Design of a bistable switch to control cellular uptake.

Science.gov (United States)

Oyarzún, Diego A; Chaves, Madalena

2015-12-06

Bistable switches are widely used in synthetic biology to trigger cellular functions in response to environmental signals. All bistable switches developed so far, however, control the expression of target genes without access to other layers of the cellular machinery. Here, we propose a bistable switch to control the rate at which cells take up a metabolite from the environment. An uptake switch provides a new interface to command metabolic activity from the extracellular space and has great potential as a building block in more complex circuits that coordinate pathway activity across cell cultures, allocate metabolic tasks among different strains or require cell-to-cell communication with metabolic signals. Inspired by uptake systems found in nature, we propose to couple metabolite import and utilization with a genetic circuit under feedback regulation. Using mathematical models and analysis, we determined the circuit architectures that produce bistability and obtained their design space for bistability in terms of experimentally tuneable parameters. We found an activation-repression architecture to be the most robust switch because it displays bistability for the largest range of design parameters and requires little fine-tuning of the promoters' response curves. Our analytic results are based on on-off approximations of promoter activity and are in excellent qualitative agreement with simulations of more realistic models. With further analysis and simulation, we established conditions to maximize the parameter design space and to produce bimodal phenotypes via hysteresis and cell-to-cell variability. Our results highlight how mathematical analysis can drive the discovery of new circuits for synthetic biology, as the proposed circuit has all the hallmarks of a toggle switch and stands as a promising design to control metabolic phenotypes across cell cultures. © 2015 The Author(s).

Single cell analysis of gene expression patterns of competence development and initiation of sporulation in Bacillus subtilis grown on chemically defined media

NARCIS (Netherlands)

Veening, J. -W.; Smits, W. K.; Hamoen, L. W.; Kuipers, O. P.

Aim: Understanding the basis for the heterogeneous (or bistable) expression patterns of competence development and sporulation in Bacillus subtilis. Methods and Results: Using flow cytometric analyses of various promoter-GFP fusions, we have determined the single-cell gene expression patterns of

Mutual repression enhances the steepness and precision of gene expression boundaries.

Directory of Open Access Journals (Sweden)

Thomas R Sokolowski

Full Text Available Embryonic development is driven by spatial patterns of gene expression that determine the fate of each cell in the embryo. While gene expression is often highly erratic, embryonic development is usually exceedingly precise. In particular, gene expression boundaries are robust not only against intra-embryonic fluctuations such as noise in gene expression and protein diffusion, but also against embryo-to-embryo variations in the morphogen gradients, which provide positional information to the differentiating cells. How development is robust against intra- and inter-embryonic variations is not understood. A common motif in the gene regulation networks that control embryonic development is mutual repression between pairs of genes. To assess the role of mutual repression in the robust formation of gene expression patterns, we have performed large-scale stochastic simulations of a minimal model of two mutually repressing gap genes in Drosophila, hunchback (hb and knirps (kni. Our model includes not only mutual repression between hb and kni, but also the stochastic and cooperative activation of hb by the anterior morphogen Bicoid (Bcd and of kni by the posterior morphogen Caudal (Cad, as well as the diffusion of Hb and Kni between neighboring nuclei. Our analysis reveals that mutual repression can markedly increase the steepness and precision of the gap gene expression boundaries. In contrast to other mechanisms such as spatial averaging and cooperative gene activation, mutual repression thus allows for gene-expression boundaries that are both steep and precise. Moreover, mutual repression dramatically enhances their robustness against embryo-to-embryo variations in the morphogen levels. Finally, our simulations reveal that diffusion of the gap proteins plays a critical role not only in reducing the width of the gap gene expression boundaries via the mechanism of spatial averaging, but also in repairing patterning errors that could arise because of the

Ca++ dependent bistability induced by serotonin in spinal motoneurons

DEFF Research Database (Denmark)

Hounsgaard, J.; Kiehn, O.

1985-01-01

The plateau potential, responsible for the bistable state of spinal motoneurons, recently described in the decerebrate cat, was suggested to depend on serotonin (Hounsgaard et al. 1984). In an in vitro preparation of the spinal cord of the turtle we now show that serotonin, applied directly...... to the bath, transforms the intrinsic response properties of motoneurons, uncovering a plateau potential and voltage sensitive bistability. The changes induced by serotonin were blocked by Mn++, while the plateau potential and the bistability remained after application of tetrodotoxin. We conclude...... that serotonin controls the expression of a Ca++ dependent plateau potential in motoneurons....

Optical Bistability in Graded Core-Shell Granular Composites