divided the plasmids of virulent isolates into five closely related types. Three of the five types had already been reported in Canadian and Japanese isolates, and the two new types had been found in French and Japanese isolates. Therefore, we tentatively designated these five types 85-kb type I (pREAT701), 85-kb type II (a new type), 87-kb type I (EcoRI and BamHI type 2 [V. M. Nicholson and J. F. Prescott, J. Clin. Microbiol. 35:738–740, 1997]), 87-kb type II (a new type), and 90-kb (pREL1) plasmids. The 85-kb type I plasmid was found in isolates from Argentina, Australia, Canada, and France. Plasmid 87-kb type I was isolated in specimens from Argentina, Canada, and France. The 85-kb type II plasmid appeared in isolates from France. On the other hand, plasmids 87-kb type II and 90-kb were found only in isolates from Japan. These results revealed geographic differences in the distribution of the virulence plasmids found in the five countries and suggested that the restriction fragment length polymorphism of virulence plasmids might be useful to elucidate the molecular epidemiology of virulent R. equi in the world. PMID:10488224

  12. Dynamic Electron Correlation Effects on the Ground State Potential Energy Surface of a Retinal Chromophore Model.

    Science.gov (United States)

    Gozem, Samer; Huntress, Mark; Schapiro, Igor; Lindh, Roland; Granovsky, Alexander A; Angeli, Celestino; Olivucci, Massimo

    2012-11-13

    The ground state potential energy surface of the retinal chromophore of visual pigments (e.g., bovine rhodopsin) features a low-lying conical intersection surrounded by regions with variable charge-transfer and diradical electronic structures. This implies that dynamic electron correlation may have a large effect on the shape of the force fields driving its reactivity. To investigate this effect, we focus on mapping the potential energy for three paths located along the ground state CASSCF potential energy surface of the penta-2,4-dieniminium cation taken as a minimal model of the retinal chromophore. The first path spans the bond length alternation coordinate and intercepts a conical intersection point. The other two are minimum energy paths along two distinct but kinetically competitive thermal isomerization coordinates. We show that the effect of introducing the missing dynamic electron correlation variationally (with MRCISD) and perturbatively (with the CASPT2, NEVPT2, and XMCQDPT2 methods) leads, invariably, to a stabilization of the regions with charge transfer character and to a significant reshaping of the reference CASSCF potential energy surface and suggesting a change in the dominating isomerization mechanism. The possible impact of such a correction on the photoisomerization of the retinal chromophore is discussed.

  13. Efficient molecular dynamics simulations with many-body potentials on graphics processing units

    Science.gov (United States)

    Fan, Zheyong; Chen, Wei; Vierimaa, Ville; Harju, Ari

    2017-09-01

    Graphics processing units have been extensively used to accelerate classical molecular dynamics simulations. However, there is much less progress on the acceleration of force evaluations for many-body potentials compared to pairwise ones. In the conventional force evaluation algorithm for many-body potentials, the force, virial stress, and heat current for a given atom are accumulated within different loops, which could result in write conflict between different threads in a CUDA kernel. In this work, we provide a new force evaluation algorithm, which is based on an explicit pairwise force expression for many-body potentials derived recently (Fan et al., 2015). In our algorithm, the force, virial stress, and heat current for a given atom can be accumulated within a single thread and is free of write conflicts. We discuss the formulations and algorithms and evaluate their performance. A new open-source code, GPUMD, is developed based on the proposed formulations. For the Tersoff many-body potential, the double precision performance of GPUMD using a Tesla K40 card is equivalent to that of the LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator) molecular dynamics code running with about 100 CPU cores (Intel Xeon CPU X5670 @ 2.93 GHz).

  14. The effect of empirical potential functions on modeling of amorphous carbon using molecular dynamics method

    International Nuclear Information System (INIS)

    Li, Longqiu; Xu, Ming; Song, Wenping; Ovcharenko, Andrey; Zhang, Guangyu; Jia, Ding

    2013-01-01

    Empirical potentials have a strong effect on the hybridization and structure of amorphous carbon and are of great importance in molecular dynamics (MD) simulations. In this work, amorphous carbon at densities ranging from 2.0 to 3.2 g/cm 3 was modeled by a liquid quenching method using Tersoff, 2nd REBO, and ReaxFF empirical potentials. The hybridization, structure and radial distribution function G(r) of carbon atoms were analyzed as a function of the three potentials mentioned above. The ReaxFF potential is capable to model the change of the structure of amorphous carbon and MD results are in a good agreement with experimental results and density function theory (DFT) at low density of 2.6 g/cm 3 and below. The 2nd REBO potential can be used when amorphous carbon has a very low density of 2.4 g/cm 3 and below. Considering the computational efficiency, the Tersoff potential is recommended to model amorphous carbon at a high density of 2.6 g/cm 3 and above. In addition, the influence of the quenching time on the hybridization content obtained with the three potentials is discussed.

  15. Design of expanded bed supports for the recovery of plasmid DNA by anion exchange adsorption

    DEFF Research Database (Denmark)

    Theodossiou, Irini; Søndergaard, M.; Thomas, Owen R. T.

    2001-01-01

    In this study we detail the rational design of new chromatographic adsorbents tailored for the capture of plasmid DNA. Features present on current chromatographic supports that can significantly enhance plasmid binding capacity have been identified in packed bed chromatography experiments...... and blueprints for improved expanded bed adsorbents have been put forward. The characterisation and testing of small (20-40 mum) high density (>3.7 g cm(-3)) pellicular expanded bed materials functionalised with various anion exchange structures is presented. In studies with calf thymus DNA, dynamic binding...... capacities of 1.2 and 3.4 mg ml(-1) were recorded for prototype diethylaminoethyl-and polyethylene imine-linked adsorbents which were respectively 25 and 70 fold higher than those of equivalently derivatised commercial expanded bed materials. The prototype polyethylene imine-coupled material exhibited severe...

  16. Spherical harmonics based descriptor for neural network potentials: Structure and dynamics of Au147 nanocluster.

    Science.gov (United States)

    Jindal, Shweta; Chiriki, Siva; Bulusu, Satya S

    2017-05-28

    We propose a highly efficient method for fitting the potential energy surface of a nanocluster using a spherical harmonics based descriptor integrated with an artificial neural network. Our method achieves the accuracy of quantum mechanics and speed of empirical potentials. For large sized gold clusters (Au 147 ), the computational time for accurate calculation of energy and forces is about 1.7 s, which is faster by several orders of magnitude compared to density functional theory (DFT). This method is used to perform the global minimum optimizations and molecular dynamics simulations for Au 147 , and it is found that its global minimum is not an icosahedron. The isomer that can be regarded as the global minimum is found to be 4 eV lower in energy than the icosahedron and is confirmed from DFT. The geometry of the obtained global minimum contains 105 atoms on the surface and 42 atoms in the core. A brief study on the fluxionality in Au 147 is performed, and it is concluded that Au 147 has a dynamic surface, thus opening a new window for studying its reaction dynamics.

  17. Horizontal gene transfer of a ColV plasmid has resulted in a dominant avian clonal type of Salmonella enterica serovar Kentucky.

    Directory of Open Access Journals (Sweden)

    Timothy J Johnson

    Full Text Available Salmonella enterica continues to be a significant cause of foodborne gastrointestinal illness in humans. A wide variety of Salmonella serovars have been isolated from production birds and from retail poultry meat. Recently, though, S. enterica subsp. enterica serovar Kentucky has emerged as one of the prominent Salmonella serovars isolated from broiler chickens. Recent work suggests that its emergence apparently coincides with its acquisition of a ColV virulence plasmid. In the present study, we examined 902 Salmonella isolates belonging to 59 different serovars for the presence of this plasmid. Of the serovars examined, the ColV plasmid was found only among isolates belonging to the serovars Kentucky (72.9%, Typhimurium (15.0% and Heidelberg (1.7%. We demonstrated that a single PFGE clonal type of S. Kentucky harbors this plasmid, and acquisition of this plasmid by S. Kentucky significantly increased its ability to colonize the chicken cecum and cause extraintestinal disease. Comparison of the completed sequences of three ColV plasmids from S. Kentucky isolated from different geographical locales, timepoints and sources revealed a nearly identical genetic structure with few single nucleotide changes or insertions/deletions. Overall, it appears that the ColV plasmid was recently acquired by a single clonal type S. Kentucky and confers to its host enhanced colonization and fitness capabilities. Thus, the potential for horizontal gene transfer of virulence and fitness factors to Salmonella from other enteric bacteria exists in poultry, representing a potential human health hazard.

  18. Dissemination of plasmid-encoded AmpC β-lactamases in antimicrobial resistant Salmonella serotypes originating from humans, pigs and the swine environment.

    Science.gov (United States)

    Keelara, Shivaramu; Thakur, Siddhartha

    2014-09-17

    The aim of this study was to characterize and determine the inter-serovar exchange of AmpC β-lactamase conferring plasmids isolated from humans, pigs and the swine environment. Plasmids isolated from a total of 21 antimicrobial resistant (AMR) Salmonella isolates representing human clinical cases (n=6), pigs (n=6) and the swine farm environment (n=9) were characterized by replicon typing and restriction digestion, inter-serovar transferability by conjugation, and presence of AmpC β-lactamase enzyme encoding gene blaCMY-2 by southern hybridization. Based on replicon typing, the majority (17/21, 81%) of the plasmids belonged to the I1-Iγ Inc group and were between 70 and 103kb. The potential for inter-serovar plasmid transfer was further confirmed by the PCR detection of AMR genes on the plasmids isolated from trans-conjugants. Plasmids from Salmonella serovars Anatum, Ouakam, Johannesburg and Typhimurium isolated from the same cohort of pigs and their environment and S. Heidelberg from a single human clinical isolate had identical plasmids based on digestion with multiple restriction enzymes (EcoRI, HindIII and PstI) and southern blotting. We demonstrated likely horizontal inter-serovar exchange of plasmid-encoding AmpC β-lactamases resistance among MDR Salmonella serotypes isolated from pigs, swine farm environment and clinical human cases. This study provides valuable information on the role of the swine farm environment and by extension other livestock farm environments, as a potential reservoir of resistant bacterial strains that potentially transmit resistance determinants to livestock, in this case, swine, humans and possibly other hosts by horizontal exchange of plasmids. Copyright © 2014 Elsevier B.V. All rights reserved.

  19. Dynamics and climate change mitigation potential of soil organic carbon sequestration.

    Science.gov (United States)

    Sommer, Rolf; Bossio, Deborah

    2014-11-01

    When assessing soil organic carbon (SOC) sequestration and its climate change (CC) mitigation potential at global scale, the dynamic nature of soil carbon storage and interventions to foster it should be taken into account. Firstly, adoption of SOC-sequestration measures will take time, and reasonably such schemes could only be implemented gradually at large-scale. Secondly, if soils are managed as carbon sinks, then SOC will increase only over a limited time, up to the point when a new SOC equilibrium is reached. This paper combines these two processes and predicts potential SOC sequestration dynamics in agricultural land at global scale and the corresponding CC mitigation potential. Assuming that global governments would agree on a worldwide effort to gradually change land use practices towards turning agricultural soils into carbon sinks starting 2014, the projected 87-year (2014-2100) global SOC sequestration potential of agricultural land ranged between 31 and 64 Gt. This is equal to 1.9-3.9% of the SRES-A2 projected 87-year anthropogenic emissions. SOC sequestration would peak 2032-33, at that time reaching 4.3-8.9% of the projected annual SRES-A2 emission. About 30 years later the sequestration rate would have reduced by half. Thus, SOC sequestration is not a C wedge that could contribute increasingly to mitigating CC. Rather, the mitigation potential is limited, contributing very little to solving the climate problem of the coming decades. However, we deliberately did not elaborate on the importance of maintaining or increasing SOC for sustaining soil health, agro-ecosystem functioning and productivity; an issue of global significance that deserves proper consideration irrespectively of any potential additional sequestration of SOC. Copyright © 2014 Elsevier Ltd. All rights reserved.

  20. Dynamical symmetry as a tool to understanding properties of supersymmetric partner potentials. Example of so(2,1) symmetry

    International Nuclear Information System (INIS)

    Wehrhahn, R.F.; Cooper, I.L.

    1992-05-01

    Analysis of the dynamical symmetry of a system is used to predict properties arising from its supersymmetric quantum mechanical treatment. Two applications of the so(2,1) algebra, the Coulomb potential and Morse oscillator potential which display different structure with respect to the dynamical symmetry, are studied. This difference is shown to be responsible for the behaviour of the respective supersymmetric partner potentials. (orig.)

  1. Non-perturbative effective potential: Lower bounds on the Higgs mass and dynamical applications

    International Nuclear Information System (INIS)

    Faivre, H.

    2006-01-01

    The purpose of this work was to assess the benefits of using non-perturbative methods to phenomenological issues in field theory. The exact equations of the Wilson renormalization group (RG) and the effective action have been used, we have computed the energy gap between the first 2 levels in double-well potential. We get a very good agreement with exact solutions inferring from the numerical solving of the Schroedinger equation. RG equations lead to a convex effective potential that is consistent with theory. We have considered the Higgs sector of the standard model. It is commonly acknowledged that the Yukawa coupling between the top quark and the Higgs boson generates the instability of the electroweak vacuum at high energy. We show that this instability does not exist, it is a mere consequence of the extrapolation of the RG equations beyond their validity range. We have also used the effective potential for the description of the time history of the mean value of the quantum field. We have defined the conditions under which the dynamics of the mean value can be described in the local potential approximation by classical equations of motion in which the effective potential replaces the classical potential. (A.C.)

  2. Critical insight into the influence of the potential energy surface on fission dynamics

    International Nuclear Information System (INIS)

    Mazurek, K.; Schmitt, C.; Wieleczko, J. P.; Ademard, G.; Nadtochy, P. N.

    2011-01-01

    The present work is dedicated to a careful investigation of the influence of the potential energy surface on the fission process. The time evolution of nuclei at high excitation energy and angular momentum is studied by means of three-dimensional Langevin calculations performed for two different parametrizations of the macroscopic potential: the Finite Range Liquid Drop Model (FRLDM) and the Lublin-Strasbourg Drop (LSD) prescription. Depending on the mass of the system, the topology of the potential throughout the deformation space of interest in fission is observed to noticeably differ within these two approaches, due to the treatment of curvature effects. When utilized in the dynamical calculation as the driving potential, the FRLDM and LSD models yield similar results in the heavy-mass region, whereas the predictions can be strongly dependent on the Potential Energy Surface (PES) for medium-mass nuclei. In particular, the mass, charge, and total kinetic energy distributions of the fission fragments are found to be narrower with the LSD prescription. The influence of critical model parameters on our findings is carefully investigated. The present study sheds light on the experimental conditions and signatures well suited for constraining the parametrization of the macroscopic potential. Its implication regarding the interpretation of available experimental data is briefly discussed.

  3. Antibiotic resistance plasmids of Staphylococcus aureus and their clinical importance

    International Nuclear Information System (INIS)

    Lacey, R.W.

    1975-01-01

    A variety of plasmids were isolated physically, and most antibiotic resistance is thought to be plasmid mediated. A number of characters (e.g., resistance to erythromycin or methicillin, and production of pigment) are determined by genes that do not give clear indications of either plasmid or chromosomal location. Although the formation of a particular plasmid is probably, even in bacterial terms, a very rare event, once formed such an element can spread rapidly among the bacterial population. The spectacular increase in the incidence of penicillinase-producing hospital strains in the late 1940's could have been due in part to this process. Evidence is stronger, however, for the intercell transfer of recently isolated plasmids coding for resistance to fusidic acid (and penicillinase production), or for neomycin, or for tetracycline resistance. Study of bacterial plasmids can resolve fundamental biochemical problems, and give some insight into the life of the cell at the molecular level. But the immediate application of the study of staphylococcal plasmids may be directed towards improving the effectiveness of antibiotic therapy. The most important aspect of future anti-staphylococcal chemotherapy should thus be the limitation of the use of antibiotics, particularly for application to the skin and nose. (U.S.)

  4. Plasmid-associated sensitivity of Bacillus thuringiensis to UV light

    International Nuclear Information System (INIS)

    Benoit, T.G.; Wilson, G.R.; Bull, D.L.; Aronson, A.I.

    1990-01-01

    Spores and vegetative cells of Bacillus thuringiensis were more sensitive to UV light than were spores or cells of plasmid-cured B. thuringiensis strains or of the closely related Bacillus cereus. Introduction of B. thuringiensis plasmids into B. cereus by cell mating increased the UV sensitivity of the cells and spores. Protoxins encoded by one or more B. thuringiensis plasmids were not involved in spore sensitivity, since a B. thuringiensis strain conditional for protoxin accumulation was equally sensitive at the permissive and nonpermissive temperatures. In addition, introduction of either a cloned protoxin gene, the cloning vector, or another plasmid not containing a protoxin gene into a plasmid-cured strain of B. thuringiensis all increased the UV sensitivity of the spores. Although the variety of small, acid-soluble proteins was the same in the spores of all strains examined, the quantity of dipicolinic acid was about twice as high in the plasmid-containing strains, and this may account for the differences in UV sensitivity of the spores. The cells of some strains harboring only B. thuringiensis plasmids were much more sensitive than cells of any of the other strains, and the differences were much greater than observed with spores

  5. Dynamic Neural State Identification in Deep Brain Local Field Potentials of Neuropathic Pain.

    Science.gov (United States)

    Luo, Huichun; Huang, Yongzhi; Du, Xueying; Zhang, Yunpeng; Green, Alexander L; Aziz, Tipu Z; Wang, Shouyan

    2018-01-01

    In neuropathic pain, the neurophysiological and neuropathological function of the ventro-posterolateral nucleus of the thalamus (VPL) and the periventricular gray/periaqueductal gray area (PVAG) involves multiple frequency oscillations. Moreover, oscillations related to pain perception and modulation change dynamically over time. Fluctuations in these neural oscillations reflect the dynamic neural states of the nucleus. In this study, an approach to classifying the synchronization level was developed to dynamically identify the neural states. An oscillation extraction model based on windowed wavelet packet transform was designed to characterize the activity level of oscillations. The wavelet packet coefficients sparsely represented the activity level of theta and alpha oscillations in local field potentials (LFPs). Then, a state discrimination model was designed to calculate an adaptive threshold to determine the activity level of oscillations. Finally, the neural state was represented by the activity levels of both theta and alpha oscillations. The relationship between neural states and pain relief was further evaluated. The performance of the state identification approach achieved sensitivity and specificity beyond 80% in simulation signals. Neural states of the PVAG and VPL were dynamically identified from LFPs of neuropathic pain patients. The occurrence of neural states based on theta and alpha oscillations were correlated to the degree of pain relief by deep brain stimulation. In the PVAG LFPs, the occurrence of the state with high activity levels of theta oscillations independent of alpha and the state with low-level alpha and high-level theta oscillations were significantly correlated with pain relief by deep brain stimulation. This study provides a reliable approach to identifying the dynamic neural states in LFPs with a low signal-to-noise ratio by using sparse representation based on wavelet packet transform. Furthermore, it may advance closed-loop deep

  6. Analogy between electromagnetic potentials and wave-like dynamic variables with connections to quantum theory

    Science.gov (United States)

    Yang, Chen

    2018-05-01

    The transitions from classical theories to quantum theories have attracted many interests. This paper demonstrates the analogy between the electromagnetic potentials and wave-like dynamic variables with their connections to quantum theory for audiences at advanced undergraduate level and above. In the first part, the counterpart relations in the classical electrodynamics (e.g. gauge transform and Lorenz condition) and classical mechanics (e.g. Legendre transform and free particle condition) are presented. These relations lead to similar governing equations of the field variables and dynamic variables. The Lorenz gauge, scalar potential and vector potential manifest a one-to-one similarity to the action, Hamiltonian and momentum, respectively. In the second part, the connections between the classical pictures of electromagnetic field and particle to quantum picture are presented. By characterising the states of electromagnetic field and particle via their (corresponding) variables, their evolution pictures manifest the same algebraic structure (isomorphic). Subsequently, pictures of the electromagnetic field and particle are compared to the quantum picture and their interconnections are given. A brief summary of the obtained results are presented at the end of the paper.

  7. AAVS1-Targeted Plasmid Integration in AAV Producer Cell Lines.

    Science.gov (United States)

    Luo, Yuxia; Frederick, Amy; Martin, John M; Scaria, Abraham; Cheng, Seng H; Armentano, Donna; Wadsworth, Samuel C; Vincent, Karen A

    2017-06-01

    Adeno-associated virus (AAV) producer cell lines are created via transfection of HeLaS3 cells with a single plasmid containing three components (the vector sequence, the AAV rep and cap genes, and a selectable marker gene). As this plasmid contains both the cis (Rep binding sites) and trans (Rep protein encoded by the rep gene) elements required for site-specific integration, it was predicted that plasmid integration might occur within the AAVS1 locus on human chromosome 19 (chr19). The objective of this study was to investigate whether integration in AAVS1 might be correlated with vector yield. Plasmid integration sites within several independent cell lines were assessed via Southern, fluorescence in situ hybridization (FISH) and PCR analyses. In the Southern analyses, the presence of fragments detected by both rep- and AAVS1-specific probes suggested that for several mid- and high-producing lines, plasmid DNA had integrated into the AAVS1 locus. Analysis with puroR and AAVS1-specific probes suggested that integration in AAVS1 was a more widespread phenomenon. High-producing AAV2-secreted alkaline phosphatase (SEAP) lines (masterwell 82 [MW82] and MW278) were evaluated via FISH using probes specific for the plasmid, AAVS1, and a chr19 marker. FISH analysis detected two plasmid integration sites in MW278 (neither in AAVS1), while a total of three sites were identified in MW82 (two in AAVS1). An inverse PCR assay confirmed integration within AAVS1 for several mid- and high-producing lines. In summary, the FISH, Southern, and PCR data provide evidence of site-specific integration of the plasmid within AAVS1 in several AAV producer cell lines. The data also suggest that integration in AAVS1 is a general phenomenon that is not necessarily restricted to high producers. The results also suggest that plasmid integration within the AAVS1 locus is not an absolute requirement for a high vector yield.

  8. The master activator of IncA/C conjugative plasmids stimulates genomic islands and multidrug resistance dissemination.

    Science.gov (United States)

    Carraro, Nicolas; Matteau, Dominick; Luo, Peng; Rodrigue, Sébastien; Burrus, Vincent

    2014-10-01

    Dissemination of antibiotic resistance genes occurs mostly by conjugation, which mediates DNA transfer between cells in direct contact. Conjugative plasmids of the IncA/C incompatibility group have become a substantial threat due to their broad host-range, the extended spectrum of antimicrobial resistance they confer, their prevalence in enteric bacteria and their very efficient spread by conjugation. However, their biology remains largely unexplored. Using the IncA/C conjugative plasmid pVCR94ΔX as a prototype, we have investigated the regulatory circuitry that governs IncA/C plasmids dissemination and found that the transcriptional activator complex AcaCD is essential for the expression of plasmid transfer genes. Using chromatin immunoprecipitation coupled with exonuclease digestion (ChIP-exo) and RNA sequencing (RNA-seq) approaches, we have identified the sequences recognized by AcaCD and characterized the AcaCD regulon. Data mining using the DNA motif recognized by AcaCD revealed potential AcaCD-binding sites upstream of genes involved in the intracellular mobility functions (recombination directionality factor and mobilization genes) in two widespread classes of genomic islands (GIs) phylogenetically unrelated to IncA/C plasmids. The first class, SGI1, confers and propagates multidrug resistance in Salmonella enterica and Proteus mirabilis, whereas MGIVmi1 in Vibrio mimicus belongs to a previously uncharacterized class of GIs. We have demonstrated that through expression of AcaCD, IncA/C plasmids specifically trigger the excision and mobilization of the GIs at high frequencies. This study provides new evidence of the considerable impact of IncA/C plasmids on bacterial genome plasticity through their own mobility and the mobilization of genomic islands.

  9. A plasmid containing the human metallothionein II gene can function as an antibody-assisted electrophoretic biosensor for heavy metals.

    Science.gov (United States)

    Wooten, Dennis C; Starr, Clarise R; Lyon, Wanda J

    2016-01-01

    Different forms of heavy metals affect biochemical systems in characteristic ways that cannot be detected with typical metal analysis methods like atomic absorption spectrometry. Further, using living systems to analyze interaction of heavy metals with biochemical systems can be laborious and unreliable. To generate a reliable easy-to-use biologically-based biosensor system, the entire human metallothionein-II (MT-II) gene was incorporated into a plasmid (pUC57-MT) easily replicated in Escherichia coli. In this system, a commercial polyclonal antibody raised against human metal-responsive transcription factor-1 protein (MTF-1 protein) could modify the electrophoretic migration patterns (i.e. cause specific decreases in agarose gel electrophoretic mobility) of the plasmid in the presence or absence of heavy metals other than zinc (Zn). In the study here, heavy metals, MTF-1 protein, and polyclonal anti-MTF-1 antibody were used to assess pUC57-MT plasmid antibody-assisted electrophoretic mobility. Anti-MTF-1 antibody bound both MTF-1 protein and pUC57-MT plasmid in a non-competitive fashion such that it could be used to differentiate specific heavy metal binding. The results showed that antibody-inhibited plasmid migration was heavy metal level-dependent. Zinc caused a unique mobility shift pattern opposite to that of other metals tested, i.e. Zn blocked the antibody ability to inhibit plasmid migration, despite a greatly increased affinity for DNA by the antibody when Zn was present. The Zn effect was reversed/modified by adding MTF-1 protein. Additionally, antibody inhibition of plasmid mobility was resistant to heat pre-treatment and trypsinization, indicating absence of residual DNA extraction-resistant bacterial DNA binding proteins. DNA binding by anti-DNA antibodies may be commonly enhanced by xenobiotic heavy metals and elevated levels of Zn, thus making them potentially effective tools for assessment of heavy metal bioavailability in aqueous solutions and

  10. Development of plasmid vector and electroporation condition for gene transfer in sporogenic lactic acid bacterium, Bacillus coagulans.

    Science.gov (United States)

    Rhee, Mun Su; Kim, Jin-Woo; Qian, Yilei; Ingram, L O; Shanmugam, K T

    2007-07-01

    Bacillus coagulans is a sporogenic lactic acid bacterium that ferments glucose and xylose, major components of plant biomass, a potential feedstock for cellulosic ethanol. The temperature and pH for optimum rate of growth of B. coagulans (50 to 55 degrees C, pH 5.0) are very similar to that of commercially developed fungal cellulases (50 degrees C; pH 4.8). Due to this match, simultaneous saccharification and fermentation (SSF) of cellulose to products by B. coagulans is expected to require less cellulase than needed if the SSF is conducted at a sub-optimal temperature, such as 30 degrees C, the optimum for yeast, the main biocatalyst used by the ethanol industry. To fully exploit B. coagulans as a platform organism, we have developed an electroporation method to transfer plasmid DNA into this genetically recalcitrant bacterium. We also constructed a B. coagulans/E. coli shuttle vector, plasmid pMSR10 that contains the rep region from a native plasmid (pMSR0) present in B. coagulans strain P4-102B. The native plasmid, pMSR0 (6823bp), has 9 ORFs, and replicates by rolling-circle mode of replication. Plasmid pNW33N, developed for Geobacillus stearothermophilus, was also transformed into this host and stably maintained while several other Bacillus/Escherichia coli shuttle vector plasmids were not transformed into B. coagulans. The transformation efficiency of B. coagulans strain P4-102B using the plasmids pNW33N or pMSR10 was about 1.5x10(16) per mole of DNA. The availability of shuttle vectors and an electroporation method is expected to aid in genetic and metabolic engineering of B. coagulans.

  11. Shifts in wind energy potential following land-use driven vegetation dynamics in complex terrain.

    Science.gov (United States)

    Fang, Jiannong; Peringer, Alexander; Stupariu, Mihai-Sorin; Pǎtru-Stupariu, Ileana; Buttler, Alexandre; Golay, Francois; Porté-Agel, Fernando

    2018-10-15

    Many mountainous regions with high wind energy potential are characterized by multi-scale variabilities of vegetation in both spatial and time dimensions, which strongly affect the spatial distribution of wind resource and its time evolution. To this end, we developed a coupled interdisciplinary modeling framework capable of assessing the shifts in wind energy potential following land-use driven vegetation dynamics in complex mountain terrain. It was applied to a case study area in the Romanian Carpathians. The results show that the overall shifts in wind energy potential following the changes of vegetation pattern due to different land-use policies can be dramatic. This suggests that the planning of wind energy project should be integrated with the land-use planning at a specific site to ensure that the expected energy production of the planned wind farm can be reached over its entire lifetime. Moreover, the changes in the spatial distribution of wind and turbulence under different scenarios of land-use are complex, and they must be taken into account in the micro-siting of wind turbines to maximize wind energy production and minimize fatigue loads (and associated maintenance costs). The proposed new modeling framework offers, for the first time, a powerful tool for assessing long-term variability in local wind energy potential that emerges from land-use change driven vegetation dynamics over complex terrain. Following a previously unexplored pathway of cause-effect relationships, it demonstrates a new linkage of agro- and forest policies in landscape development with an ultimate trade-off between renewable energy production and biodiversity targets. Moreover, it can be extended to study the potential effects of micro-climatic changes associated with wind farms on vegetation development (growth and patterning), which could in turn have a long-term feedback effect on wind resource distribution in mountainous regions. Copyright © 2018 Elsevier B.V. All rights

  12. Generation of Footprint-Free Induced Pluripotent Stem Cells from Human Fibroblasts Using Episomal Plasmid Vectors.

    Science.gov (United States)

    Ovchinnikov, Dmitry A; Sun, Jane; Wolvetang, Ernst J

    2015-01-01

    Human induced pluripotent stem cells (hiPSCs) have provided novel insights into the etiology of disease and are set to transform regenerative medicine and drug screening over the next decade. The generation of human iPSCs free of a genetic footprint of the reprogramming process is crucial for the realization of these potential uses. Here we describe in detail the generation of human iPSC from control and disease-carrying individuals' fibroblasts using episomal plasmids.

  13. Dynamical properties of a particle in a time-dependent double-well potential

    International Nuclear Information System (INIS)

    Leonel, Edson D; McClintock, P V E

    2004-01-01

    Some chaotic properties of a classical particle interacting with a time-dependent double-square-well potential are studied. The dynamics of the system is characterized using a two-dimensional nonlinear area-preserving map. Scaling arguments are used to study the chaotic sea in the low-energy domain. It is shown that the distributions of successive reflections and of corresponding successive reflection times obey power laws with the same exponent. If one or both wells move randomly, the particle experiences the phenomenon of Fermi acceleration in the sense that it has unlimited energy growth

  14. Momentum distribution, vibrational dynamics, and the potential of mean force in ice

    Science.gov (United States)

    Lin, Lin; Morrone, Joseph A.; Car, Roberto; Parrinello, Michele

    2011-06-01

    By analyzing the momentum distribution obtained from path integral and phonon calculations we find that the protons in hexagonal ice experience an anisotropic quasiharmonic effective potential with three distinct principal frequencies that reflect molecular orientation. Due to the importance of anisotropy, anharmonic features of the environment cannot be extracted from existing experimental distributions that involve the spherical average. The full directional distribution is required, and we give a theoretical prediction for this quantity that could be verified in future experiments. Within the quasiharmonic context, anharmonicity in the ground-state dynamics of the proton is substantial and has quantal origin, a finding that impacts the interpretation of several spectroscopies.

  15. Dynamic Mobile RobotNavigation Using Potential Field Based Immune Network

    Directory of Open Access Journals (Sweden)

    Guan-Chun Luh

    2007-04-01

    Full Text Available This paper proposes a potential filed immune network (PFIN for dynamic navigation of mobile robots in an unknown environment with moving obstacles and fixed/moving targets. The Velocity Obstacle method is utilized to determine imminent obstacle collision of a robot moving in the time-varying environment. The response of the overall immune network is derived by the aid of fuzzy system. Simulation results are presented to verify the effectiveness of the proposed methodology in unknown environments with single and multiple moving obstacles

  16. On potential energies and constraints in the dynamics of rigid bodies and particles

    Directory of Open Access Journals (Sweden)

    O'reilly Oliver M.

    2002-01-01

    Full Text Available A new treatment of kinematical constraints and potential energies arising in the dynamics of systems of rigid bodies and particles is presented which is suited to Newtonian and Lagrangian formulations. Its novel feature is the imposing of invariance requirements on the constraint functions and potential energy functions. These requirements are extensively used in continuum mechanics and, in the present context, one finds certain generalizations of Newton's third law of motion and an elucidation of the nature of constraint forces and moments. One motivation for such a treatment can be found by considering approaches where invariance requirements are ignored. In contrast to the treatment presented in this paper, it is shown that this may lead to a difficulty in formulating the equations governing the motion of the system.

  17. Deep Potential Molecular Dynamics: A Scalable Model with the Accuracy of Quantum Mechanics

    Science.gov (United States)

    Zhang, Linfeng; Han, Jiequn; Wang, Han; Car, Roberto; E, Weinan

    2018-04-01

    We introduce a scheme for molecular simulations, the deep potential molecular dynamics (DPMD) method, based on a many-body potential and interatomic forces generated by a carefully crafted deep neural network trained with ab initio data. The neural network model preserves all the natural symmetries in the problem. It is first-principles based in the sense that there are no ad hoc components aside from the network model. We show that the proposed scheme provides an efficient and accurate protocol in a variety of systems, including bulk materials and molecules. In all these cases, DPMD gives results that are essentially indistinguishable from the original data, at a cost that scales linearly with system size.

  18. Atomistic simulations of TeO₂-based glasses: interatomic potentials and molecular dynamics.

    Science.gov (United States)

    Gulenko, Anastasia; Masson, Olivier; Berghout, Abid; Hamani, David; Thomas, Philippe

    2014-07-21

    In this work we present for the first time empirical interatomic potentials that are able to reproduce TeO2-based systems. Using these potentials in classical molecular dynamics simulations, we obtained first results for the pure TeO2 glass structure model. The calculated pair distribution function is in good agreement with the experimental one, which indicates a realistic glass structure model. We investigated the short- and medium-range TeO2 glass structures. The local environment of the Te atom strongly varies, so that the glass structure model has a broad Q polyhedral distribution. The glass network is described as weakly connected with a large number of terminal oxygen atoms.

  19. Dynamical behavior of the wave packets on adiabatic potential surfaces observed by femtosecond luminescence spectroscopy

    International Nuclear Information System (INIS)

    Suemoto, Tohru; Nakajima, Makoto; Matsuoka, Taira; Yasukawa, Keizo; Koyama, Takeshi

    2007-01-01

    The wave packet dynamics on adiabatic potential surfaces studied by means of time-resolved luminescence spectroscopy is reviewed and the advantages of this method are discussed. In quasi-one-dimensional bromine-bridged platinum complexes, a movie representing the time evolution of the wave packet motion and shape was constructed. A two-dimensional Lissajous-like motion of the wave packet was suggested in the same material at low temperature. In F-centers in KI, evidence for tunneling of the wave packet between the adjacent adiabatic potential surfaces was found. Selective observation of the wave packet motion on the excited state was demonstrated for F-centers in KBr and compared with the results from pump-and-probe experiments in literature

  20. How to combine binary collision approximation and multi-body potential for molecular dynamics

    International Nuclear Information System (INIS)

    Saito, Seiki; Nakamura, Hiroaki; Takayama, Arimichi; Ito, Atsushi M.; Kenmotsu, Takahiro

    2010-01-01

    Our group has been developing a hybrid simulation of the molecular dynamics (MD) and the binary collision approximation (BCA) simulation. One of the main problems of this hybridization model is that the multi-body potential suddenly appears at the moment when the simulation method switches from the BCA to the MD. This instantaneously emerged multi-body potential causes the acceleration or deceleration of atoms of the system. To solve this problem, the kinetic energy of atoms should be corrected to conserve the total energy in the system. This paper gives the solution. The hybrid simulation for hydrogen atom injection into a graphite material is executed in order to demonstrate the solution. (author)

  1. Dynamic Potential Intensity: An improved representation of the ocean’s impact on tropical cyclones

    Energy Technology Data Exchange (ETDEWEB)

    Balaguru, Karthik; Foltz, Gregory R.; Leung, Lai-Yung; D' Asaro, Eric; Emanuel, Kerry A.; Liu, Hailong; Zedler, Sarah E.

    2015-08-18

    To incorporate the effects of tropical cyclone (TC)-induced upper ocean mixing and sea surface temperature (SST) cooling on TC intensification, a vertical average of temperature down to a fixed depth was proposed as a replacement for SST within the framework of air-sea coupled Potential Intensity (PI). However, the depth to which TC-induced mixing penetrates may vary substantially with ocean stratification and storm state. To account for these effects, here we develop a “Dynamic Potential Intensity” (DPI) based on considerations of stratified fluid turbulence. For the Argo period 2004–2013 and the three major TC basins of the Northern Hemisphere, we show that the DPI explains 11–32% of the variance in TC intensification, compared to 0–16% using previous methods. The improvement obtained using the DPI is particularly large in the eastern Pacific where the thermocline is shallow and ocean stratification effects are strong.

  2. The effect of temperature on Anopheles mosquito population dynamics and the potential for malaria transmission.

    Directory of Open Access Journals (Sweden)

    Lindsay M Beck-Johnson

    Full Text Available The parasites that cause malaria depend on Anopheles mosquitoes for transmission; because of this, mosquito population dynamics are a key determinant of malaria risk. Development and survival rates of both the Anopheles mosquitoes and the Plasmodium parasites that cause malaria depend on temperature, making this a potential driver of mosquito population dynamics and malaria transmission. We developed a temperature-dependent, stage-structured delayed differential equation model to better understand how climate determines risk. Including the full mosquito life cycle in the model reveals that the mosquito population abundance is more sensitive to temperature than previously thought because it is strongly influenced by the dynamics of the juvenile mosquito stages whose vital rates are also temperature-dependent. Additionally, the model predicts a peak in abundance of mosquitoes old enough to vector malaria at more accurate temperatures than previous models. Our results point to the importance of incorporating detailed vector biology into models for predicting the risk for vector borne diseases.

  3. Potential impact of harvesting on the population dynamics of two epiphytic bromeliads

    Science.gov (United States)

    Toledo-Aceves, Tarin; Hernández-Apolinar, Mariana; Valverde, Teresa

    2014-08-01

    Large numbers of epiphytes are extracted from cloud forests for ornamental use and illegal trade in Latin America. We examined the potential effects of different harvesting regimes on the population dynamics of the epiphytic bromeliads Tillandsia multicaulis and Tillandsia punctulata. The population dynamics of these species were studied over a 2-year period in a tropical montane cloud forest in Veracruz, Mexico. Prospective and retrospective analyses were used to identify which demographic processes and life-cycle stages make the largest relative contribution to variation in population growth rate (λ). The effect of simulated harvesting levels on population growth rates was analysed for both species. λ of both populations was highly influenced by survival (stasis), to a lesser extent by growth, and only slightly by fecundity. Vegetative growth played a central role in the population dynamics of these organisms. The λ value of the studied populations did not differ significantly from unity: T. multicaulis λ (95% confidence interval) = 0.982 (0.897-1.060) and T. punctulata λ = 0.967 (0.815-1.051), suggesting population stability. However, numerical simulation of different levels of extraction showed that λ would drop substantially even under very low (2%) harvesting levels. Matrix analysis revealed that T. multicaulis and T. punctulata populations are likely to decline and therefore commercial harvesting would be unsustainable. Based on these findings, management recommendations are outlined.

  4. Synaptic potentiation facilitates memory-like attractor dynamics in cultured in vitro hippocampal networks.

    Directory of Open Access Journals (Sweden)

    Mark Niedringhaus

    Full Text Available Collective rhythmic dynamics from neurons is vital for cognitive functions such as memory formation but how neurons self-organize to produce such activity is not well understood. Attractor-based computational models have been successfully implemented as a theoretical framework for memory storage in networks of neurons. Additionally, activity-dependent modification of synaptic transmission is thought to be the physiological basis of learning and memory. The goal of this study is to demonstrate that using a pharmacological treatment that has been shown to increase synaptic strength within in vitro networks of hippocampal neurons follows the dynamical postulates theorized by attractor models. We use a grid of extracellular electrodes to study changes in network activity after this perturbation and show that there is a persistent increase in overall spiking and bursting activity after treatment. This increase in activity appears to recruit more "errant" spikes into bursts. Phase plots indicate a conserved activity pattern suggesting that a synaptic potentiation perturbation to the attractor leaves it unchanged. Lastly, we construct a computational model to demonstrate that these synaptic perturbations can account for the dynamical changes seen within the network.

  5. Magneto-responsive liquid crystalline elastomer nanocomposites as potential candidates for dynamic cell culture substrates

    International Nuclear Information System (INIS)

    Herrera-Posada, Stephany; Mora-Navarro, Camilo; Ortiz-Bermudez, Patricia; Torres-Lugo, Madeline; McElhinny, Kyle M.; Evans, Paul G.; Calcagno, Barbara O.; Acevedo, Aldo

    2016-01-01

    Recently, liquid crystalline elastomers (LCEs) have been proposed as active substrates for cell culture due to their potential to attach and orient cells, and impose dynamic mechanical signals through the application of external stimuli. In this report, the preparation of anisotropic and oriented nematic magnetic-sensitized LCEs with iron oxide nanoparticles, and the evaluation of the effect of particle addition at low concentrations on the resultant structural, thermal, thermo-mechanical, and mechanical properties is presented. Phase transformations produced by heating in alternating magnetic fields were investigated in LCEs in contact with air, water, and a common liquid cell culture medium was also evaluated. The inclusion of nanoparticles into the elastomers displaced the nematic-to-isotropic phase transition, without affecting the nematic structure as evidenced by similar values of the order parameter, while reducing the maximum thermomechanical deformations. Remote and reversible deformations of the magnetic LCEs were achieved through the application of alternating magnetic fields, which induces the nematic–isotropic phase transition through nanoparticle heat generation. Formulation parameters can be modified to allow for remote actuation at values closer to the human physiological temperature range and within the range of deformations that can affect the cellular behavior of fibroblasts. Finally, a collagen surface treatment was performed to improve compatibility with NIH-3T3 fibroblast cultures, which enabled the attachment and proliferation of fibroblasts on substrates with and without magnetic particles under quiescent conditions. The LCEs developed in this work, which are able to deform and experience stress changes by remote contact-less magnetic stimulation, may allow for further studies on the effect of substrate morphology changes and dynamic mechanical properties during in vitro cell culture. - Highlights: • Magnetic LCE nanocomposites were

  6. Magneto-responsive liquid crystalline elastomer nanocomposites as potential candidates for dynamic cell culture substrates

    Energy Technology Data Exchange (ETDEWEB)

    Herrera-Posada, Stephany; Mora-Navarro, Camilo; Ortiz-Bermudez, Patricia; Torres-Lugo, Madeline [Department of Chemical Engineering, Call Box 9000, University of Puerto Rico, Mayagüez PR 00681 (Puerto Rico); McElhinny, Kyle M.; Evans, Paul G. [Department of Materials Science and Engineering, 1509 University Avenue, University of Wisconsin-Madison, WI 53706 (United States); Calcagno, Barbara O. [Department of General Engineering, Call Box 9000, University of Puerto Rico, Mayagüez PR 00681 (Puerto Rico); Acevedo, Aldo, E-mail: aldo.acevedo@upr.edu [Department of Chemical Engineering, Call Box 9000, University of Puerto Rico, Mayagüez PR 00681 (Puerto Rico)

    2016-08-01

    Recently, liquid crystalline elastomers (LCEs) have been proposed as active substrates for cell culture due to their potential to attach and orient cells, and impose dynamic mechanical signals through the application of external stimuli. In this report, the preparation of anisotropic and oriented nematic magnetic-sensitized LCEs with iron oxide nanoparticles, and the evaluation of the effect of particle addition at low concentrations on the resultant structural, thermal, thermo-mechanical, and mechanical properties is presented. Phase transformations produced by heating in alternating magnetic fields were investigated in LCEs in contact with air, water, and a common liquid cell culture medium was also evaluated. The inclusion of nanoparticles into the elastomers displaced the nematic-to-isotropic phase transition, without affecting the nematic structure as evidenced by similar values of the order parameter, while reducing the maximum thermomechanical deformations. Remote and reversible deformations of the magnetic LCEs were achieved through the application of alternating magnetic fields, which induces the nematic–isotropic phase transition through nanoparticle heat generation. Formulation parameters can be modified to allow for remote actuation at values closer to the human physiological temperature range and within the range of deformations that can affect the cellular behavior of fibroblasts. Finally, a collagen surface treatment was performed to improve compatibility with NIH-3T3 fibroblast cultures, which enabled the attachment and proliferation of fibroblasts on substrates with and without magnetic particles under quiescent conditions. The LCEs developed in this work, which are able to deform and experience stress changes by remote contact-less magnetic stimulation, may allow for further studies on the effect of substrate morphology changes and dynamic mechanical properties during in vitro cell culture. - Highlights: • Magnetic LCE nanocomposites were

  7. Dynamic Action Potential Restitution Contributes to Mechanical Restitution in Right Ventricular Myocytes From Pulmonary Hypertensive Rats.

    Science.gov (United States)

    Hardy, Matthew E L; Pervolaraki, Eleftheria; Bernus, Olivier; White, Ed

    2018-01-01

    We investigated the steepened dynamic action potential duration (APD) restitution of rats with pulmonary artery hypertension (PAH) and right ventricular (RV) failure and tested whether the observed APD restitution properties were responsible for negative mechanical restitution in these myocytes. PAH and RV failure were provoked in male Wistar rats by a single injection of monocrotaline (MCT) and compared with saline-injected animals (CON). Action potentials were recorded from isolated RV myocytes at stimulation frequencies between 1 and 9 Hz. Action potential waveforms recorded at 1 Hz were used as voltage clamp profiles (action potential clamp) at stimulation frequencies between 1 and 7 Hz to evoke rate-dependent currents. Voltage clamp profiles mimicking typical CON and MCT APD restitution were applied and cell shortening simultaneously monitored. Compared with CON myocytes, MCT myocytes were hypertrophied; had less polarized diastolic membrane potentials; had action potentials that were triggered by decreased positive current density and shortened by decreased negative current density; APD was longer and APD restitution steeper. APD90 restitution was unchanged by exposure to the late Na + -channel blocker (5 μM) ranolazine or the intracellular Ca 2+ buffer BAPTA. Under AP clamp, stimulation frequency-dependent inward currents were smaller in MCT myocytes and were abolished by BAPTA. In MCT myocytes, increasing stimulation frequency decreased contraction amplitude when depolarization duration was shortened, to mimic APD restitution, but not when depolarization duration was maintained. We present new evidence that the membrane potential of PAH myocytes is less stable than normal myocytes, being more easily perturbed by external currents. These observations can explain increased susceptibility to arrhythmias. We also present novel evidence that negative APD restitution is at least in part responsible for the negative mechanical restitution in PAH myocytes. Thus

  8. Alternative future analysis for assessing the potential impact of climate change on urban landscape dynamics.

    Science.gov (United States)

    He, Chunyang; Zhao, Yuanyuan; Huang, Qingxu; Zhang, Qiaofeng; Zhang, Da

    2015-11-01

    Assessing the impact of climate change on urban landscape dynamics (ULD) is the foundation for adapting to climate change and maintaining urban landscape sustainability. This paper demonstrates an alternative future analysis by coupling a system dynamics (SD) and a cellular automata (CA) model. The potential impact of different climate change scenarios on ULD from 2009 to 2030 was simulated and evaluated in the Beijing-Tianjin-Tangshan megalopolis cluster area (BTT-MCA). The results suggested that the integrated model, which combines the advantages of the SD and CA model, has the strengths of spatial quantification and flexibility. Meanwhile, the results showed that the influence of climate change would become more severe over time. In 2030, the potential urban area affected by climate change will be 343.60-1260.66 km(2) (5.55 -20.37 % of the total urban area, projected by the no-climate-change-effect scenario). Therefore, the effects of climate change should not be neglected when designing and managing urban landscape. Copyright © 2015 Elsevier B.V. All rights reserved.

  9. Comparative assessment of plasmid DNA delivery by encapsulation ...

    African Journals Online (AJOL)

    Tropical Journal of Pharmaceutical Research January 2018; 17 (1): 1-10 ... Purpose: To compare the gene delivery effectiveness of plasmid DNA (pDNA) ..... Intramuscular delivery of DNA ... copolymeric system for gene delivery in complete.

  10. The technology of large-scale pharmaceutical plasmid purification ...

    African Journals Online (AJOL)

    STORAGESEVER

    2010-01-04

    Jan 4, 2010 ... DNA vaccine, the cost of purification must be decreased. Although commonly .... Three mice were killed every 4 days interval. Tissues of heart, liver, .... Now, methods such as chromatography had good prospects in plasmid ...

  11. Mechanisms of Evolution in High-Consequence Drug Resistance Plasmids

    Directory of Open Access Journals (Sweden)

    Susu He

    2016-12-01

    Full Text Available The dissemination of resistance among bacteria has been facilitated by the fact that resistance genes are usually located on a diverse and evolving set of transmissible plasmids. However, the mechanisms generating diversity and enabling adaptation within highly successful resistance plasmids have remained obscure, despite their profound clinical significance. To understand these mechanisms, we have performed a detailed analysis of the mobilome (the entire mobile genetic element content of a set of previously sequenced carbapenemase-producing Enterobacteriaceae (CPE from the National Institutes of Health Clinical Center. This analysis revealed that plasmid reorganizations occurring in the natural context of colonization of human hosts were overwhelmingly driven by genetic rearrangements carried out by replicative transposons working in concert with the process of homologous recombination. A more complete understanding of the molecular mechanisms and evolutionary forces driving rearrangements in resistance plasmids may lead to fundamentally new strategies to address the problem of antibiotic resistance.

  12. Photoinduced silver nanoparticles/nanorings on plasmid DNA scaffolds.

    Science.gov (United States)

    Liu, Jianhua; Zhang, Xiaoliang; Yu, Mei; Li, Songmei; Zhang, Jindan

    2012-01-23

    Biological scaffolds are being actively explored for the synthesis of nanomaterials with novel structures and unexpected properties. Toroidal plasmid DNA separated from the Bacillus host is applied as a sacrificial mold for the synthesis of silver nanoparticles and nanorings. The photoirradiation method is applied to reduce Ag(I) on the plasmid. The nanoparticles are obtained by varying the concentration of the Ag(I) ion solution and the exposure time of the plasmid-Ag(I) complex under UV light at 254 nm and room temperature. It is found that the plasmid serves not only as a template but also as a reductant to drive the silver nucleation and deposition. The resulting nanoparticles have a face-centered cubic (fcc) crystal structure and 20-30 nm average diameter. The detailed mechanism is discussed, and other metals or alloys could also be synthesized with this method. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  13. Antipersistent dynamics in short time scale variability of self-potential signals

    Directory of Open Access Journals (Sweden)

    M. Ragosta

    2000-06-01

    Full Text Available Time scale properties of self-potential signals are investigated through the analysis of the second order structure function (variogram, a powerful tool to investigate the spatial and temporal variability of observational data. In this work we analyse two sequences of self-potential values measured by means of a geophysical monitoring array located in a seismically active area of Southern Italy. The range of scales investigated goes from a few minutes to several days. It is shown that signal fluctuations are characterised by two time scale ranges in which self-potential variability appears to follow slightly different dynamical behaviours. Results point to the presence of fractal, non stationary features expressing a long term correlation with scaling coefficients which are the clue of stabilising mechanisms. In the scale ranges in which the series show scale invariant behaviour, self-potentials evolve like fractional Brownian motions with anticorrelated increments typical of processes regulated by negative feedback mechanisms (antipersistence. On scales below about 6 h the strength of such an antipersistence appears to be slightly greater than that observed on larger time scales where the fluctuations are less efficiently stabilised.

  14. Spike-threshold adaptation predicted by membrane potential dynamics in vivo.

    Directory of Open Access Journals (Sweden)

    Bertrand Fontaine

    2014-04-01

    Full Text Available Neurons encode information in sequences of spikes, which are triggered when their membrane potential crosses a threshold. In vivo, the spiking threshold displays large variability suggesting that threshold dynamics have a profound influence on how the combined input of a neuron is encoded in the spiking. Threshold variability could be explained by adaptation to the membrane potential. However, it could also be the case that most threshold variability reflects noise and processes other than threshold adaptation. Here, we investigated threshold variation in auditory neurons responses recorded in vivo in barn owls. We found that spike threshold is quantitatively predicted by a model in which the threshold adapts, tracking the membrane potential at a short timescale. As a result, in these neurons, slow voltage fluctuations do not contribute to spiking because they are filtered by threshold adaptation. More importantly, these neurons can only respond to input spikes arriving together on a millisecond timescale. These results demonstrate that fast adaptation to the membrane potential captures spike threshold variability in vivo.

  15. Isolation and properties of plasmids from Deinococcus radiodurans Sark

    International Nuclear Information System (INIS)

    Sjarief, S.H.; Kikuchi, Masahiro; Kurita, Hiromi; Kitayama, Shigeru; Watanabe, Hiroshi.

    1990-05-01

    Radioresistant bacterium, Deinococcus radiodurans, can repair completely almost all of DNA damages including double strand breaks induced by gamma-rays up to about 5 kGy. In order to reveal the repair mechanism, it is necessary to develop a cloning vector available for the genetic analysis. We tried to isolate plasmids from D.radiodurans Sark strain. In the present paper the isolation and properties of plasmids were described. (author)

  16. Mechanisms of Evolution in High-Consequence Drug Resistance Plasmids.

    Science.gov (United States)

    He, Susu; Chandler, Michael; Varani, Alessandro M; Hickman, Alison B; Dekker, John P; Dyda, Fred

    2016-12-06

    The dissemination of resistance among bacteria has been facilitated by the fact that resistance genes are usually located on a diverse and evolving set of transmissible plasmids. However, the mechanisms generating diversity and enabling adaptation within highly successful resistance plasmids have remained obscure, despite their profound clinical significance. To understand these mechanisms, we have performed a detailed analysis of the mobilome (the entire mobile genetic element content) of a set of previously sequenced carbapenemase-producing Enterobacteriaceae (CPE) from the National Institutes of Health Clinical Center. This analysis revealed that plasmid reorganizations occurring in the natural context of colonization of human hosts were overwhelmingly driven by genetic rearrangements carried out by replicative transposons working in concert with the process of homologous recombination. A more complete understanding of the molecular mechanisms and evolutionary forces driving rearrangements in resistance plasmids may lead to fundamentally new strategies to address the problem of antibiotic resistance. The spread of antibiotic resistance among Gram-negative bacteria is a serious public health threat, as it can critically limit the types of drugs that can be used to treat infected patients. In particular, carbapenem-resistant members of the Enterobacteriaceae family are responsible for a significant and growing burden of morbidity and mortality. Here, we report on the mechanisms underlying the evolution of several plasmids carried by previously sequenced clinical Enterobacteriaceae isolates from the National Institutes of Health Clinical Center (NIH CC). Our ability to track genetic rearrangements that occurred within resistance plasmids was dependent on accurate annotation of the mobile genetic elements within the plasmids, which was greatly aided by access to long-read DNA sequencing data and knowledge of their mechanisms. Mobile genetic elements such as

  17. Effect of TiO2 on conjugative transfer of RP4 plasmid

    International Nuclear Information System (INIS)

    Qian Di; Zhang Buchang; Yang Dong; Chen Zhaoli; Jin Min; Qiu Zhigang; Li Junwen

    2013-01-01

    Objective: To explore the effect and law of nano-titanium dioxide on the conjugative transfer of RP4 plasmid. Methods: Mating was conducted between Escherichia coli HB101 (RP4) and E. coli K12Rif in saline without stirring under certain conditions and the donor per recipient ratio was 1:1 constantly. The selective LB agar medium plates containing appropriate antibiotics were used to count the number of transconjugants and the conjugative transfer frequency. Results: Nano-titanium dioxide could promote the conjugative transfer of RP4. The nano-titanium dioxide concentration, bacterial concentration, mating temperature and mating time could affect the conjugative transfer of RP4. Conclusion: Nano-titanium dioxide can promote plasmid conjugal transfer in the liquid phase under certain conditions, which may pose a potential hazard to environmental and human health. (authors)

  18. The characteristics of micrococcus (deinococcus) radiodurans sark plasmids

    International Nuclear Information System (INIS)

    Sjarief, Sri Hariani; Kikuchi, Masahiro; Watanabe, Hiroshi.

    1994-01-01

    The characterization of micrococcus (deinococcus) radiodurans sark plasmids. This bacterium has been classified as a new genus deinococcus radiodurans which is resistant to gamma-rays. It can repair itself completely almost all of DNA damages including double strand breaks induced by gamma-rays up to about 5 KGy. To reveal the repair mechanism, several investigations had been done to develop a cloning vector available for the genetic analysis. For this purpose D. radiodurans Sark are to be prepared as a vector by studying the characteristics of its plasmid. Plasmids were isolated by electrophoresis using 0.6% low-melting-temperature agarose in TAE and run for 5.5 hours, followed by the identification. An antibiotic marker was also carried out in this experiment to identify its location in the genetic materials of the cell, beside making a restriction map of the plasmid. Results have shown that D. radiodurans Sark has 4 plasmids (P1, P2, P3, and P4) and the refampicin resistant genes were not found in the plasmid. (authors). 14 refs; 4 figs

  19. Fluoride enhances transfection activity of carbonate apatite by increasing cytoplasmic stability of plasmid DNA

    International Nuclear Information System (INIS)

    Chowdhury, E.H.

    2011-01-01

    Highlights: → Cytoplasmic stability of plasmid DNA is enhanced by fluoride incorporation into carbonate apatite carrier. → Fluoridated carbonate apatite promotes a robust increase in transgene expression. → Controlled dissolution of fluoridated carbonate apatite in endosomal acidic environment might buffer the endosomes and prevent degradation of the released DNA. -- Abstract: Intracellular delivery of a functional gene or a nucleic acid sequence to specifically knockdown a harmful gene is a potential approach to precisely treat a critical human disease. The intensive efforts in the last few decades led to the development of a number of viral and non-viral synthetic vectors. However, an ideal delivery tool in terms of the safety and efficacy has yet to be established. Recently, we have developed pH-sensing inorganic nanocrystals of carbonate apatite for efficient and cell-targeted delivery of gene and gene-silencing RNA. Here we show that addition of very low level of fluoride to the particle-forming medium facilitates a robust increase in transgene expression following post-incubation of the particles with HeLa cells. Confocal microscopic observation and Southern blotting prove the cytoplasmic existence of plasmid DNA delivered by likely formed fluoridated carbonate apatite particles while degradation of plasmid DNA presumably by cytoplasmic nucleases was noticed following delivery with apatite particles alone. The beneficial role of fluoride in enhancing carbonate apatite-mediated gene expression might be due to the buffering potential of generated fluoridated apatite in endosomal acidic environment, thereby increasing the half-life of delivered plasmid DNA.

  20. Fluoride enhances transfection activity of carbonate apatite by increasing cytoplasmic stability of plasmid DNA

    Energy Technology Data Exchange (ETDEWEB)

    Chowdhury, E.H., E-mail: md.ezharul.hoque@med.monash.edu.my [Jeffrey Cheah School of Medicine and Health Sciences, Monash University Sunway Campus, Jalan Lagoon Selatan, Bandar Sunway, Selangor Darul Ehsan (Malaysia)

    2011-06-17

    Highlights: {yields} Cytoplasmic stability of plasmid DNA is enhanced by fluoride incorporation into carbonate apatite carrier. {yields} Fluoridated carbonate apatite promotes a robust increase in transgene expression. {yields} Controlled dissolution of fluoridated carbonate apatite in endosomal acidic environment might buffer the endosomes and prevent degradation of the released DNA. -- Abstract: Intracellular delivery of a functional gene or a nucleic acid sequence to specifically knockdown a harmful gene is a potential approach to precisely treat a critical human disease. The intensive efforts in the last few decades led to the development of a number of viral and non-viral synthetic vectors. However, an ideal delivery tool in terms of the safety and efficacy has yet to be established. Recently, we have developed pH-sensing inorganic nanocrystals of carbonate apatite for efficient and cell-targeted delivery of gene and gene-silencing RNA. Here we show that addition of very low level of fluoride to the particle-forming medium facilitates a robust increase in transgene expression following post-incubation of the particles with HeLa cells. Confocal microscopic observation and Southern blotting prove the cytoplasmic existence of plasmid DNA delivered by likely formed fluoridated carbonate apatite particles while degradation of plasmid DNA presumably by cytoplasmic nucleases was noticed following delivery with apatite particles alone. The beneficial role of fluoride in enhancing carbonate apatite-mediated gene expression might be due to the buffering potential of generated fluoridated apatite in endosomal acidic environment, thereby increasing the half-life of delivered plasmid DNA.

  1. D2 dissociative adsorption on and associative desorption from Si(100): Dynamic consequences of an ab initio potential energy surface

    DEFF Research Database (Denmark)

    Luntz, A. C.; Kratzer, Peter

    1996-01-01

    favors the symmetric one. Under the conditions of many experiments, either could dominate. The calculations show quite weak dynamic coupling to the Si lattice for both paths, i.e., weak surface temperature dependences to dissociation and small energy loss to the lattice upon desorption......Dynamical calculations are reported for D-2 dissociative chemisorption on and associative desorption from a Si(100) surface. These calculations use the dynamically relevant effective potential which is based on an ab initio potential energy surface for the ''pre-paired'' species. Three coordinates...

  2. Dynamic Reference Electrode development for redox potential measurements in fluoride molten salt at high temperature

    International Nuclear Information System (INIS)

    Durán-Klie, Gabriela; Rodrigues, Davide; Delpech, Sylvie

    2016-01-01

    Measurement of redox potential in fluoride media is a major problem due to the difficulty to design a reference electrode with high stability, high mechanical resistance and high accuracy. In the frame of molten salt reactor studies, a dynamic reference electrode (DRE) is developed to measure redox potential in fluoride molten salt at high temperature. DRE is based on the in-situ generation of a transient redox system. The choice of the redox couple corresponds to the cathodic limit of the molten salt considered. As a preliminary step, the demonstration of feasibility of generating a DRE was done in LiF-NaF-KF (46.5–11.5–42 mol%) media at 500 °C. In this salt, the reference redox system generated by coulometry at applied current is KF/K, metallic potassium being electrodeposited on a tungsten wire electrode. The validation of the DRE response and the experimental optimization parameters for DRE generation were realized by following the NiF 2 /Ni redox potential evolution as a function of NiF 2 concentration in the fused salt. The current value applied for DRE generation was optimized. It depends on the amount of metallic cations contained in the fused salt and which can be electrochemically reduced simultaneously during the DRE generation. The current corresponding to the DRE generation has to be 4 times greater than the current corresponding to the reduction of the other elements.

  3. The Dynamics of the Scientific Potential of Personnel in Terms of the Regions of Ukraine

    Directory of Open Access Journals (Sweden)

    Zhuravka Andrey V.

    2017-11-01

    Full Text Available Innovation development as well as economic growth of the country and its regions depend on the availability of scientific potential of personnel and its effective use. A brief review on this issue has been undertaken. The dynamics of scientific potential of personnel for the period of independence of Ukraine (1991–2015 in all its regions was studied. The scientific potential of personnel is considered in the context of all specialists, performing research and advanced development, and also separately in terms of candidates and doctors of sciences. It has been shown that the number of specialists, performing research and advanced development, across all Ukraine considering the period under review has decreased more than five times. During the same period, the decline in the number of candidates of science was 3,7 times, and in the doctors of science – 1.6 times. A forecast calculation of the number of specialists, performing research and advanced development, on the regression exponential dependence at the level of 2020 showed that it will reach 43,3 thousand persons, which is less than the considered number at the beginning of the «Dobrov period» (46,7 thousand people in 1960.

  4. Dynamical symmetry breaking of λφ4 theory in the two loop effective potential

    International Nuclear Information System (INIS)

    Yang Jifeng; Ruan Jianhong

    2002-01-01

    The two loop effective potential of massless λφ 4 theory is presented in several regularization and renormalization prescriptions and the dynamical symmetry breaking solution is obtained in the strong-coupling situation in several prescriptions except the Coleman-Weinberg prescription. The beta function in the broken phase becomes negative and the UV fixed point turns out to be a strong-coupling one, and its numeric value varies with the renormalization prescriptions, a detail which is different from the asymptotic-free solution in the one loop case. The symmetry-breaking phase is shown to be an entirely strong-coupling phase. The reason for the relevance of the renormalization prescriptions is shown to be due to the nonperturbative nature of the effective potential. We also reanalyze the two loop effective potential by adopting a differential equation approach based on the understanding that all the quantum field theories are ill-defined formulations of the 'low-energy' effective theories of a complete underlying theory. The relevance of the prescriptions of fixing the local ambiguities to physical properties such as symmetry breaking is further emphasized. We also tentatively propose a rescaling insensitivity argument for fixing the quadratic ambiguities. Some detailed properties of the strongly coupled broken phase and related issues are discussed

  5. A binary plasmid system for shuffling combinatorial antibody libraries.

    Science.gov (United States)

    Collet, T A; Roben, P; O'Kennedy, R; Barbas, C F; Burton, D R; Lerner, R A

    1992-11-01

    We have used a binary system of replicon-compatible plasmids to test the potential for promiscuous recombination of heavy and light chains within sets of human Fab fragments isolated from combinatorial antibody libraries. Antibody molecules showed a surprising amount of promiscuity in that a particular heavy chain could recombine with multiple light chains with retention of binding to a protein antigen. The degree to which a given heavy chain productively paired with any light chain to bind antigen varied from 43% to 100% and depended strongly on the heavy-chain sequence. Such productive crosses resulted in a set of Fab fragments of similar apparent binding constants, which seemed to differ mainly in the amount of active Fab fragment produced in the bacterial cell. The dominance of the heavy chain in the antibody-antigen interaction was further explored in a set of directed crosses, in which heavy and light chains derived from antigen-specific clones were crossed with nonrelated heavy and light chains. In these crosses, an Fab fragment retained antigen binding only if it contained a heavy chain from an antigen-specific clone. In no case did the light chain confer detectable affinity when paired with indifferent heavy chains. The surprising promiscuity of heavy chains has ramifications for the evaluation of the diversity of combinatorial libraries made against protein antigens and should allow the combination of one such promiscuous heavy chain with an engineered light chain to form an Fab fragment carrying synthetic cofactors to assist in antibody catalysis.

  6. Assessing groundwater depletion and dynamics using GRACE and InSAR: Potential and limitations

    Science.gov (United States)

    Castellazzi, Pascal; Martel, Richard; Galloway, Devin L.; Longuevergne, Laurent; Rivera, Alfonso

    2016-01-01

    In the last decade, remote sensing of the temporal variation of ground level and gravity has improved our understanding of groundwater dynamics and storage. Mass changes are measured by GRACE (Gravity Recovery and Climate Experiment) satellites, whereas ground deformation is measured by processing synthetic aperture radar satellites data using the InSAR (Interferometry of Synthetic Aperture Radar) techniques. Both methods are complementary and offer different sensitivities to aquifer system processes. GRACE is sensitive to mass changes over large spatial scales (more than 100,000 km2). As such, it fails in providing groundwater storage change estimates at local or regional scales relevant to most aquifer systems, and at which most groundwater management schemes are applied. However, InSAR measures ground displacement due to aquifer response to fluid-pressure changes. InSAR applications to groundwater depletion assessments are limited to aquifer systems susceptible to measurable deformation. Furthermore, the inversion of InSAR-derived displacement maps into volume of depleted groundwater storage (both reversible and largely irreversible) is confounded by vertical and horizontal variability of sediment compressibility. During the last decade, both techniques have shown increasing interest in the scientific community to complement available in situ observations where they are insufficient. In this review, we present the theoretical and conceptual bases of each method, and present idealized scenarios to highlight the potential benefits and challenges of combining these techniques to remotely assess groundwater storage changes and other aspects of the dynamics of aquifer systems.

  7. First principles molecular dynamics of metal/water interfaces under bias potential

    Science.gov (United States)

    Pedroza, Luana; Brandimarte, Pedro; Rocha, Alexandre; Fernandez-Serra, Marivi

    2014-03-01

    Understanding the interaction of the water-metal system at an atomic level is extremely important in electrocatalysts for fuel cells, photocatalysis among other systems. The question of the interface energetics involves a detailed study of the nature of the interactions between water-water and water-substrate. A first principles description of all components of the system is the most appropriate methodology in order to advance understanding of electrochemically processes. In this work we describe, using first principles molecular dynamics simulations, the dynamics of a combined surface(Au and Pd)/water system both in the presence and absence of an external bias potential applied to the electrodes, as one would come across in electrochemistry. This is accomplished using a combination of density functional theory (DFT) and non-equilibrium Green's functions methods (NEGF), thus accounting for the fact that one is dealing with an out-of-equilibrium open system, with and without van der Waals interactions. DOE Early Career Award No. DE-SC0003871.

  8. Prediction of Liquefaction Potential of Dredge Fill Sand by DCP and Dynamic Probing

    International Nuclear Information System (INIS)

    Alam, Md. Jahangir; Azad, Abul Kalam; Rahman, Ziaur

    2008-01-01

    From many research it is proved that liquefaction potential of sand is function of mainly relative density and confining pressure. During routine site investigations, high-quality sampling and laboratory testing of sands are not feasible because of inevitable sample disturbance effects and budgetary constraints. On the other hand quality control of sand fill can be done by determining in situ density of sand in layer by layer which is expensive and time consuming. In this paper TRL DCP (Transportation Research Laboratory Dynamic Cone Penetration) and DPL (Dynamic Probing Light) are calibrated to predict the relative density of sand deposit. For this purpose sand of known relative density is prepared in a calibration chamber which is a mild steel cylinder with diameter 0.5 m and height 1.0 m. Relative density of sand is varied by controlling height of fall and diameter of hole of sand discharge bowl. After filling, every time DPL and DCP tests are performed and for every blow the penetration of cone is recorded. N10 is then calculated from penetration records. Thus a database is compiled where N10 and relative densities are known. A correlation is made between N 10 and relative density for two types of sand. A good correlation of N 10 and relative density is found

  9. Estimation of Nanodiamond Surface Charge Density from Zeta Potential and Molecular Dynamics Simulations.

    Science.gov (United States)

    Ge, Zhenpeng; Wang, Yi

    2017-04-20

    Molecular dynamics simulations of nanoparticles (NPs) are increasingly used to study their interactions with various biological macromolecules. Such simulations generally require detailed knowledge of the surface composition of the NP under investigation. Even for some well-characterized nanoparticles, however, this knowledge is not always available. An example is nanodiamond, a nanoscale diamond particle with surface dominated by oxygen-containing functional groups. In this work, we explore using the harmonic restraint method developed by Venable et al., to estimate the surface charge density (σ) of nanodiamonds. Based on the Gouy-Chapman theory, we convert the experimentally determined zeta potential of a nanodiamond to an effective charge density (σ eff ), and then use the latter to estimate σ via molecular dynamics simulations. Through scanning a series of nanodiamond models, we show that the above method provides a straightforward protocol to determine the surface charge density of relatively large (> ∼100 nm) NPs. Overall, our results suggest that despite certain limitation, the above protocol can be readily employed to guide the model construction for MD simulations, which is particularly useful when only limited experimental information on the NP surface composition is available to a modeler.

  10. An In Vitro Chicken Gut Model Demonstrates Transfer of a Multidrug Resistance Plasmid from Salmonella to Commensal Escherichia coli.

    Science.gov (United States)

    Card, Roderick M; Cawthraw, Shaun A; Nunez-Garcia, Javier; Ellis, Richard J; Kay, Gemma; Pallen, Mark J; Woodward, Martin J; Anjum, Muna F

    2017-07-18

    The chicken gastrointestinal tract is richly populated by commensal bacteria that fulfill various beneficial roles for the host, including helping to resist colonization by pathogens. It can also facilitate the conjugative transfer of multidrug resistance (MDR) plasmids between commensal and pathogenic bacteria which is a significant public and animal health concern as it may affect our ability to treat bacterial infections. We used an in vitro chemostat system to approximate the chicken cecal microbiota, simulate colonization by an MDR Salmonella pathogen, and examine the dynamics of transfer of its MDR plasmid harboring several genes, including the extended-spectrum beta-lactamase bla CTX-M1 We also evaluated the impact of cefotaxime administration on plasmid transfer and microbial diversity. Bacterial community profiles obtained by culture-independent methods showed that Salmonella inoculation resulted in no significant changes to bacterial community alpha diversity and beta diversity, whereas administration of cefotaxime caused significant alterations to both measures of diversity, which largely recovered. MDR plasmid transfer from Salmonella to commensal Escherichia coli was demonstrated by PCR and whole-genome sequencing of isolates purified from agar plates containing cefotaxime. Transfer occurred to seven E. coli sequence types at high rates, even in the absence of cefotaxime, with resistant strains isolated within 3 days. Our chemostat system provides a good representation of bacterial interactions, including antibiotic resistance transfer in vivo It can be used as an ethical and relatively inexpensive approach to model dissemination of antibiotic resistance within the gut of any animal or human and refine interventions that mitigate its spread before employing in vivo studies. IMPORTANCE The spread of antimicrobial resistance presents a grave threat to public health and animal health and is affecting our ability to respond to bacterial infections

  11. Complete nucleotide sequence and analysis of two conjugative broad host range plasmids from a marine microbial biofilm.

    Directory of Open Access Journals (Sweden)

    Peter Norberg

    Full Text Available The complete nucleotide sequence of plasmids pMCBF1 and pMCBF6 was determined and analyzed. pMCBF1 and pMCBF6 form a novel clade within the IncP-1 plasmid family designated IncP-1 ς. The plasmids were exogenously isolated earlier from a marine biofilm. pMCBF1 (62 689 base pairs; bp and pMCBF6 (66 729 bp have identical backbones, but differ in their mercury resistance transposons. pMCBF1 carries Tn5053 and pMCBF6 carries Tn5058. Both are flanked by 5 bp direct repeats, typical of replicative transposition. Both insertions are in the vicinity of a resolvase gene in the backbone, supporting the idea that both transposons are "res-site hunters" that preferably insert close to and use external resolvase functions. The similarity of the backbones indicates recent insertion of the two transposons and the ongoing dynamics of plasmid evolution in marine biofilms. Both plasmids also carry the insertion sequence ISPst1, albeit without flanking repeats. ISPs1is located in an unusual site within the control region of the plasmid. In contrast to most known IncP-1 plasmids the pMCBF1/pMCBF6 backbone has no insert between the replication initiation gene (trfA and the vegetative replication origin (oriV. One pMCBF1/pMCBF6 block of about 2.5 kilo bases (kb has no similarity with known sequences in the databases. Furthermore, insertion of three genes with similarity to the multidrug efflux pump operon mexEF and a gene from the NodT family of the tripartite multi-drug resistance-nodulation-division (RND system in Pseudomonas aeruginosa was found. They do not seem to confer antibiotic resistance to the hosts of pMCBF1/pMCBF6, but the presence of RND on promiscuous plasmids may have serious implications for the spread of antibiotic multi-resistance.

  12. Molecular Dynamics simulations of Inhibitor of Apoptosis Proteins and identification of potential small molecule inhibitors.

    Science.gov (United States)

    Jayakumar, Jayanthi; Anishetty, Sharmila

    2014-05-01

    Chemotherapeutic resistance due to over expression of Inhibitor of Apoptosis Proteins (IAPs) XIAP, survivin and livin has been observed in various cancers. In the current study, Molecular Dynamics (MD) simulations were carried out for all three IAPs and a common ligand binding scaffold was identified. Further, a novel sequence based motif specific to these IAPs was designed. SMAC is an endogenous inhibitor of IAPs. Screening of ChemBank for compounds similar to lead SMAC-non-peptidomimetics yielded a cemadotin related compound NCIMech_000654. Cemadotin is a derivative of natural anti-tumor peptide dolastatin-15; hence these compounds were docked against all three IAPs. Based on our analysis, we propose that NCIMech_000654/dolastatin-15/cemadotin derivatives may be investigated for their potential in inhibiting XIAP, survivin and livin. Copyright © 2014 Elsevier Ltd. All rights reserved.

  13. Coupled dynamics of interacting spin-1 bosons in a double-well potential

    Science.gov (United States)

    Carvalho, D. W. S.; Foerster, A.; Gusmão, M. A.

    2018-03-01

    We present a detailed analysis of dynamical processes involving two or three particles in a double-well potential. Motivated by experimental realizations of such a system with optically trapped cold atoms, we focus on spin-1 bosons with special attention on the effects of a spin-dependent interaction in addition to the usual Hubbard-like repulsive one. For a sufficiently weak tunneling amplitude in comparison to the dominant Hubbard coupling, particle motion is strongly correlated, occurring only under fine-tuned relationships between well-depth asymmetry and interactions. We highlight processes involving tunneling of coupled particle pairs and triads, emphasizing the role of the spin-dependent interaction in resonance conditions.

  14. Chaotic Dynamics of a Josephson Junction with a Ratchet Potential and Current-Modulating Damping

    Science.gov (United States)

    Li, Fei; Li, Wenwu; Xu, Lan

    2018-04-01

    The chaotic dynamics of a Josephson junction with a ratchet potential and current-modulating damping are studied. Under the first-order approximation, we construct the general solution of the first-order equation whose boundedness condition contains the famous Melnikov chaotic criterion. Based on the general solution, the incomputability and unpredictability of the system's chaotic behavior are discussed. For the case beyond perturbation conditions, the evolution of stroboscopic Poincaré sections shows that the system undergoes a quasi-periodic transition to chaos with an increasing intensity of the rf-current. Through a suitable feedback controlling strategy, the chaos can be effectively suppressed and the intensity of the controller can vary in a large range. It is also found that the current between the two separated superconductors increases monotonously in some specific parameter spaces.

  15. Comparing the temporal dynamics of thematic and taxonomic processing using event-related potentials.

    Directory of Open Access Journals (Sweden)

    Olivera Savic

    Full Text Available We report the results of a study comparing the temporal dynamics of thematic and taxonomic knowledge activation in a picture-word priming paradigm using event-related potentials. Although we found no behavioral differences between thematic and taxonomic processing, ERP data revealed distinct patterns of N400 and P600 amplitude modulation for thematic and taxonomic priming. Thematically related target stimuli elicited less negativity than taxonomic targets between 280-460 ms after stimulus onset, suggesting easier semantic processing of thematic than taxonomic relationships. Moreover, P600 mean amplitude was significantly increased for taxonomic targets between 520-600 ms, consistent with a greater need for stimulus reevaluation in that condition. These results offer novel evidence in favor of a dissociation between thematic and taxonomic thinking in the early phases of conceptual evaluation.

  16. Comparing the temporal dynamics of thematic and taxonomic processing using event-related potentials.

    Science.gov (United States)

    Savic, Olivera; Savic, Andrej M; Kovic, Vanja

    2017-01-01

    We report the results of a study comparing the temporal dynamics of thematic and taxonomic knowledge activation in a picture-word priming paradigm using event-related potentials. Although we found no behavioral differences between thematic and taxonomic processing, ERP data revealed distinct patterns of N400 and P600 amplitude modulation for thematic and taxonomic priming. Thematically related target stimuli elicited less negativity than taxonomic targets between 280-460 ms after stimulus onset, suggesting easier semantic processing of thematic than taxonomic relationships. Moreover, P600 mean amplitude was significantly increased for taxonomic targets between 520-600 ms, consistent with a greater need for stimulus reevaluation in that condition. These results offer novel evidence in favor of a dissociation between thematic and taxonomic thinking in the early phases of conceptual evaluation.

  17. Modulations of 'late' event-related brain potentials in humans by dynamic audiovisual speech stimuli.

    Science.gov (United States)

    Lebib, Riadh; Papo, David; Douiri, Abdel; de Bode, Stella; Gillon Dowens, Margaret; Baudonnière, Pierre-Marie

    2004-11-30

    Lipreading reliably improve speech perception during face-to-face conversation. Within the range of good dubbing, however, adults tolerate some audiovisual (AV) discrepancies and lipreading, then, can give rise to confusion. We used event-related brain potentials (ERPs) to study the perceptual strategies governing the intermodal processing of dynamic and bimodal speech stimuli, either congruently dubbed or not. Electrophysiological analyses revealed that non-coherent audiovisual dubbings modulated in amplitude an endogenous ERP component, the N300, we compared to a 'N400-like effect' reflecting the difficulty to integrate these conflicting pieces of information. This result adds further support for the existence of a cerebral system underlying 'integrative processes' lato sensu. Further studies should take advantage of this 'N400-like effect' with AV speech stimuli to open new perspectives in the domain of psycholinguistics.

  18. Burst analysis tool for developing neuronal networks exhibiting highly varying action potential dynamics

    Directory of Open Access Journals (Sweden)

    Fikret Emre eKapucu

    2012-06-01

    Full Text Available In this paper we propose a firing statistics based neuronal network burst detection algorithm for neuronal networks exhibiting highly variable action potential dynamics. Electrical activity of neuronal networks is generally analyzed by the occurrences of spikes and bursts both in time and space. Commonly accepted analysis tools employ burst detection algorithms based on predefined criteria. However, maturing neuronal networks, such as those originating from human embryonic stem cells (hESC, exhibit highly variable network structure and time-varying dynamics. To explore the developing burst/spike activities of such networks, we propose a burst detection algorithm which utilizes the firing statistics based on interspike interval (ISI histograms. Moreover, the algorithm calculates interspike interval thresholds for burst spikes as well as for pre-burst spikes and burst tails by evaluating the cumulative moving average and skewness of the ISI histogram. Because of the adaptive nature of the proposed algorithm, its analysis power is not limited by the type of neuronal cell network at hand. We demonstrate the functionality of our algorithm with two different types of microelectrode array (MEA data recorded from spontaneously active hESC-derived neuronal cell networks. The same data was also analyzed by two commonly employed burst detection algorithms and the differences in burst detection results are illustrated. The results demonstrate that our method is both adaptive to the firing statistics of the network and yields successful burst detection from the data. In conclusion, the proposed method is a potential tool for analyzing of hESC-derived neuronal cell networks and thus can be utilized in studies aiming to understand the development and functioning of human neuronal networks and as an analysis tool for in vitro drug screening and neurotoxicity assays.

  19. The influence of saltmarsh restoration on sediment dynamics and the potential impact on carbon sequestration

    Science.gov (United States)

    Taylor, Benjamin; Paterson, David

    2017-04-01

    Coastal wetland ecosystems can act as large-capacity carbon sinks, providing a valuable climate change mitigation function. Globally, saltmarshes are estimated to accumulate an average of 244.7g C m-2 yr-1 (Ouyang & Lee 2014). Saltmarsh areas have experienced rapid loss in the recent past of approximately 1-2% per year (Duarte et al. 2008). Efforts to restore these areas could result in additional carbon storage due to extended vegetation cover and altered burial due to changing sediment dynamics. The influence of restoration through transplantation on sediment dynamics within a small estuary on the east coast of Scotland was assessed. Restoration efforts have been implemented since the early 2000s providing examples of old established sites ("old", >10years), young recently planted sites ("young", percentage organic matter content of deposited material is significantly lower in mudflat and young areas (3.78 ± 0.59% and 3.66 ± 0.79% respectively) versus those of natural and old areas (12.08 ± 2.27% and 6.70 ± 1.30% respectively). This relationship suggests that older restored areas are potentially offering the most potential benefit in terms of carbon sequestration, due to higher rates of deposition from the potential load and higher percentage organic content of those deposits. Furthermore, measurements of sediment accretion rates over the same period show natural and old areas to be the most effective at retaining sediment, with average elevation changes of 6.99 ± 1.64mm and 6.56 ± 0.94mm respectively, in comparison to young areas, 4.44 ± 1.58mm, and mudflats, 1.51 ± 1.23mm. Factors influencing these differences could be attributed to type and density of vegetation present and elevation of each area (or immersion period). However, the data suggests restoration could play an important role, which once established, appears to facilitate efficient sediment deposition from potential sediment load and crucially the effective accumulation of organic rich

  20. Plasmids and rickettsial evolution: insight from Rickettsia felis.

    Directory of Open Access Journals (Sweden)

    Joseph J Gillespie

    2007-03-01

    Full Text Available The genome sequence of Rickettsia felis revealed a number of rickettsial genetic anomalies that likely contribute not only to a large genome size relative to other rickettsiae, but also to phenotypic oddities that have confounded the categorization of R. felis as either typhus group (TG or spotted fever group (SFG rickettsiae. Most intriguing was the first report from rickettsiae of a conjugative plasmid (pRF that contains 68 putative open reading frames, several of which are predicted to encode proteins with high similarity to conjugative machinery in other plasmid-containing bacteria.Using phylogeny estimation, we determined the mode of inheritance of pRF genes relative to conserved rickettsial chromosomal genes. Phylogenies of chromosomal genes were in agreement with other published rickettsial trees. However, phylogenies including pRF genes yielded different topologies and suggest a close relationship between pRF and ancestral group (AG rickettsiae, including the recently completed genome of R. bellii str. RML369-C. This relatedness is further supported by the distribution of pRF genes across other rickettsiae, as 10 pRF genes (or inactive derivatives also occur in AG (but not SFG rickettsiae, with five of these genes characteristic of typical plasmids. Detailed characterization of pRF genes resulted in two novel findings: the identification of oriV and replication termination regions, and the likelihood that a second proposed plasmid, pRFdelta, is an artifact of the original genome assembly.Altogether, we propose a new rickettsial classification scheme with the addition of a fourth lineage, transitional group (TRG rickettsiae, that is unique from TG and SFG rickettsiae and harbors genes from possible exchanges with AG rickettsiae via conjugation. We offer insight into the evolution of a plastic plasmid system in rickettsiae, including the role plasmids may have played in the acquirement of virulence traits in pathogenic strains, and the

  1. Multilayer network representation of membrane potential and cytosolic calcium concentration dynamics in beta cells

    International Nuclear Information System (INIS)

    Gosak, Marko; Dolenšek, Jurij; Markovič, Rene; Slak Rupnik, Marjan; Marhl, Marko; Stožer, Andraž

    2015-01-01

    Highlights: • Physiological processes within and among pancreatic beta cells are very complex. • We analyze the simultaneous recordings of membrane potential and calcium dynamics. • We represent the interaction patterns among beta cells as a multilayer network. • The nature of the intracellular dynamics is found to rely on the network structure. - Abstract: Modern theory of networks has been recognized as a very successful methodological concept for the description and analysis of complex systems. However, some complex systems are more complex than others. For instance, several real-life systems are constituted by interdependent subsystems and their elements are subjected to different types of interactions that can also change with time. Recently, the multilayer network formalism has been proposed as a general theoretical framework for the description and analysis of such multi-dimensional complex systems and is acquiring more and more prominence in terms of a new research direction. In the present study, we use this methodology for the description of functional connectivity patterns and signal propagation between pancreatic beta cells in an islet of Langerhans at the levels of membrane potential (MP) and cytosolic calcium concentration ([Ca"2"+]_c) dynamics to study the extent of overlap in the two networks and to clarify whether time lags between the two signals in individual cells are in any way dependent on the role these cells play in the functional networks. The two corresponding network layers are constructed on the basis of signal directions and pairwise correlations, whereas the interlayer connections represent the time lag between both measured signals. Our results confirm our previous finding that both MP and [Ca"2"+]_c change spread across an islet in the form of a depolarization and a [Ca"2"+]_c wave, respectively. Both types of waves follow nearly the same path and the networks in both layers have a similar but not entirely the same structure

  2. Gene Electrotransfer of Plasmid with Tissue Specific Promoter Encoding shRNA against Endoglin Exerts Antitumor Efficacy against Murine TS/A Tumors by Vascular Targeted Effects.

    Directory of Open Access Journals (Sweden)

    Monika Stimac

    Full Text Available Vascular targeted therapies, targeting specific endothelial cell markers, are promising approaches for the treatment of cancer. One of the targets is endoglin, transforming growth factor-β (TGF-β co-receptor, which mediates proliferation, differentiation and migration of endothelial cells forming neovasculature. However, its specific, safe and long-lasting targeting remains the challenge. Therefore, in our study we evaluated the transfection efficacy, vascular targeted effects and therapeutic potential of the plasmid silencing endoglin with the tissue specific promoter, specific for endothelial cells marker endothelin-1 (ET (TS plasmid, in comparison to the plasmid with constitutive promoter (CON plasmid, in vitro and in vivo. Tissue specificity of TS plasmid was demonstrated in vitro on several cell lines, and its antiangiogenic efficacy was demonstrated by reducing tube formation of 2H11 endothelial cells. In vivo, on a murine mammary TS/A tumor model, we demonstrated good antitumor effect of gene electrotransfer (GET of either of both plasmids in treatment of smaller tumors still in avascular phase of growth, as well as on bigger tumors, already well vascularized. In support to the observations on predominantly vascular targeted effects of endoglin, histological analysis has demonstrated an increase in necrosis and a decrease in the number of blood vessels in therapeutic groups. A significant antitumor effect was observed in tumors in avascular and vascular phase of growth, possibly due to both, the antiangiogenic and the vascular disrupting effect. Furthermore, the study indicates on the potential use of TS plasmid in cancer gene therapy since the same efficacy as of CON plasmid was determined.

  3. Gene Electrotransfer of Plasmid with Tissue Specific Promoter Encoding shRNA against Endoglin Exerts Antitumor Efficacy against Murine TS/A Tumors by Vascular Targeted Effects.

    Science.gov (United States)

    Stimac, Monika; Dolinsek, Tanja; Lampreht, Ursa; Cemazar, Maja; Sersa, Gregor

    2015-01-01

    Vascular targeted therapies, targeting specific endothelial cell markers, are promising approaches for the treatment of cancer. One of the targets is endoglin, transforming growth factor-β (TGF-β) co-receptor, which mediates proliferation, differentiation and migration of endothelial cells forming neovasculature. However, its specific, safe and long-lasting targeting remains the challenge. Therefore, in our study we evaluated the transfection efficacy, vascular targeted effects and therapeutic potential of the plasmid silencing endoglin with the tissue specific promoter, specific for endothelial cells marker endothelin-1 (ET) (TS plasmid), in comparison to the plasmid with constitutive promoter (CON plasmid), in vitro and in vivo. Tissue specificity of TS plasmid was demonstrated in vitro on several cell lines, and its antiangiogenic efficacy was demonstrated by reducing tube formation of 2H11 endothelial cells. In vivo, on a murine mammary TS/A tumor model, we demonstrated good antitumor effect of gene electrotransfer (GET) of either of both plasmids in treatment of smaller tumors still in avascular phase of growth, as well as on bigger tumors, already well vascularized. In support to the observations on predominantly vascular targeted effects of endoglin, histological analysis has demonstrated an increase in necrosis and a decrease in the number of blood vessels in therapeutic groups. A significant antitumor effect was observed in tumors in avascular and vascular phase of growth, possibly due to both, the antiangiogenic and the vascular disrupting effect. Furthermore, the study indicates on the potential use of TS plasmid in cancer gene therapy since the same efficacy as of CON plasmid was determined.

  4. Intrathecal injection of naked plasmid DNA provides long-term expression of secreted proteins.

    Science.gov (United States)

    Hughes, Travis S; Langer, Stephen J; Johnson, Kirk W; Chavez, Raymond A; Watkins, Linda R; Milligan, Erin D; Leinwand, Leslie A

    2009-01-01

    Therapeutic benefit has been reported to result from intrathecal (i.t.) injection of transgene vectors, including naked DNA. However, most studies using naked DNA have measured only the transgene expression of intracellular proteins. Here we demonstrate that i.t. injection of naked DNA can result in long-term expression of secreted proteins. Plasmids expressing either secreted alkaline phosphatase (SEAP) or human interleukin-10 (hIL-10) were injected into the i.t. space in rats, and transgene products were repeatedly measured in the cerebrospinal fluid (CSF). Both SEAP and hIL-10 were maximal at 1 and 2 days after the injection and still detectable at 4 months. The utilization of a plasmid having two features that are hypothesized to increase gene expression (matrix attachment regions (MARs) and lack of CpG dinucleotides) resulted in a significant increase in gene expression. Reinjection of SEAP or hIL-10 plasmids after 4 months significantly increased protein levels at 1 and 14 days after the reinjection. SEAP was uniformly distributed between the DNA delivery site (approximately vertebral level T13) and the lumbar puncture site (L5/L6 inter-vertebral space), was reduced at the cisterna magna, and was detectable, though at much lower levels, in serum. These data suggest that naked DNA has the potential to be used as a therapeutic tool for applications that require long-term release of transgenes into the CSF.

  5. Binding mechanisms for histamine and agmatine ligands in plasmid deoxyribonucleic acid purifications.

    Science.gov (United States)

    Sousa, Ângela; Pereira, Patrícia; Sousa, Fani; Queiroz, João A

    2014-10-31

    Histamine and agmatine amino acid derivatives were immobilized into monolithic disks, in order to combine the specificity and selectivity of the ligand with the high mass transfer and binding capacity offered by monolithic supports, to purify potential plasmid DNA biopharmaceuticals. Different elution strategies were explored by changing the type and salt concentration, as well as the pH, in order to understand the retention pattern of different plasmids isoforms The pVAX1-LacZ supercoiled isoform was isolated from a mixture of pDNA isoforms by using NaCl increasing stepwise gradient and also by ammonium sulfate decreasing stepwise gradient, in both histamine and agmatine monoliths. Acidic pH in the binding buffer mainly strengthened ionic interactions with both ligands in the presence of sodium chloride. Otherwise, for histamine ligand, pH values higher than 7 intensified hydrophobic interactions in the presence of ammonium sulfate. In addition, circular dichroism spectroscopy studies revealed that the binding and elution chromatographic conditions, such as the combination of high ionic strength with extreme pH values can reversibly influence the structural stability of the target nucleic acid. Therefore, ascending sodium chloride gradients with pH manipulation can be preferable chromatographic conditions to be explored in the purification of plasmid DNA biopharmaceuticals, in order to avoid the environmental impact of ammonium sulfate. Copyright © 2014. Published by Elsevier B.V.

  6. THE ENDOGENOUS BACILLUS-SUBTILIS (NATTO) PLASMIDS PTA1015 AND PTA1040 CONTAIN SIGNAL PEPTIDASE-ENCODING GENES - IDENTIFICATION OF A NEW STRUCTURAL MODULE ON CRYPTIC PLASMIDS

    NARCIS (Netherlands)

    MEIJER, WJJ; DEJONG, A; BEA, G; WISMAN, A; TJALSMA, H; VENEMA, G; BRON, S; MAARTEN, J; VANDIJL, JM

    Various strains of Bacillus subtilis (natto) contain small cryptic plasmids that replicate via the rolling-circle mechanism. Like plasmids from other Gram-positive bacteria, these plasmids are composed of several distinct structural modules. A new structural module was identified on the B. subtilis

  7. Potential and flux field landscape theory. II. Non-equilibrium thermodynamics of spatially inhomogeneous stochastic dynamical systems

    International Nuclear Information System (INIS)

    Wu, Wei; Wang, Jin

    2014-01-01

    We have established a general non-equilibrium thermodynamic formalism consistently applicable to both spatially homogeneous and, more importantly, spatially inhomogeneous systems, governed by the Langevin and Fokker-Planck stochastic dynamics with multiple state transition mechanisms, using the potential-flux landscape framework as a bridge connecting stochastic dynamics with non-equilibrium thermodynamics. A set of non-equilibrium thermodynamic equations, quantifying the relations of the non-equilibrium entropy, entropy flow, entropy production, and other thermodynamic quantities, together with their specific expressions, is constructed from a set of dynamical decomposition equations associated with the potential-flux landscape framework. The flux velocity plays a pivotal role on both the dynamic and thermodynamic levels. On the dynamic level, it represents a dynamic force breaking detailed balance, entailing the dynamical decomposition equations. On the thermodynamic level, it represents a thermodynamic force generating entropy production, manifested in the non-equilibrium thermodynamic equations. The Ornstein-Uhlenbeck process and more specific examples, the spatial stochastic neuronal model, in particular, are studied to test and illustrate the general theory. This theoretical framework is particularly suitable to study the non-equilibrium (thermo)dynamics of spatially inhomogeneous systems abundant in nature. This paper is the second of a series

  8. The real-time link between person perception and action: brain potential evidence for dynamic continuity.

    Science.gov (United States)

    Freeman, Jonathan B; Ambady, Nalini; Midgley, Katherine J; Holcomb, Phillip J

    2011-01-01

    Using event-related potentials, we investigated how the brain extracts information from another's face and translates it into relevant action in real time. In Study 1, participants made between-hand sex categorizations of sex-typical and sex-atypical faces. Sex-atypical faces evoked negativity between 250 and 550 ms (N300/N400 effects), reflecting the integration of accumulating sex-category knowledge into a coherent sex-category interpretation. Additionally, the lateralized readiness potential revealed that the motor cortex began preparing for a correct hand response while social category knowledge was still gradually evolving in parallel. In Study 2, participants made between-hand eye-color categorizations as part of go/no-go trials that were contingent on a target's sex. On no-go trials, although the hand did not actually move, information about eye color partially prepared the motor cortex to move the hand before perception of sex had finalized. Together, these findings demonstrate the dynamic continuity between person perception and action, such that ongoing results from face processing are immediately and continuously cascaded into the motor system over time. The preparation of action begins based on tentative perceptions of another's face before perceivers have finished interpreting what they just saw. © 2010 Psychology Press, an imprint of the Taylor & Francis Group, an Informa business

  9. A Two-Stage Method to Determine Optimal Product Sampling considering Dynamic Potential Market

    Science.gov (United States)

    Hu, Zhineng; Lu, Wei; Han, Bing

    2015-01-01

    This paper develops an optimization model for the diffusion effects of free samples under dynamic changes in potential market based on the characteristics of independent product and presents a two-stage method to figure out the sampling level. The impact analysis of the key factors on the sampling level shows that the increase of the external coefficient or internal coefficient has a negative influence on the sampling level. And the changing rate of the potential market has no significant influence on the sampling level whereas the repeat purchase has a positive one. Using logistic analysis and regression analysis, the global sensitivity analysis gives a whole analysis of the interaction of all parameters, which provides a two-stage method to estimate the impact of the relevant parameters in the case of inaccuracy of the parameters and to be able to construct a 95% confidence interval for the predicted sampling level. Finally, the paper provides the operational steps to improve the accuracy of the parameter estimation and an innovational way to estimate the sampling level. PMID:25821847

  10. Finite-size effects in the dynamics of few bosons in a ring potential

    Science.gov (United States)

    Eriksson, G.; Bengtsson, J.; Karabulut, E. Ö.; Kavoulakis, G. M.; Reimann, S. M.

    2018-02-01

    We study the temporal evolution of a small number N of ultra-cold bosonic atoms confined in a ring potential. Assuming that initially the system is in a solitary-wave solution of the corresponding mean-field problem, we identify significant differences in the time evolution of the density distribution of the atoms when it instead is evaluated with the many-body Schrödinger equation. Three characteristic timescales are derived: the first is the period of rotation of the wave around the ring, the second is associated with a ‘decay’ of the density variation, and the third is associated with periodic ‘collapses’ and ‘revivals’ of the density variations, with a factor of \\sqrt{N} separating each of them. The last two timescales tend to infinity in the appropriate limit of large N, in agreement with the mean-field approximation. These findings are based on the assumption of the initial state being a mean-field state. We confirm this behavior by comparison to the exact solutions for a few-body system stirred by an external potential. We find that the exact solutions of the driven system exhibit similar dynamical features.

  11. Multilocus sequence typing of IncN plasmids

    DEFF Research Database (Denmark)

    García-Fernández, Aurora; Villa, Laura; Moodley, Arshnee

    2011-01-01

    that spread and persistence of this particular IncN-carrying blaVIM-1 lineage in Greece. CONCLUSIONS: This study proposes the use of pMLST as a suitable and rapid method for identification of IncN epidemic plasmid lineages. The recent spread of blaCTX-M-1 among humans and animals seems to be associated......OBJECTIVES: Incompatibility group N (IncN) plasmids have been associated with the dissemination of antimicrobial resistance and are a major vehicle for the spread of blaVIM-1 in humans and blaCTX-M-1 in animals. A plasmid multilocus sequence typing (pMLST) scheme was developed for rapid...... in different countries from both animals and humans belonged to ST1, suggesting dissemination of an epidemic plasmid through the food chain. Fifteen of 17 plasmids carrying blaVIM-1 from Klebsiella pneumoniae and Escherichia coli, isolated during a 5year period in Greece were assigned to ST10, suggesting...

  12. Assessment of Tumor Radioresponsiveness and Metastatic Potential by Dynamic Contrast-Enhanced Magnetic Resonance Imaging

    International Nuclear Information System (INIS)

    Ovrebo, Kirsti Marie; Gulliksrud, Kristine; Mathiesen, Berit; Rofstad, Einar K.

    2011-01-01

    Purpose: It has been suggested that gadolinium diethylene-triamine penta-acetic acid (Gd-DTPA)-based dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) may provide clinically useful biomarkers for personalized cancer treatment. In this preclinical study, we investigated the potential of DCE-MRI as a noninvasive method for assessing the radioresponsiveness and metastatic potential of tumors. Methods and Materials: R-18 melanoma xenografts growing in BALB/c nu/nu mice were used as experimental tumor models. Fifty tumors were subjected to DCE-MRI, and parametric images of K trans (the volume transfer constant of Gd-DTPA) and v e (the fractional distribution volume of Gd-DTPA) were produced by pharmacokinetic analysis of the DCE-MRI series. The tumors were irradiated after the DCE-MRI, either with a single dose of 10 Gy for detection of radiobiological hypoxia (30 tumors) or with five fractions of 4 Gy in 48 h for assessment of radioresponsiveness (20 tumors). The host mice were then euthanized and examined for lymph node metastases, and the primary tumors were resected for measurement of cell survival in vitro. Results: Tumors with hypoxic cells showed significantly lower K trans values than tumors without significant hypoxia (p trans decreased with increasing cell surviving fraction for tumors given fractionated radiation treatment (p trans values than tumors in metastasis-negative mice (p e and tumor hypoxia, radioresponsiveness, or metastatic potential could not be detected. Conclusions: R-18 tumors with low K trans values are likely to be resistant to radiation treatment and have a high probability of developing lymph node metastases. The general validity of these observations should be investigated further by studying preclinical tumor models with biological properties different from those of the R-18 tumors.

  13. REDOX POTENTIAL AND DYNAMICS OF PROTEIN AND FAT DESTRUCTION DURING STORAGE OF CANNED MEAT IN PIECES

    Directory of Open Access Journals (Sweden)

    V. B. Krylova

    2016-01-01

    Full Text Available The studies on the dynamics of the redox potential of systems and its relationship with the processes of protein and fat destruction in canned foods during their storage are fragmented and not systemized, which highlight their topicality. The aim of the research was to obtain the experimental data on the Eh values and physico-chemical indicators of canned food quality during storage in order to establish their possible correlation. It was shown that the dynamics of Eh, the content of free amino acids and fatty acid fractions in the canned products from beef and pork was different during storage. For example, a decrease in the Eh value and free amino acid content in the canned products from beef had a smooth character, while in the canned products from pork several periods were observed, which differed in the character of the change in the quality indicators.A linear character of the changes in the proportion of fatty acid fractions during storage of the canned products from beef and pork was noticed. With that, both canned food items had an increase in the saturated fatty acid content at the concomitant decrease in the sum of mono- and polyunsaturated fatty acids. The value of an increase in the proportion of saturated fatty acids associated with the process of reduction of mono- and polyunsaturated fatty acids did not depend on the kind of meat in the canned foods and was on average 6%. A decrease in the proportion of mono- and polyunsaturated fatty acids in the canned products from pork was about 4 times more intensive compared to the canned products from beef.

  14. Potential for Assessing Dynamic Problem-Solving at the Beginning of Higher Education Studies

    Science.gov (United States)

    Csapó, Benő; Molnár, Gyöngyvér

    2017-01-01

    There is a growing demand for assessment instruments which can be used in higher education, which cover a broader area of competencies than the traditional tests for disciplinary knowledge and domain-specific skills, and which measure students' most important general cognitive capabilities. Around the age of the transition from secondary to tertiary education, such assessments may serve several functions, including selecting the best-prepared candidates for certain fields of study. Dynamic problem-solving (DPS) is a good candidate for such a role, as tasks that assess it involve knowledge acquisition and knowledge utilization as well. The purpose of this study is to validate an online DPS test and to explore its potential for assessing students' DPS skills at the beginning of their higher education studies. Participants in the study were first-year students at a major Hungarian university (n = 1468). They took five tests that measured knowledge from their previous studies: Hungarian language and literature, mathematics, history, science and English as a Foreign Language (EFL). A further, sixth test based on the MicroDYN approach, assessed students' DPS skills. A brief questionnaire explored learning strategies and collected data on students' background. The testing took place at the beginning of the first semester in three 2-h sessions. Problem-solving showed relatively strong correlations with mathematics (r = 0.492) and science (r = 0.401), and moderate correlations with EFL (r = 0.227), history (r = 0.192), and Hungarian (r = 0.125). Weak but still significant correlations were found with certain learning strategies, positive correlations with elaboration strategies, and a negative correlation with memorization strategies. Significant differences were observed between male and female students; men performed significantly better in DPS than women. Results indicated the dominant role of the first phase of solving dynamic problems, as knowledge acquisition

  15. Potential for Assessing Dynamic Problem-Solving at the Beginning of Higher Education Studies

    Directory of Open Access Journals (Sweden)

    Benő Csapó

    2017-11-01

    Full Text Available There is a growing demand for assessment instruments which can be used in higher education, which cover a broader area of competencies than the traditional tests for disciplinary knowledge and domain-specific skills, and which measure students' most important general cognitive capabilities. Around the age of the transition from secondary to tertiary education, such assessments may serve several functions, including selecting the best-prepared candidates for certain fields of study. Dynamic problem-solving (DPS is a good candidate for such a role, as tasks that assess it involve knowledge acquisition and knowledge utilization as well. The purpose of this study is to validate an online DPS test and to explore its potential for assessing students' DPS skills at the beginning of their higher education studies. Participants in the study were first-year students at a major Hungarian university (n = 1468. They took five tests that measured knowledge from their previous studies: Hungarian language and literature, mathematics, history, science and English as a Foreign Language (EFL. A further, sixth test based on the MicroDYN approach, assessed students' DPS skills. A brief questionnaire explored learning strategies and collected data on students' background. The testing took place at the beginning of the first semester in three 2-h sessions. Problem-solving showed relatively strong correlations with mathematics (r = 0.492 and science (r = 0.401, and moderate correlations with EFL (r = 0.227, history (r = 0.192, and Hungarian (r = 0.125. Weak but still significant correlations were found with certain learning strategies, positive correlations with elaboration strategies, and a negative correlation with memorization strategies. Significant differences were observed between male and female students; men performed significantly better in DPS than women. Results indicated the dominant role of the first phase of solving dynamic problems, as knowledge

  16. Potential for Assessing Dynamic Problem-Solving at the Beginning of Higher Education Studies.

    Science.gov (United States)

    Csapó, Benő; Molnár, Gyöngyvér

    2017-01-01

    There is a growing demand for assessment instruments which can be used in higher education, which cover a broader area of competencies than the traditional tests for disciplinary knowledge and domain-specific skills, and which measure students' most important general cognitive capabilities. Around the age of the transition from secondary to tertiary education, such assessments may serve several functions, including selecting the best-prepared candidates for certain fields of study. Dynamic problem-solving (DPS) is a good candidate for such a role, as tasks that assess it involve knowledge acquisition and knowledge utilization as well. The purpose of this study is to validate an online DPS test and to explore its potential for assessing students' DPS skills at the beginning of their higher education studies. Participants in the study were first-year students at a major Hungarian university ( n = 1468). They took five tests that measured knowledge from their previous studies: Hungarian language and literature, mathematics, history, science and English as a Foreign Language (EFL). A further, sixth test based on the MicroDYN approach, assessed students' DPS skills. A brief questionnaire explored learning strategies and collected data on students' background. The testing took place at the beginning of the first semester in three 2-h sessions. Problem-solving showed relatively strong correlations with mathematics ( r = 0.492) and science ( r = 0.401), and moderate correlations with EFL ( r = 0.227), history ( r = 0.192), and Hungarian ( r = 0.125). Weak but still significant correlations were found with certain learning strategies, positive correlations with elaboration strategies, and a negative correlation with memorization strategies. Significant differences were observed between male and female students; men performed significantly better in DPS than women. Results indicated the dominant role of the first phase of solving dynamic problems, as knowledge acquisition

  17. Plasmids in Vibrio parahemolyticus strains isolated in Japan and Bangladesh with special reference to different distributions.

    Science.gov (United States)

    Arai, T; Ando, T; Kusakabe, A; Ullah, M A

    1983-01-01

    We surveyed plasmids in naturally occurring Vibrio parahemolyticus strains isolated in Japan and Bangladesh. Among the strains isolated in Japan, about half of the strains isolated from stools of patients of domestic diarrhea outbreaks as well as of travelers returning from East Asia were found to have plasmids, but no strains from foods had plasmids. In contrast, among the strains isolated in Bangladesh, none of the four strains isolated from patients had plasmids, but two out of eight strains isolated from water had plasmids, suggesting that plasmids are common in strains from the water in Bangladesh. All plasmids so far reported in V. parahemolyticus were detected in strains isolated from stools of patients. Incidences of plasmids in this organism were not so high in either area. In Japan, all plasmids were detected in strains from human intestines at 37 C, but in Bangladesh, where the temperature is around 30-40 C, the plasmids were detected in strains from the natural environment. These results suggested the possibility that these plasmids can come from different bacteria under rather high temperatures and that incidences of plasmids are influenced by the incidences of plasmids in bacteria present in the vicinity of V. parahemolyticus strains. None of these plasmids were found to have any relation to the biological characters tested.

  18. Potentials and Influencing Factors of Dynamic Pricing in Business: Empirical Insights of European Experts

    OpenAIRE

    Christopher Reichstein; Ralf-Christian Härting; Martina Häußler

    2017-01-01

    With a continuously increasing speed of information exchange on the World Wide Web, retailers in the E-Commerce sector are faced with immense possibilities regarding different online purchase processes like dynamic price settings. By use of Dynamic Pricing, retailers are able to set short time price changes in order to optimize producer surplus. The empirical research illustrates the basics of Dynamic Pricing and identifies six influencing factors of Dynamic Pricing. The results of a structur...

  19. The READY program: Building a global potential energy surface and reactive dynamic simulations for the hydrogen combustion.

    Science.gov (United States)

    Mogo, César; Brandão, João

    2014-06-30

    READY (REActive DYnamics) is a program for studying reactive dynamic systems using a global potential energy surface (PES) built from previously existing PESs corresponding to each of the most important elementary reactions present in the system. We present an application to the combustion dynamics of a mixture of hydrogen and oxygen using accurate PESs for all the systems involving up to four oxygen and hydrogen atoms. Results at the temperature of 4000 K and pressure of 2 atm are presented and compared with model based on rate constants. Drawbacks and advantages of this approach are discussed and future directions of research are pointed out. Copyright © 2014 Wiley Periodicals, Inc.

  20. Genetic characterization of plasmid pRJ5 of Staphylococcus aureus compared to plasmid pE194

    International Nuclear Information System (INIS)

    Oliveira, S.S. de; Freire Bastos, M.C. de

    1993-01-01

    The pRJ5, a naturally occurring constitutive macrolide, lincosamide and streptogramin B (MLS) resistance plasmid of Staphylococcus aureus, was compared to pE194, a plasmid that confers the inducible phenotype. pRJ5 was stable in all strains of S. aureus tested, even under growth at 43 O C, which distinguished it from pE194 which was shown to be thermo-sensitive for replication. pRJ5, like pE194, was highly unstable in Bacillus subtilis when the cells were grown in nonselective conditions. Multimeric forms of pRJ5 DNA were detected in the few cells of B. subtilis that retained this plasmid. pE194 was transduced by phages φ 11 and φ 443 at frequencies 400 and 20-fold higher, respectively, than pRJ5. Both plasmids were co-transduced with the plasmid pRJ4. pRJ5 was shown to be compatible with pE194. Therefore they belong to distinct Inc groups. Hybridization studies revealed that pRJ5 shares a 1.35 kb region of homology to pE194, which is limited to the erm gene, conferring MLS resistance. (author)

  1. Cloning of a Recombinant Plasmid Encoding Thiol-Specific Antioxidant Antigen (TSA) Gene of Leishmania majorand Expression in the Chinese Hamster Ovary Cell Line.

    Science.gov (United States)

    Fatemeh, Ghaffarifar; Fatemeh, Tabatabaie; Zohreh, Sharifi; Abdolhosein, Dalimiasl; Mohammad Zahir, Hassan; Mehdi, Mahdavi

    2012-01-01

    TSA (thiol-specific antioxidant antigen) is the immune-dominant antigen of Leishmania major and is considered to be the most promising candidate molecule for a recombinant or DNA vaccine against leishmaniasis. The aim of the present work was to express a plasmid containing the TSA gene in eukaryotic cells. Genomic DNA was extracted, and the TSA gene was amplified by polymerase chain reaction (PCR). The PCR product was cloned into the pTZ57R/T vector, followed by subcloning into the eukaryotic expression vector pcDNA3 (EcoRI and HindIII sites). The recombinant plasmid was characterised by restriction digest and PCR. Eukaryotic Chinese hamster ovary cells were transfected with the plasmid containing the TSA gene. Expression of the L. major TSA gene was confirmed by sodium dodecyl sulphate-polyacrylamide gel electrophoresis and Western blotting. The plasmid containing the TSA gene was successfully expressed, as demonstrated by a band of 22.1 kDa on Western blots. The plasmid containing the TSA gene can be expressed in a eukaryotic cell line. Thus, the recombinant plasmid may potentially be used as a DNA vaccine in animal models.

  2. Molecular characterization of a 21.4 kilobase antibiotic resistance plasmid from an α-hemolytic Escherichia coli O108:H- human clinical isolate.

    Directory of Open Access Journals (Sweden)

    Fay E Dawes

    Full Text Available This study characterizes the 21.4 kilobase plasmid pECTm80 isolated from Escherichia coli strain 80, an α hemolytic human clinical diarrhoeal isolate (serotype O108:H-. DNA sequence analysis of pECTm80 revealed it belonged to incompatibility group X1, and contained plasmid partition and toxin-antitoxin systems, an R6K-like triple origin (ori replication system, genes required for replication regulation, insertion sequences IS1R, ISEc37 and a truncated transposase gene (Tn3-like ΔtnpA of the Tn3 family, and carried a class 2 integron. The class 2 integron of pECTm80 contains an intact cassette array dfrA1-sat2, encoding resistance to trimethoprim and streptothricin, and an aadA1 gene cassette truncated by the insertion of IS1R. The complex plasmid replication system includes α, β and γ origins of replication. Pairwise BLASTn comparison of pECTm80 with plasmid pE001 reveals a conserved plasmid backbone suggestive of a common ancestral lineage. Plasmid pECTm80 is of potential clinical importance, as it carries multiple genes to ensure its stable maintenance through successive bacterial cell divisions and multiple antibiotic resistance genes.

  3. Mitochondrial pAL2-1 plasmid homologs are senescence factors in Podospora anserina independent of intrinsic senescence

    NARCIS (Netherlands)

    Diepeningen, van A.D.; Debets, A.J.M.; Slakhorst-Wandel, S.M.; Hoekstra, R.F.

    2008-01-01

    Since the first description of a linear mitochondrial plasmid in Podospora anserina, pAL2-1, and homologous plasmids have gone from being considered beneficial longevity plasmids, via neutral genetic elements, toward mutator plasmids causing senescence. The plasmid has an invertron structure, with

  4. Mitochondrial pAL2-1 plasmid homologs are senescence factors in Podospora anserina independent of intrinsic senescence

    NARCIS (Netherlands)

    van Diepeningen, Anne D; Debets, Alfons J M; Slakhorst, S Marijke; Hoekstra, Rolf F

    Since the first description of a linear mitochondrial plasmid in Podospora anserina, pAL2-1, and homologous plasmids have gone from being considered beneficial longevity plasmids, via neutral genetic elements, toward mutator plasmids causing senescence. The plasmid has an invertron structure, with

  5. Recombinogenic engineering of conjugative plasmids with fluorescent marker cassettes

    DEFF Research Database (Denmark)

    Reisner, A.; Molin, Søren; Zechner, E.L.

    2002-01-01

    An efficient approach for the insertion of fluorescent marker genes with sequence specificity into conjugative plasmids in Escherichia coli is described. For this purpose, homologous recombination of linear double-stranded targeting DNA was mediated by the bacteriophage lambda recombination...... resistance genes and fluorescent markers. The choice of 5' non-homologous extensions in primer pairs used for amplifying the marker cassettes determines the site specificity of the targeting DNA. This methodology is applicable to the modification of all plasmids that replicate in E coli and is not restricted...

  6. Infectious alphavirus production from a simple plasmid transfection+

    Directory of Open Access Journals (Sweden)

    Olson Ken E

    2011-07-01

    Full Text Available Abstract We have developed a new method for producing infectious double subgenomic alphaviruses from plasmids transfected into mammalian cells. A double subgenomic Sindbis virus (TE3'2J was transcribed from a cytomegalovirus PolII promoter, which results in the production of infectious virus. Transfection of as little as 125 ng of plasmid is able to produce 1 × 108 plaque forming units/ml (PFU/ml of infectious virus 48 hours post-transfection. This system represents a more efficient method for producing recombinant Sindbis viruses.

  7. Unmasking of spiral ganglion neuron firing dynamics by membrane potential and neurotrophin-3.

    Science.gov (United States)

    Crozier, Robert A; Davis, Robin L

    2014-07-16

    Type I spiral ganglion neurons have a unique role relative to other sensory afferents because, as a single population, they must convey the richness, complexity, and precision of auditory information as they shape signals transmitted to the brain. To understand better the sophistication of spiral ganglion response properties, we compared somatic whole-cell current-clamp recordings from basal and apical neurons obtained during the first 2 postnatal weeks from CBA/CaJ mice. We found that during this developmental time period neuron response properties changed from uniformly excitable to differentially plastic. Low-frequency, apical and high-frequency basal neurons at postnatal day 1 (P1)-P3 were predominantly slowly accommodating (SA), firing at low thresholds with little alteration in accommodation response mode induced by changes in resting membrane potential (RMP) or added neurotrophin-3 (NT-3). In contrast, P10-P14 apical and basal neurons were predominately rapidly accommodating (RA), had higher firing thresholds, and responded to elevation of RMP and added NT-3 by transitioning to the SA category without affecting the instantaneous firing rate. Therefore, older neurons appeared to be uniformly less excitable under baseline conditions yet displayed a previously unrecognized capacity to change response modes dynamically within a remarkably stable accommodation framework. Because the soma is interposed in the signal conduction pathway, these specializations can potentially lead to shaping and filtering of the transmitted signal. These results suggest that spiral ganglion neurons possess electrophysiological mechanisms that enable them to adapt their response properties to the characteristics of incoming stimuli and thus have the capacity to encode a wide spectrum of auditory information. Copyright © 2014 the authors 0270-6474/14/349688-15$15.00/0.

  8. Molecular dynamics simulation of nano-indentation of (111) cubic boron nitride with optimized Tersoff potential

    International Nuclear Information System (INIS)

    Zhao, Yinbo; Peng, Xianghe; Fu, Tao; Huang, Cheng; Feng, Chao; Yin, Deqiang; Wang, Zhongchang

    2016-01-01

    Highlights: • We optimize Tersoff potential to simulate the cBN better under nanoidentation. • Dislocations slip more easily along and directions on the {111} plane. • Shuffle-set dislocation slip along direction on {111} plane first. • A tetrahedron structure is found in the initial stage of the indentation. - Abstract: We conduct molecular dynamics simulation of nanoindentation on (111) surface of cubic boron nitride and find that shuffle-set dislocations slip along direction on {111} plane at the initial stage of the indentation. The shuffle-set dislocations are then found to meet together, forming surfaces of a tetrahedron. We also find that the surfaces are stacking-fault zones, which intersect with each other, forming edges of stair-rod dislocations along direction. Moreover, we also calculate the generalized stacking fault (GSF) energies along various gliding directions on several planes and find that the GSF energies of the {111} and {111} systems are relatively smaller, indicating that dislocations slip more easily along and directions on the {111} plane.

  9. Molecular dynamics simulation of nano-indentation of (111) cubic boron nitride with optimized Tersoff potential

    Energy Technology Data Exchange (ETDEWEB)

    Zhao, Yinbo [College of Aerospace Engineering, Chongqing University, Chongqing 400044 (China); Peng, Xianghe, E-mail: xhpeng@cqu.edu.cn [College of Aerospace Engineering, Chongqing University, Chongqing 400044 (China); State Key Laboratory of Coal Mine Disaster Dynamics and Control, Chongqing University, Chongqing 400044 (China); Fu, Tao; Huang, Cheng; Feng, Chao [College of Aerospace Engineering, Chongqing University, Chongqing 400044 (China); Yin, Deqiang [School of Manufacturing Science and Engineering, Sichuan University, Chengdu 610065 (China); Wang, Zhongchang, E-mail: zcwang@wpi-aimr.tohoku.ac.jp [College of Aerospace Engineering, Chongqing University, Chongqing 400044 (China); Advanced Institute for Materials Research, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577 (Japan)

    2016-09-30

    Highlights: • We optimize Tersoff potential to simulate the cBN better under nanoidentation. • Dislocations slip more easily along <110> and <112> directions on the {111} plane. • Shuffle-set dislocation slip along <112> direction on {111} plane first. • A tetrahedron structure is found in the initial stage of the indentation. - Abstract: We conduct molecular dynamics simulation of nanoindentation on (111) surface of cubic boron nitride and find that shuffle-set dislocations slip along <112> direction on {111} plane at the initial stage of the indentation. The shuffle-set dislocations are then found to meet together, forming surfaces of a tetrahedron. We also find that the surfaces are stacking-fault zones, which intersect with each other, forming edges of stair-rod dislocations along <110> direction. Moreover, we also calculate the generalized stacking fault (GSF) energies along various gliding directions on several planes and find that the GSF energies of the <112>{111} and <110>{111} systems are relatively smaller, indicating that dislocations slip more easily along <110> and <112> directions on the {111} plane.

  10. Directed Magnetic Particle Transport above Artificial Magnetic Domains Due to Dynamic Magnetic Potential Energy Landscape Transformation.

    Science.gov (United States)

    Holzinger, Dennis; Koch, Iris; Burgard, Stefan; Ehresmann, Arno

    2015-07-28

    An approach for a remotely controllable transport of magnetic micro- and/or nanoparticles above a topographically flat exchange-bias (EB) thin film system, magnetically patterned into parallel stripe domains, is presented where the particle manipulation is achieved by sub-mT external magnetic field pulses. Superparamagnetic core-shell particles are moved stepwise by the dynamic transformation of the particles' magnetic potential energy landscape due to the external magnetic field pulses without affecting the magnetic state of the thin film system. The magnetic particle velocity is adjustable in the range of 1-100 μm/s by the design of the substrate's magnetic field landscape (MFL), the particle-substrate distance, and the magnitude of the applied external magnetic field pulses. The agglomeration of magnetic particles is avoided by the intrinsic magnetostatic repulsion of particles due to the parallel alignment of the particles' magnetic moments perpendicular to the transport direction and parallel to the surface normal of the substrate during the particle motion. The transport mechanism is modeled by a quantitative theory based on the precise knowledge of the sample's MFL and the particle-substrate distance.

  11. Dynamic reponse of a cylindrical shell immersed in a potential fluid

    International Nuclear Information System (INIS)

    Cummings, G.E.

    1978-01-01

    A numerical solution technique is presented for determining the dynamic response of a thin, elastic, circular, cylindrical shell of constant wall thickness and density, immersed in a potential fluid. The shell may be excited by an arbitrary radial forcing function with a specified time history and spatial distribution. In addition, a pressure history may be specified over a segment of the fluid outer boundary. Any of the natural shell end conditions may be prescribed. A numerical instability prevented direct solutions where the ratio of the hydrodynamic forces to shell inertial forces is greater than two. This instability is believed to be the result of the weak coupling between the equations describing the fluid to those describing the shell. To circumvent this instability, an effective mass was calculated and added to the shell. Comparison of numerical to experimental results are made using a 1 / 12 scale model of a nuclear reactor core support barrel. Natural frequencies and modes are determined for this model in air, water, and oil. The computed frequencies compare to experimental results to within 15%. The use of this numerical technique is illustrated by comparing it to an analytical solution for shell beam modes and an uncertainty in the analytical technique concerning the proper effective mass to use, is resolved

  12. A Cantorian potential theory for describing dynamical systems on El Naschie's space-time

    International Nuclear Information System (INIS)

    Iovane, G.; Gargiulo, G.; Zappale, E.

    2006-01-01

    In this paper we analyze classical systems, in which motion is not on a classical continuous path, but rather on a Cantorian one. Starting from El Naschie's space-time we introduce a mathematical approach based on a potential to describe the interaction system-support. We study some relevant force fields on Cantorian space and analyze the differences with respect to the analogous case on a continuum in the context of Lagrangian formulation. Here we confirm the idea proposed by the first author in dynamical systems on El Naschie's o (∞) Cantorian space-time that a Cantorian space could explain some relevant stochastic and quantum processes, if the space acts as an harmonic oscillating support, such as that found in Nature. This means that a quantum process could sometimes be explained as a classical one, but on a nondifferential and discontinuous support. We consider the validity of this point of view, that in principle could be more realistic, because it describes the real nature of matter and space. These do not exist in Euclidean space or curved Riemanian space-time, but in a Cantorian one. The consequence of this point of view could be extended in many fields such as biomathematics, structural engineering, physics, astronomy, biology and so on

  13. Membrane potential dynamics of populations of cortical neurons during auditory streaming

    Science.gov (United States)

    Farley, Brandon J.

    2015-01-01

    How a mixture of acoustic sources is perceptually organized into discrete auditory objects remains unclear. One current hypothesis postulates that perceptual segregation of different sources is related to the spatiotemporal separation of cortical responses induced by each acoustic source or stream. In the present study, the dynamics of subthreshold membrane potential activity were measured across the entire tonotopic axis of the rodent primary auditory cortex during the auditory streaming paradigm using voltage-sensitive dye imaging. Consistent with the proposed hypothesis, we observed enhanced spatiotemporal segregation of cortical responses to alternating tone sequences as their frequency separation or presentation rate was increased, both manipulations known to promote stream segregation. However, across most streaming paradigm conditions tested, a substantial cortical region maintaining a response to both tones coexisted with more peripheral cortical regions responding more selectively to one of them. We propose that these coexisting subthreshold representation types could provide neural substrates to support the flexible switching between the integrated and segregated streaming percepts. PMID:26269558

  14. Dynamic reponse of a cylindrical shell immersed in a potential fluid

    Energy Technology Data Exchange (ETDEWEB)

    Cummings, G.E.

    1978-04-18

    A numerical solution technique is presented for determining the dynamic response of a thin, elastic, circular, cylindrical shell of constant wall thickness and density, immersed in a potential fluid. The shell may be excited by an arbitrary radial forcing function with a specified time history and spatial distribution. In addition, a pressure history may be specified over a segment of the fluid outer boundary. Any of the natural shell end conditions may be prescribed. A numerical instability prevented direct solutions where the ratio of the hydrodynamic forces to shell inertial forces is greater than two. This instability is believed to be the result of the weak coupling between the equations describing the fluid to those describing the shell. To circumvent this instability, an effective mass was calculated and added to the shell. Comparison of numerical to experimental results are made using a /sup 1///sub 12/ scale model of a nuclear reactor core support barrel. Natural frequencies and modes are determined for this model in air, water, and oil. The computed frequencies compare to experimental results to within 15%. The use of this numerical technique is illustrated by comparing it to an analytical solution for shell beam modes and an uncertainty in the analytical technique concerning the proper effective mass to use, is resolved.

  15. DNA sequence analysis of plasmids from multidrug resistant Salmonella enterica serotype Heidelberg isolates.

    Directory of Open Access Journals (Sweden)

    Jing Han

    Full Text Available Salmonella enterica serovar Heidelberg is among the most detected serovars in swine and poultry, ranks among the top five serotypes associated with human salmonellosis and is disproportionately associated with invasive infections and mortality in humans. Salmonella are known to carry plasmids associated with antimicrobial resistance and virulence. To identify plasmid-associated genes in multidrug resistant S. enterica serovar Heidelberg, antimicrobial resistance plasmids from five isolates were sequenced using the 454 LifeSciences pyrosequencing technology. Four of the isolates contained incompatibility group (Inc A/C multidrug resistance plasmids harboring at least eight antimicrobial resistance genes. Each of these strains also carried a second resistance plasmid including two IncFIB, an IncHI2 and a plasmid lacking an identified Inc group. The fifth isolate contained an IncI1 plasmid, encoding resistance to gentamicin, streptomycin and sulfonamides. Some of the IncA/C plasmids lacked the full concert of transfer genes and yet were able to be conjugally transferred, likely due to the transfer genes carried on the companion plasmids in the strains. Several non-IncA/C resistance plasmids also carried putative virulence genes. When the sequences were compared to previously sequenced plasmids, it was found that while all plasmids demonstrated some similarity to other plasmids, they were unique, often due to differences in mobile genetic elements in the plasmids. Our study suggests that Salmonella Heidelberg isolates harbor plasmids that co-select for antimicrobial resistance and virulence, along with genes that can mediate the transfer of plasmids within and among other bacterial isolates. Prevalence of such plasmids can complicate efforts to control the spread of S. enterica serovar Heidelberg in food animal and human populations.

  16. Characterization of pLAC1, a cryptic plasmid isolated from Lactobacillus acidipiscis and comparative analysis with its related plasmids.

    Science.gov (United States)

    Asteri, Ioanna-Areti; Papadimitriou, Konstantinos; Boutou, Effrossyni; Anastasiou, Rania; Pot, Bruno; Vorgias, Constantinos E; Tsakalidou, Effie

    2010-07-15

    The pLAC1 plasmid of Lactobacillus acidipiscis ACA-DC 1533, a strain isolated from traditional Kopanisti cheese, was characterised. Nucleotide sequence analysis revealed a circular molecule of 3478bp with a G+C content of 37.2%. Ab initio annotation indicated four putative open reading frames (orfs). orf1 and orf4 were found to encode a replication initiation protein (Rep) and a mobilization protein (Mob), respectively. The deduced products of orf2 and orf3 revealed no significant homology to other known proteins. However, in silico examination of the plasmid sequence supported the existence of a novel operon that includes rep, orf2 and orf3 in pLAC1 and that this operon is highly conserved also in plasmids pLB925A02, pSMA23, pLC88 and pC7. RT-PCR experiments allowed us to verify that these three genes are co-transcribed as a single polycistronic mRNA species. Furthermore, phylogenetic analysis of pLAC1 Rep and Mob proteins demonstrated that they may have derived from different plasmid origins, suggesting that pLAC1 is a product of a modular evolution process. Comparative analysis of full length nucleotide sequences of pLAC1 and related Lactobacillus plasmids showed that pLAC1 shares a very similar replication backbone with pLB925A02, pSMA23 and pLC88. In contrast, mob of pLAC1 was almost identical with the respective gene of plasmids pLAB1000, pLB4 and pPB1. These findings lead to the conclusion that pLAC1 acquired mob probably via an ancestral recombination event. Our overall work highlights the importance of characterizing plasmids deriving from non-starter 'wild' isolates in order to better appreciate plasmid divergence and evolution of lactic acid bacteria. 2010 Elsevier B.V. All rights reserved.

  17. Development of a chromosome-plasmid balanced lethal system for Lactobacillus acidophilus with thyA gene as selective marker.

    Science.gov (United States)

    Fu, X; Xu, J G

    2000-01-01

    A chromosome-plasmid balanced lethal gene delivery system for Lactobacillus acidophilus based on the thyA gene was developed. The selected L. acidophilus DOM La strain carries a mutated thyA gene and has an obligate requirement for thymidine. This strain can be used as a host for the constructed shuttle vector pFXL03, lacking antibiotic-resistant markers but having the wild-type thyA gene from L. casei which complements the thyA chromosomal mutation. The vector also contains the replicon region from plasmid pUC19 and that of the Lactococcus plasmid pWV01, which allows the transfer between Escherichia coli, L. casei and L. acidophilus. Eight unique restriction sites (i.e., PstI, HindIII, SphI, SalI, AccI, XbaI, KpnI and SacI) are available for cloning. After 40-time transfers in modified MRS medium, no plasmid loss was observed. The vector pFXL03 is potentially useful as a food-grade vaccine delivery system for L. acidophilus.

  18. Abortive phage-infection and UV-protection markers on ColI plasmids from epidemic strains of Salmonella

    International Nuclear Information System (INIS)

    Barker, R.M.

    1988-01-01

    Cultures of Escherichia coli carrying ColI plasmids received in conjugation from strains of Salmonella typhimurium and S. agona were examined for abortive infection (Abi) of phage BF23 and for enhanced resistance to the lethal action of UV-irradiation (Uvr). The Abi character of stored cultures of E. coli was also compared with the reaction of the same stock culture tested 5 years before. Seven of the eight potential types differentiated by three characters were represented among 160 ColI plasmids: ColIa Abi + Uvr + (3 plasmids), ColIa Abi - Uvr + (1), ColIa Abi - Uvr-> (2), ColIb Abi + Uvr + (85), ColIb Abi + Uvr - (5), ColIb Abi - Uvr + (4), ColIb Abi-? Uvr - (60). Recognition that different plasmid types could be carried by strains of a clone proved useful in the interpretation of the epidemic spread of strains of S. typhimurium of phage type/biotype 141/9f in Scotland and in tracing the ancestry of a recently emerged rhamnose non-fermenting mutant strain of S. agona. (author)

  19. Dynamic. cap alpha. -transfer polarisation potentials and the large angle scattering of /sup 16/O + /sup 28/Si

    Energy Technology Data Exchange (ETDEWEB)

    Hussein, M S; Aleixo, A N; Canto, L F; Carrilho, P; Donangelo, R; Paula, L.S. de

    1987-07-01

    A closed expression is derived for the dynamic ..cap alpha..-transfer polarisation potential for heavy-ion elastic scattering. The back-angle angular distributions for the elastic scattering of /sup 16/O + /sup 28/Si obtained by adding this polarisation potential to the E-18 interaction are shown to be in good agreement with the data if an ..cap alpha..-transfer spectroscopic factor of 0.4 is used.

  20. The potential of positron emission tomography for intratreatment dynamic lung tumor tracking: A phantom study

    International Nuclear Information System (INIS)

    Yang, Jaewon; Yamamoto, Tokihiro; Mazin, Samuel R.; Graves, Edward E.; Keall, Paul J.

    2014-01-01

    Purpose: This study aims to evaluate the potential and feasibility of positron emission tomography for dynamic lung tumor tracking during radiation treatment. The authors propose a center of mass (CoM) tumor tracking algorithm using gated-PET images combined with a respiratory monitor and investigate the geometric accuracy of the proposed algorithm. Methods: The proposed PET dynamic lung tumor tracking algorithm estimated the target position information through the CoM of the segmented target volume on gated PET images reconstructed from accumulated coincidence events. The information was continuously updated throughout a scan based on the assumption that real-time processing was supported (actual processing time at each frame ≈10 s). External respiratory motion and list-mode PET data were acquired from a phantom programmed to move with measured respiratory traces (external respiratory motion and internal target motion) from human subjects, for which the ground truth target position was known as a function of time. The phantom was cylindrical with six hollow sphere targets (10, 13, 17, 22, 28, and 37 mm in diameter). The measured respiratory traces consisted of two sets: (1) 1D-measured motion from ten healthy volunteers and (2) 3D-measured motion from four lung cancer patients. The authors evaluated the geometric accuracy of the proposed algorithm by quantifying estimation errors (Euclidean distance) between the actual motion of targets (1D-motion and 3D-motion traces) and CoM trajectories estimated by the proposed algorithm as a function of time. Results: The time-averaged error of 1D-motion traces over all trajectories of all targets was 1.6 mm. The error trajectories decreased with time as coincidence events were accumulated. The overall error trajectory of 1D-motion traces converged to within 2 mm in approximately 90 s. As expected, more accurate results were obtained for larger targets. For example, for the 37 mm target, the average error over all 1D

  1. Plasmid containing a DNA ligase gene from Haemophilus influenzae

    International Nuclear Information System (INIS)

    McCarthy, D.; Griffin, K.; Setlow, J.K.

    1984-01-01

    A ligase gene from Haemophilus influenzae was cloned into the shuttle vector pDM2. Although the plasmid did not affect X-ray sensitivity, it caused an increase in UV sensitivity of the wild-type but not excision-defective H. influenzae and a decrease in UV sensitivity of the rec-1 mutant. 14 references, 2 figures

  2. Antibiogram and plasmid profiling of carbapenemase and extended ...

    African Journals Online (AJOL)

    Background: The increased reports of ESBL dissemination from various centres in south western, Nigeria and the recent emergence of carbapenem resistant bacteria prompted the conception of this study. Objectives: To demonstrate the relationship between high molecular weight plasmids and the expression of antibiotic ...

  3. Quinolones Resistance And R-Plasmids Of Clinical Isolates Of ...

    African Journals Online (AJOL)

    Background: There has been reported incidence in the emergence of. Quinolones resistance in clinical isolates in Nigeria and the level in resistance has been on the increase. Objective: To determine the antimicrobial resistance patterns and plasmids profiles of 67 clinical Pseudomonas species from a teaching hospital ...

  4. Chromosomal context and replication properties of ARS plasmids in ...

    Indian Academy of Sciences (India)

    2015-11-28

    Nov 28, 2015 ... plasmid but only a subset of them functions as replication origins in their ... except that they are rich in A + T content (As on one strand and Ts .... different unique, terminal, PCR-generated restriction sites used for cloning each fragment are ..... Hall TA 1999 BioEdit: a user-friendly biological sequence align-.

  5. a positive control plasmid for reporter gene assay

    African Journals Online (AJOL)

    STORAGESEVER

    2008-07-04

    Jul 4, 2008 ... qualification as a positive control for luciferase reporter gene assays. Key words: Reporter gene plasmid, luciferase assay, cytomegalovirus promoter/enhancer, human melanoma cell line. INTRODUCTION. Reporter genes, often called reporters, have become a precious tool in studies of gene expression ...

  6. Pharmaceutical development of the plasmid DNA vaccine pDERMATT

    NARCIS (Netherlands)

    Quaak, S.G.L.

    2009-01-01

    The discovery of tumor specific antigens and self tolerance mechanisms against these antigens led to the assumption that antigens circulating at sufficient concentration levels could break this self tolerance mechanism and evoke immunological antitumor effects. pDERMATT (plasmid DNA encoding

  7. plasmid mediated resistance in multidrug resistant bacteria isolated

    African Journals Online (AJOL)

    User

    PLASMID MEDIATED RESISTANCE IN MULTIDRUG RESISTANT BACTERIA. ISOLATED FROM CHILDREN WITH SUSPECTED SEPTICAEMIA IN ZARIA,. NIGERIA. AbdulAziz, Z. A.,1* Ehinmidu, J. O.,1 Adeshina, G. O.,1 Pala, Y. Y2., Yusuf, S. S2. and. Bugaje, M. A.3. 1Department of Pharmaceutics and Pharmaceutical ...

  8. Resistant plasmid profile analysis of multidrug resistant Escherichia ...

    African Journals Online (AJOL)

    Background: Multi-drug resistant Escherichia coli has become a major threat and cause of many urinary tract infections (UTIs) in Abeokuta, Nigeria. Objectives: This study was carried out to determine the resistant plasmids of multidrug resistant Escherichia coli isolated from (Urinary tract infections)UTIs in Abeokuta.

  9. Effect of Surfactants on Plasmid DNA Stability and Release from ...

    African Journals Online (AJOL)

    Purpose: To evaluate the effect of surfactants on plasmid DNA during preparation and release from polylactic glycolide (PLGA) microspheres. Methods: Various surfactants, both ionic and non-ionic (Span, Tween, Triton X100, cetyltrimethylammonium bromide and sodium dodecyl sulphate), were added during the ...

  10. Screening of degradative plasmids from Arthrobacter sp. HW08 and ...

    African Journals Online (AJOL)

    Administrator

    2011-06-08

    Jun 8, 2011 ... Media were solidified, if necessary, by the addition of 15 g agar ... genome extraction reagent kit, plasmid DNA fast extraction kit and. DNA segments ... spectrophotometer (Spectronic Instruments, Rochester, NY) and. SW content .... cultivation on LB slant for 100 times at 30 °C for 2 days, it was found that ...

  11. Antibiogram and plasmid profiling of carbapenemase and extended ...

    African Journals Online (AJOL)

    EB

    susceptibility was recorded against the Quinolone class of antibiotics; Meropenem remained the most active antibiotic against ESBL isolates ... Conclusion: Due to the relationship between high molecular weight plasmids and multi-drug resistance, we hereby recommend ..... Agents. Chemotherapy 2005; 49: 2137-. 2139. 7.

  12. Plasmid-encoded diacetyl (acetoin) reductase in Leuconostoc pseudomesenteroides

    DEFF Research Database (Denmark)

    Rattray, Fergal P; Myling-Petersen, Dorte; Larsen, Dianna

    2003-01-01

    A plasmid-borne diacetyl (acetoin) reductase (butA) from Leuconostoc pseudomesenteroides CHCC2114 was sequenced and cloned. Nucleotide sequence analysis revealed an open reading frame encoding a protein of 257 amino acids which had high identity at the amino acid level to diacetyl (acetoin...

  13. Comparative assessment of plasmid DNA delivery by encapsulation ...

    African Journals Online (AJOL)

    Purpose: To compare the gene delivery effectiveness of plasmid DNA (pDNA) encapsulated within poly (D,L-lactide-co-glycolide) (PLGA) nanoparticles with that adsorbed on PLGA nanoparticles. Methods: PLGA nanoparticles were prepared using solvent-evaporation method. To encapsulate pDNA within the particles, ...

  14. Dynamics of action potential backpropagation in basal dendrites of prefrontal cortical pyramidal neurons.

    Science.gov (United States)

    Zhou, Wen-Liang; Yan, Ping; Wuskell, Joseph P; Loew, Leslie M; Antic, Srdjan D

    2008-02-01

    Basal dendrites of neocortical pyramidal neurons are relatively short and directly attached to the cell body. This allows electrical signals arising in basal dendrites to strongly influence the neuronal output. Likewise, somatic action potentials (APs) should readily propagate back into the basilar dendritic tree to influence synaptic plasticity. Two recent studies, however, determined that sodium APs are severely attenuated in basal dendrites of cortical pyramidal cells, so that they completely fail in distal dendritic segments. Here we used the latest improvements in the voltage-sensitive dye imaging technique (Zhou et al., 2007) to study AP backpropagation in basal dendrites of layer 5 pyramidal neurons of the rat prefrontal cortex. With a signal-to-noise ratio of > 15 and minimal temporal averaging (only four sweeps) we were able to sample AP waveforms from the very last segments of individual dendritic branches (dendritic tips). We found that in short- (< 150 microm) and medium (150-200 microm in length)-range basal dendrites APs backpropagated with modest changes in AP half-width or AP rise-time. The lack of substantial changes in AP shape and dynamics of rise is inconsistent with the AP-failure model. The lack of substantial amplitude boosting of the third AP in the high-frequency burst also suggests that in short- and medium-range basal dendrites backpropagating APs were not severely attenuated. Our results show that the AP-failure concept does not apply in all basal dendrites of the rat prefrontal cortex. The majority of synaptic contacts in the basilar dendritic tree actually received significant AP-associated electrical and calcium transients.

  15. Competitive Semantic Memory Retrieval: Temporal Dynamics Revealed by Event-Related Potentials.

    Directory of Open Access Journals (Sweden)

    Robin Hellerstedt

    Full Text Available Memories compete for retrieval when they are related to a common retrieval cue. Previous research has shown that retrieval of a target memory may lead to subsequent retrieval-induced forgetting (RIF of currently irrelevant competing memories. In the present study, we investigated the time course of competitive semantic retrieval and examined the neurocognitive mechanisms underlying RIF. We contrasted two theoretical accounts of RIF by examining a critical aspect of this memory phenomenon, namely the extent to which it depends on successful retrieval of the target memory. Participants first studied category-exemplar word-pairs (e.g. Fruit-Apple. Next, we recorded electrophysiological measures of brain activity while the participants performed a competitive semantic cued-recall task. In this task, the participants were provided with the studied categories but they were instructed to retrieve other unstudied exemplars (e.g. Fruit-Ma__?. We investigated the event-related potential (ERP correlates of retrieval success by comparing ERPs from successful and failed retrieval trials. To isolate the ERP correlates of continuous retrieval attempts from the ERP correlates of retrieval success, we included an impossible retrieval condition, with incompletable word-stem cues (Drinks-Wy__ and compared it with a non-retrieval presentation baseline condition (Occupation-Dentist. The participants' memory for all the studied exemplars was tested in the final phase of the experiment. Taken together, the behavioural results suggest that RIF is independent of target retrieval. Beyond investigating the mechanisms underlying RIF, the present study also elucidates the temporal dynamics of semantic cued-recall by isolating the ERP correlates of retrieval attempt and retrieval success. The ERP results revealed that retrieval attempt is reflected in a late posterior negativity, possibly indicating construction of candidates for completing the word-stem cue and retrieval

  16. Competitive Semantic Memory Retrieval: Temporal Dynamics Revealed by Event-Related Potentials

    Science.gov (United States)

    Hellerstedt, Robin; Johansson, Mikael

    2016-01-01

    Memories compete for retrieval when they are related to a common retrieval cue. Previous research has shown that retrieval of a target memory may lead to subsequent retrieval-induced forgetting (RIF) of currently irrelevant competing memories. In the present study, we investigated the time course of competitive semantic retrieval and examined the neurocognitive mechanisms underlying RIF. We contrasted two theoretical accounts of RIF by examining a critical aspect of this memory phenomenon, namely the extent to which it depends on successful retrieval of the target memory. Participants first studied category-exemplar word-pairs (e.g. Fruit—Apple). Next, we recorded electrophysiological measures of brain activity while the participants performed a competitive semantic cued-recall task. In this task, the participants were provided with the studied categories but they were instructed to retrieve other unstudied exemplars (e.g. Fruit—Ma__?). We investigated the event-related potential (ERP) correlates of retrieval success by comparing ERPs from successful and failed retrieval trials. To isolate the ERP correlates of continuous retrieval attempts from the ERP correlates of retrieval success, we included an impossible retrieval condition, with incompletable word-stem cues (Drinks—Wy__) and compared it with a non-retrieval presentation baseline condition (Occupation—Dentist). The participants’ memory for all the studied exemplars was tested in the final phase of the experiment. Taken together, the behavioural results suggest that RIF is independent of target retrieval. Beyond investigating the mechanisms underlying RIF, the present study also elucidates the temporal dynamics of semantic cued-recall by isolating the ERP correlates of retrieval attempt and retrieval success. The ERP results revealed that retrieval attempt is reflected in a late posterior negativity, possibly indicating construction of candidates for completing the word-stem cue and retrieval

  17. Modulation of actin dynamics as potential macrophage subtype-targeting anti-tumour strategy.

    Science.gov (United States)

    Pergola, Carlo; Schubert, Katrin; Pace, Simona; Ziereisen, Jana; Nikels, Felix; Scherer, Olga; Hüttel, Stephan; Zahler, Stefan; Vollmar, Angelika M; Weinigel, Christina; Rummler, Silke; Müller, Rolf; Raasch, Martin; Mosig, Alexander; Koeberle, Andreas; Werz, Oliver

    2017-01-30

    Tumour-associated macrophages mainly comprise immunosuppressive M2 phenotypes that promote tumour progression besides anti-tumoural M1 subsets. Selective depletion or reprogramming of M2 may represent an innovative anti-cancer strategy. The actin cytoskeleton is central for cellular homeostasis and is targeted for anti-cancer chemotherapy. Here, we show that targeting G-actin nucleation using chondramide A (ChA) predominantly depletes human M2 while promoting the tumour-suppressive M1 phenotype. ChA reduced the viability of M2, with minor effects on M1, but increased tumour necrosis factor (TNF)α release from M1. Interestingly, ChA caused rapid disruption of dynamic F-actin filaments and polymerization of G-actin, followed by reduction of cell size, binucleation and cell division, without cellular collapse. In M1, but not in M2, ChA caused marked activation of SAPK/JNK and NFκB, with slight or no effects on Akt, STAT-1/-3, ERK-1/2, and p38 MAPK, seemingly accounting for the better survival of M1 and TNFα secretion. In a microfluidically-supported human tumour biochip model, circulating ChA-treated M1 markedly reduced tumour cell viability through enhanced release of TNFα. Together, ChA may cause an anti-tumoural microenvironment by depletion of M2 and activation of M1, suggesting induction of G-actin nucleation as potential strategy to target tumour-associated macrophages in addition to neoplastic cells.

  18. Analysis of potential dynamic concealed factors in the difficulty of lower third molar extraction.

    Science.gov (United States)

    Singh, P; Ajmera, D-H; Xiao, S-S; Yang, X-Z; Liu, X; Peng, B

    2016-11-01

    The purpose of this study was to identify potential concealed variables associated with the difficulty of lower third molar (M3) extractions. To address the research purpose, we implemented a prospective study and enrolled a sample of subjects presenting for M3 removal. Predictor variables were categorized into Group-I and Group-II, based on predetermined criteria. The primary outcome variable was the difficulty of extraction, measured as extraction time. Appropriate univariate and multivariate statistics were computed using ordinal logistic regression. The sample comprised of 1235 subjects with a mean age of 29.49 +/- 8.92 years in Group-I and 26.20 +/- 11.55 years in Group-II subjects. The mean operating time per M3 extraction was 21.24 +/- 12.80 and 20.24 +/- 12.50 minutes for Group-I and Group-II subjects respectively. Three linear parameters including B-M2 height (distance between imaginary point B on the inferior border of mandibular body, and M2), lingual cortical thickness, bone density and one angular parameter including Rc-Cs angle (angle between ramus curvature and curve of spee), in addition to patient's age, profile type, facial type, cant of occlusal plane, and decreased overbite, were found to be statistically associated ( p < or = 0.05) with extraction difficulty under regression models. In conclusion, our study indicates that the difficulty of lower M3 extractions is possibly governed by morphological and biomechanical factors with substantial influence of myofunctional factors. Preoperative evaluation of dynamic concealed factors may not only help in envisaging the difficulty and planning of surgical approach but might also help in better time management in clinical practice.

  19. Plasmon dispersion and dynamic exchange-correlation potential from two-pair excitations in degenerate plasmas

    International Nuclear Information System (INIS)

    Boehm, H.M.; Conti, S.; Tosi, M.P.

    1995-11-01

    Electron energy loss experiments have shown a rapid softening of the bulk plasmon dispersion across the series of the alkali metals. Motivated by these observations, we reconsider the evaluation of the dynamic, long-wavelength exchange-correlation potential f xc (ω) in the electron fluid, which is of interest for applications in time-dependent density functional theory. The value of Re[f xc (ω pl )] at the plasma frequency ω pl determines the exchange-correlation contribution to the leading plasmon dispersion coefficient in the homogeneous electron fluid. Whereas an interpolation scheme originally proposed by Gross and Kohn assumes a monotonic increase of Re[f xc (ω) - f xc (0)] across the plasma frequency, we examine the possibility of strongly non-monotonic behaviour arising from a resonance process between plasmons and two-pair excitations. This process is evaluated with the help of sum rules and selfconsistency requirements with a single-pole approximation of the dielectric function. The cases of a fermion plasma and of a boson plasma are treated in parallel and the reliability of the results for the fermion plasma at low coupling is tested by calculations within a random phase approximation for the dielectric function. In all cases it is found that the resonance process accumulates oscillator strength in the neighbourhood of 2ω pl , thus decreasing the value of Re[f xc (ω pl )] below the static value f xc (0) fixed by the compressibility sum rule. Although this lowering does not suffice to account by itself for the measured plasmon dispersion coefficient in the low-density alkali metals, our results provide useful input for combined band-structure and exchange-correlation calculations. (author). 40 refs, 9 figs, 2 tabs

  20. Dynamics of host-reservoir transmission of Ebola with spillover potential to humans

    Directory of Open Access Journals (Sweden)

    Berge Tsanou

    2018-04-01

    Full Text Available Ebola virus disease (EVD is a zoonotic borne disease (i.e. disease that is spread from animals to people. Therefore human beings can be infected through direct contact with an infected animal (fruit-eating bat or great ape. It has been demonstrated that fruit-eating bats of pteropodidae family are potential reservoir of EVD. Moreover, it has been biologically shown that fruit-eating bats do not die due to EVD and bear the Ebola viruses lifelong. We develop in this paper, a mathematical model to assess the impact of the reservoir on the dynamics of EVD. Our model couples a bat-to-bat model with a human-to-human model and the indirect environmental contamination through a spillover process (i.e. process by which a zoonotic pathogen moves (regardless of transmission mode from an animal host (or environmental reservoir to a human host from bats to humans. The sub-models and the coupled models exhibit each a threshold behavior with the corresponding basic reproduction numbers being the bifurcation parameters. Existence of equilibria, their global stability are established by combining monotone operator theory, Lyapunov-LaSalle techniques and graph theory. Control strategies are assessed by using the target reproduction numbers. The efforts required to control EVD are assessed as well through S-control. The spillover event is shown to be highly detrimental to EVD by allowing the disease to switch from bats to humans even though the disease was not initially endemic in the human population. Precisely, we show that the spillover phenomenon contributes to speed up the disease outbreak. This suggests that the manipulation and consumption of fruit-bats play an important role in sustaining EVD in a given environment.

  1. Competitive Semantic Memory Retrieval: Temporal Dynamics Revealed by Event-Related Potentials.

    Science.gov (United States)

    Hellerstedt, Robin; Johansson, Mikael

    2016-01-01

    Memories compete for retrieval when they are related to a common retrieval cue. Previous research has shown that retrieval of a target memory may lead to subsequent retrieval-induced forgetting (RIF) of currently irrelevant competing memories. In the present study, we investigated the time course of competitive semantic retrieval and examined the neurocognitive mechanisms underlying RIF. We contrasted two theoretical accounts of RIF by examining a critical aspect of this memory phenomenon, namely the extent to which it depends on successful retrieval of the target memory. Participants first studied category-exemplar word-pairs (e.g. Fruit-Apple). Next, we recorded electrophysiological measures of brain activity while the participants performed a competitive semantic cued-recall task. In this task, the participants were provided with the studied categories but they were instructed to retrieve other unstudied exemplars (e.g. Fruit-Ma__?). We investigated the event-related potential (ERP) correlates of retrieval success by comparing ERPs from successful and failed retrieval trials. To isolate the ERP correlates of continuous retrieval attempts from the ERP correlates of retrieval success, we included an impossible retrieval condition, with incompletable word-stem cues (Drinks-Wy__) and compared it with a non-retrieval presentation baseline condition (Occupation-Dentist). The participants' memory for all the studied exemplars was tested in the final phase of the experiment. Taken together, the behavioural results suggest that RIF is independent of target retrieval. Beyond investigating the mechanisms underlying RIF, the present study also elucidates the temporal dynamics of semantic cued-recall by isolating the ERP correlates of retrieval attempt and retrieval success. The ERP results revealed that retrieval attempt is reflected in a late posterior negativity, possibly indicating construction of candidates for completing the word-stem cue and retrieval monitoring

  2. Potential of an ensemble Kalman smoother for stratospheric chemical-dynamical data assimilation

    Directory of Open Access Journals (Sweden)

    Thomas Milewski

    2013-02-01

    Full Text Available A new stratospheric ensemble Kalman smoother (EnKS system is introduced, and the potential of assimilating posterior stratospheric observations to better constrain the whole model state at analysis time is investigated. A set of idealised perfect-model Observation System Simulation Experiments (OSSE assimilating synthetic limb-sounding temperature or ozone retrievals are performed with a chemistry–climate model. The impact during the analysis step is characterised in terms of the root mean square error reduction between the forecast state and the analysis state. The performances of (1 a fixed-lag EnKS assimilating observations spread over 48 hours and (2 an ensemble Kalman Filter (EnKF assimilating a denser network of observations are compared with a reference EnKF. The ozone assimilation with EnKS shows a significant additional reduction of analysis error of the order of 10% for dynamical and chemical variables in the extratropical upper troposphere lower stratosphere (UTLS and Polar Vortex regions when compared to the reference EnKF. This reduction has similar magnitude to the one achieved by the denser-network EnKF assimilation. Similarly, the temperature assimilation with EnKS significantly decreases the error in the UTLS for the wind variables like the denser-network EnKF assimilation. However, the temperature assimilation with EnKS has little or no significant impact on the temperature and ozone analyses, whereas the denser-network EnKF shows improvement with respect to the reference EnKF. The different analysis impacts from the assimilation of current and posterior ozone observations indicate the capacity of time-lagged background-error covariances to represent temporal interactions up to 48 hours between variables during the ensemble data assimilation analysis step, and the possibility to use posterior observations whenever additional current observations are unavailable. The possible application of the EnKS for reanalyses is

  3. A new hydrocarbon empirical potential in angle bending calculation for the molecular dynamics simulation

    Energy Technology Data Exchange (ETDEWEB)

    Ping, Tan Ai; Hoe, Yeak Su [Department of Mathematical Sciences, Faculty of Science, Universiti Teknologi Malaysia, 81310 UTM Skudai, Johor Bahru, Johor Darul Takzim (Malaysia)

    2014-07-10

    Typically, short range potential only depends on neighbouring atoms and its parameters function can be categorized into bond stretching, angle bending and bond rotation potential. In this paper, we present our work called Angle Bending (AB) potential, whereas AB potential is the extension of our previous work namely Bond Stretching (BS) potential. Basically, potential will tend to zero after truncated region, potential in specific region can be represented by different piecewise polynomial. We proposed the AB piecewise potential which is possible to solve a system involving three atoms. AB potential able to handle the potential of covalent bonds for three atoms as well as two atoms cases due to its degeneracy properties. Continuity for the piecewise polynomial has been enforced by coupling with penalty methods. There are still plenty of improvement spaces for this AB potential. The improvement for three atoms AB potential will be studied and further modified into torsional potential which are the ongoing current research.

  4. Survival and evolution of a large multidrug resistance plasmid in new clinical bacterial hosts

    DEFF Research Database (Denmark)

    Porse, Andreas; Schønning, Kristian; Munck, Christian

    2016-01-01

    Large conjugative plasmids are important drivers of bacterial evolution and contribute significantly to the dissemination of antibiotic resistance. Although plasmid borne multidrug resistance is recognized as one of the main challenges in modern medicine, the adaptive forces shaping the evolution...

  5. A rapid matrix-assisted laser desorption ionization-time of flight mass spectrometry-based method for single-plasmid tracking in an outbreak of carbapenem-resistant Enterobacteriaceae.

    Science.gov (United States)

    Lau, Anna F; Wang, Honghui; Weingarten, Rebecca A; Drake, Steven K; Suffredini, Anthony F; Garfield, Mark K; Chen, Yong; Gucek, Marjan; Youn, Jung-Ho; Stock, Frida; Tso, Hanna; DeLeo, Jim; Cimino, James J; Frank, Karen M; Dekker, John P

    2014-08-01

    Carbapenem-resistant Enterobacteriaceae (CRE) have spread globally and represent a serious and growing threat to public health. Rapid methods for tracking plasmids carrying carbapenemase genes could greatly benefit infection control efforts. Here, we demonstrate that real-time, direct tracking of a single plasmid in a bacterial strain responsible for an outbreak is possible using a commercial matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) system. In this case, we retrospectively tracked the bla(KPC) carbapenemase gene-bearing pKpQIL plasmid responsible for a CRE outbreak that occurred at the NIH Clinical Center in 2011. An ∼ 11,109-Da MS peak corresponding to a gene product of the bla(KPC) pKpQIL plasmid was identified and characterized using a combination of proteomics and molecular techniques. This plasmid peak was present in spectra from retrospectively analyzed K. pneumoniae outbreak isolates, concordant with results from whole-genome sequencing, and absent from a diverse control set of bla(KPC)-negative clinical Enterobacteriaceae isolates. Notably, the gene characterized here is located adjacent to the bla(KPC) Tn4401 transposon on the pKpQIL plasmid. Sequence analysis demonstrates the presence of this gene in other bla(KPC) Tn4401-containing plasmids and suggests that this signature MS peak may be useful in tracking other plasmids conferring carbapenem resistance. Plasmid identification using this MALDI-TOF MS method was accomplished in as little as 10 min from isolated colonies and 30 min from positive (spiked) blood cultures, demonstrating the potential clinical utility for real-time plasmid tracking in an outbreak. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

  6. A Rapid Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry-Based Method for Single-Plasmid Tracking in an Outbreak of Carbapenem-Resistant Enterobacteriaceae

    Science.gov (United States)

    Lau, Anna F.; Wang, Honghui; Weingarten, Rebecca A.; Drake, Steven K.; Suffredini, Anthony F.; Garfield, Mark K.; Chen, Yong; Gucek, Marjan; Youn, Jung-Ho; Stock, Frida; Tso, Hanna; DeLeo, Jim; Cimino, James J.; Frank, Karen M.

    2014-01-01

    Carbapenem-resistant Enterobacteriaceae (CRE) have spread globally and represent a serious and growing threat to public health. Rapid methods for tracking plasmids carrying carbapenemase genes could greatly benefit infection control efforts. Here, we demonstrate that real-time, direct tracking of a single plasmid in a bacterial strain responsible for an outbreak is possible using a commercial matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) system. In this case, we retrospectively tracked the blaKPC carbapenemase gene-bearing pKpQIL plasmid responsible for a CRE outbreak that occurred at the NIH Clinical Center in 2011. An ∼11,109-Da MS peak corresponding to a gene product of the blaKPC pKpQIL plasmid was identified and characterized using a combination of proteomics and molecular techniques. This plasmid peak was present in spectra from retrospectively analyzed K. pneumoniae outbreak isolates, concordant with results from whole-genome sequencing, and absent from a diverse control set of blaKPC-negative clinical Enterobacteriaceae isolates. Notably, the gene characterized here is located adjacent to the blaKPC Tn4401 transposon on the pKpQIL plasmid. Sequence analysis demonstrates the presence of this gene in other blaKPC Tn4401-containing plasmids and suggests that this signature MS peak may be useful in tracking other plasmids conferring carbapenem resistance. Plasmid identification using this MALDI-TOF MS method was accomplished in as little as 10 min from isolated colonies and 30 min from positive (spiked) blood cultures, demonstrating the potential clinical utility for real-time plasmid tracking in an outbreak. PMID:24850353

  7. Genomic Analysis of Hospital Plumbing Reveals Diverse Reservoir of Bacterial Plasmids Conferring Carbapenem Resistance

    Directory of Open Access Journals (Sweden)

    Rebecca A. Weingarten

    2018-02-01

    Full Text Available The hospital environment is a potential reservoir of bacteria with plasmids conferring carbapenem resistance. Our Hospital Epidemiology Service routinely performs extensive sampling of high-touch surfaces, sinks, and other locations in the hospital. Over a 2-year period, additional sampling was conducted at a broader range of locations, including housekeeping closets, wastewater from hospital internal pipes, and external manholes. We compared these data with previously collected information from 5 years of patient clinical and surveillance isolates. Whole-genome sequencing and analysis of 108 isolates provided comprehensive characterization of blaKPC/blaNDM-positive isolates, enabling an in-depth genetic comparison. Strikingly, despite a very low prevalence of patient infections with blaKPC-positive organisms, all samples from the intensive care unit pipe wastewater and external manholes contained carbapenemase-producing organisms (CPOs, suggesting a vast, resilient reservoir. We observed a diverse set of species and plasmids, and we noted species and susceptibility profile differences between environmental and patient populations of CPOs. However, there were plasmid backbones common to both populations, highlighting a potential environmental reservoir of mobile elements that may contribute to the spread of resistance genes. Clear associations between patient and environmental isolates were uncommon based on sequence analysis and epidemiology, suggesting reasonable infection control compliance at our institution. Nonetheless, a probable nosocomial transmission of Leclercia sp. from the housekeeping environment to a patient was detected by this extensive surveillance. These data and analyses further our understanding of CPOs in the hospital environment and are broadly relevant to the design of infection control strategies in many infrastructure settings.

  8. Presence of Glycopeptide-Encoding Plasmids in Enterococcal Isolates from Food and Humans in Denmark

    DEFF Research Database (Denmark)

    Migura, Lourdes Garcia; Valenzuela, Antonio Jesus Sanchez; Jensen, Lars Bogø

    2011-01-01

    developed techniques for classification of plasmids. Replicons associated with sex pheromone-inducible plasmids were detected in all GR E. faecalis, whereas GR Enterococcus faecium contained plasmids known to be widely distributed among enterococci. vanA resistance is common in E. faecium isolates from meat...... and animals in Europe and is rarely found in E. faecalis. This article describes the first characterization of MGE from vanA mediated E. faecalis, thus linking this resistance genotype to pheromone responding plasmids....

  9. Genotoxic activity of 4,4',5'-trimethylazapsoralen on plasmid DNA.

    Science.gov (United States)

    Lagatolla, C; Dolzani, L; Granzotto, M; Monti-Bragadin, C

    1998-01-01

    The genotoxic activities of 8-methoxypsoralen (8-MOP) and 4,4',5'-trimethylazapsoralen (4,4',5'-TMAP) on plasmid DNA have been compared. In a previous work, 4,4',5'-TMAP, a methyl derivative of a psoralen isoster, had shown potential photochemotherapeutic activity. The mutagenic activity of mono- and bifunctional lesions caused by these compounds was evaluated both after UVA irradiation, which causes the formation of both kinds of lesions, and after a two-step irradiation procedure of the psoralen-plasmid DNA complex, which allowed monoadducts and interstrand crosslinks to be studied separately. Furthermore, we used a procedure that allowed us to evaluate both the mutagenic and recombinogenic activity of the two compounds. Results indicate that the most important difference between 8-MOP and 4,4',5'-TMAP consists in their mode of photoreaction with DNA rather than in their mutagenic potential. In fact, in all of the experimental procedures, 4,4',5'-TMAP shows a lower ability than 8-MOP to generate interstrand crosslinks. However, when comparable toxicity levels are reached, the two compounds show the same mutagenic potentiality.

  10. Potential and flux field landscape theory. I. Global stability and dynamics of spatially dependent non-equilibrium systems.

    Science.gov (United States)

    Wu, Wei; Wang, Jin

    2013-09-28

    We established a potential and flux field landscape theory to quantify the global stability and dynamics of general spatially dependent non-equilibrium deterministic and stochastic systems. We extended our potential and flux landscape theory for spatially independent non-equilibrium stochastic systems described by Fokker-Planck equations to spatially dependent stochastic systems governed by general functional Fokker-Planck equations as well as functional Kramers-Moyal equations derived from master equations. Our general theory is applied to reaction-diffusion systems. For equilibrium spatially dependent systems with detailed balance, the potential field landscape alone, defined in terms of the steady state probability distribution functional, determines the global stability and dynamics of the system. The global stability of the system is closely related to the topography of the potential field landscape in terms of the basins of attraction and barrier heights in the field configuration state space. The effective driving force of the system is generated by the functional gradient of the potential field alone. For non-equilibrium spatially dependent systems, the curl probability flux field is indispensable in breaking detailed balance and creating non-equilibrium condition for the system. A complete characterization of the non-equilibrium dynamics of the spatially dependent system requires both the potential field and the curl probability flux field. While the non-equilibrium potential field landscape attracts the system down along the functional gradient similar to an electron moving in an electric field, the non-equilibrium flux field drives the system in a curly way similar to an electron moving in a magnetic field. In the small fluctuation limit, the intrinsic potential field as the small fluctuation limit of the potential field for spatially dependent non-equilibrium systems, which is closely related to the steady state probability distribution functional, is

  11. Plasmid vectors for Xylella fastidiosa utilizing a toxin-antitoxin system for plasmid stability in the absence of antibiotic selection

    Science.gov (United States)

    The phytopathogen Xylella fastidiosa causes disease in a variety of important crop and landscape plants. Functional genetic studies have led to a broader understanding of virulence mechanisms used by this pathogen in the grapevine host. Plasmid shuttle vectors are important tools in studies of bacte...

  12. Dynamic functional coupling of high resolution EEG potentials related to unilateral internally triggered one-digit movements.

    Science.gov (United States)

    Urbano, A; Babiloni, C; Onorati, P; Babiloni, F

    1998-06-01

    Between-electrode cross-covariances of delta (0-3 Hz)- and theta (4-7 Hz)-filtered high resolution EEG potentials related to preparation, initiation. and execution of human unilateral internally triggered one-digit movements were computed to investigate statistical dynamic coupling between these potentials. Significant (P planning, starting, and performance of unilateral movement. The involvement of these cortical areas is supported by the observation that averaged spatially enhanced delta- and theta-bandpassed potentials were computed from the scalp regions where task-related electrical activation of primary sensorimotor areas and supplementary motor area was roughly represented.

  13. Isolation of novel IncA/C and IncN fluoroquinolone resistance plasmids from an antibiotic-polluted lake.

    Science.gov (United States)

    Flach, Carl-Fredrik; Johnning, Anna; Nilsson, Ida; Smalla, Kornelia; Kristiansson, Erik; Larsson, D G Joakim

    2015-10-01

    Antibiotic-polluted environments may function as reservoirs for novel resistance plasmids not yet encountered in pathogens. The aims of this study were to assess the potential of resistance transfer between bacteria from such environments and Escherichia coli, and to characterize the conjugative elements involved. Sediment samples from Kazipally lake and Asanikunta tank, two Indian lakes with a history of severe pollution with fluoroquinolones, were investigated. Proportions of resistant bacteria were determined by selective cultivation, while horizontal gene transfer was studied using a GFP-tagged E. coli as recipient. Retrieved transconjugants were tested for susceptibility by Etest(®) and captured conjugative resistance elements were characterized by WGS. The polluted lakes harboured considerably higher proportions of ciprofloxacin-resistant and sulfamethoxazole-resistant bacteria than did other Indian and Swedish lakes included for comparison (52% versus 2% and 60% versus 7%, respectively). Resistance plasmids were captured from Kazipally lake, but not from any of the other lakes; in the case of Asanikunta tank because of high sediment toxicity. Eight unique IncA/C and IncN resistance plasmids were identified among 11 sequenced transconjugants. Five plasmids were fully assembled, and four of these carried the quinolone resistance gene qnrVC1, which has previously only been found on chromosomes. Acquired resistance genes, in the majority of cases associated with class 1 integrons, could be linked to decreased susceptibility to several different classes of antibiotics. Our study shows that environments heavily polluted with antibiotics contain novel multiresistance plasmids transferrable to E. coli. © The Author 2015. Published by Oxford University Press on behalf of the British Society for Antimicrobial Chemotherapy. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  14. Characterization of a novel plasmid type and various genetic contexts of bla OXA-58 in Acinetobacter spp. from multiple cities in China.

    Directory of Open Access Journals (Sweden)

    Yiqi Fu

    Full Text Available BACKGROUND/OBJECTIVE: Several studies have described the epidemiological distribution of blaOXA-58-harboring Acinetobacter baumannii in China. However, there is limited data concerning the replicon types of blaOXA-58-carrying plasmids and the genetic context surrounding blaOXA-58 in Acinetobacter spp. in China. METHODOLOGY/PRINCIPAL FINDINGS: Twelve non-duplicated blaOXA-58-harboring Acinetobacter spp. isolates were collected from six hospitals in five different cities between 2005 and 2010. The molecular epidemiology of the isolates was carried out using PFGE and multilocus sequence typing. Carbapenemase-encoding genes and plasmid replicase genes were identified by PCR. The genetic location of blaOXA-58 was analyzed using S1-nuclease method. Plasmid conjugation and electrotransformation were performed to evaluate the transferability of blaOXA-58-harboring plasmids. The genetic structure surrounding blaOXA-58 was determined by cloning experiments. The twelve isolates included two Acinetobacter pittii isolates (belong to one pulsotype, three Acinetobacter nosocomialis isolates (belong to two pulsotypes and seven Acinetobacter baumannii isolates (belong to two pulsotypes/sequence types. A. baumannii ST91 was found to be a potential multidrug resistant risk clone carrying both blaOXA-58 and blaOXA-23. blaOXA-58 located on plasmids varied from ca. 52 kb to ca. 143 kb. All plasmids can be electrotransformed to A. baumannii recipient, but were untypeable by the current replicon typing scheme. A novel plasmid replicase named repAci10 was identified in blaOXA-58-harboring plasmids of two A. pittii isolates, three A. nosocomialis isolates and two A. baumannii isolates. Four kinds of genetic contexts of blaOXA-58 were identified. The transformants of plasmids with structure of IS6 family insertion sequence (ISOur1, IS1008 or IS15-ΔISAba3-like element-blaOXA-58 displayed carbapenem nonsusceptible, while others with structure of intact ISAba3-like element

  15. Structural and functional analysis of the kid toxin protein from E. coli Plasmid R1

    NARCIS (Netherlands)

    Hargreaves, D.; Santos-Sierra, S.; Giraldo, R.; Sabariegos-Jareño, R.; de la Cueva-Méndez, G.; Boelens, R.|info:eu-repo/dai/nl/070151407; Díaz-Orejas, R.; Rafferty, J.B.

    2002-01-01

    We have determined the structure of Kid toxin protein from E. coli plasmid R1 involved in stable plasmid inheritance by postsegregational killing of plasmid-less daughter cells. Kid forms a two-component system with its antagonist, Kis antitoxin. Our 1.4 Å crystal structure of Kid reveals a 2-fold

  16. Movement and equipositioning of plasmids by ParA filament disassembly

    DEFF Research Database (Denmark)

    Ringgaard, Simon; van Zon, Jeroen; Howard, Martin

    2009-01-01

    , plasmids consistently migrate behind disassembling ParA cytoskeletal structures, suggesting that ParA filaments pull plasmids by depolymerization. The perpetual cycles of ParA assembly and disassembly result in continuous relocation of plasmids, which, on time averaging, results in equidistribution...

  17. Studies on the expression of plasmid-borne genes in the endosymbiotic state of Rhizobium leguminosarum

    NARCIS (Netherlands)

    Krol, A.J.M.

    1982-01-01

    The subject matter of the research reported in this thesis is the role of plasmid-borne genes of Rhizobium in symbiosis and nitrogen fixation. Plasmid DNA was isolated from Rhizobium leguminosarum strain PRE and the expression of plasmid DNA in nitrogen

  18. Direct Quantum Dynamics Using Grid-Based Wave Function Propagation and Machine-Learned Potential Energy Surfaces.

    Science.gov (United States)

    Richings, Gareth W; Habershon, Scott

    2017-09-12

    We describe a method for performing nuclear quantum dynamics calculations using standard, grid-based algorithms, including the multiconfiguration time-dependent Hartree (MCTDH) method, where the potential energy surface (PES) is calculated "on-the-fly". The method of Gaussian process regression (GPR) is used to construct a global representation of the PES using values of the energy at points distributed in molecular configuration space during the course of the wavepacket propagation. We demonstrate this direct dynamics approach for both an analytical PES function describing 3-dimensional proton transfer dynamics in malonaldehyde and for 2- and 6-dimensional quantum dynamics simulations of proton transfer in salicylaldimine. In the case of salicylaldimine we also perform calculations in which the PES is constructed using Hartree-Fock calculations through an interface to an ab initio electronic structure code. In all cases, the results of the quantum dynamics simulations are in excellent agreement with previous simulations of both systems yet do not require prior fitting of a PES at any stage. Our approach (implemented in a development version of the Quantics package) opens a route to performing accurate quantum dynamics simulations via wave function propagation of many-dimensional molecular systems in a direct and efficient manner.

  19. Evaluation of dynamic message signs and their potential impact on traffic flow.

    Science.gov (United States)

    2013-04-01

    Maryland State Highway Administration (SHA) has a rich data archive of the messages posted to the : Dynamic Message Signs (DMS) and the time stamps when they were posted and taken down. The archive : also contains traffic information surrounding the ...

  20. Simulating the room-temperature dynamic motion of a ferromagnetic vortex in a bistable potential

    Science.gov (United States)

    Haber, E.; Badea, R.; Berezovsky, J.

    2018-05-01

    The ability to precisely and reliably control the dynamics of ferromagnetic (FM) vortices could lead to novel nonvolatile memory devices and logic gates. Intrinsic and fabricated defects in the FM material can pin vortices and complicate the dynamics. Here, we simulated switching a vortex between bistable pinning sites using magnetic field pulses. The dynamic motion was modeled with the Thiele equation for a massless, rigid vortex subject to room-temperature thermal noise. The dynamics were explored both when the system was at zero temperature and at room-temperature. The probability of switching for different pulses was calculated, and the major features are explained using the basins of attraction map of the two pinning sites.

  1. Redox potential dynamics in a grassed swale used for storage and treatment

    Science.gov (United States)

    Vorenhout, Michel; Boogaard, Floris Cornelis

    2016-04-01

    Treatment wetlands are used to remove pollutants from water. Most swales are designed to infiltrate stormwater into the subsurface. A combination of both functions can help to enhance water quality and reduce flooding risks in urban areas. The chemical forms and possible removal of pollutants such as nitrate and heavy metals in wetlands are highly dependent on the redox conditions. The redox conditions are expected to be highly dynamic and dependent on water levels and flow. We studied the correlation between these factors in an urban grassed swale system, and show that more factors play a role in these systems than water levels alone. The study system is located in the World Heritage site "Bryggen" in the city of Bergen, Norway. It consists of a series of SUDS, a socalled treatment train. The system is fed by storm water, which is at first stored in a rain garden then led to grassed swales. Water infiltrates into the subsurface in the swales. The reason for implementation of the system at this site is the protection of the highly organic archaeological layers at the site, which requires reduced conditions. Swales 1 and 2 were equipped with pressure loggers and multi-level redox and temperature probes (-2, -5, -10 and -20cm from surface). Redox and temperature probes were connected to a HYPNOS system. Measurements were taken for more than 1 year at 15 minute interval. A weather station supplemented the dataset with precipitation measurements. The redox potential in the swales show a strong correlation with water level. The regularly flooded swale 2 shows frequent anoxic events (Eh < 200mV) where as swale 1 shows oxic conditions (Eh = 650mV) throughout the same measurement period. Swale 1 has fewer flooding events than Swale 2 and a more coarse soil with less organic matter than swale 2. These redox results are as expected given the local conditions, and show that redox conditions are localised phenomena that depend on local soil conditions. Analysis of the redox

  2. Potentials and challenges associated with automated closed dynamic chamber measurements of soil CO2 fluxes

    Science.gov (United States)

    Görres, Carolyn-Monika; Kammann, Claudia; Ceulemans, Reinhart

    2015-04-01

    Soil respiration fluxes are influenced by natural factors such as climate and soil type, but also by anthropogenic activities in managed ecosystems. As a result, soil CO2 fluxes show a large intra- and interannual as well as intra- and intersite variability. Most of the available soil CO2 flux data giving insights into this variability have been measured with manually closed static chambers, but technological advances in the past 15 years have also led to an increased use of automated closed chamber systems. The great advantage of automated chambers in comparison to manually operated chambers is the higher temporal resolution of the flux data. This is especially important if we want to better understand the effects of short-term events, e.g. fertilization or heavy rainfall, on soil CO2 flux variability. However, the chamber method is an invasive measurement method which can potentially alter soil CO2 fluxes and lead to biased measurement results. In the peer-reviewed literature, many papers compare the field performance and results of different closed static chamber designs, or compare manual chambers with automated chamber systems, to identify potential biases in CO2 flux measurements, and thus help to reduce uncertainties in the flux data. However, inter-comparisons of different automated closed dynamic chamber systems are still lacking. Here we are going to present a field comparison of the most-cited automated chamber system, the LI-8100A Automated Soil Flux System, with the also commercially available Greenhouse Gas Monitoring System AGPS. Both measurement systems were installed side by side at a recently harvested poplar bioenergy plantation (POPFULL, http://uahost.uantwerpen.be/popfull/) from April 2014 until August 2014. The plantation provided optimal comparison conditions with a bare field situation after the harvest and a regrowing canopy resulting in a broad variety of microclimates. Furthermore, the plantation was planted in a double-row system with

  3. Virtual screening for potential inhibitors of Mcl-1 conformations sampled by normal modes, molecular dynamics, and nuclear magnetic resonance

    Directory of Open Access Journals (Sweden)

    Glantz-Gashai Y

    2017-06-01

    Full Text Available Yitav Glantz-Gashai,* Tomer Meirson,* Eli Reuveni, Abraham O Samson Faculty of Medicine in the Galilee, Bar Ilan University, Safed, Israel *These authors contributed equally to this work Abstract: Myeloid cell leukemia-1 (Mcl-1 is often overexpressed in human cancer and is an important target for developing antineoplastic drugs. In this study, a data set containing 2.3 million lead-like molecules and a data set of all the US Food and Drug Administration (FDA-approved drugs are virtually screened for potential Mcl-1 ligands using Protein Data Bank (PDB ID 2MHS. The potential Mcl-1 ligands are evaluated and computationally docked on to three conformation ensembles generated by normal mode analysis (NMA, molecular dynamics (MD, and nuclear magnetic resonance (NMR, respectively. The evaluated potential Mcl-1 ligands are then compared with their clinical use. Remarkably, half of the top 30 potential drugs are used clinically to treat cancer, thus partially validating our virtual screen. The partial validation also favors the idea that the other half of the top 30 potential drugs could be used in the treatment of cancer. The normal mode-, MD-, and NMR-based conformation greatly expand the conformational sampling used herein for in silico identification of potential Mcl-1 inhibitors. Keywords: virtual screening, Mcl-1, molecular dynamics, NMR, normal modes

  4. Contrasting dynamics of leaf potential and gas exchange during progressive drought cycles and recovery in Amorpha fruticosa and Robinia pseudoacacia.

    Science.gov (United States)

    Yan, Weiming; Zheng, Shuxia; Zhong, Yangquanwei; Shangguan, Zhouping

    2017-06-30

    Leaf gas exchange is closely associated with water relations; however, less attention has been given to this relationship over successive drought events. Dynamic changes in gas exchange and water potential in the seedlings of two woody species, Amorpha fruticosa and Robinia pseudoacacia, were monitored during recurrent drought. The pre-dawn leaf water potential declined in parallel with gas exchange in both species, and sharp declines in gas exchange occurred with decreasing water potential. A significant correlation between pre-dawn water potential and gas exchange was observed in both species and showed a right shift in R. pseudoacacia in the second drought. The results suggested that stomatal closure in early drought was mediated mainly by elevated foliar abscisic acid (ABA) in R. pseudoacacia, while a shift from ABA-regulated to leaf-water-potential-driven stomatal closure was observed in A. fruticosa. After re-watering, the pre-dawn water potential recovered quickly, whereas stomatal conductance did not fully recover from drought in R. pseudoacacia, which affected the ability to tightly control transpiration post-drought. The dynamics of recovery from drought suggest that stomatal behavior post-drought may be restricted mainly by hydraulic factors, but non-hydraulic factors may also be involved in R. pseudoacacia.

  5. Pseudo hard-sphere potential for use in continuous molecular-dynamics simulation of spherical and chain molecules.

    Science.gov (United States)

    Jover, J; Haslam, A J; Galindo, A; Jackson, G; Müller, E A

    2012-10-14

    We present a continuous pseudo-hard-sphere potential based on a cut-and-shifted Mie (generalized Lennard-Jones) potential with exponents (50, 49). Using this potential one can mimic the volumetric, structural, and dynamic properties of the discontinuous hard-sphere potential over the whole fluid range. The continuous pseudo potential has the advantage that it may be incorporated directly into off-the-shelf molecular-dynamics code, allowing the user to capitalise on existing hardware and software advances. Simulation results for the compressibility factor of the fluid and solid phases of our pseudo hard spheres are presented and compared both to the Carnahan-Starling equation of state of the fluid and published data, the differences being indistinguishable within simulation uncertainty. The specific form of the potential is employed to simulate flexible chains formed from these pseudo hard spheres at contact (pearl-necklace model) for m(c) = 4, 5, 7, 8, 16, 20, 100, 201, and 500 monomer segments. The compressibility factor of the chains per unit of monomer, m(c), approaches a limiting value at reasonably small values, m(c) theory. Simulation results are also presented for highly asymmetric mixtures of pseudo hard spheres, with diameter ratios of 3:1, 5:1, 20:1 over the whole composition range.

  6. On finding the analytic dependencies of the external field potential on the control function when optimizing the beam dynamics

    Science.gov (United States)

    Ovsyannikov, A. D.; Kozynchenko, S. A.; Kozynchenko, V. A.

    2017-12-01

    When developing a particle accelerator for generating the high-precision beams, the injection system design is of importance, because it largely determines the output characteristics of the beam. At the present paper we consider the injection systems consisting of electrodes with given potentials. The design of such systems requires carrying out simulation of beam dynamics in the electrostatic fields. For external field simulation we use the new approach, proposed by A.D. Ovsyannikov, which is based on analytical approximations, or finite difference method, taking into account the real geometry of the injection system. The software designed for solving the problems of beam dynamics simulation and optimization in the injection system for non-relativistic beams has been developed. Both beam dynamics and electric field simulations in the injection system which use analytical approach and finite difference method have been made and the results presented in this paper.

  7. The significance of the amorphous potential energy landscape for dictating glassy dynamics and driving solid-state crystallisation

    DEFF Research Database (Denmark)

    Ruggiero, Michael T; Krynski, Marcin; Kissi, Eric Ofosu

    2017-01-01

    clear experimental and computational evidence in support of a theory that proposes that the shape and structure of the potential-energy surface (PES) is the fundamental factor underlying the glass-transition processes, regardless of the frequency that experimental methods probe. Whilst this has been....... Combined, these findings provide compelling evidence that the PES landscape, and the corresponding energy barriers, are the ultimate controlling feature behind the atomic and molecular dynamics of disordered solids, regardless of the frequency at which they occur....... proposed previously, we demonstrate, using ab initio molecular-dynamics (AIMD) simulations, that it is of critical importance to carefully consider the complete PES - both the intra-molecular and inter-molecular features - in order to fully understand the entire range of atomic-dynamical processes...

  8. Development of inducer-free expression plasmids based on IPTG-inducible promoters for Bacillus subtilis.

    Science.gov (United States)

    Tran, Dinh Thi Minh; Phan, Trang Thi Phuong; Huynh, Thanh Kieu; Dang, Ngan Thi Kim; Huynh, Phuong Thi Kim; Nguyen, Tri Minh; Truong, Tuom Thi Tinh; Tran, Thuoc Linh; Schumann, Wolfgang; Nguyen, Hoang Duc

    2017-07-25

    the inducible vector using the same promoter. Finally, we used gfp as a reporter gene in combination with the two promoters Pgrac01 and Pgrac100 to test the new vector types. The GFP expression levels could be repressed at least 1.5 times for the Pgrac01-gfp+ inducer-free construct in E. coli. The inducer-free constructs Pgrac01-gfp+ and Pgrac100-gfp+ allowed GFP expression at high levels from 23 × 10 4 to 32 × 10 4 RFU units and 9-13% of total intracellular proteins. We could reconfirm the two major advantages of the new inducer-free expression plasmids: (1) Strong repression of the target gene expression in the E. coli cloning strain, and (2) production of the target protein at high levels in B. subtilis in the absence of the inducer. We propose a general strategy to generate inducer-free expression vector by using IPTG-inducible vectors, and more specifically we developed inducer-free expression plasmids using IPTG-inducible promoters in the absence of the LacI repressor. These plasmids could be an excellent choice for high-level production of recombinant proteins in B. subtilis without the addition of inducer and at the same time maintaining a low basal level of the recombinant proteins in E. coli. The repression of the recombinant gene expression would facilitate cloning of genes that potentially inhibit the growth of E. coli cloning strains. The inducer-free expression plasmids will be extended versions of the current available IPTG-inducible expression vectors for B. subtilis, in which all these vectors use the same cognate promoters. These inducer-free and previously developed IPTG-inducible expression plasmids will be a useful cassette to study gene expression at a small scale up to a larger scale up for the production of recombinant proteins.

  9. Investigation of diversity of plasmids carrying the blaTEM-52 gene

    DEFF Research Database (Denmark)

    Bielak, Eliza Maria; Bergenholtz, Rikke D.; Jørgensen, Mikael Skaanning

    2011-01-01

    OBJECTIVES: To investigate the diversity of plasmids that carry blaTEM-52 genes among Escherichia coli and Salmonella enterica originating from animals, meat products and humans. METHODS: A collection of 22 blaTEM-52-encoding plasmids was characterized by restriction fragment length polymorphism...... of self-transfer to a plasmid-free E. coli recipient. CONCLUSIONS: The blaTEM-52 gene found in humans could have been transmitted on transferable plasmids originating from animal sources. Some of the blaTEM-52 plasmids carry replicons that differ from the classical ones. Two novel replicons were detected...

  10. Does the QCD vacuum build up a colour chemical potential dynamically?

    International Nuclear Information System (INIS)

    Sailer, K.; Greiner, W.

    1998-01-01

    The one-loop effective theory is found for QCD assuming an overcritical homogeneous gluon vector potential background that corresponds to a non-vanishing colour chemical potential. It is found that the vacuum is unstable against building up a non-vanishing colour chemical potential for sufficiently large number of flavours. (author)

  11. Comparison of ionospheric convection and the transpolar potential before and after solar wind dynamic pressure fronts: implications for magnetospheric reconnection

    Science.gov (United States)

    Boudouridis, A.; Zesta, E.; Lyons, L. R.; Kim, H.-J.; Lummerzheim, D.; Wiltberger, M.; Weygand, J. M.; Ruohoniemi, J. M.; Ridley, A. J.

    2012-04-01

    The solar wind dynamic pressure, both through its steady state value and through its variations, plays an important role in the determination of the state of the terrestrial magnetosphere and ionosphere, its effects being only secondary to those of the Interplanetary Magnetic Field (IMF). Recent studies have demonstrated the significant effect solar wind dynamic pressure enhancements have on ionospheric convection and the transpolar potential. Further studies have shown a strong response of the polar cap boundary and thus the open flux content of the magnetosphere. These studies clearly illustrate the strong coupling of solar wind dynamic pressure fronts to the terrestrial magnetosphere-ionosphere system. We present statistical studies of the response of Super Dual Auroral Radar Network (SuperDARN) flows, and Assimilative Mapping of Ionospheric Electrodynamics (AMIE) transpolar potentials to sudden enhancements in solar wind dynamic pressure. The SuperDARN results show that the convection is enhanced within both the dayside and nightside ionosphere. The dayside response is more clear and immediate, while the response on the nightside is slower and more evident for low IMF By values. AMIE results show that the overall convection, represented by the transpolar potential, has a strong response immediately after an increase in pressure, with magnitude and duration modulated by the background IMF Bz conditions. We compare the location of the SuperDARN convection enhancements with the location and motion of the polar cap boundary, as determined by POLAR Ultra-Violet Imager (UVI) images and runs of the Lyon-Fedder-Mobarry (LFM) global magnetohydrodynamic model for specific events. We find that the boundary exhibits a poleward motion after the increase in dynamic pressure. The enhanced ionospheric flows and the poleward motion of the boundary on the nightside are both signatures of enhanced tail reconnection, a conclusion that is reinforced by the observation of the

  12. Plasmids and packaging cell lines for use in phage display

    Science.gov (United States)

    Bradbury, Andrew M.

    2012-07-24

    The invention relates to a novel phagemid display system for packaging phagemid DNA into phagemid particles which completely avoids the use of helper phage. The system of the invention incorporates the use of bacterial packaging cell lines which have been transformed with helper plasmids containing all required phage proteins but not the packaging signals. The absence of packaging signals in these helper plasmids prevents their DNA from being packaged in the bacterial cell, which provides a number of significant advantages over the use of both standard and modified helper phage. Packaged phagemids expressing a protein or peptide of interest, in fusion with a phage coat protein such as g3p, are generated simply by transfecting phagemid into the packaging cell line.

  13. Plasmid DNA damage induced by helium atmospheric pressure plasma jet

    Science.gov (United States)

    Han, Xu; Cantrell, William A.; Escobar, Erika E.; Ptasinska, Sylwia

    2014-03-01

    A helium atmospheric pressure plasma jet (APPJ) is applied to induce damage to aqueous plasmid DNA. The resulting fractions of the DNA conformers, which indicate intact molecules or DNA with single- or double-strand breaks, are determined using agarose gel electrophoresis. The DNA strand breaks increase with a decrease in the distance between the APPJ and DNA samples under two working conditions of the plasma source with different parameters of applied electric pulses. The damage level induced in the plasmid DNA is also enhanced with increased plasma irradiation time. The reactive species generated in the APPJ are characterized by optical emission spectra, and their roles in possible DNA damage processes occurring in an aqueous environment are also discussed.

  14. Transfer of the lambdadv plasmid to new bacterial hosts

    International Nuclear Information System (INIS)

    Kellenberger-Gujer, G.; Boy de la Tour, E.; Berg, D.E.

    1974-01-01

    Lambda dv, which was derived from bacteriophage lambda, replicates autonomously as a plasmid in Escherichia coli and consists of only the immunity region (imm/sup lambda/) and DNA replication genes (O, P) of the ancestral phage. Addition phages (lambda imm 21 --lambda dv) carry the lambda dv fragment inserted as a tandem duplication in their genome (sequence A imm 21 O P imm/sup lambda/ O P R) are formed as recombinants after lambda imm 21 infection of strains carrying lambda dv. Addition phages were used to transfer lambda dv to new bacterial hosts. Lambda dv transfer by excision of the lambda dv segment from the addition phage genome requires a bacterial Rec or a phage Red recombination system. Successful transfer is stimulated by uv irradiation of the addition phage before infection. Some properties of the newly transferred lambda dv plasmids are described. (U.S.)

  15. Quasi-potential and Two-Scale Large Deviation Theory for Gillespie Dynamics

    KAUST Repository

    Li, Tiejun

    2016-01-07

    The construction of energy landscape for bio-dynamics is attracting more and more attention recent years. In this talk, I will introduce the strategy to construct the landscape from the connection to rare events, which relies on the large deviation theory for Gillespie-type jump dynamics. In the application to a typical genetic switching model, the two-scale large deviation theory is developed to take into account the fast switching of DNA states. The comparison with other proposals are also discussed. We demonstrate different diffusive limits arise when considering different regimes for genetic translation and switching processes.

  16. {lambda}{sub MS} from the static potential for QCD with n{sub f}=2 dynamical quark flavors

    Energy Technology Data Exchange (ETDEWEB)

    Jansen, Karl [Deutsches Elektronen-Synchrotron (DESY), Zeuthen (Germany); Roma Univ. ' ' Tor Vergata' ' (Italy). Dipt. di Fisica; INFN, Roma (Italy); Karbstein, Felix [Helmholtz-Institut Jena (Germany); Jena Univ. (Germany). Theoretisch-Physikalisches Inst.; Nagy, Attila [Humboldt Univ. Berlin (Germany); Wagner, Marc [Frankfurt Univ. (Germany). Inst. fuer Theoretische Physik

    2011-12-15

    We determine {lambda}{sub MS} for QCD with n{sub f}=2 dynamical quark flavors by fitting the Q anti Q static potential known analytically in the perturbative regime up to terms of O({alpha}{sub s}{sup 4}) and {proportional_to}{alpha}{sub s}{sup 4} ln{alpha}{sub s} to corresponding results obtained from lattice simulations. This has become possible, due to recent advances in both perturbative calculations, namely the determination and publication of the last missing contribution to the Q anti Q static potential at O({alpha}{sub s}{sup 4}), and lattice simulations with n{sub f}=2 dynamical quark flavors performed at the rather fine lattice spacing of a{approx}0.042 fm. Imposing conservative error estimates we obtain {lambda}{sub MS}=315(30) MeV. (orig.)

  17. Presence and analysis of plasmids in human and animal associated arcobacter species.

    Directory of Open Access Journals (Sweden)

    Laid Douidah

    Full Text Available In this study, we report the screening of four Arcobacter species for the presence of small and large plasmids. Plasmids were present in 9.9% of the 273 examined strains. One Arcobacter cryaerophilus and four Arcobacter butzleri plasmids were selected for further sequencing. The size of three small plasmids isolated from A. butzleri and the one from A. cryaerophilus strains ranged between 4.8 and 5.1 kb, and the size of the large plasmid, isolated from A. butzleri, was 27.4 kbp. The G+C content of all plasmids ranged between 25.4% and 26.2%. A total of 95% of the large plasmid sequence represents coding information, which contrasts to the 20 to 30% for the small plasmids. Some of the open reading frames showed a high homology to putative conserved domains found in other related organisms, such as replication, mobilization and genes involved in type IV secretion system. The large plasmid carried 35 coding sequences, including seven genes in a contiguous region of 11.6 kbp that encodes an orthologous type IV secretion system found in the Wolinella succinogenes genome, Helicobacter pylori and Campylobacter jejuni plasmids, which makes this plasmid interesting for further exploration.

  18. Proton-induced direct and indirect damage of plasmid DNA

    Czech Academy of Sciences Publication Activity Database

    Vyšín, Luděk; Pachnerová Brabcová, Kateřina; Štěpán, V.; Moretto-Capelle, P.; Bugler, B.; Legube, G.; Cafarelli, P.; Casta, R.; Champeaux, J. P.; Sence, M.; Vlk, M.; Wagner, Richard; Štursa, Jan; Zach, Václav; Incerti, S.; Juha, Libor; Davídková, Marie

    2015-01-01

    Roč. 54, č. 3 (2015), s. 343-352 ISSN 0301-634X R&D Projects: GA ČR GA13-28721S; GA MŠk LD12008; GA MŠk LM2011019 Institutional support: RVO:68378271 ; RVO:61389005 Keywords : proton radiation * DNA plasmid * direct and indirect effects * clustered damage * repair enzymes Subject RIV: BO - Biophysics Impact factor: 1.923, year: 2015

  19. Differences in the stability of the plasmids of Yersinia pestis cultures in vitro: impact on virulence

    Directory of Open Access Journals (Sweden)

    TC Leal-Balbino

    2004-11-01

    Full Text Available Plasmid and chromosomal genes encode determinants of virulence for Yersinia pestis, the causative agent of plague. However, in vitro, Y. pestis genome is very plastic and several changes have been described. To evaluate the alterations in the plasmid content of the cultures in vitro and the impact of the alterations to their pathogenicity, three Y. pestis isolates were submitted to serial subculture, analysis of the plasmid content, and testing for the presence of characteristic genes in each plasmid of colonies selected after subculture. Different results were obtained with each strain. The plasmid content of one of them was shown to be stable; no apparent alteration was produced through 32 subcultures. In the other two strains, several alterations were observed. LD50 in mice of the parental strains and the derived cultures with different plasmid content were compared. No changes in the virulence plasmid content could be specifically correlated with changes in the LD50.

  20. Ab initio interaction potentials for X and B excited states of He-I2 for studying dynamics

    International Nuclear Information System (INIS)

    Prosmiti, Rita; Garcia-Gutierrez, Leonor; Delgado-Tellez, Laura; Valdes, Alvaro; Villarreal, Pablo; Delgado-Barrio, Gerardo

    2009-01-01

    Ab initio CCSD(T) and MRCI approaches were employed to construct potential energy surfaces of the ground and the B electronic excited states of He-I 2 complex, while full quantum mechanical methods were applied to study its spectroscopy and dynamics. A description of the approach adopted, together with the results obtained and their comparison with recent experimental data, as well as further improvements are presented.

  1. Damage of plasmid DNA by high energy ions

    International Nuclear Information System (INIS)

    Michaelidesova, A.; Pachnerova Brabcova, K.; Davidkova, M.

    2018-01-01

    The aim of the study was to determine the degree of direct DNA damage by high-energy ions, which are one of the components of cosmic rays, and therefore the knowledge of the biological effects of these ions is key to long-term space missions with human crew. The pBR322 plasmid containing 4361 base pairs was used in this study. The aqueous solution of plasmid pBR322 was transferred on ice to Japan to the Heavy Ion Medical Accelerator in Chiba, the Research Center for Charged Particle Therapy. Just before the experiment, the droplets of solution of known concentration were applied to the slides and the water was allowed to evaporate to produce dry DNA samples. Half of the slides were irradiated with 290 MeV/u of carbon ions and a dose rate of 20 Gy/min. The other half of the slides were irradiated with helium nuclei of 150 MeV/hr and a dose rate of 12.6 Gy/min. Both sets of slides were irradiated with doses of 0-1,400 Gy with a 200 Gy step. After irradiation, the samples were re-dissolved in distilled water, frozen and transported on ice to the Czech Republic for processing. Samples were analyzed by agarose gel electrophoresis. The plasmid was evaluated separately to determine the degree of radiation induced lesions and further to incubation with enzymes recognizing basal damage. (authors)

  2. Dynamical properties for an ensemble of classical particles moving in a driven potential well with different time perturbation

    International Nuclear Information System (INIS)

    Costa, Diogo Ricardo da; Caldas, I.L.; Leonel, Edson D.

    2013-01-01

    We consider dynamical properties for an ensemble of classical particles confined to an infinite box of potential and containing a time-dependent potential well described by different nonlinear functions. For smooth functions, the phase space contains chaotic trajectories, periodic islands and invariant spanning curves preventing the unlimited particle diffusion along the energy axis. Average properties of the chaotic sea are characterised as a function of the control parameters and exponents describing their behaviour show no dependence on the perturbation functions. Given invariant spanning curves are present in the phase space, a sticky region was observed and show to modify locally the diffusion of the particles

  3. Dynamic Tear test and its potential for evaluating the toughness of welds

    International Nuclear Information System (INIS)

    Mara, G.L.

    1975-01-01

    The Dynamic Tear (DT) test is used to evaluate the influence of electron beam welding on the mechanical properties of HP-9-4-20 and 250 maraging steel. Basic trade-offs in strength and toughness are identified thereby revealing the usefulness and degree of sensitivity of the test. (auth)

  4. Quasi-potential and Two-Scale Large Deviation Theory for Gillespie Dynamics

    KAUST Repository

    Li, Tiejun; Li, Fangting; Li, Xianggang; Lu, Cheng

    2016-01-01

    theory for Gillespie-type jump dynamics. In the application to a typical genetic switching model, the two-scale large deviation theory is developed to take into account the fast switching of DNA states. The comparison with other proposals are also

  5. Membrane Potential Dynamics of Spontaneous and Visually Evoked Gamma Activity in V1 of Awake Mice

    NARCIS (Netherlands)

    Perrenoud, Q.; Pennartz, C.M.A.; Gentet, L.J.

    2016-01-01

    Cortical gamma activity (30-80 Hz) is believed to play important functions in neural computation and arises from the interplay of parvalbumin-expressing interneurons (PV) and pyramidal cells (PYRs). However, the subthreshold dynamics underlying its emergence in the cortex of awake animals remain

  6. Dynamic Wolbachia prevalence in Acromyrmex leaf‐cutting ants: potential for a nutritional symbiosis

    DEFF Research Database (Denmark)

    Andersen, S. B.; Boye, Mette; Nash, D. R.

    2012-01-01

    Wolbachia are renowned as reproductive parasites, but their phenotypic effects in eusocial insects are not well understood. We used a combination of qrt‐PCR, fluorescence in situ hybridization and laser scanning confocal microscopy to evaluate the dynamics of Wolbachia infections in the leaf‐cutting...

  7. Potential effects of timber harvest and water management on streamflow dynamics and sediment transport

    Science.gov (United States)

    C. A. Troendle; W. K. Olsen

    1994-01-01

    The sustainability of aquatic and riparian ecological systems is strongly tied to the dynamics of the streamflow regime. Timber harvest can influence the flow regime by increasing total flow, altering peak discharge rate, and changing the duration of flows of differing frequency of occurrence. These changes in the energy and sediment transporting capability of the...

  8. [Adaptogenic potentialities of dynamic magnetotherapy in the treatment and prevention of ENT pathology in ailing children].

    Science.gov (United States)

    Bolotova, N V; Grinkevich, A V; Grishchenko, T P; Raĭgorodskiĭ, Iu M; Tupkin, V D

    2007-01-01

    Efficacy of dynamic magnetotherapy (in transcranial and adrenal variants) for treatment of ENT pathology and prevention of its exacerbations is demonstrated in 126 ailing children. Mechanism of action of this magnetotherapy is due to formation of adequate adaptation reactions raising resistance to pathogens.

  9. Development of EEM based silicon–water and silica–water wall potentials for non-reactive molecular dynamics simulations

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Junghan; Iype, Eldhose; Frijns, Arjan J.H.; Nedea, Silvia V.; Steenhoven, Anton A. van

    2014-07-01

    Molecular dynamics simulations of heat transfer in gases are computationally expensive when the wall molecules are explicitly modeled. To save computational time, an implicit boundary function is often used. Steele's potential has been used in studies of fluid–solid interface for a long time. In this work, the conceptual idea of Steele's potential was extended in order to simulate water–silicon and water–silica interfaces. A new wall potential model is developed by using the electronegativity-equalization method (EEM), a ReaxFF empirical force field and a non-reactive molecular dynamics package PumMa. Contact angle simulations were performed in order to validate the wall potential model. Contact angle simulations with the resulting tabulated wall potentials gave a silicon–water contact angle of 129°, a quartz–water contact angle of 0°, and a cristobalite–water contact angle of 40°, which are in reasonable agreement with experimental values.

  10. Characterization of a Large Antibiotic Resistance Plasmid Found in Enteropathogenic Escherichia coli Strain B171 and Its Relatedness to Plasmids of Diverse E. coli and Shigella Strains.

    Science.gov (United States)

    Hazen, Tracy H; Michalski, Jane; Nagaraj, Sushma; Okeke, Iruka N; Rasko, David A

    2017-09-01

    Enteropathogenic Escherichia coli (EPEC) is a leading cause of severe infantile diarrhea in developing countries. Previous research has focused on the diversity of the EPEC virulence plasmid, whereas less is known regarding the genetic content and distribution of antibiotic resistance plasmids carried by EPEC. A previous study demonstrated that in addition to the virulence plasmid, reference EPEC strain B171 harbors a second, larger plasmid that confers antibiotic resistance. To further understand the genetic diversity and dissemination of antibiotic resistance plasmids among EPEC strains, we describe the complete sequence of an antibiotic resistance plasmid from EPEC strain B171. The resistance plasmid, pB171_90, has a completed sequence length of 90,229 bp, a GC content of 54.55%, and carries protein-encoding genes involved in conjugative transfer, resistance to tetracycline ( tetA ), sulfonamides ( sulI ), and mercury, as well as several virulence-associated genes, including the transcriptional regulator hha and the putative calcium sequestration inhibitor ( csi ). In silico detection of the pB171_90 genes among 4,798 publicly available E. coli genome assemblies indicates that the unique genes of pB171_90 ( csi and traI ) are primarily restricted to genomes identified as EPEC or enterotoxigenic E. coli However, conserved regions of the pB171_90 plasmid containing genes involved in replication, stability, and antibiotic resistance were identified among diverse E. coli pathotypes. Interestingly, pB171_90 also exhibited significant similarity with a sequenced plasmid from Shigella dysenteriae type I. Our findings demonstrate the mosaic nature of EPEC antibiotic resistance plasmids and highlight the need for additional sequence-based characterization of antibiotic resistance plasmids harbored by pathogenic E. coli . Copyright © 2017 American Society for Microbiology.

  11. The broad-host-range plasmid pSFA231 isolated from petroleum-contaminated sediment represents a new member of the PromA plasmid family.

    Science.gov (United States)

    Li, Xiaobin; Top, Eva M; Wang, Yafei; Brown, Celeste J; Yao, Fei; Yang, Shan; Jiang, Yong; Li, Hui

    2014-01-01

    A self-transmissible broad-host-range (BHR) plasmid pSFA231 was isolated from petroleum-contaminated sediment in Shen-fu wastewater irrigation zone, China, using the triparental mating exogenous plasmid capture method. Based on its complete sequence the plasmid has a size of 41.5 kb and codes for 50 putative open reading frames (orfs), 29 of which represent genes involved in replication, partitioning and transfer functions of the plasmid. Phylogenetic analysis grouped pSFA231 into the newly defined PromA plasmid family, which currently includes five members. Further comparative genomic analysis shows that pSFA231 shares the common backbone regions with the other PromA plasmids, i.e., genes involved in replication, maintenance and control, and conjugative transfer. Nevertheless, phylogenetic divergence was found in specific gene products. We propose to divide the PromA group into two subgroups, PromA-α (pMRAD02, pSB102) and PromA-β (pMOL98, pIPO2T, pSFA231, pTer331), based on the splits network analysis of the RepA protein. Interestingly, a cluster of hypothetical orfs located between parA and traA of pSFA231 shows high similarity with the corresponding regions on pMOL98, pIPO2T, and pTer331, suggesting these hypothetical orfs may represent "essential" plasmid backbone genes for the PromA-β subgroup. Alternatively, they may also be accessory genes that were first acquired and then stayed as the plasmid diverged. Our study increases the available collection of complete genome sequences of BHR plasmids, and since pSFA231 is the only characterized PromA plasmid from China, our findings also enhance our understanding of the genetic diversity of this plasmid group in different parts of the world.

  12. The broad-host-range plasmid pSFA231 isolated from petroleum-contaminated sediment represents a new member of the PromA plasmid family

    Directory of Open Access Journals (Sweden)

    Xiaobin eLi

    2015-01-01

    Full Text Available A self-transmissible broad-host-range (BHR plasmid pSFA231 was isolated from petroleum-contaminated sediment in Shen-fu wastewater irrigation zone, China, using the triparental mating exogenous plasmid capture method. Based on its complete sequence the plasmid has a size of 41.5 kb and codes for 50 putative open reading frames (orfs, 28 of which represent genes involved in replication, partitioning and transfer functions of the plasmid. Phylogenetic analysis grouped pSFA231 into the newly defined PromA plasmid family, which currently includes five members. Further comparative genomic analysis shows that pSFA231 shares the common backbone regions with the other PromA plasmids, i.e., genes involved in replication, maintenance and control, and conjugative transfer. Nevertheless, phylogenetic divergence was found in specific gene products. We propose to divide the PromA group into two subgroups, PromA-α (pMRAD02, pSB102 and PromA-β (pMOL98, pIPO2T, pSFA231, pTer331, based on the splits network analysis of the RepA protein. Interestingly, a cluster of hypothetical orfs located between parA and traA of pSFA231 shows high similarity with the corresponding regions on pMOL98, pIPO2T and pTer331, suggesting these hypothetical orfs may represent ‘‘essential’’ plasmid backbone genes for the PromA-β subgroup. Alternatively, they may also be accessory genes that were first acquired and then stayed as the plasmid diverged. Our study increases the available collection of complete genome sequences of BHR plasmids, and since pSFA231 is the only characterized PromA plasmid from China, our findings also enhance our understanding of the genetic diversity of this plasmid group in different parts of the world.

  13. On computing stress in polymer systems involving multi-body potentials from molecular dynamics simulation

    Science.gov (United States)

    Fu, Yao; Song, Jeong-Hoon

    2014-08-01

    Hardy stress definition has been restricted to pair potentials and embedded-atom method potentials due to the basic assumptions in the derivation of a symmetric microscopic stress tensor. Force decomposition required in the Hardy stress expression becomes obscure for multi-body potentials. In this work, we demonstrate the invariance of the Hardy stress expression for a polymer system modeled with multi-body interatomic potentials including up to four atoms interaction, by applying central force decomposition of the atomic force. The balance of momentum has been demonstrated to be valid theoretically and tested under various numerical simulation conditions. The validity of momentum conservation justifies the extension of Hardy stress expression to multi-body potential systems. Computed Hardy stress has been observed to converge to the virial stress of the system with increasing spatial averaging volume. This work provides a feasible and reliable linkage between the atomistic and continuum scales for multi-body potential systems.

  14. Effect of thiol pendant conjugates on plasmid DNA binding, release, and stability of polymeric delivery vectors.

    Science.gov (United States)

    Bacalocostantis, Irene; Mane, Viraj P; Kang, Michael S; Goodley, Addison S; Muro, Silvia; Kofinas, Peter

    2012-05-14

    Polymers have attracted much attention as potential gene delivery vectors due to their chemical and structural versatility. However, several challenges associated with polymeric carriers, including low transfection efficiencies, insufficient cargo release, and high cytotoxicity levels have prevented clinical implementation. Strong electrostatic interactions between polymeric carriers and DNA cargo can prohibit complete cargo release within the cell. As a result, cargo DNA never reaches the cell's nucleus where gene expression takes place. In addition, highly charged cationic polymers have been correlated with high cytotoxicity levels, making them unsuitable carriers in vivo. Using poly(allylamine) (PAA) as a model, we investigated how pH-sensitive disulfide cross-linked polymer networks can improve the delivery potential of cationic polymer carriers. To accomplish this, we conjugated thiol-terminated pendant chains onto the primary amines of PAA using 2-iminothiolane, developing three new polymer vectors with 5, 13, or 20% thiol modification. Unmodified PAA and thiol-conjugated polymers were tested for their ability to bind and release plasmid DNA, their capacity to protect genetic cargo from enzymatic degradation, and their potential for endolysosomal escape. Our results demonstrate that polymer-plasmid complexes (polyplexes) formed by the 13% thiolated polymer demonstrate the greatest delivery potential. At high N/P ratios, all thiolated polymers (but not unmodified counterparts) were able to resist decomplexation in the presence of heparin, a negatively charged polysaccharide used to mimic in vivo polyplex-protein interactions. Further, all thiolated polymers exhibited higher buffering capacities than unmodified PAA and, therefore, have a greater potential for endolysosomal escape. However, 5 and 20% thiolated polymers exhibited poor DNA binding-release kinetics, making them unsuitable carriers for gene delivery. The 13% thiolated polymers, on the other hand

  15. Closure of orbits and dynamical symmetry of screened Coulomb potential and isotropic harmonic oscillator

    International Nuclear Information System (INIS)

    Zeng Bei; Zeng Jinyan

    2002-01-01

    It is shown that for any central potential V(r) there exist a series of conserved aphelion and perihelion vectors R-tilde=pxL-g(r)r, g(r)=rV ' (r). However, if and only if V(r) is a pure or screened Coulomb potential, R-tilde and L constitute an SO 4 algebra in the subspace spanned by the degenerate states with a given energy eigenvalue E ' . While dR/dt=0 always holds, dR ' /dt=0 holds only at the aphelia and perihelia. Moreover, the space spanning the SO 4 algebra for a screened Coulomb potential is smaller than that for a pure Coulomb potential. The relation of closed orbits for a screened Coulomb potential with that for a pure Coulomb potential is clarified. The ratio of the radial frequency ω r and angular frequency ω φ , ω r /ω φ =κ=1 for a pure Coulomb potential irrespective of the angular momentum L and energy E(<0). For a screened Coulomb potential κ is determined by the angular momentum L, and when κ is any rational number (κ<1), the orbit is closed. The situation for a pure or screened isotropic harmonic oscillator is similar

  16. Potential energy savings using dynamically optimizing control in refrigeration systems under daily variations in ambient temperature

    DEFF Research Database (Denmark)

    Larsen, Lars Finn Sloth; Thybo, Claus; Wisniewski, Rafal

    2007-01-01

    The objective of this study is to investigate the energy saving potential for refrigeration systems by refrigeration more at the colder night time than at the warmer day time. The potential is evaluated using an optimal control policy and illustrated on a simulation example. The results show...

  17. F-127-PEI co-delivering docetaxel and TFPI-2 plasmid for nasopharyngeal cancer therapy

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Tao, E-mail: taoliu18@126.com [Department of Otolaryngology, Zhujiang Hospital, Southern Medical University, Guangzhou 510282 (China); Zhang, Xinyu [Department of Otolaryngology, Zhujiang Hospital, Southern Medical University, Guangzhou 510282 (China); Ke, Bo [Jiangxi Key Laboratory of Hematological Oncology and Cell Biology, Jiangxi Provincial People' s Hospital, Nanchang 330006 (China); Wang, Yigang [School of Life Sciences, Zhejiang Sci-Tech University, Hangzhou 310018 (China); Wu, Xidong [Department of Pharmacology, Jiangxi Institute of Materia Medica,Nanchang 330029 (China); Jiang, Gang [Department of Otolaryngology, Zhujiang Hospital, Southern Medical University, Guangzhou 510282 (China); Wu, Ting [Department of Light Chemical Engineering, Guangdong Polytechnic, Foshan 528041 (China); Nie, Guohui, E-mail: nghui@21cn.com [Department of Otolaryngological, Peking University Shenzhen Hospital, Shenzhen 518036 (China)

    2016-04-01

    The co-delivery of drug and gene has become the primary strategy in cancer therapy. However, to construct one safe co-delivering system with higher drug loading and gene transfection efficiency for cancer therapy is still challenging. Herein, a novel degradable nanocarriers were synthesized and characterized in this study, which was composed of polyethylenimine (PEI)-linked PEO–PPO–PEO (Pluronic F127), called F127-PEI. Then the nanocarrier was used for hydrophobic docetaxel (DOC) and functional gene (TFPI-2 plasmid) co-delivery to treat nasopharyngeal cancer (NPC). The results indicated that F127-PEI nanocarriers had higher DOC loading amount and possessed good gene delivery effect in vitro. For co-delivery analysis, the obtained F127-PEI/DOC/TFPI-2 complexes could induce a more significant apoptosis than DOC or TFPI-2 alone, and decreased invasive capacity of NPC HNE-1 cells more obviously. Moreover, the F127-PEI copolymer exhibited better blood compatibility and lower cytotoxicity compared to PEI-25k by the hemolysis and MTT assays, which suggests a promising potential for NPC therapy. - Highlights: • F127-PEI was synthesized and used for drug and gene co-delivery. • F127-PEI showed good delivery ability to docetaxel and TFPI-2 plasmid. • The co-loaded complexes showed synergistic effect to nasopharyngeal carcinoma. • F127-PEI showed better blood safety and lower cytotoxicity compared to PEI-25k.

  18. Generation of Induced Pluripotent Stem Cells from Frozen Buffy Coats using Non-integrating Episomal Plasmids.

    Science.gov (United States)

    Meraviglia, Viviana; Zanon, Alessandra; Lavdas, Alexandros A; Schwienbacher, Christine; Silipigni, Rosamaria; Di Segni, Marina; Chen, Huei-Sheng Vincent; Pramstaller, Peter P; Hicks, Andrew A; Rossini, Alessandra

    2015-06-05

    Somatic cells can be reprogrammed into induced pluripotent stem cells (iPSCs) by forcing the expression of four transcription factors (Oct-4, Sox-2, Klf-4, and c-Myc), typically expressed by human embryonic stem cells (hESCs). Due to their similarity with hESCs, iPSCs have become an important tool for potential patient-specific regenerative medicine, avoiding ethical issues associated with hESCs. In order to obtain cells suitable for clinical application, transgene-free iPSCs need to be generated to avoid transgene reactivation, altered gene expression and misguided differentiation. Moreover, a highly efficient and inexpensive reprogramming method is necessary to derive sufficient iPSCs for therapeutic purposes. Given this need, an efficient non-integrating episomal plasmid approach is the preferable choice for iPSC derivation. Currently the most common cell type used for reprogramming purposes are fibroblasts, the isolation of which requires tissue biopsy, an invasive surgical procedure for the patient. Therefore, human peripheral blood represents the most accessible and least invasive tissue for iPSC generation. In this study, a cost-effective and viral-free protocol using non-integrating episomal plasmids is reported for the generation of iPSCs from human peripheral blood mononuclear cells (PBMNCs) obtained from frozen buffy coats after whole blood centrifugation and without density gradient separation.

  19. Plasmid DNA loaded chitosan nanoparticles for nasal mucosal immunization against hepatitis B.

    Science.gov (United States)

    Khatri, Kapil; Goyal, Amit K; Gupta, Prem N; Mishra, Neeraj; Vyas, Suresh P

    2008-04-16

    This work investigates the preparation and in vivo efficacy of plasmid DNA loaded chitosan nanoparticles for nasal mucosal immunization against hepatitis B. Chitosan pDNA nanoparticles were prepared using a complex coacervation process. Prepared nanoparticles were characterized for size, shape, surface charge, plasmid loading and ability of nanoparticles to protect DNA against nuclease digestion and for their transfection efficacy. Nasal administration of nanoparticles resulted in serum anti-HBsAg titre that was less compared to that elicited by naked DNA and alum adsorbed HBsAg, but the mice were seroprotective within 2 weeks and the immunoglobulin level was above the clinically protective level. However, intramuscular administration of naked DNA and alum adsorbed HBsAg did not elicit sIgA titre in mucosal secretions that was induced by nasal immunization with chitosan nanoparticles. Similarly, cellular responses (cytokine levels) were poor in case of alum adsorbed HBsAg. Chitosan nanoparticles thus produced humoral (both systemic and mucosal) and cellular immune responses upon nasal administration. The study signifies the potential of chitosan nanoparticles as DNA vaccine carrier and adjuvant for effective immunization through non-invasive nasal route.

  20. F-127-PEI co-delivering docetaxel and TFPI-2 plasmid for nasopharyngeal cancer therapy

    International Nuclear Information System (INIS)

    Liu, Tao; Zhang, Xinyu; Ke, Bo; Wang, Yigang; Wu, Xidong; Jiang, Gang; Wu, Ting; Nie, Guohui

    2016-01-01

    The co-delivery of drug and gene has become the primary strategy in cancer therapy. However, to construct one safe co-delivering system with higher drug loading and gene transfection efficiency for cancer therapy is still challenging. Herein, a novel degradable nanocarriers were synthesized and characterized in this study, which was composed of polyethylenimine (PEI)-linked PEO–PPO–PEO (Pluronic F127), called F127-PEI. Then the nanocarrier was used for hydrophobic docetaxel (DOC) and functional gene (TFPI-2 plasmid) co-delivery to treat nasopharyngeal cancer (NPC). The results indicated that F127-PEI nanocarriers had higher DOC loading amount and possessed good gene delivery effect in vitro. For co-delivery analysis, the obtained F127-PEI/DOC/TFPI-2 complexes could induce a more significant apoptosis than DOC or TFPI-2 alone, and decreased invasive capacity of NPC HNE-1 cells more obviously. Moreover, the F127-PEI copolymer exhibited better blood compatibility and lower cytotoxicity compared to PEI-25k by the hemolysis and MTT assays, which suggests a promising potential for NPC therapy. - Highlights: • F127-PEI was synthesized and used for drug and gene co-delivery. • F127-PEI showed good delivery ability to docetaxel and TFPI-2 plasmid. • The co-loaded complexes showed synergistic effect to nasopharyngeal carcinoma. • F127-PEI showed better blood safety and lower cytotoxicity compared to PEI-25k

  1. ZVI Addition in Continuous Anaerobic Digestion Systems Dramatically Decreases P Recovery Potential: Dynamic Modelling

    DEFF Research Database (Denmark)

    Puyol, D.; Flores Alsina, Xavier; Segura, Y.

    2017-01-01

    The objective of this study is to show the preliminary results of a (dynamic) mathematical model describing the effects of zero valent iron (ZVI) addition during the anaerobic digestion of waste activated sludge from wastewater treatment systems. A modified version of the Anaerobic Digestion Model...... No. 1 (ADM1) upgraded with an improved physico-chemical description, ZVI corrosion, propionate uptake enhancement and multiple mineral precipitation is used as a modelling platform. The proposed approach is tested against two case studies which correspond to two lab scale anaerobic digesters (AD2, AD....... Simulations demonstrate that the model is capable to satisfactorily reproduce the dynamics of hydrolysis, acetogenesis, acidogenesis, nutrient release, pH and methanogenesis in the control anaerobic digester (AD1). This study also evidences the enhancement of methane production by the influence of ZVI...

  2. Soliton dynamical properties of Bose—Einstein condensates trapped in a double square well potential

    International Nuclear Information System (INIS)

    Li Jin-Hui; Li Zhi-Jian

    2011-01-01

    We first present an analytical solution of the single and double solitions of Bose—Einstein condensates trapped in a double square well potential using the multiple-scale method. Then, we show by numerical calculation that a dark soliton can be transmitted through the square well potential. With increasing depth of the square well potential, the amplitude of the dark soliton becomes larger, and the soliton propagates faster. In particular, we treat the collision behaviour of the condensates trapped in either equal or different depths of the double square well potential. If we regard the double square well potential as the output source of the solitons, the collision locations (position and time) between two dark solitons can be controlled by its depth. (general)

  3. Expansion of a plasmid classification system for Gram-positive bacteria and determination of the diversity of plasmids in Staphylococcus aureus strains of human, animal, and food origins

    DEFF Research Database (Denmark)

    Lozano, C.; Garcia-Migura, L.; Aspiroz, C.

    2012-01-01

    An expansion of a previously described plasmid classification was performed and used to reveal the plasmid content of a collection of 92 Staphylococcus aureus strains of different origins. rep genes of other genera were detected in Staphylococcus. S1 pulsed-field gel electrophoresis (PFGE) hybrid...

  4. Potential role of vegetation dynamics on recent extreme droughts over tropical South America

    Science.gov (United States)

    Wang, G.; Erfanian, A.; Fomenko, L.

    2017-12-01

    Tropical South America is a drought hot spot. In slightly over a decade (2005-2016), the region encountered three extreme droughts (2005, 2010, and 2016). Recurrent extreme droughts not only impact the region's eco-hydrology and socio-economy, but are also globally important as they can transform the planet's largest rainforest, the Amazon, from a carbon sink to a carbon source. Understanding drought drivers and mechanisms underlying extreme droughts in tropical South America can help better project the fate of the Amazon rainforest in a changing climate. In this study we use a regional climate model (RegCM4.3.4) coupled with a comprehensive land-surface model (CLM4.5) to study the present-day hydroclimate of the region, focusing specifically on what might have caused the frequent recurrence of extreme droughts. In the context of observation natural variability of the global oceanic forcing, we tackle the role of land-atmosphere interactions and ran the model with and without dynamic vegetation to study how vegetation dynamics and carbon-nitrogen cycles may have influenced the drought characteristics. Our results demonstrate skillful simulation of the South American climate in the model, and indicate substantial sensitivity of the region's hydroclimatology to vegetation dynamics. This presentation will compare the role of global oceanic forcing versus regional land surface feedback in the recent recurrent droughts, and will characterize the effects of vegetation dynamics in enhancing the drought severity. Preliminary results on future projections of the regional ecosystem and droughts perspective will be also presented.

  5. Efficient Exploration of Reactive Potential Energy Surfaces Using Car-Parrinello Molecular Dynamics

    OpenAIRE

    Iannuzzi, Marcella; Laio, Alessandro; Parrinello, Michele

    2003-01-01

    The possibility of observing chemical reactions in ab initio molecular dynamics runs is severely hindered by the short simulation time accessible. We propose a new method for accelerating the reaction process, based on the ideas of the extended Lagrangian and coarse-grained non-Markovian metady- namics. We demonstrate that by this method it is possible to simulate reactions involving complex atomic rearrangements and very large energy barriers in runs of a few picoseconds.

  6. North Korea after Kim Chong-il: Leadership Dynamics and Potential Crisis Scenarios

    Science.gov (United States)

    2011-11-01

    legal responsibility, and with specified procedures , the actual process is different.3 To date, regime dynamics in the Kim Chong-il era have been... procedures and regulations provide the outlines of formal rule, the 3 For a detailed examination of how...was also made an alternate member. It is also worth noting that 10 of the 12 members of the NDC were represented in the new Politburo lineup , thus

  7. Is the Potential for International Diversification Disappearing? A Dynamic Copula Approach

    DEFF Research Database (Denmark)

    Christoffersen, Peter; Errunza, Vihang; Jacobs, Kris

    International equity markets are characterized by nonlinear dependence and asymmetries. We propose a new dynamic asymmetric copula model to capture long-run and short-run dependence, multivariate nonnormality, and asymmetries in large cross-sections. We find that copula correlations have increased...... and nonlinear dependence. The bene…fits from international diversi…cation have reduced over time, drastically so for DMs. EMs still offer signi…cant diversi…cation bene…ts, especially during large market downturns....

  8. Potential for Assessing Dynamic Problem-Solving at the Beginning of Higher Education Studies

    OpenAIRE

    Benő Csapó; Gyöngyvér Molnár

    2017-01-01

    There is a growing demand for assessment instruments which can be used in higher education, which cover a broader area of competencies than the traditional tests for disciplinary knowledge and domain-specific skills, and which measure students' most important general cognitive capabilities. Around the age of the transition from secondary to tertiary education, such assessments may serve several functions, including selecting the best-prepared candidates for certain fields of study. Dynamic pr...

  9. Peircean semiotics and transmedia dynamics. Communicational potentiality of the model of Semiosis

    Directory of Open Access Journals (Sweden)

    Geane Carvalho Alzamora

    2014-11-01

    Full Text Available In this article, we discuss the pragmatic relationship between semiosis and communication in order to characterize transmedia dynamics as a pragmatic offshoot of semiosis in media, a perspective that accounts for the incompleteness of the interpretant in its meditated actions. The theoretical approach is based on the communication perspective of the sign developed by Charles Sanders Peirce and his contemporary commentators, such as Parmentier (1985, Colapietro (1995, 2004, Santaella (1992, 1995, 2003, 2004, and Bergman (2000, 2003, 2007. In addition, transmedia dynamics are explored according to Jenkins (2001, 2006, 2013, Göran (2012, and Jansson (2013. We discuss the notion of media as sign mediation and transmedia dynamics as an improvement of semiosis, based on the pragmatic approach to the latter. Transmedia narratives refer to integrated media experiences that unfold across a variety of platforms, attracting audience engagement and offering new and pertinent content. Moreover, the productive incompleteness of the interpretant is taken as a conceptual parameter for understanding the way in which media consumption regulates habits and delineates the transmedia narrative in the sign process of network associations. In conclusion, we stress how the semiotic operation of representation, associating new signs and collateral experience, without losing the narrative reference (semiotic operation of determination, emerged in transmedia environments.

  10. Equilibrium Molecular Dynamics (MD Simulation Study of Thermal Conductivity of Graphene Nanoribbon: A Comparative Study on MD Potentials

    Directory of Open Access Journals (Sweden)

    Asir Intisar Khan

    2015-12-01

    Full Text Available The thermal conductivity of graphene nanoribbons (GNRs has been investigated using equilibrium molecular dynamics (EMD simulation based on Green-Kubo (GK method to compare two interatomic potentials namely optimized Tersoff and 2nd generation Reactive Empirical Bond Order (REBO. Our comparative study includes the estimation of thermal conductivity as a function of temperature, length and width of GNR for both the potentials. The thermal conductivity of graphene nanoribbon decreases with the increase of temperature. Quantum correction has been introduced for thermal conductivity as a function of temperature to include quantum effect below Debye temperature. Our results show that for temperatures up to Debye temperature, thermal conductivity increases, attains its peak and then falls off monotonically. Thermal conductivity is found to decrease with the increasing length for optimized Tersoff potential. However, thermal conductivity has been reported to increase with length using 2nd generation REBO potential for the GNRs of same size. Thermal conductivity, for the specified range of width, demonstrates an increasing trend with the increase of width for both the concerned potentials. In comparison with 2nd generation REBO potential, optimized Tersoff potential demonstrates a better modeling of thermal conductivity as well as provides a more appropriate description of phonon thermal transport in graphene nanoribbon. Such comparative study would provide a good insight for the optimization of the thermal conductivity of graphene nanoribbons under diverse conditions.

  11. Type 3 Fimbriae Encoded on Plasmids Are Expressed from a Unique Promoter without Affecting Host Motility, Facilitating an Exceptional Phenotype That Enhances Conjugal Plasmid Transfer

    DEFF Research Database (Denmark)

    Madsen, Jonas Stenlokke; Riber, Leise; Kot, Witold

    2016-01-01

    Horizontal gene transfer (HGT), the transmission of genetic material to a recipient that is not the progeny of the donor, is fundamental in bacterial evolution. HGT is often mediated by mobile genetic elements such as conjugative plasmids, which may be in conflict with the chromosomal elements...... of the genome because they are independent replicons that may petition their own evolutionary strategy. Here we study differences between type 3 fimbriae encoded on wild type plasmids and in chromosomes. Using known and newly characterized plasmids we show that the expression of type 3 fimbriae encoded...... on plasmids is systematically different, as MrkH, a c-di-GMP dependent transcriptional activator is not needed for strong expression of the fimbriae. MrkH is required for expression of type 3 fimbriae of the Klebsiella pneumoniae chromosome, wherefrom the fimbriae operon (mrkABCDF) of plasmids is believed...

  12. Solar Potential Analysis and Integration of the Time-Dependent Simulation Results for Semantic 3d City Models Using Dynamizers

    Science.gov (United States)

    Chaturvedi, K.; Willenborg, B.; Sindram, M.; Kolbe, T. H.

    2017-10-01

    Semantic 3D city models play an important role in solving complex real-world problems and are being adopted by many cities around the world. A wide range of application and simulation scenarios directly benefit from the adoption of international standards such as CityGML. However, most of the simulations involve properties, whose values vary with respect to time, and the current generation semantic 3D city models do not support time-dependent properties explicitly. In this paper, the details of solar potential simulations are provided operating on the CityGML standard, assessing and estimating solar energy production for the roofs and facades of the 3D building objects in different ways. Furthermore, the paper demonstrates how the time-dependent simulation results are better-represented inline within 3D city models utilizing the so-called Dynamizer concept. This concept not only allows representing the simulation results in standardized ways, but also delivers a method to enhance static city models by such dynamic property values making the city models truly dynamic. The dynamizer concept has been implemented as an Application Domain Extension of the CityGML standard within the OGC Future City Pilot Phase 1. The results are given in this paper.

  13. Rift Valley fever in a zone potentially occupied by Aedes vexans in Senegal: dynamics and risk mapping

    Directory of Open Access Journals (Sweden)

    Cécile Vignolles

    2009-05-01

    Full Text Available This paper presents an analysis of the interaction between the various variables associated with Rift Valley fever (RVF such as the mosquito vector, available hosts and rainfall distribution. To that end, the varying zones potentially occupied by mosquitoes (ZPOM, rainfall events and pond dynamics, and the associated exposure of hosts to the RVF virus by Aedes vexans, were analyzed in the Barkedji area of the Ferlo, Senegal, during the 2003 rainy season. Ponds were identified by remote sensing using a high-resolution SPOT-5 satellite image. Additional data on ponds and rainfall events from the Tropical Rainfall Measuring Mission were combined with in-situ entomological and limnimetric measurements, and the localization of vulnerable ruminant hosts (data derived from QuickBird satellite. Since “Ae. vexans productive events” are dependent on the timing of rainfall for their embryogenesis (six days without rain are necessary to trigger hatching, the dynamic spatio-temporal distribution of Ae. vexans density was based on the total rainfall amount and pond dynamics. Detailed ZPOM mapping was obtained on a daily basis and combined with aggressiveness temporal profiles. Risks zones, i.e. zones where hazards and vulnerability are combined, are expressed by the percentages of parks where animals are potentially exposed to mosquito bites. This new approach, simply relying upon rainfall distribution evaluated from space, is meant to contribute to the implementation of a new, operational early warning system for RVF based on environmental risks linked to climatic and environmental conditions.

  14. Water dissociating on rigid Ni(100): A quantum dynamics study on a full-dimensional potential energy surface

    Science.gov (United States)

    Liu, Tianhui; Chen, Jun; Zhang, Zhaojun; Shen, Xiangjian; Fu, Bina; Zhang, Dong H.

    2018-04-01

    We constructed a nine-dimensional (9D) potential energy surface (PES) for the dissociative chemisorption of H2O on a rigid Ni(100) surface using the neural network method based on roughly 110 000 energies obtained from extensive density functional theory (DFT) calculations. The resulting PES is accurate and smooth, based on the small fitting errors and the good agreement between the fitted PES and the direct DFT calculations. Time dependent wave packet calculations also showed that the PES is very well converged with respect to the fitting procedure. The dissociation probabilities of H2O initially in the ground rovibrational state from 9D quantum dynamics calculations are quite different from the site-specific results from the seven-dimensional (7D) calculations, indicating the importance of full-dimensional quantum dynamics to quantitatively characterize this gas-surface reaction. It is found that the validity of the site-averaging approximation with exact potential holds well, where the site-averaging dissociation probability over 15 fixed impact sites obtained from 7D quantum dynamics calculations can accurately approximate the 9D dissociation probability for H2O in the ground rovibrational state.

  15. Comparative genomics of the IncA/C multidrug resistance plasmid family.

    Science.gov (United States)

    Fricke, W Florian; Welch, Timothy J; McDermott, Patrick F; Mammel, Mark K; LeClerc, J Eugene; White, David G; Cebula, Thomas A; Ravel, Jacques

    2009-08-01

    Multidrug resistance (MDR) plasmids belonging to the IncA/C plasmid family are widely distributed among Salmonella and other enterobacterial isolates from agricultural sources and have, at least once, also been identified in a drug-resistant Yersinia pestis isolate (IP275) from Madagascar. Here, we present the complete plasmid sequences of the IncA/C reference plasmid pRA1 (143,963 bp), isolated in 1971 from the fish pathogen Aeromonas hydrophila, and of the cryptic IncA/C plasmid pRAx (49,763 bp), isolated from Escherichia coli transconjugant D7-3, which was obtained through pRA1 transfer in 1980. Using comparative sequence analysis of pRA1 and pRAx with recent members of the IncA/C plasmid family, we show that both plasmids provide novel insights into the evolution of the IncA/C MDR plasmid family and the minimal machinery necessary for stable IncA/C plasmid maintenance. Our results indicate that recent members of the IncA/C plasmid family evolved from a common ancestor, similar in composition to pRA1, through stepwise integration of horizontally acquired resistance gene arrays into a conserved plasmid backbone. Phylogenetic comparisons predict type IV secretion-like conjugative transfer operons encoded on the shared plasmid backbones to be closely related to a group of integrating conjugative elements, which use conjugative transfer for horizontal propagation but stably integrate into the host chromosome during vegetative growth. A hipAB toxin-antitoxin gene cluster found on pRA1, which in Escherichia coli is involved in the formation of persister cell subpopulations, suggests persistence as an early broad-spectrum antimicrobial resistance mechanism in the evolution of IncA/C resistance plasmids.

  16. NVU dynamics. I. Geodesic motion on the constant-potential-energy hypersurface

    DEFF Research Database (Denmark)

    Ingebrigtsen, Trond; Toxværd, Søren; Heilmann, Ole

    2011-01-01

    that ensures potential-energy and step-length conservation; center-of-mass drift is also eliminated. Analytical arguments confirmed by simulations demonstrate that the modified NVU algorithm is absolutely stable. Finally, we present simulations showing that the NVU algorithm and the standard leap-frog NVE......An algorithm is derived for computer simulation of geodesics on the constant-potential-energy hypersurface of a system of N classical particles. First, a basic time-reversible geodesic algorithm is derived by discretizing the geodesic stationarity condition and implementing the constant......-potential-energy constraint via standard Lagrangian multipliers. The basic NVU algorithm is tested by single-precision computer simulations of the Lennard-Jones liquid. Excellent numerical stability is obtained if the force cutoff is smoothed and the two initial configurations have identical potential energy within machine...

  17. Evaluation of dynamic message signs and their potential impact on traffic flow : [research summary].

    Science.gov (United States)

    2013-04-01

    The objective of this research was to understand the potential impact of DMS messages on traffic : flow and evaluate their accuracy, timeliness, relevance and usefulness. Additionally, Bluetooth : sensors were used to track and analyze the diversion ...

  18. "Helios Dynamics" A Potential Future Power Source for the Greek Islands

    National Research Council Canada - National Science Library

    Deligiannidis, Ioannis; Angelis, Ioannis

    2007-01-01

    .... Environmental concerns, economic benefits but most of all the potential exhaustion of the current sources of energy, such as fossil fuels, have alarmed the international community and gave incentives...

  19. Trophic dynamics and fishery potentials of the Indian Occean - critical assessment

    Digital Repository Service at National Institute of Oceanography (India)

    Dalal, S.G.; Parulekar, A.H.

    A critical review of the status of the Indian Ocean marine fisheries reveals that the presently exploited annual catch is less than one third of the projected potentials as estimated from the biological productivity and exploratory fishery survey...

  20. Antipersistent dynamics in short time scale variability of self-potential signals

    OpenAIRE

    Cuomo, V.; Lanfredi, M.; Lapenna, V.; Macchiato, M.; Ragosta, M.; Telesca, L.

    2000-01-01

    Time scale properties of self-potential signals are investigated through the analysis of the second order structure function (variogram), a powerful tool to investigate the spatial and temporal variability of observational data. In this work we analyse two sequences of self-potential values measured by means of a geophysical monitoring array located in a seismically active area of Southern Italy. The range of scales investigated goes from a few minutes to several days. It is shown that signal...

  1. High throughput static and dynamic small animal imaging using clinical PET/CT: potential preclinical applications

    International Nuclear Information System (INIS)

    Aide, Nicolas; Desmonts, Cedric; Agostini, Denis; Bardet, Stephane; Bouvard, Gerard; Beauregard, Jean-Mathieu; Roselt, Peter; Neels, Oliver; Beyer, Thomas; Kinross, Kathryn; Hicks, Rodney J.

    2010-01-01

    The objective of the study was to evaluate state-of-the-art clinical PET/CT technology in performing static and dynamic imaging of several mice simultaneously. A mouse-sized phantom was imaged mimicking simultaneous imaging of three mice with computation of recovery coefficients (RCs) and spillover ratios (SORs). Fifteen mice harbouring abdominal or subcutaneous tumours were imaged on clinical PET/CT with point spread function (PSF) reconstruction after injection of [18F]fluorodeoxyglucose or [18F]fluorothymidine. Three of these mice were imaged alone and simultaneously at radial positions -5, 0 and 5 cm. The remaining 12 tumour-bearing mice were imaged in groups of 3 to establish the quantitative accuracy of PET data using ex vivo gamma counting as the reference. Finally, a dynamic scan was performed in three mice simultaneously after the injection of 68 Ga-ethylenediaminetetraacetic acid (EDTA). For typical lesion sizes of 7-8 mm phantom experiments indicated RCs of 0.42 and 0.76 for ordered subsets expectation maximization (OSEM) and PSF reconstruction, respectively. For PSF reconstruction, SOR air and SOR water were 5.3 and 7.5%, respectively. A strong correlation (r 2 = 0.97, p 2 = 0.98; slope = 0.89, p 2 = 0.96; slope = 0.62, p 68 Ga-EDTA dynamic acquisition. New generation clinical PET/CT can be used for simultaneous imaging of multiple small animals in experiments requiring high throughput and where a dedicated small animal PET system is not available. (orig.)

  2. Disease dynamics and potential mitigation among restored and wild staghorn coral, Acropora cervicornis

    Science.gov (United States)

    Lohr, Kathryn E.; Cameron, Caitlin M.; Williams, Dana E.; Peters, Esther C.

    2014-01-01

    The threatened status (both ecologically and legally) of Caribbean staghorn coral, Acropora cervicornis, has prompted rapidly expanding efforts in culture and restocking, although tissue loss diseases continue to affect populations. In this study, disease surveillance and histopathological characterization were used to compare disease dynamics and conditions in both restored and extant wild populations. Disease had devastating effects on both wild and restored populations, but dynamics were highly variable and appeared to be site-specific with no significant differences in disease prevalence between wild versus restored sites. A subset of 20 haphazardly selected colonies at each site observed over a four-month period revealed widely varying disease incidence, although not between restored and wild sites, and a case fatality rate of 8%. A tropical storm was the only discernable environmental trigger associated with a consistent spike in incidence across all sites. Lastly, two field mitigation techniques, (1) excision of apparently healthy branch tips from a diseased colony, and (2) placement of a band of epoxy fully enclosing the diseased margin, gave equivocal results with no significant benefit detected for either treatment compared to controls. Tissue condition of associated samples was fair to very poor; unsuccessful mitigation treatment samples had severe degeneration of mesenterial filament cnidoglandular bands. Polyp mucocytes in all samples were infected with suspect rickettsia-like organisms; however, no bacterial aggregates were found. No histological differences were found between disease lesions with gross signs fitting literature descriptions of white-band disease (WBD) and rapid tissue loss (RTL). Overall, our results do not support differing disease quality, quantity, dynamics, nor health management strategies between restored and wild colonies of A. cervicornis in the Florida Keys. PMID:25210660

  3. Dynamic chaos interference in Hamiltonian systems: experiment and potential radiophysics applications

    International Nuclear Information System (INIS)

    Evdokimov, Nikolai V; Komolov, Pavel V; Komolov, Vladimir P

    2001-01-01

    The sign correlation of quasiperiodic oscillations with close incommensurable frequencies forms a dynamic chaos, which interferes like noise with a single interference peak and is controlled by the delay of its constituent oscillations. This property of oscillations with incommensurable frequencies can be employed in multichannel information transfer systems to form radar reception patterns and obtain uninterrupted coherent key streams in symmetric cryptographic systems. The review of known results on the generation and properties of quasiperiodic oscillations is complemented by a description of new experiments. (methodological notes)

  4. Dynamic NMR under nonstationary conditions: Theoretical model, numerical calculation, and potential of application

    Energy Technology Data Exchange (ETDEWEB)

    Babailov, S. P., E-mail: babajlov@niic.nsc.ru [A. V. Nikolaevs Institute of Inorganic Chemistry, Siberian Branch, Russian Academy of Sciences, Novosibirsk (Russian Federation); National Research Tomsk Polytechnic University, Lenin Avenue 30, Tomsk 634050 (Russian Federation); Purtov, P. A. [Voevodsky Institute of Chemical Kinetics and Combustion, Siberian Branch of the Russian Academy of Sciences, Insitutskaya 3, 630090 Novosibirsk (Russian Federation); Fomin, E. S. [Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Av. Lavrentyev 10, 630090 Novosibirsk (Russian Federation)

    2016-08-07

    An expression has been derived for the time dependence of the NMR line shape for systems with multi-site chemical exchange in the absence of spin-spin coupling, in a zero saturation limit. The dynamics of variation of the NMR line shape with time is considered in detail for the case of two-site chemical exchange. Mathematical programs have been designed for numerical simulation of the NMR spectra of chemical exchange systems. The analytical expressions obtained are useful for NMR line shape simulations for systems with photoinduced chemical exchange.

  5. Price dynamics of the financial markets using the stochastic differential equation for a potential double well

    Science.gov (United States)

    Lima, L. S.; Miranda, L. L. B.

    2018-01-01

    We have used the Itô's stochastic differential equation for the double well with additive white noise as a mathematical model for price dynamics of the financial market. We have presented a model which allows us to test within the same framework the comparative explanatory power of rational agents versus irrational agents, with respect to the facts of financial markets. We have obtained the mean price in terms of the β parameter that represents the force of the randomness term of the model.

  6. Survey of potential use of dynamic line phantom for quality control of Gamma camera

    International Nuclear Information System (INIS)

    Trindev, P.; Ozturk, N.

    2004-01-01

    Different phantoms, used to evaluate the essential for image quality parameters of gamma cameras in order to avoid artefacts, are presented. The prices are significant and it is a sensible approach to optimise the type and number of phantoms necessary for quality control. Among all phantoms the price of 'Dynamic Line Phantom' (DLP) is impressive, but it is announced to substitute several 'passive' and 'active' phantoms. The goal of this paper is to justify this statement. The programs, based on image profile are discussed in the paper and the practical uses of the different programs are given

  7. Mobility and Attenuation Dynamics of Potentially Toxic Chemical Species at an Abandoned Copper Mine Tailings Dump

    Directory of Open Access Journals (Sweden)

    Wilson Mugera Gitari

    2018-02-01

    Full Text Available Large volumes of disposed mine tailings abound in several regions of South Africa, as a consequence of unregulated, unsustainable long years of mining activities. Tailings dumps occupy a large volume of valuable land, and present a potential risk for aquatic systems, through leaching of potentially toxic chemical species. This paper reports on the evaluation of the geochemical processes controlling the mobility of potentially toxic chemical species within the tailings profile, and their potential risk with regard to surface and groundwater systems. Combination of X-ray fluorescence (XRF, X-ray diffraction (XRD, and scanning electron microscopy-energy dispersive spectroscopy (SEM-EDS techniques, show that the tailing profiles are uniform, weakly altered, and vary slightly with depth in both physical and geochemical properties, as well as mineralogical composition. Mineralogical analysis showed the following order of abundance: quartz > epidote > chlorite > muscovite > calcite > hematite within the tailings profiles. The neutralization of the dominant alumino-silicate minerals and the absence of sulfidic minerals, have produced medium alkaline pH conditions (7.97–8.37 at all depths and low concentrations of dissolved Cu (20.21–47.9 µg/L, Zn (0.88–1.80 µg/L, Pb (0.27–0.34 µg/L, and SO42− (15.71–55.94 mg/L in the tailings profile leachates. The relative percentage leach for the potentially toxic chemical species was low in the aqueous phase (Ni 0.081%, Cu 0.006%, and Zn 0.05%. This indicates that the transport load of potentially toxic chemical species from tailings to the aqueous phase is very low. The precipitation of secondary hematite has an important known ability to trap and attenuate the mobility of potentially toxic chemical species (Cu, Zn, and Pb by adsorption on the surface area. Geochemical modelling MINTEQA2 showed that the tailings leachates were below saturation regarding oxyhydroxide minerals, but oversaturated with Cu

  8. Complex forest dynamics indicate potential for slowing carbon accumulation in the southeastern United States.

    Science.gov (United States)

    Coulston, John W; Wear, David N; Vose, James M

    2015-01-23

    Over the past century forest regrowth in Europe and North America expanded forest carbon (C) sinks and offset C emissions but future C accumulation is uncertain. Policy makers need insights into forest C dynamics as they anticipate emissions futures and goals. We used land use and forest inventory data to estimate how forest C dynamics have changed in the southeastern United States and attribute changes to land use, management, and disturbance causes. From 2007-2012, forests yielded a net sink of C because of net land use change (+6.48 Tg C yr(-1)) and net biomass accumulation (+75.4 Tg C yr(-1)). Forests disturbed by weather, insect/disease, and fire show dampened yet positive forest C changes (+1.56, +1.4, +5.48 Tg C yr(-1), respectively). Forest cutting caused net decreases in C (-76.7 Tg C yr(-1)) but was offset by forest growth (+143.77 Tg C yr(-1)). Forest growth rates depend on age or stage of development and projected C stock changes indicate a gradual slowing of carbon accumulation with anticipated forest aging (a reduction of 9.5% over the next five years). Additionally, small shifts in land use transitions consistent with economic futures resulted in a 40.6% decrease in C accumulation.

  9. Non-Gaussian wave packet dynamics in anharmonic potential: Cumulant expansion treatment

    International Nuclear Information System (INIS)

    Toutounji, Mohamad

    2015-01-01

    This manuscript utilizes cumulant expansion as an alternative algebraic approach to evaluating integrals and solving a system of nonlinear differential equations for probing anharmonic dynamics in condensed phase systems using Morse oscillator. These integrals and differential equations become harder to solve as the anharmonicity of the system goes beyond that of Morse oscillator description. This algebraic approach becomes critically important in case of Morse oscillator as it tends to exhibit divergent dynamics and numerical uncertainties at low temperatures. The autocorrelation function is calculated algebraically and compared to the exact one for they match perfectly. It is also compared to the approximate autocorrelation function using the differential equations technique reported in Toutounji (2014) for weak and strong electron–phonon coupling cases. It is found that the present cumulant method is more efficient, and easier to use, than the exact expression. Deviation between the approximate autocorrelation function and the exact autocorrelation function starts to arise as the electron–phonon coupling strength increases. The autocorrelation function obtained using cumulants identically matches the exact autocorrelation function, thereby surpassing the approach presented in Toutounji (2014). The advantage of the present methodology is its applicability to various types of electron–phonon coupling cases. Additionally, the herein approach only uses algebraic techniques, thereby avoiding both the divergence integral and solving a set of linear first- and second-order partial differential equations as was done in previous work. Model calculations are presented to demonstrate the accuracy of the herein work

  10. Probing the dynamic response of antivortex, interstitial and trapped vortex lattices on magnetic periodic pinning potentials

    International Nuclear Information System (INIS)

    Gomez, A; Gonzalez, E M; Vicent, J L; Gilbert, D A; Liu Kai; Milošević, M V

    2013-01-01

    The dynamics of the pinned vortex, antivortex and interstitial vortex have been studied in superconducting/magnetic hybrids consisting of arrays of Co/Pd multilayer nanodots embedded in Nb films. The magnetic nanodots show out-of-plane magnetization at the remanent state. This magnetic state allows for superconducting vortex lattices of different types in an applied homogeneous magnetic field. We experimentally and theoretically show three such lattices: (i) a lattice containing only antivortices; (ii) a vortex lattice entirely pinned on the dots; and (iii) a vortex lattice with pinned and interstitial vortices. Between the flux creep (low vortex velocity) and the free flux flow (high vortex velocity) regimes the interaction between the magnetic array and the vortex lattice governs the vortex dynamics, which in turn enables distinguishing experimentally the type of vortex lattice which governs the dissipation. We show that the vortex lattice with interstitial vortices has the highest onset velocity where the lattice becomes ordered, whereas the pinned vortex lattice has the smallest onset velocity. Further, for this system, we directly estimate that the external force needed to depin vortices is 60% larger than the one needed to depin antivortices; therefore we are able to decouple the antivortex–vortex motion. (paper)

  11. Gauge-invariant dynamical quantities of QED with decomposed gauge potentials

    International Nuclear Information System (INIS)

    Zhou Baohua; Huang Yongchang

    2011-01-01

    We discover an inner structure of the QED system; i.e., by decomposing the gauge potential into two orthogonal components, we obtain a new expansion of the Lagrangian for the electron-photon system, from which, we realize the orthogonal decomposition of the canonical momentum conjugate to the gauge potential with the canonical momentum's two components conjugate to the gauge potential's two components, respectively. Using the new expansion of Lagrangian and by the general method of field theory, we naturally derive the gauge invariant separation of the angular momentum of the electron-photon system from Noether theorem, which is the rational one and has the simplest form in mathematics, compared with the other four versions of the angular momentum separation available in literature. We show that it is only the longitudinal component of the gauge potential that is contained in the orbital angular momentum of the electron, as Chen et al. have said. A similar gauge invariant separation of the momentum is given. The decomposed canonical Hamiltonian is derived, from which we construct the gauge invariant energy operator of the electron moving in the external field generated by a proton [Phys. Rev. A 82, 012107 (2010)], where we show that the form of the kinetic energy containing the longitudinal part of the gauge potential is due to the intrinsic requirement of the gauge invariance. Our method provides a new perspective to look on the nucleon spin crisis and indicates that this problem can be solved strictly and systematically.

  12. Action Potential Dynamics in Fine Axons Probed with an Axonally Targeted Optical Voltage Sensor.

    Science.gov (United States)

    Ma, Yihe; Bayguinov, Peter O; Jackson, Meyer B

    2017-01-01

    The complex and malleable conduction properties of axons determine how action potentials propagate through extensive axonal arbors to reach synaptic terminals. The excitability of axonal membranes plays a major role in neural circuit function, but because most axons are too thin for conventional electrical recording, their properties remain largely unexplored. To overcome this obstacle, we used a genetically encoded hybrid voltage sensor (hVOS) harboring an axonal targeting motif. Expressing this probe in transgenic mice enabled us to monitor voltage changes optically in two populations of axons in hippocampal slices, the large axons of dentate granule cells (mossy fibers) in the stratum lucidum of the CA3 region and the much finer axons of hilar mossy cells in the inner molecular layer of the dentate gyrus. Action potentials propagated with distinct velocities in each type of axon. Repetitive firing broadened action potentials in both populations, but at an intermediate frequency the degree of broadening differed. Repetitive firing also attenuated action potential amplitudes in both mossy cell and granule cell axons. These results indicate that the features of use-dependent action potential broadening, and possible failure, observed previously in large nerve terminals also appear in much finer unmyelinated axons. Subtle differences in the frequency dependences could influence the propagation of activity through different pathways to excite different populations of neurons. The axonally targeted hVOS probe used here opens up the diverse repertoire of neuronal processes to detailed biophysical study.

  13. Multiple drug resistant carbapenemases producing Acinetobacter baumannii isolates harbours multiple R-plasmids

    Directory of Open Access Journals (Sweden)

    Rajagopalan Saranathan

    2014-01-01

    Full Text Available Background & objectives: The nosocomial human pathogen Acinetobacter baumannii has high propensity to develop resistance to antimicrobials and to become multidrug resistant (MDR, consequently complicating the treatment. This study was carried out to investigate the presence of resistant plasmids (R-plasmids among the clinical isolates of A. baumannii. In addition, the study was performed to check the presence of common β-lactamases encoding genes on these plasmids. Methods: A total of 55 clinical isolates of A. baumannii were included in the study and all were subjected to plasmid DNA isolation, followed by PCR to check the presence of resistance gene determinants such as blaOXA-23 , blaOXA-51, blaOXA-58 and blaIMP-1 on these plasmids that encode for oxacillinase (OXA and metallo-β-lactamase (MBL type of carbapenemases. Plasmid curing experiments were carried out on selected isolates using ethidium bromide and acridine orange as curing agents and the antibiotic resistance profiles were evaluated before and after curing. Results: All the isolates were identified as A. baumannii by 16SrDNA amplification and sequencing. Plasmid DNA isolated from these isolates showed the occurrence of multiple plasmids with size ranging from 500bp to ≥ 25 kb. The percentage of blaOXA-51 and blaOXA-23 on plasmids were found to be 78 and 42 per cent, respectively and 20 isolates (36% carried blaIMP-1 gene on plasmids. Significant difference was observed in the antibiograms of plasmid cured isolates when compared to their parental ones. The clinical isolates became susceptible to more than two antibiotic classes after curing of plasmids indicating plasmid borne resistance. Interpretation & conclusions: Our study determined the plasmid mediated resistance mechanisms and occurrence of different resistance genes on various plasmids isolated from MDR A. baumannii. The present findings showed the evidence for antibiotic resistance mediated through multiple plasmids in

  14. The significance of the amorphous potential energy landscape for dictating glassy dynamics and driving solid-state crystallisation.

    Science.gov (United States)

    Ruggiero, Michael T; Krynski, Marcin; Kissi, Eric Ofosu; Sibik, Juraj; Markl, Daniel; Tan, Nicholas Y; Arslanov, Denis; van der Zande, Wim; Redlich, Britta; Korter, Timothy M; Grohganz, Holger; Löbmann, Korbinian; Rades, Thomas; Elliott, Stephen R; Zeitler, J Axel

    2017-11-15

    The fundamental origins surrounding the dynamics of disordered solids near their characteristic glass transitions continue to be fiercely debated, even though a vast number of materials can form amorphous solids, including small-molecule organic, inorganic, covalent, metallic, and even large biological systems. The glass-transition temperature, T g , can be readily detected by a diverse set of techniques, but given that these measurement modalities probe vastly different processes, there has been significant debate regarding the question of why T g can be detected across all of them. Here we show clear experimental and computational evidence in support of a theory that proposes that the shape and structure of the potential-energy surface (PES) is the fundamental factor underlying the glass-transition processes, regardless of the frequency that experimental methods probe. Whilst this has been proposed previously, we demonstrate, using ab initio molecular-dynamics (AIMD) simulations, that it is of critical importance to carefully consider the complete PES - both the intra-molecular and inter-molecular features - in order to fully understand the entire range of atomic-dynamical processes in disordered solids. Finally, we show that it is possible to utilise this dependence to directly manipulate and harness amorphous dynamics in order to control the behaviour of such solids by using high-powered terahertz pulses to induce crystallisation and preferential crystal-polymorph growth in glasses. Combined, these findings provide compelling evidence that the PES landscape, and the corresponding energy barriers, are the ultimate controlling feature behind the atomic and molecular dynamics of disordered solids, regardless of the frequency at which they occur.

  15. Attractive short-range interatomic potential in the lattice dynamics of niobium and tantalum

    International Nuclear Information System (INIS)

    Onwuagba, B.N.; Pal, S.

    1987-01-01

    It is shown in the framework of the pseudopotential approach that there is a sizable attractive short-range component of the interatomic potential due to the s-d interaction which has the same functional form in real space as the Born-Mayer repulsion due to the overlap of core electron wave functions centred on neighbouring ions. The magnitude of this attractive component is such as to completely cancel the conventional Born-Mayer repulsion, making the resultant short-range interatomic potential attractive rather than repulsive. Numerical calculations show that the attractive interatomics potential, which represents the local-field correction, leads to a better understanding of the occurrence of the soft modes in the phonon dispersion curves of niobium and tantalum

  16. Common misconceptions about the dynamical theory of crystal lattices: Cauchy relations, lattice potentials and infinite crystals

    International Nuclear Information System (INIS)

    Elcoro, Luis; Etxebarria, Jesus

    2011-01-01

    The requirement of rotational invariance for lattice potential energies is investigated. Starting from this condition, it is shown that the Cauchy relations for the elastic constants are fulfilled if the lattice potential is built from pair interactions or when the first-neighbour approximation is adopted. This is seldom recognized in widely used solid-state textbooks. Frequently, pair interaction is even considered to be the most general situation. In addition, it is shown that the demand of rotational invariance in an infinite crystal leads to inconsistencies in the symmetry of the elastic tensor. However, for finite crystals, no problems arise, and the Huang conditions are deduced using exclusively a microscopic approach for the elasticity theory, without making any reference to macroscopic parameters. This work may be useful in both undergraduate and graduate level courses to point out the crudeness of the pair-potential interaction and to explore the limits of the infinite-crystal approximation.

  17. Ab initio study on stacking sequences, free energy, dynamical stability and potential energy surfaces of graphite structures

    International Nuclear Information System (INIS)

    Anees, P; Valsakumar, M C; Chandra, Sharat; Panigrahi, B K

    2014-01-01

    Ab initio simulations have been performed to study the structure, energetics and stability of several plausible stacking sequences in graphite. These calculations suggest that in addition to the standard structures, graphite can also exist in AA-simple hexagonal, AB-orthorhombic and ABC-hexagonal type stacking. The free energy difference between these structures is very small (∼1 meV/atom), and hence all the structures can coexist from purely energetic considerations. Calculated x-ray diffraction patterns are similar to those of the standard structures for 2θ ⩽ 70°. Shear elastic constant C 44 is negative in AA-simple hexagonal, AB-orthorhombic and ABC-hexagonal structures, suggesting that these structures are mechanically unstable. Phonon dispersions show that the frequencies of some modes along the Γ–A direction in the Brillouin zone are imaginary in all of the new structures, implying that these structures are dynamically unstable. Incorporation of zero point vibrational energy via the quasi-harmonic approximation does not result in the restoration of dynamical stability. Potential energy surfaces for the unstable normal modes are seen to have the topography of a potential hill for all the new structures, confirming that all of the new structures are inherently unstable. The fact that the potential energy surface is not in the form of a double well implies that the structures are linearly as well as globally unstable. (paper)

  18. The inherent dynamics of a molecular liquid: Geodesic pathways through the potential energy landscape of a liquid of linear molecules

    Science.gov (United States)

    Jacobson, Daniel; Stratt, Richard M.

    2014-05-01

    Because the geodesic pathways that a liquid follows through its potential energy landscape govern its slow, diffusive motion, we suggest that these pathways are logical candidates for the title of a liquid's "inherent dynamics." Like their namesake "inherent structures," these objects are simply features of the system's potential energy surface and thus provide views of the system's structural evolution unobstructed by thermal kinetic energy. This paper shows how these geodesic pathways can be computed for a liquid of linear molecules, allowing us to see precisely how such molecular liquids mix rotational and translational degrees of freedom into their dynamics. The ratio of translational to rotational components of the geodesic path lengths, for example, is significantly larger than would be expected on equipartition grounds, with a value that scales with the molecular aspect ratio. These and other features of the geodesics are consistent with a picture in which molecular reorientation adiabatically follows translation—molecules largely thread their way through narrow channels available in the potential energy landscape.

  19. Coupled iterated map models of action potential dynamics in a one-dimensional cable of cardiac cells

    International Nuclear Information System (INIS)

    Wang Shihong; Xie Yuanfang; Qu Zhilin

    2008-01-01

    Low-dimensional iterated map models have been widely used to study action potential dynamics in isolated cardiac cells. Coupled iterated map models have also been widely used to investigate action potential propagation dynamics in one-dimensional (1D) coupled cardiac cells, however, these models are usually empirical and not carefully validated. In this study, we first developed two coupled iterated map models which are the standard forms of diffusively coupled maps and overcome the limitations of the previous models. We then determined the coupling strength and space constant by quantitatively comparing the 1D action potential duration profile from the coupled cardiac cell model described by differential equations with that of the coupled iterated map models. To further validate the coupled iterated map models, we compared the stability conditions of the spatially uniform state of the coupled iterated maps and those of the 1D ionic model and showed that the coupled iterated map model could well recapitulate the stability conditions, i.e. the spatially uniform state is stable unless the state is chaotic. Finally, we combined conduction into the developed coupled iterated map model to study the effects of coupling strength on wave stabilities and showed that the diffusive coupling between cardiac cells tends to suppress instabilities during reentry in a 1D ring and the onset of discordant alternans in a periodically paced 1D cable

  20. Plasmid DNA damage caused by stibine and trimethylstibine

    International Nuclear Information System (INIS)

    Andrewes, Paul; Kitchin, Kirk T.; Wallace, Kathleen

    2004-01-01

    Antimony is classified as 'possibly carcinogenic to humans' and there is also sufficient evidence for antimony carcinogenicity in experimental animals. Stibine is a volatile inorganic antimony compound to which humans can be exposed in occupational settings (e.g., lead-acid battery charging). Because it is highly toxic, stibine is considered a significant health risk; however, its genotoxicity has received little attention. For the work reported here, stibine was generated by sodium borohydride reduction of potassium antimony tartrate. Trimethylstibine is a volatile organometallic antimony compound found commonly in landfill and sewage fermentation gases at concentrations ranging between 0.1 and 100 μg/m 3 . Trimethylstibine is generally considered to pose little environmental or health risk. In the work reported here, trimethylstibine was generated by reduction of trimethylantimony dichloride using either sodium borohydride or the thiol compounds, dithioerythritol (DTE), L-cysteine, and glutathione. Here we report the evaluation of the in vitro genotoxicities of five antimony compounds--potassium antimony tartrate, stibine, potassium hexahydroxyantimonate, trimethylantimony dichloride, and trimethylstibine--using a plasmid DNA-nicking assay. Of these five antimony compounds, only stibine and trimethylstibine were genotoxic (significant nicking to pBR 322 plasmid DNA). We found stibine and trimethylstibine to be about equipotent with trimethylarsine using this plasmid DNA-nicking assay. Reaction of trimethylantimony dichloride with either glutathione or L-cysteine to produce DNA-damaging trimethylstibine was observed with a trimethylantimony dichloride concentration as low as 50 μM and L-cysteine or glutathione concentrations as low as 500 and 200 μM, respectively, for a 24 h incubation

  1. Reversible entrapment of plasmid deoxyribonucleic acid on different chromatographic supports.

    Science.gov (United States)

    Gabor, Boštjan; Černigoj, Urh; Barut, Miloš; Štrancar, Aleš

    2013-10-11

    HPLC based analytical assay is a powerful technique that can be used to efficiently monitor plasmid DNA (pDNA) purity and quantity throughout the entire purification process. Anion exchange monolithic and non-porous particle based stationary phases were used to study the recovery of the different pDNA isoforms from the analytical column. Three differently sized pDNA molecules of 3.0kbp, 5.2kbp and 14.0kbp were used. Plasmid DNA was injected onto columns under the binding conditions and the separation of the isoforms took place by increasing the ionic strength of the elution buffer. While there was no substantial decrease of the recovered supercoiled and linear isoforms of the pDNA with the increase of the plasmid size and with the increase of the flow rate (recoveries in all cases larger than 75%), a pronounced decrease of the oc isoform recovery was observed. The entrapment of the oc pDNA isoform occurred under non-binding conditions as well. The partial oc isoform elution from the column could be achieved by decreasing the flow rate of the elution mobile phase. The results suggested a reversible entrapment of the oc isoform in the restrictions within the pores of the monolithic material as well as within the intra-particle space of the non-porous particles. This phenomenon was observed on both types of the stationary phase morphologies and could only be connected to the size of a void space through which the pDNA needs to migrate. A prediction of reversible pDNA entrapment was successfully estimated with the calculation of Peclet numbers, Pe, which defines the ratio between a convective and diffusive mass transport. Copyright © 2013 Elsevier B.V. All rights reserved.

  2. Controllability of pure states for the Poeschl-Teller potential with a dynamical group SU(2)

    International Nuclear Information System (INIS)

    Dong, S.-H.; Tang Yu; Sun, G.-H.; Lara-Rosano, F.; Lozada-Cassou, M.

    2005-01-01

    The controllability of a quantum system for the modified Poeschl-Teller (MPT) potential with the discrete bound states is investigated. The creation and annihilation operators of this potential are constructed directly from the normalized wave function with the factorization method and associated to an su(2) algebra. It is shown that this quantum system with the nondegenerate discrete bound states can, in principle, be strongly completely controllable, i.e., the system eigenstates can be guided by the external field to approach arbitrarily close to a target state, which could be theoretically realized by the actions of the creation and annihilation operators on the ground state

  3. Construction of adeno-associated virus packaging plasmids and cells that directly select for AAV helper functions.

    Science.gov (United States)

    Whiteway, Alistair; Deru, Wale; Prentice, H Grant; Anderson, Robert

    2003-12-01

    Recombinant adeno-associated virus type 2 (rAAV) has promise for use as a gene therapy vector. Potential problems in the production of rAAV stocks are both the limited amount of recombinant virus that is produced by traditional methods and the possibility of wild-type replication competent adeno-associated virus (wtAAV) contamination. The presence of these contaminants is largely dependent upon the helper plasmid used. Whilst wtAAV is not a pathogen, the presence of these contaminants is undesirable as they may affect experiments concerning the biology of rAAV. Additionally as protocols using rAAV with altered tropism are becoming more prevalent, it is important that no recombination be permitted that may cause the creation of a replication competent AAV with modified (targeting) capsids. Many experimental protocols require the generation of large amounts of high titre rAAV stocks. We describe the production of several AAV helper plasmids and cell lines designed to achieve this goal. These plasmids possess split AAV rep and cap genes to eliminate the production of wtAAV and they possess a selection mechanism which is operatively linked to expression from the AAV cap gene. This allows positive selection of those cells expressing the highest level of the structural capsid proteins and therefore those cells which yield the highest amount of rAAV.

  4. Recombinant plasmid-based quantitative Real-Time PCR analysis of Salmonella enterica serotypes and its application to milk samples.

    Science.gov (United States)

    Gokduman, Kurtulus; Avsaroglu, M Dilek; Cakiris, Aris; Ustek, Duran; Gurakan, G Candan

    2016-03-01

    The aim of the current study was to develop, a new, rapid, sensitive and quantitative Salmonella detection method using a Real-Time PCR technique based on an inexpensive, easy to produce, convenient and standardized recombinant plasmid positive control. To achieve this, two recombinant plasmids were constructed as reference molecules by cloning the two most commonly used Salmonella-specific target gene regions, invA and ttrRSBC. The more rapid detection enabled by the developed method (21 h) compared to the traditional culture method (90 h) allows the quantitative evaluation of Salmonella (quantification limits of 10(1)CFU/ml and 10(0)CFU/ml for the invA target and the ttrRSBC target, respectively), as illustrated using milk samples. Three advantages illustrated by the current study demonstrate the potential of the newly developed method to be used in routine analyses in the medical, veterinary, food and water/environmental sectors: I--The method provides fast analyses including the simultaneous detection and determination of correct pathogen counts; II--The method is applicable to challenging samples, such as milk; III--The method's positive controls (recombinant plasmids) are reproducible in large quantities without the need to construct new calibration curves. Copyright © 2016 Elsevier B.V. All rights reserved.

  5. Assessing the sustainable development and intensification potential of beef cattle production in Sumbawa, Indonesia, using a system dynamics approach.

    Science.gov (United States)

    Dahlanuddin; Henderson, Benjamin; Dizyee, Kanar; Hermansyah; Ash, Andrew

    2017-01-01

    The intensification of beef cattle production in dryland areas of East Indonesia has the potential to substantially raise the incomes of smallholder farmers that dominate the sector. In this study we assess the potential for intensifying beef production on Sumbawa Island, by introducing a household feedlot production system (2-20 animals) based on the Leucaena leucocephala (leucanea) tree legume as an improved source of feed. We used a system dynamics approach to model the entire value chain, accounting for herd dynamics, demand dynamics and seasonality. Our findings complement the growing body of biophysical evidence about the potential success of this intervention, by simulating improvements in the annual profitability for beef farmers in the project area of up to 415% by 2023. Increases in farm profit were shown to depend near equally on the higher productivity of the leucaena feeding system and an associated price premium, demonstrating the importance of supporting improved agricultural production with better marketing practices. The intervention was also shown to generate positive or neutral benefits for the main post-farm value chain actors. Importantly, it also reduced the GHG emission intensity of outputs from the beef herd by 16% by 2020. We explored number of scale-out pathways, including a relatively moderate pace of autonomous adoption for our main analysis, resulting in the accumulation of 3,444 hectares of leucaena 20-years after the initial project phase, which could sustain the fattening of 37,124 male cattle per year. More ambitious rates of scale-out were found to be possible without exceeding the animal and land resources of the island.

  6. IncA/C plasmids: An emerging threat to human and animal health?

    Science.gov (United States)

    Johnson, Timothy J; Lang, Kevin S

    2012-01-01

    Incompatibility group IncA/C plasmids are large, low copy, theta-replicating plasmids that have been described in the literature for over 40 years. However, they have only recently been intensively studied on the genomic level because of their associations with the emergence of multidrug resistance in enteric pathogens of humans and animals. These plasmids are unique among other enterobacterial plasmids in many aspects, including their modular structure and gene content. While the IncA/C plasmid genome structure has now been well defined, many questions remain pertaining to their basic biological mechanisms of dissemination and regulation. Here, we discuss the history of IncA/C plasmids in light of our recent understanding of their population distribution, genomics, and effects on host bacteria.

  7. Strategies and approaches in plasmidome studies—uncovering plasmid diversity disregarding of linear elements?

    Science.gov (United States)

    Dib, Julián R.; Wagenknecht, Martin; Farías, María E.; Meinhardt, Friedhelm

    2015-01-01

    The term plasmid was originally coined for circular, extrachromosomal genetic elements. Today, plasmids are widely recognized not only as important factors facilitating genome restructuring but also as vehicles for the dissemination of beneficial characters within bacterial communities. Plasmid diversity has been uncovered by means of culture-dependent or -independent approaches, such as endogenous or exogenous plasmid isolation as well as PCR-based detection or transposon-aided capture, respectively. High-throughput-sequencing made possible to cover total plasmid populations in a given environment, i.e., the plasmidome, and allowed to address the quality and significance of self-replicating genetic elements. Since such efforts were and still are rather restricted to circular molecules, here we put equal emphasis on the linear plasmids which—despite their frequent occurrence in a large number of bacteria—are largely neglected in prevalent plasmidome conceptions. PMID:26074886

  8. Novel archaeal plasmid pAH1 and its interactions with the lipothrixvirus AFV1

    DEFF Research Database (Denmark)

    Basta, Tamara; Smyth, John; Forterre, Patrick

    2009-01-01

    . Although nucleotide sequence comparisons revealed extensive intergenomic exchange during the evolution of archaeal conjugative plasmids, pAH1 was shown to be stably maintained suggesting that the host system is suitable for studying plasmid-virus interactions. AFV1 infection and propagation leads to a loss...... of the circular form of pAH1 and this effect correlates positively with the increase in the intracellular quantity of AFV1 DNA. We infer that the virus inhibits plasmid replication since no pAH1 degradation was observed. This mechanism of archaeal viral inhibition of plasmid propagation is not observed...... in bacteria where relevant bacteriophages either are dependent on a conjugative plasmid for successful infection or are excluded by a resident plasmid....

  9. Adenovirus or HA-2 fusogenic peptide-assisted lipofection increases cytoplasmic levels of plasmid in nondividing endothelium with little enhancement of transgene expression.

    Science.gov (United States)

    Subramanian, Ajit; Ma, Haiching; Dahl, Kris N; Zhu, Jingya; Diamond, Scott L

    2002-01-01

    Adenovirus-assisted lipofection has been reported to increase transfection efficiency through mechanisms potentially involving endosome escape and/or nuclear targeting activity. Similarly, transfection with the viral fusogenic peptide HA-2 of the influenza virus hemagglutinin can increase transfection efficiency. However, there are few studies examining the mechanism and intracellular trafficking of these viral and/or viral fusogenic peptide-assisted lipofections. Endosome escape was directly assayed with T7 RNA polymerase bound to plasmid (pTM beta gal) expressing beta-galactosidase under a T7 promoter to detect transcribable plasmid that escapes the endosomal compartment. Lipofection of pTM beta gal with replication-deficient adenovirus (Ad5-null) at a multiplicity of infection (MOI) of 100 and 1000 increased cytoplasmic levels of transcribable plasmid by 24- and 117-fold, respectively, over lipofection alone, without an effect on total plasmid uptake. However, lipofection of pCMV beta gal with Ad5-null at a MOI of 100 and 1000 increased transgene expression only seven- and eight-fold, respectively, over lipofection alone. Thus, a 24-fold increase in endosome escape saturated expression from pCMV beta gal and provided only a seven-fold benefit in nondividing cells, which was not significantly increased with further increases in endosome escape. A cationic form of HA-2 (HA-K(4)) also caused significant enhancements in endosome escape, as detected with the cytoplasmic transcription assay. However, HA-K(4) enhancement of endosome escape did not correlate with transgene expression from pCMV beta gal, consistent with the detection of HA-K(4)-mediated partitioning of plasmid to the insoluble fraction of the cell lysate. These results indicate that enhancement of endosome escape in nondividing cells does not fully alleviate rate limits related to nuclear import of the plasmid. Copyright 2001 John Wiley & Sons, Ltd.

  10. The diurnal vertical dynamics of cape hake and their potential prey ...

    African Journals Online (AJOL)

    cephalopods. Together with their cohabitant potential prey, hake are known to undertake diurnal vertical migrations, aggregating near the bottom during daylight, but migrating off the bottom at night. An attempt to determine the ... predation dominating. This may indicate a feeding strategy where vision is not important.

  11. Temporal Dynamics of Late Second Language Acquisition: Evidence from Event-Related Brain Potentials

    Science.gov (United States)

    Steinhauer, Karsten; White, Erin J.; Drury, John E.

    2009-01-01

    The ways in which age of acquisition (AoA) may affect (morpho)syntax in second language acquisition (SLA) are discussed. We suggest that event-related brain potentials (ERPs) provide an appropriate online measure to test some such effects. ERP findings of the past decade are reviewed with a focus on recent and ongoing research. It is concluded…

  12. Joint Attention in Infant-Toddler Early Childhood Programs: Its Dynamics and Potential for Collaborative Learning

    Science.gov (United States)

    Degotardi, Sheila

    2017-01-01

    This article examines how joint attention episodes constitute a core feature of relational pedagogy for infants and toddlers. It draws on social interactionist approaches to language and cognitive development to propose that joint attention may afford significant current and future potential for young children's learning. However, most joint…

  13. Quantifying the potential of automated dynamic solar shading in office buildings through integrated simulations of energy and daylight

    DEFF Research Database (Denmark)

    Nielsen, Martin Vraa; Svendsen, Svend; Bjerregaard Jensen, Lotte

    2011-01-01

    The façade design is and should be considered a central issue in the design of energy-efficient buildings. That is why dynamic façade components are increasingly used to adapt to both internal and external impacts, and to cope with a reduction in energy consumption and an increase in occupant...... them with various window heights and orientations. Their performance was evaluated on the basis of the building’s total energy demand, its energy demand for heating, cooling and lighting, and also its daylight factors. Simulation results comparing the three façade alternatives show potential...

  14. New ab initio potential surfaces and three-dimensional quantum dynamics for transition state spectroscopy in ozone photodissociation

    Science.gov (United States)

    Yamashita, Koichi; Morokuma, Keiji; Le Quéré, Frederic; Leforestier, Claude

    1992-04-01

    New ab initio potential energy surfaces (PESs) of the ground and B ( 1B 2) states of ozone have been calculated with the CASSCF-SECI/DZP method to describe the three-dimensional photodissociation process. The dissociation energy of the ground state and the vertical barrier height of the B PES are obtained to be 0.88 and 1.34 eV, respectively, in better agreement with the experimental values than the previous calculation. The photodissociation autocorrelation function, calculated on the new B PES, based on exact three-dimensional quantum dynamics, reproduces well the main recurrence feature extracted from the experimental spectra.

  15. Assessment of the potential of urban organic carbon dynamics to off-set urban anthropogenic emissions

    Science.gov (United States)

    Gottschalk, P.; Churkina, G.; Wattenbach, M.; Cubasch, U.

    2010-12-01

    The impact of urban systems on current and future global carbon emissions has been a focus of several studies. Many mitigation options in terms of increasing energy efficiency are discussed. However, apart from technical mitigation potential urban systems also have a considerable biogenic potential to mitigate carbon through an optimized management of organic carbon pools of vegetation and soil. Berlin city area comprises almost 50% of areas covered with vegetation or largely covered with vegetation. This potentially offers various areas for carbon mitigation actions. To assess the mitigation potentials our first objective is to estimate how large current vegetation and soil carbon stocks of Berlin are. We use publicly available forest and soil inventories to calculate soil organic carbon of non-pervious areas and forest standing biomass carbon. This research highlights data-gaps and assigns uncertainty ranges to estimated carbon resources. The second objective is to assess the carbon mitigation potential of Berlin’s vegetation and soils using a biogeochemical simulation model. BIOME-BGC simulates carbon-, nitrogen- and water-fluxes of ecosystems mechanistically. First, its applicability for Berlin forests is tested at selected sites. A spatial application gives an estimate of current net carbon fluxes. The application of such a model allows determining the sensitivity of key ecosystem processes (e.g. carbon gains through photosynthesis, carbon losses through decomposition) towards external drivers. This information can then be used to optimise forest management in terms of carbon mitigation. Initial results of Berlin’s current carbon stocks and its spatial distribution and preliminary simulations results will be presented.

  16. Role of plasmids in Lactobacillus brevis BSO 464 hop tolerance and beer spoilage.

    Science.gov (United States)

    Bergsveinson, Jordyn; Baecker, Nina; Pittet, Vanessa; Ziola, Barry

    2015-02-01

    Specific isolates of lactic acid bacteria (LAB) can grow in the harsh beer environment, thus posing a threat to brew quality and the economic success of breweries worldwide. Plasmid-localized genes, such as horA, horC, and hitA, have been suggested to confer hop tolerance, a trait required for LAB survival in beer. The presence and expression of these genes among LAB, however, do not universally correlate with the ability to grow in beer. Genome sequencing of the virulent beer spoilage organism Lactobacillus brevis BSO 464 revealed the presence of eight plasmids, with plasmids 1, 2, and 3 containing horA, horC, and hitA, respectively. To investigate the roles that these and the other five plasmids play in L. brevis BSO 464 growth in beer, plasmid curing with novobiocin was used to derive 10 plasmid variants. Multiplex PCRs were utilized to determine the presence or absence of each plasmid, and how plasmid loss affected hop tolerance and growth in degassed (noncarbonated) beer was assessed. Loss of three of the eight plasmids was found to affect hop tolerance and growth in beer. Loss of plasmid 2 (horC and 28 other genes) had the most dramatic effect, with loss of plasmid 4 (120 genes) and plasmid 8 (47 genes) having significant, but smaller, impacts. These results support the contention that genes on mobile genetic elements are essential for bacterial growth in beer and that beer spoilage ability is not dependent solely on the three previously described hop tolerance genes or on the chromosome of a beer spoilage LAB isolate.

  17. Cefotaxime resistant Escherichia coli collected from a healthy volunteer; characterisation and the effect of plasmid loss.

    Directory of Open Access Journals (Sweden)

    Miranda Kirchner

    Full Text Available In this study 6 CTX-M positive E. coli isolates collected during a clinical study examining the effect of antibiotic use in a human trial were analysed. The aim of the study was to analyse these isolates and assess the effect of full or partial loss of plasmid genes on bacterial fitness and pathogenicity. A DNA array was utilised to assess resistance and virulence gene carriage. Plasmids were characterised by PCR-based replicon typing and addiction system multiplex PCR. A phenotypic array and insect virulence model were utilised to assess the effect of plasmid-loss in E. coli of a large multi-resistance plasmid. All six E. coli carrying bla CTX-M-14 were detected from a single participant and were identical by pulse field gel electrophoresis and MLST. Plasmid profiling and arrays indicated absence of a large multi-drug resistance (MDR F-replicon plasmid carrying blaTEM, aadA4, strA, strB, dfrA17/19, sul1, and tetB from one isolate. Although this isolate partially retained the plasmid it showed altered fitness characteristics e.g. inability to respire in presence of antiseptics, similar to a plasmid-cured strain. However, unlike the plasmid-cured or plasmid harbouring strains, the survival rate for Galleria mellonella infected by the former strain was approximately 5-times lower, indicating other possible changes accompanying partial plasmid loss. In conclusion, our results demonstrated that an apparently healthy individual can harbour bla CTX-M-14 E. coli strains. In one such strain, isolated from the same individual, partial absence of a large MDR plasmid resulted in altered fitness and virulence characteristics, which may have implications in the ability of this strain to infect and any subsequent treatment.

  18. Persistence of plasmids, cholera toxin genes, and prophage DNA in classical Vibrio cholerae O1.

    OpenAIRE

    Cook, W L; Wachsmuth, K; Johnson, S R; Birkness, K A; Samadi, A R

    1984-01-01

    Plasmid profiles, the location of cholera toxin subunit A genes, and the presence of the defective VcA1 prophage genome in classical Vibrio cholerae isolated from patients in Bangladesh in 1982 were compared with those in older classical strains isolated during the sixth pandemic and with those in selected eltor and nontoxigenic O1 isolates. Classical strains typically had two plasmids (21 and 3 megadaltons), eltor strains typically had no plasmids, and nontoxigenic O1 strains had zero to thr...

  19. Plasmid profiles and antibiotic susceptibility patterns of Staphylococcus aureus isolates from Nigeria.

    Science.gov (United States)

    Olukoya, D K; Asielue, J O; Olasupo, N A; Ikea, J K

    1995-06-01

    In an investigation into the problems of infections due to Staphylococcus aureus in Nigeria, 100 strains were isolated from various hospitals in Lagos. The strains were screened for the presence of plasmids and for susceptibility to antimicrobial agents. Plasmids were extracted by modification of the method of Takahashi and Nagono[1]. The plasmids were diverse in nature. The strains were found to be highly resistant to commonly prescribed antibiotics.

  20. Cloning in Streptococcus lactis of plasmid-mediated UV resistance and effect on prophage stability

    International Nuclear Information System (INIS)

    Chopin, M.C.; Chopin, A.; Rouault, A.; Simon, D.

    1986-01-01

    Plasmid pIL7 (33 kilobases) from Streptococcus lactis enhances UV resistance and prophage stability. A 5.4-kilobase pIL7 fragment carrying genes coding for both characters was cloned into S. lactis, using plasmid pHV1301 as the cloning vector. The recombinant plasmid was subsequently transferred to three other S. lactis strains by transformation or protoplast fusion. Cloned genes were expressed in all tested strains

  1. Stem loop sequences specific to transposable element IS605 are found linked to lipoprotein genes in Borrelia plasmids.

    Directory of Open Access Journals (Sweden)

    Nicholas Delihas

    Full Text Available BACKGROUND: Plasmids of Borrelia species are dynamic structures that contain a large number of repetitive genes, gene fragments, and gene fusions. In addition, the transposable element IS605/200 family, as well as degenerate forms of this IS element, are prevalent. In Helicobacter pylori, flanking regions of the IS605 transposase gene contain sequences that fold into identical small stem loops. These function in transposition at the single-stranded DNA level. METHODOLOGY/PRINCIPAL FINDINGS: In work reported here, bioinformatics techniques were used to scan Borrelia plasmid genomes for IS605 transposable element specific stem loop sequences. Two variant stem loop motifs are found in the left and right flanking regions of the transposase gene. Both motifs appear to have dispersed in plasmid genomes and are found "free-standing" and phylogenetically conserved without the associated IS605 transposase gene or the adjacent flanking sequence. Importantly, IS605 specific stem loop sequences are also found at the 3' ends of lipoprotein genes (PFam12 and PFam60, however the left and right sequences appear to develop their own evolutionary patterns. The lipoprotein gene-linked left stem loop sequences maintain the IS605 stem loop motif in orthologs but only at the RNA level. These show mutations whereby variants fold into phylogenetically conserved RNA-type stem loops that contain the wobble non-Watson-Crick G-U base-pairing. The right flanking sequence is associated with the family lipoprotein-1 genes. A comparison of homologs shows that the IS605 stem loop motif rapidly dissipates, but a more elaborate secondary structure appears to develop in its place. CONCLUSIONS/SIGNIFICANCE: Stem loop sequences specific to the transposable element IS605 are present in plasmid regions devoid of a transposase gene and significantly, are found linked to lipoprotein genes in Borrelia plasmids. These sequences are evolutionarily conserved and/or structurally developed in

  2. Molecular dynamics simulation study of the influence of the lattice atom potential function upon atom ejection processes

    International Nuclear Information System (INIS)

    Harrison, D.E. Jr.; Webb, R.P.

    1982-01-01

    A molecular dynamics simulation has been used to investigate the sensitivity of atom ejection processes from a single-crystal target to changes in the atom-atom potential function. Four functions, three constructed from the Gibson potentials with Anderman's attractive well, and a fouth specifically developed for this investigation, were investigated in the Cu/Ar/sup +/ system over a range of ion energies from 1.0 to 10.0 kev with the KSE-B ion-atom potential. Well depths and widths also were varied. The calculations were done at normal incidence on the fcc (111) crystal orientation. Computed values were compared with experimental data where they exist. Sputtering yields, multimer yield ratios, layer yield ratios, and the ejected atom energy distribution vary systematically with the parameters of the atom-atom potential function. Calculations also were done with the modified Moliere function. Yields and other properties fall exactly into the positions predicted from the Born-Mayer function analysis. Simultaneous analysis of the ejected atom energy distribution and the ion energy dependence of the sputtering yield curve provides information about the parameters of both the wall and well portions of the atom-atom potential function

  3. On calculation of the electrostatic potential of a phosphatidylinositol phosphate-containing phosphatidylcholine lipid membrane accounting for membrane dynamics.

    Directory of Open Access Journals (Sweden)

    Jonathan C Fuller

    Full Text Available Many signaling events require the binding of cytoplasmic proteins to cell membranes by recognition of specific charged lipids, such as phosphoinositol-phosphates. As a model for a protein-membrane binding site, we consider one charged phosphoinositol phosphate (PtdIns(3P embedded in a phosphatidylcholine bilayer. As the protein-membrane binding is driven by electrostatic interactions, continuum solvent models require an accurate representation of the electrostatic potential of the phosphoinositol phosphate-containing membrane. We computed and analyzed the electrostatic potentials of snapshots taken at regular intervals from molecular dynamics simulations of the bilayer. We observe considerable variation in the electrostatic potential of the bilayer both along a single simulation and between simulations performed with the GAFF or CHARMM c36 force fields. However, we find that the choice of GAFF or CHARMM c36 parameters has little effect on the electrostatic potential of a given configuration of the bilayer with a PtdIns(3P embedded in it. From our results, we propose a remedian averaging method for calculating the electrostatic potential of a membrane system that is suitable for simulations of protein-membrane binding with a continuum solvent model.

  4. Optimised cut-off function for Tersoff-like potentials for a BN nanosheet: a molecular dynamics study

    International Nuclear Information System (INIS)

    Kumar, Rajesh; Rajasekaran, G; Parashar, Avinash

    2016-01-01

    In this article, molecular dynamics based simulations were carried out to study the tensile behaviour of boron nitride nanosheets (BNNSs). Four different sets of Tersoff potential parameters were used in the simulations for estimating the interatomic interactions between boron and nitrogen atoms. Modifications were incorporated in the Tersoff cut-off function to improve the accuracy of results with respect to fracture stress, fracture strain and Young’s modulus. In this study, the original cut-off function was optimised in such a way that small and large cut-off distances were made equal, and hence a single cut-off distance was used with all sets of Tersoff potential parameters. The single value of cut-off distance for the Tersoff potential was chosen after analysing the potential energy and bond forces experienced by boron and nitrogen atoms subjected to bond stretching. The simulations performed with the optimised cut-off function help in identifying the Tersoff potential parameters that reproduce the experimentally evaluated mechanical behaviour of BNNSs. (paper)

  5. Compatibility and entry exclusion of IncA and IncC plasmids revisited: IncA and IncC plasmids are compatible.

    Science.gov (United States)

    Ambrose, Stephanie J; Harmer, Christopher J; Hall, Ruth M

    2018-02-24

    In an early study, IncA and IncC plasmids that were reported to be compatible were grouped as the "A-C complex" based on similarities and on strong entry exclusion. However, recently, the term IncA/C has been used frequently to describe plasmids belonging to both of these two groups. Granted that the supporting data was not included in the original reports and that the consensus iteron sequences have since been shown to be essentially identical, we have addressed the question again. The original IncA plasmid, RA1, and the IncC plasmid pRMH760, were introduced into the same cell by transformation, and were found to be maintained stably for over 100 generations in the absence of selection for either plasmid, i.e. they were compatible. We conclude that use of the term IncA/C for this important plasmid group is indeed incorrect and it causes unnecessary confusion. Granted the importance of IncC plasmids in the spread of antibiotic resistance genes, we recommend that use of the misleading terms IncA/C, IncA/C 1 and IncA/C 2 should cease. In addition, RA1 and pRMH760 were shown to each completely prevent entry of the other via conjugative transfer into the cell they reside in. Copyright © 2018 Elsevier Inc. All rights reserved.

  6. High-temperature dynamic behavior in bulk liquid water: A molecular dynamics simulation study using the OPC and TIP4P-Ew potentials

    Science.gov (United States)

    Gabrieli, Andrea; Sant, Marco; Izadi, Saeed; Shabane, Parviz Seifpanahi; Onufriev, Alexey V.; Suffritti, Giuseppe B.

    2018-02-01

    Classical molecular dynamics simulations were performed to study the high-temperature (above 300 K) dynamic behavior of bulk water, specifically the behavior of the diffusion coefficient, hydrogen bond, and nearest-neighbor lifetimes. Two water potentials were compared: the recently proposed "globally optimal" point charge (OPC) model and the well-known TIP4P-Ew model. By considering the Arrhenius plots of the computed inverse diffusion coefficient and rotational relaxation constants, a crossover from Vogel-Fulcher-Tammann behavior to a linear trend with increasing temperature was detected at T* ≈ 309 and T* ≈ 285 K for the OPC and TIP4P-Ew models, respectively. Experimentally, the crossover point was previously observed at T* ± 315-5 K. We also verified that for the coefficient of thermal expansion α P ( T, P), the isobaric α P ( T) curves cross at about the same T* as in the experiment. The lifetimes of water hydrogen bonds and of the nearest neighbors were evaluated and were found to cross near T*, where the lifetimes are about 1 ps. For T T*, water behaves more like a simple liquid. The fact that T* falls within the biologically relevant temperature range is a strong motivation for further analysis of the phenomenon and its possible consequences for biomolecular systems.

  7. Selfish restriction modification genes: resistance of a resident R/M plasmid to displacement by an incompatible plasmid mediated by host killing.

    Science.gov (United States)

    Naito, Y; Naito, T; Kobayashi, I

    1998-01-01

    Previous work from this laboratory demonstrated that plasmids carrying a type II restriction-modification gene complex are not easily lost from their bacterial host because plasmid-free segregant cells are killed through chromosome cleavage. Here, we have followed the course of events that takes place when an Escherichia coli rec BC sbcA strain carrying a plasmid coding for the PaeR7I restriction-modification (R/M) gene complex is transformed by a plasmid with an identical origin of replication. The number of transformants that appeared was far fewer than with the restriction-minus (r-) control. Most of the transformants were very small. After prolonged incubation, the number and the size of the colonies increased, but this increase never attained the level of the r- control. Most of the transformed colonies retained the drug-resistance of the resident, r+ m+ plasmid. These results indicate that post-segregational host killing occurs when a plasmid bearing an R/M gene complex is displaced by an incompatible plasmid. Such cell killing eliminates the competitor plasmid along with the host and, thus, would allow persistence of the R/M plasmid in the neighboring, clonal host cells in nature. This phenomenon is reminiscent of mammalian apoptosis and other forms of altruistic cell death strategy against infection. This type of resistance to displacement was also studied in a wild type Escherichia coli strain that was normal for homologous recombination (rec+). A number of differences between the recBC sbcA strain and the rec+ strain were observed and these will be discussed.

  8. Glass Formation of n-Butanol: Coarse-grained Molecular Dynamics Simulations Using Gay-Berne Potential Model

    Science.gov (United States)

    Xie, Gui-long; Zhang, Yong-hong; Huang, Shi-ping

    2012-04-01

    Using coarse-grained molecular dynamics simulations based on Gay-Berne potential model, we have simulated the cooling process of liquid n-butanol. A new set of GB parameters are obtained by fitting the results of density functional theory calculations. The simulations are carried out in the range of 290-50 K with temperature decrements of 10 K. The cooling characteristics are determined on the basis of the variations of the density, the potential energy and orientational order parameter with temperature, whose slopes all show discontinuity. Both the radial distribution function curves and the second-rank orientational correlation function curves exhibit splitting in the second peak. Using the discontinuous change of these thermodynamic and structure properties, we obtain the glass transition at an estimate of temperature Tg=120±10 K, which is in good agreement with experimental results 110±1 K.

  9. Plasmid marker rescue transformation proceeds by breakage-reunion in Bacillus subtilis

    International Nuclear Information System (INIS)

    Weinrauch, Y.; Dubnau, D.

    1987-01-01

    Bacillus subtilis carrying a plasmid which replicates with a copy number of about 1 was transformed with linearized homologous plasmid DNA labeled with the heavy isotopes 2 H and 15 N, in the presence of 32 Pi and 6-(p-hydroxyphenylazo)-uracil to inhibit DNA replication. Plasmid DNA was isolated from the transformed culture and fractionated in cesium chloride density gradients. The distribution of total and donor plasmid DNA was examined, using specific hybridization probes. The synthesis of new DNA, associated with the integration of donor moiety, was also monitored. Donor-specific sequences were present at a density intermediate between that of light and hybrid DNA. This recombinant DNA represented 1.4% of total plasmid DNA. The latter value corresponded well with the transforming activity (1.7%) obtained for the donor marker. Newly synthesized material associated with plasmid DNA at the recombinant density amounted to a minor portion of the recombinant plasmid DNA. These data suggest that, like chromosomal transformation, plasmid marker rescue transformation does not require replication for the integration of donor markers and, also like chromosomal transformation, proceeds by a breakage-reunion mechanism. The extent of donor DNA replacement of recipient DNA per plasmid molecule of 54 kilobases (27 kilobase pairs) was estimated as 16 kilobases

  10. Nucleotide Sequences and Comparison of Two Large Conjugative Plasmids from Different Campylobacter species

    National Research Council Canada - National Science Library

    Batchelor, Roger A; Pearson, Bruce M; Friis, Lorna M; Guerry, Patricia; Wells, Jerry M

    2004-01-01

    .... Both plasmids are mosaic in structure, having homologues of genes found in a variety of different commensal and pathogenic bacteria, but nevertheless, showed striking similarities in DNA sequence...

  11. Genetic characterization of blaNDM-harboring plasmids in carbapenem-resistant Escherichia coli from Myanmar.

    Directory of Open Access Journals (Sweden)

    Yo Sugawara

    Full Text Available The bacterial enzyme New Delhi metallo-β-lactamase hydrolyzes almost all β-lactam antibiotics, including carbapenems, which are drugs of last resort for severe bacterial infections. The spread of carbapenem-resistant Enterobacteriaceae that carry the New Delhi metallo-β-lactamase gene, blaNDM, poses a serious threat to public health. In this study, we genetically characterized eight carbapenem-resistant Escherichia coli isolates from a tertiary care hospital in Yangon, Myanmar. The eight isolates belonged to five multilocus-sequence types and harbored multiple antimicrobial-resistance genes, resulting in resistance against nearly all of the antimicrobial agents tested, except colistin and fosfomycin. Nine plasmids harboring blaNDM genes were identified from these isolates. Multiple blaNDM genes were found in the distinct Inc-replicon types of the following plasmids: an IncA/C2 plasmid harboring blaNDM-1 (n = 1, IncX3 plasmids harboring blaNDM-4 (n = 2 or blaNDM-7 (n = 1, IncFII plasmids harboring blaNDM-4 (n = 1 or blaNDM-5 (n = 3, and a multireplicon F plasmid harboring blaNDM-5 (n = 1. Comparative analysis highlighted the diversity of the blaNDM-harboring plasmids and their distinct characteristics, which depended on plasmid replicon types. The results indicate circulation of phylogenetically distinct strains of carbapenem-resistant E. coli with various plasmids harboring blaNDM genes in the hospital.

  12. Repair of UV-irradiated plasmid DNA in excision repair deficient mutants of Saccharomyces cerevisiae

    International Nuclear Information System (INIS)

    Ikai, K.; Tano, K.; Ohnishi, T.; Nozu, K.

    1985-01-01

    The repair of UV-irradiated DNA of plasmid YEp13 was studied in the incision defective strains by measurement of cell transformation frequency. In Saccharomyces cerevisiae, rad1,2,3 and 4 mutants could repair UV-damaged plasmid DNA. In Escherichia coli, uvrA mutant was unable to repair UV-damaged plasmid DNA; however, pretreatment of the plasmid with Micrococcus luteus endonuclease increased repair. It was concluded that all the mutations of yeast were probably limited only to the nuclear DNA. (author)

  13. Plasmids which make their host bacteria mutable as well as resistant to ultraviolet irradiation

    International Nuclear Information System (INIS)

    Arai, Toshihiko; Ando, Takao

    1980-01-01

    Some of the naturally occurring Iα, I zeta, M, N, O and T group plasmids increase both the mutability and UV resistance of their host bacteria, while group H and S plasmids only increase mutability. This suggests that these two plasmid-mediated repair functions are separable. The two functions have no direct relation to their restriction-modification systems and nitrofuran resistant functions. In addition, the close linking between the restriction-modification genes and these repair function genes was suggested in group N plasmids. (author)

  14. Computational design and characterization of a temperature-sensitive plasmid replicon for gram positive thermophiles

    Directory of Open Access Journals (Sweden)

    Olson Daniel G

    2012-05-01

    Full Text Available Abstract Background Temperature-sensitive (Ts plasmids are useful tools for genetic engineering, but there are currently none compatible with the gram positive, thermophilic, obligate anaerobe, Clostridium thermocellum. Traditional mutagenesis techniques yield Ts mutants at a low frequency, and therefore requires the development of high-throughput screening protocols, which are also not available for this organism. Recently there has been progress in the development of computer algorithms which can predict Ts mutations. Most plasmids currently used for genetic modification of C. thermocellum are based on the replicon of plasmid pNW33N, which replicates using the RepB replication protein. To address this problem, we set out to create a Ts plasmid by mutating the gene coding for the RepB replication protein using an algorithm designed by Varadarajan et al. (1996 for predicting Ts mutants based on the amino-acid sequence of the protein. Results A library of 34 mutant plasmids was designed, synthesized and screened, resulting in 6 mutants which exhibited a Ts phenotype. Of these 6, the one with the most temperature-sensitive phenotype (M166A was compared with the original plasmid. It exhibited lower stability at 48°C and was completely unable to replicate at 55°C. Conclusions The plasmid described in this work could be useful in future efforts to genetically engineer C. thermocellum, and the method used to generate this plasmid may be useful for others trying to make Ts plasmids.

  15. Regulation of Mnemiopsis leidyi dynamics by potential changes in temperature and zooplankton conditions in the Black Sea.

    Science.gov (United States)

    Salihoglu, B.; Fach, B.; Oguz, T.

    2009-04-01

    Providing a comprehensive understanding of the effects that cause formations of ctenophore blooms in the Black Sea is the main objective of this study. In order to analyse ctenophore dynamics in the Black Sea a zero-dimensional population based model of the ctenophore Mnemiopsis leidyi is developed. The stage resolving ctenophore model combines the modified form of stage resolving approach of Fennel, 2001 with the growth dynamics model of Kremer, 1976; Kremer and Reeve, 1989 under 4 stages of model-ctenophore. These stages include the different growth characteristics of egg, juvenile, transitional and adult stages. The dietary patterns of the different stages follows the observations obtained from the literature. The model is able to represent consistent development patterns, while reflecting the physiological complexity of a population of Mnemiopsis leidyi. Model results suggest that different nutritional requirement of each stage may serve as the bottlenecks for population growth and only when growth conditions are favorable for both larval and lobate stages, the high overall population growth rates may occur. Model is also used to analyse the influence of climatic changes on Mnemiopsis leidyi reproduction and outburst. This study presents and discussed how potential changes in temperature and zooplankton conditions in the Black Sea may regulate Mnemiopsis leidyi dynamics.

  16. Studying the potential of point detectors in time-resolved dose verification of dynamic radiotherapy

    International Nuclear Information System (INIS)

    Beierholm, A.R.; Behrens, C.F.; Andersen, C.E.

    2015-01-01

    Modern megavoltage x-ray radiotherapy with high spatial and temporal dose gradients puts high demands on the entire delivery system, including not just the linear accelerator and the multi-leaf collimator, but also algorithms used for optimization and dose calculations, and detectors used for quality assurance and dose verification. In this context, traceable in-phantom dosimetry using a well-characterized point detector is often an important supplement to 2D-based quality assurance methods based on radiochromic film or detector arrays. In this study, an in-house developed dosimetry system based on fiber-coupled plastic scintillator detectors was evaluated and compared with a Farmer-type ionization chamber and a small-volume ionization chamber. An important feature of scintillator detectors is that the sensitive volume of the detector can easily be scaled, and five scintillator detectors of different scintillator length were thus employed to quantify volume averaging effects by direct measurement. The dosimetric evaluation comprised several complex-shape static fields as well as simplified dynamic deliveries using RapidArc, a volumetric-modulated arc therapy modality often used at the participating clinic. The static field experiments showed that the smallest scintillator detectors were in the best agreement with dose calculations, while needing the smallest volume averaging corrections. Concerning total dose measured during RapidArc, all detectors agreed with dose calculations within 1.1 ± 0.7% when positioned in regions of high homogenous dose. Larger differences were observed for high dose gradient and organ at risk locations, were differences between measured and calculated dose were as large as 8.0 ± 5.5%. The smallest differences were generally seen for the small-volume ionization chamber and the smallest scintillators. The time-resolved RapidArc dose profiles revealed volume-dependent discrepancies between scintillator and ionization chamber response

  17. Rapid and inexpensive method for isolating plasmid DNA

    International Nuclear Information System (INIS)

    Aljanabi, S. M.; Al-Awadi, S. J.; Al-Kazaz, A. A.; Baghdad Univ.

    1997-01-01

    A small-scale and economical method for isolating plasmid DNA from bacteria is described. The method provides DNA of suitable quality for most DNA manipulation techniques. This DNA can be used for restriction endonuclease digestion, southern blot hybridization, nick translation and end labeling of DNA probes, Polymerase Chain Reaction (PCR) -based techniques, transformation, DNA cycle-sequencing, and Chain-termination method for DNA sequencing. The entire procedure is adapted to 1.5 ml microfuge tubes and takes approximately 30 mins. The DNA isolated by this method has the same purity produced by CTAB and cesium chloride precipitation and purification procedures respectively. The two previous methods require many hours to obtain the final product and require the use of very expensive equipment as ultracentrifuge. This method is well suited for the isolation of plasmid DNA from a large number of bacterial samples and in a very short time and low cost in laboratories where chemicals, expensive equipment and finance are limited factors in conducting molecular research. (authors). 11refs. 11refs

  18. Rib Geometry Explains Variation in Dynamic Structural Response: Potential Implications for Frontal Impact Fracture Risk.

    Science.gov (United States)

    Murach, Michelle M; Kang, Yun-Seok; Goldman, Samuel D; Schafman, Michelle A; Schlecht, Stephen H; Moorhouse, Kevin; Bolte, John H; Agnew, Amanda M

    2017-09-01

    The human thorax is commonly injured in motor vehicle crashes, and despite advancements in occupant safety rib fractures are highly prevalent. The objective of this study was to quantify the ability of gross and cross-sectional geometry, separately and in combination, to explain variation of human rib structural properties. One hundred and twenty-two whole mid-level ribs from 76 fresh post-mortem human subjects were tested in a dynamic frontal impact scenario. Structural properties (peak force and stiffness) were successfully predicted (p rib cross-sectional geometry obtained via direct histological imaging (total area, cortical area, and section modulus) and were improved further when utilizing a combination of cross-sectional and gross geometry (robusticity, whole bone strength index). Additionally, preliminary application of a novel, adaptive thresholding technique, allowed for total area and robusticity to be measured on a subsample of standard clinical CT scans with varied success. These results can be used to understand variation in individual rib response to frontal loading as well as identify important geometric parameters, which could ultimately improve injury criteria as well as the biofidelity of anthropomorphic test devices (ATDs) and finite element (FE) models of the human thorax.

  19. Dynamic Wolbachia prevalence in Acromyrmex leaf-cutting ants: potential for a nutritional symbiosis.

    Science.gov (United States)

    Andersen, S B; Boye, M; Nash, D R; Boomsma, J J

    2012-07-01

    Wolbachia are renowned as reproductive parasites, but their phenotypic effects in eusocial insects are not well understood. We used a combination of qrt-PCR, fluorescence in situ hybridization and laser scanning confocal microscopy to evaluate the dynamics of Wolbachia infections in the leaf-cutting ant Acromyrmex octospinosus across developmental stages of sterile workers. We confirm that workers are infected with one or two widespread wsp genotypes of Wolbachia, show that colony prevalence is always 100% and characterize two rare recombinant genotypes. One dominant genotype is always present and most abundant, whereas another only proliferates in adult workers of some colonies and is barely detectable in larvae and pupae. An explanation may be that Wolbachia genotypes compete for host resources in immature stages while adult tissues provide substantially more niche space. Tissue-specific prevalence of the two genotypes differs, with the rarer genotype being over-represented in the adult foregut and thorax muscles. Both genotypes occur extracellularly in the foregut, suggesting an unknown mutualistic function in worker ant nutrition. Both genotypes are also abundant in the faecal fluid of the ants, suggesting that they may have extended functional phenotypes in the fungus garden that the ants manure with their own faeces. © 2012 The Authors. Journal of Evolutionary Biology © 2012 European Society For Evolutionary Biology.

  20. Dynamic causal modeling of touch-evoked potentials in the rubber hand illusion.

    Science.gov (United States)

    Zeller, Daniel; Friston, Karl J; Classen, Joseph

    2016-09-01

    The neural substrate of bodily ownership can be disclosed by the rubber hand illusion (RHI); namely, the illusory self-attribution of an artificial hand that is induced by synchronous tactile stimulation of the subject's hand that is hidden from view. Previous studies have pointed to the premotor cortex (PMC) as a pivotal area in such illusions. To investigate the effective connectivity between - and within - sensory and premotor areas involved in bodily perceptions, we used dynamic causal modeling of touch-evoked responses in 13 healthy subjects. Each subject's right hand was stroked while viewing their own hand ("REAL"), or an artificial hand presented in an anatomically plausible ("CONGRUENT") or implausible ("INCONGRUENT") position. Bayesian model comparison revealed strong evidence for a differential involvement of the PMC in the generation of touch-evoked responses under the three conditions, confirming a crucial role of PMC in bodily self-attribution. In brief, the extrinsic (forward) connection from left occipital cortex to left PMC was stronger for CONGRUENT and INCONGRUENT as compared to REAL, reflecting the augmentation of bottom-up visual input when multisensory integration is challenged. Crucially, intrinsic connectivity in the primary somatosensory cortex (S1) was attenuated in the CONGRUENT condition, during the illusory percept. These findings support predictive coding models of the functional architecture of multisensory integration (and attenuation) in bodily perceptual experience. Copyright © 2016 Elsevier Inc. All rights reserved.

  1. Towards high dynamic range extensions of HEVC: subjective evaluation of potential coding technologies

    Science.gov (United States)

    Hanhart, Philippe; Řeřábek, Martin; Ebrahimi, Touradj

    2015-09-01

    This paper reports the details and results of the subjective evaluations conducted at EPFL to evaluate the responses to the Call for Evidence (CfE) for High Dynamic Range (HDR) and Wide Color Gamut (WCG) Video Coding issued by Moving Picture Experts Group (MPEG). The CfE on HDR/WCG Video Coding aims to explore whether the coding efficiency and/or the functionality of the current version of HEVC standard can be signi_cantly improved for HDR and WCG content. In total, nine submissions, five for Category 1 and four for Category 3a, were compared to the HEVC Main 10 Profile based Anchor. More particularly, five HDR video contents, compressed at four bit rates by each proponent responding to the CfE, were used in the subjective evaluations. Further, the side-by-side presentation methodology was used for the subjective experiment to discriminate small differences between the Anchor and proponents. Subjective results shows that the proposals provide evidence that the coding efficiency can be improved in a statistically noticeable way over MPEG CfE Anchors in terms of perceived quality within the investigated content. The paper further benchmarks the selected objective metrics based on their correlations with the subjective ratings. It is shown that PSNR-DE1000, HDRVDP- 2, and PSNR-Lx can reliably detect visible differences between the proposed encoding solutions and current HEVC standard.

  2. Fast and efficient three-step target-specific curing of a virulence plasmid in Salmonella enterica.

    Science.gov (United States)

    de Moraes, Marcos H; Teplitski, Max

    2015-12-01

    Virulence plasmids borne by serovars of Salmonella enterica carry genes involved in its pathogenicity, as well as other functions. Characterization of phenotypes associated with virulence plasmids requires a system for efficiently curing strains of their virulence plasmids. Here, we developed a 3-step protocol for targeted curing of virulence plasmids. The protocol involves insertion of an I-SecI restriction site linked to an antibiotic resistance gene into the target plasmid using λ-Red mutagenesis, followed by the transformation with a temperature-sensitive auxiliary plasmid which carries I-SecI nuclease expressed from a tetracycline-inducible promoter. Finally, the auxiliary plasmid is removed by incubation at 42 °C and the plasmid-less strains are verified on antibiotic-containing media. This method is fast and very efficient: over 90 % of recovered colonies lacked their virulence plasmid.

  3. Synchronization in primate cerebellar granule cell layer local field potentials: Basic anisotropy and dynamic changes during active expectancy

    Directory of Open Access Journals (Sweden)

    Richard Courtemanche

    2009-07-01

    Full Text Available The cerebellar cortex is remarkable for its organizational regularity, out of which task-related neural networks should emerge. So, in Purkinje cells, both complex and simple spike network patterns are evident in sensorimotor behavior. However, task-related patterns of activity in the granule cell layer (GCL have been less studied. We recorded local field potential (LFP activity simultaneously in pairs of GCL sites in monkeys performing an active expectancy (lever-press task, in passive expectancy, and at rest. LFP sites were selected when they showed strong 10-25 Hz oscillations; pair orientation was in stereotaxic sagittal and coronal (mainly, and diagonal. As shown previously, LFP oscillations at each site were modulated during the lever-press task. Synchronization across LFP pairs showed an evident basic anisotropy at rest: sagittal pairs of LFPs were better synchronized (more than double the cross-correlation coefficients than coronal pairs, and more than diagonal pairs. On the other hand, this basic anisotropy was modifiable: during the active expectancy condition, where sagittal and coronal orientations were tested, synchronization of LFP pairs would increase just preceding movement, most notably for the coronal pairs. This lateral extension of synchronization was not observed in passive expectancy. The basic pattern of synchronization at rest, favoring sagittal synchrony, thus seemed to adapt in a dynamic fashion, potentially extending laterally to include more cerebellar cortex elements. This dynamic anisotropy in LFP synchronization could underlie GCL network organization in the context of sensorimotor tasks.

  4. Electric Potential and Electric Field Imaging with Dynamic Applications: 2017 Research Award Innovation

    Science.gov (United States)

    Generazio, Ed

    2017-01-01

    The technology and methods for remote quantitative imaging of electrostatic potentials and electrostatic fields in and around objects and in free space is presented. Electric field imaging (EFI) technology may be applied to characterize intrinsic or existing electric potentials and electric fields, or an externally generated electrostatic field may be used for illuminating volumes to be inspected with EFI. The baseline sensor technology (e-Sensor) and its construction, optional electric field generation (quasi-static generator), and current e- Sensor enhancements (ephemeral e-Sensor) are discussed. Critical design elements of current linear and real-time two-dimensional (2D) measurement systems are highlighted, and the development of a three dimensional (3D) EFI system is presented. Demonstrations for structural, electronic, human, and memory applications are shown. Recent work demonstrates that phonons may be used to create and annihilate electric dipoles within structures. Phonon induced dipoles are ephemeral and their polarization, strength, and location may be quantitatively characterized by EFI providing a new subsurface Phonon-EFI imaging technology. Initial results from real-time imaging of combustion and ion flow, and their measurement complications, will be discussed. These new EFI capabilities are demonstrated to characterize electric charge distribution creating a new field of study embracing areas of interest including electrostatic discharge (ESD) mitigation, crime scene forensics, design and materials selection for advanced sensors, combustion science, on-orbit space potential, container inspection, remote characterization of electronic circuits and level of activation, dielectric morphology of structures, tether integrity, organic molecular memory, atmospheric science, and medical diagnostic and treatment efficacy applications such as cardiac polarization wave propagation and electromyography imaging.

  5. On the dynamics of the power law inflation due to an exponential potential

    International Nuclear Information System (INIS)

    Yokohama, Jun'ichi; Maeda, Kei-ichi; Tokyo Univ.

    1988-01-01

    The power law inflationary universe model induced by a scalar field with an exponential potential is studied. A dissipation term due to particle creation is introduced in the inflation's classical equation of motion. It is shown that the power index of the inflation increases prominently with an adequate viscosity. Consequently, even in theories with a rather steep exponential such as some supergravity or superstring models, it turns out that a 'realistic' power law inflation (with a power index p> or approx.10) is possible. (orig.)

  6. Soil CO2 Dynamics in a Tree Island Soil of the Pantanal: The Role of Soil Water Potential

    Science.gov (United States)

    Johnson, Mark S.; Couto, Eduardo Guimarães; Pinto Jr, Osvaldo B.; Milesi, Juliana; Santos Amorim, Ricardo S.; Messias, Indira A. M.; Biudes, Marcelo Sacardi

    2013-01-01

    The Pantanal is a biodiversity hotspot comprised of a mosaic of landforms that differ in vegetative assemblages and flooding dynamics. Tree islands provide refuge for terrestrial fauna during the flooding period and are particularly important to the regional ecosystem structure. Little soil CO2 research has been conducted in this region. We evaluated soil CO2 dynamics in relation to primary controlling environmental parameters (soil temperature and soil water). Soil respiration was computed using the gradient method using in situ infrared gas analyzers to directly measure CO2 concentration within the soil profile. Due to the cost of the sensors and associated equipment, this study was unreplicated. Rather, we focus on the temporal relationships between soil CO2 efflux and related environmental parameters. Soil CO2 efflux during the study averaged 3.53 µmol CO2 m−2 s−1, and was equivalent to an annual soil respiration of 1220 g C m−2 y−1. This efflux value, integrated over a year, is comparable to soil C stocks for 0–20 cm. Soil water potential was the measured parameter most strongly associated with soil CO2 concentrations, with high CO2 values observed only once soil water potential at the 10 cm depth approached zero. This relationship was exhibited across a spectrum of timescales and was found to be significant at a daily timescale across all seasons using conditional nonparametric spectral Granger causality analysis. Hydrology plays a significant role in controlling CO2 efflux from the tree island soil, with soil CO2 dynamics differing by wetting mechanism. During the wet-up period, direct precipitation infiltrates soil from above and results in pulses of CO2 efflux from soil. The annual flood arrives later, and saturates soil from below. While CO2 concentrations in soil grew very high under both wetting mechanisms, the change in soil CO2 efflux was only significant when soils were wet from above. PMID:23762259

  7. Patch-Clamp Recording from Human Induced Pluripotent Stem Cell-Derived Cardiomyocytes: Improving Action Potential Characteristics through Dynamic Clamp

    Science.gov (United States)

    Veerman, Christiaan C.; Zegers, Jan G.; Mengarelli, Isabella; Bezzina, Connie R.

    2017-01-01

    Human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) hold great promise for studying inherited cardiac arrhythmias and developing drug therapies to treat such arrhythmias. Unfortunately, until now, action potential (AP) measurements in hiPSC-CMs have been hampered by the virtual absence of the inward rectifier potassium current (IK1) in hiPSC-CMs, resulting in spontaneous activity and altered function of various depolarising and repolarising membrane currents. We assessed whether AP measurements in “ventricular-like” and “atrial-like” hiPSC-CMs could be improved through a simple, highly reproducible dynamic clamp approach to provide these cells with a substantial IK1 (computed in real time according to the actual membrane potential and injected through the patch-clamp pipette). APs were measured at 1 Hz using perforated patch-clamp methodology, both in control cells and in cells treated with all-trans retinoic acid (RA) during the differentiation process to increase the number of cells with atrial-like APs. RA-treated hiPSC-CMs displayed shorter APs than control hiPSC-CMs and this phenotype became more prominent upon addition of synthetic IK1 through dynamic clamp. Furthermore, the variability of several AP parameters decreased upon IK1 injection. Computer simulations with models of ventricular-like and atrial-like hiPSC-CMs demonstrated the importance of selecting an appropriate synthetic IK1. In conclusion, the dynamic clamp-based approach of IK1 injection has broad applicability for detailed AP measurements in hiPSC-CMs. PMID:28867785

  8. Assessing Bioinspired Topographies for their Antifouling Potential Control Using Computational Fluid Dynamics (CFD

    Directory of Open Access Journals (Sweden)

    Ling Jacky

    2018-01-01

    Full Text Available Biofouling is the accumulation of unwanted material on surfaces submerged or semi submerged over an extended period. This study investigates the antifouling performance of a new bioinspired topography design. A shark riblets inspired topography was designed with Solidworks and CFD simulations were antifouling performance. The study focuses on the fluid flow velocity, the wall shear stress and the appearance of vortices are to be noted to determine the possible locations biofouling would most probably occur. The inlet mass flow rate is 0.01 kgs-1 and a no-slip boundary condition was applied to the walls of the fluid domain. Simulations indicate that Velocity around the topography averaged at 7.213 x 10-3 ms-1. However, vortices were observed between the gaps. High wall shear stress is observed at the peak of each topography. In contrast, wall shear stress is significantly low at the bed of the topography. This suggests the potential location for the accumulation of biofouling. Results show that bioinspired antifouling topography can be improved by reducing the frequency of gaps between features. Linear surfaces on the topography should also be minimized. This increases the avenues of flow for the fluid, thus potentially increasing shear stresses with surrounding fluid leading to better antifouling performance.

  9. Investigating potential correlations between jet engine noise and plume dynamics in the hypertemporal infrared domain

    Science.gov (United States)

    Cunio, Phillip M.; Weber, Reed; Knobel, Kimberly; Wager, Jason; Lopez, Gerardo

    2014-09-01

    Jet engine noise can be a hazard and environmental pollutant, affecting personnel working in close proximity to jet engines. Mitigating the effects of jet engine noise could reduce the potential for hearing loss in runway workers, but engine noise is not yet sufficiently well-characterized that it can easily be mitigated for new engine designs. That is, there exists a very complex relationship between jet engine design parameters, operating conditions, and resultant noise power levels. In this paper, we propose to evaluate the utility of high-speed imaging (also called hypertemporal imaging) in correlating the infrared signatures of jet aircraft engines with acoustic noise from the jet engines. This paper will focus on a theoretical analysis of jet engine infrared signatures, and will define potentially-detectable characteristics of such signatures in the hypertemporal domain. A systematic test campaign to determine whether such signatures actually exist and can be correlated with acoustic jet engine characteristics will be proposed. The detection of any hypertemporal signatures in association with acoustic signatures of jet engines will enable the use of a new domain in characterizing jet engine noise. This may in turn enable new methods of predicting or mitigating jet engine noise, which could lead to benefits for operators of large numbers of jet engines.

  10. Enhanced Regenerative Braking Strategies for Electric Vehicles: Dynamic Performance and Potential Analysis

    Directory of Open Access Journals (Sweden)

    Boyi Xiao

    2017-11-01

    Full Text Available A regenerative braking system and hydraulic braking system are used in conjunction in the majority of electric vehicles worldwide. We propose a new regenerative braking distribution strategy that is based on multi-input fuzzy control logic while considering the influences of the battery’s state of charge, the brake strength and the motor speed. To verify the braking performance and recovery economy, this strategy was applied to a battery electric vehicle model and compared with two other improved regenerative braking strategies. The performance simulation was performed using standard driving cycles (NEDC, LA92, and JP1015 and a real-world-based urban cycle in China. The tested braking strategies satisfied the general safety requirements of Europe (as specified in ECE-13H, and the emergency braking scenario and economic potential were tested. The simulation results demonstrated the differences in the braking force distribution performance of these three regenerative braking strategies, the feasibility of the braking methods for the proposed driving cycles and the energy economic potential of the three strategies.

  11. Neural Temporal Dynamics of Social Exclusion Elicited by Averted Gaze: An Event-Related Potentials Study

    Directory of Open Access Journals (Sweden)

    Yue Leng

    2018-02-01

    Full Text Available Eye gaze plays a fundamental role in social communication. The averted eye gaze during social interaction, as the most common form of silent treatment, conveys a signal of social exclusion. In the present study, we examined the time course of brain response to social exclusion by using a modified version of Eye-gaze paradigm. The event-related potentials (ERPs data and the subjective rating data showed that the frontocentral P200 was positively correlated with negative mood of excluded events, whereas, the centroparietal late positive potential (LPP was positively correlated with the perceived ostracism intensity. Both the P200 and LPP were more positive-going for excluded events than for included events. These findings suggest that brain responses sensitive to social exclusion can be divided into the early affective processing stage, linking to the early pre-cognitive warning system; and the late higher-order processes stage, demanding attentional resources for elaborate stimuli evaluation and categorization generally not under specific situation.

  12. Amorphization induced by chemical disorder in crystalline NiZr2: A molecular-dynamics study based on an n-body potential

    International Nuclear Information System (INIS)

    Massobrio, C.; Pontikis, V.; Martin, G.

    1989-01-01

    We present the first molecular-dynamics study of the amorphization of a crystalline alloy (NiZr 2 ) induced by chemical disorder. We used a n-body potential in conjunction with isobaric-isothermal molecular dynamics. The behavior of the pair distribution function suggests that the instability leading to the amorphous state is a first-order phase transformation

  13. Dynamic Support Culture of Murine Skeletal Muscle-Derived Stem Cells Improves Their Cardiogenic Potential In Vitro

    Directory of Open Access Journals (Sweden)

    Klaus Neef

    2015-01-01

    Full Text Available Ischemic heart disease is the main cause of death in western countries and its burden is increasing worldwide. It typically involves irreversible degeneration and loss of myocardial tissue leading to poor prognosis and fatal outcome. Autologous cells with the potential to regenerate damaged heart tissue would be an ideal source for cell therapeutic approaches. Here, we compared different methods of conditional culture for increasing the yield and cardiogenic potential of murine skeletal muscle-derived stem cells. A subpopulation of nonadherent cells was isolated from skeletal muscle by preplating and applying cell culture conditions differing in support of cluster formation. In contrast to static culture conditions, dynamic culture with or without previous hanging drop preculture led to significantly increased cluster diameters and the expression of cardiac specific markers on the protein and mRNA level. Whole-cell patch-clamp studies revealed similarities to pacemaker action potentials and responsiveness to cardiac specific pharmacological stimuli. This data indicates that skeletal muscle-derived stem cells are capable of adopting enhanced cardiac muscle cell-like properties by applying specific culture conditions. Choosing this route for the establishment of a sustainable, autologous source of cells for cardiac therapies holds the potential of being clinically more acceptable than transgenic manipulation of cells.

  14. First-principles model potentials for lattice-dynamical studies: general methodology and example of application to ferroic perovskite oxides.

    Science.gov (United States)

    Wojdeł, Jacek C; Hermet, Patrick; Ljungberg, Mathias P; Ghosez, Philippe; Íñiguez, Jorge

    2013-07-31

    We present a scheme to construct model potentials, with parameters computed from first principles, for large-scale lattice-dynamical simulations of materials. We mimic the traditional solid-state approach to the investigation of vibrational spectra, i.e., we start from a suitably chosen reference configuration of the compound and describe its energy as a function of arbitrary atomic distortions by means of a Taylor series. Such a form of the potential-energy surface is general, trivial to formulate for any material, and physically transparent. Further, such models involve clear-cut approximations, their precision can be improved in a systematic fashion, and their simplicity allows for convenient and practical strategies to compute/fit the potential parameters. We illustrate our scheme with two challenging cases in which the model potential is strongly anharmonic, namely, the ferroic perovskite oxides PbTiO3 and SrTiO3. Studying these compounds allows us to better describe the connection between the so-called effective-Hamiltonian method and ours (which may be seen as an extension of the former), and to show the physical insight and predictive power provided by our approach-e.g., we present new results regarding the factors controlling phase-transition temperatures, novel phase transitions under elastic constraints, an improved treatment of thermal expansion, etc.

  15. Dynamic monitoring of transmembrane potential changes: a study of ion channels using an electrical double layer-gated FET biosensor.

    Science.gov (United States)

    Pulikkathodi, Anil Kumar; Sarangadharan, Indu; Chen, Yi-Hong; Lee, Geng-Yen; Chyi, Jen-Inn; Lee, Gwo-Bin; Wang, Yu-Lin

    2018-03-27

    In this research, we have designed, fabricated and characterized an electrical double layer (EDL)-gated AlGaN/GaN high electron mobility transistor (HEMT) biosensor array to study the transmembrane potential changes of cells. The sensor array platform is designed to detect and count circulating tumor cells (CTCs) of colorectal cancer (CRC) and investigate cellular bioelectric signals. Using the EDL FET biosensor platform, cellular responses can be studied in physiological salt concentrations, thereby eliminating complex automation. Upon investigation, we discovered that our sensor response follows the transmembrane potential changes of captured cells. Our whole cell sensor platform can be used to monitor the dynamic changes in the membrane potential of cells. The effects of continuously changing electrolyte ion concentrations and ion channel blocking using cadmium are investigated. This methodology has the potential to be used as an electrophysiological probe for studying ion channel gating and the interaction of biomolecules in cells. The sensor can also be a point-of-care diagnostic tool for rapid screening of diseases.

  16. A toxicological study of inhalable particulates in an industrial region of Lanzhou City, northwestern China: Results from plasmid scission assay

    Science.gov (United States)

    Xiao, Zhenghui; Shao, Longyi; Zhang, Ning; Wang, Jing; Chuang, Hsiao-Chi; Deng, Zhenzhen; Wang, Zhen; BéruBé, Kelly

    2014-09-01

    The city of Lanzhou in northwestern China experiences serious air pollution episodes in the form of PM10 that is characterized by having high levels of heavy metals. The Xigu District represents the industrial core area of Lanzhou City and is denoted by having the largest petrochemical bases in western China. This study investigates heavy metal compositions and oxidative potential of airborne PM10 (particulate matter with aerodynamic diameter of 10 μm or less) collected in Xigu District in the summer and winter of 2010. An in vitro plasmid scission assay (PSA) was employed to study the oxidative potential of airborne PM10 and inductively coupled plasma-mass spectrometry (ICP-MS) was used to examine heavy metal compositions. Transmission electron microscopy coupled with energy-dispersive X-ray spectrometry (TEM/EDX) was used to investigate elemental compositions and mixing states of PM10. The average mass concentrations of PM10 collected in Xigu District were generally higher than the national standard for daily PM10 (150 μg/m3). Cr, Zn, Pb and Mn were the most abundant metals in the intact whole particles of PM10. Zn, Mn and As was the most abundant metal in the water-soluble fraction, while Cr, Pb, and V existed primarily in insoluble forms. TD20 values (i.e. toxic dosage of PM10 causing 20% of plasmid DNA damage) varied considerably in both winter and summer (from 19 μg/mL to >1000 μg/mL) but were typically higher in summer, suggesting that the winter PM10 exhibited greater bioreactivity. In addition, the PM10 collected during a dust storm episode had a highest TD20 value and thus the least oxidative damage to supercoiled plasmid DNA, while the particles collected on a hazy day had a lowest TD20 value and thus the highest oxidative damage to supercoiled plasmid DNA. The particles collected on the first day after snow fall and on a day of cold air intrusion exhibited minor oxidative potential (i.e. caused limited DNA damage). The water-soluble Zn, Mn, As, and

  17. Dynamics

    CERN Document Server

    Goodman, Lawrence E

    2001-01-01

    Beginning text presents complete theoretical treatment of mechanical model systems and deals with technological applications. Topics include introduction to calculus of vectors, particle motion, dynamics of particle systems and plane rigid bodies, technical applications in plane motions, theory of mechanical vibrations, and more. Exercises and answers appear in each chapter.

  18. Searching Nearest Potential of Children with Intellectual Disability – Dynamic Assessment

    Directory of Open Access Journals (Sweden)

    Kulesza Ewa Maria

    2015-08-01

    Full Text Available The article discussed the issue of the diagnosis with the use of task-support-task procedure. A theoretical model of diagnosis based on the concepts by L. S. Vygotski, R. Case, and A. Bandura was described and developed. The model was tested on a group of non-disabled preschool children, and children with mild and moderate intellectual disability who were paired up accordingly to their mental age. Each pair was given a set of developmentally adapted tasks. The tool (44 tasks was reliable and valid. The task-support-task procedure significantly affected the level of the task performance in all the children and allowed to define the scope of potential abilities, especially in the children with mild and moderate intellectual disabilities. Most of the task they did fell into the zone of proximal development.

  19. Dynamic Changes in Numbers and Properties of Circulating Tumor Cells and Their Potential Applications

    International Nuclear Information System (INIS)

    Tseng, Ju-Yu; Yang, Chih-Yung; Liang, Shu-Ching; Liu, Ren-Shyan; Jiang, Jeng-Kai; Lin, Chi-Hung

    2014-01-01

    Circulating tumor cells (CTCs) can be detected in the blood of different types of early or advanced cancer using immunology-based assays or nucleic acid methods. The detection and quantification of CTCs has significant clinical utility in the prognosis of metastatic breast, prostate, and colorectal cancers. CTCs are a heterogeneous population of cells and often different from those of their respective primary tumor. Understanding the biology of CTCs may provide useful predictive information for the selection of the most appropriate treatment. Therefore, CTC detection and characterization could become a valuable tool to refine prognosis and serve as a “real-time biopsy” and has the potential to guide precision cancer therapies, monitor cancer treatment, and investigate the process of metastasis

  20. Phytoplankton dynamics in contrasting early stage North Atlantic spring blooms: composition, succession, and potential drivers

    DEFF Research Database (Denmark)

    Daniels, C.J.; Poulton, A. J.; Esposito, M.

    2015-01-01

    The spring bloom is a key annual event in the phenology of pelagic ecosystems, making a major contribution to the oceanic biological carbon pump through the production and export of organic carbon. However, there is little consensus as to the main drivers of spring bloom formation, exacerbated......) of the 2012 North Atlantic spring bloom. The plankton composition and characteristics of the initial stages of the bloom were markedly different between the two basins. The Iceland Basin (ICB) appeared well mixed to > 400 m, yet surface chlorophyll a (0.27–2.2 mg m–3) and primary production (0.06–0.66 mmol C...... suggest micro-zooplankton grazing, potentially coupled with the lack of a seed population of bloom forming diatoms, was restricting diatom growth in the NWB, and that large diatoms may be absent in NWB spring blooms. Despite both phytoplankton communities being in the early stages of bloom formation...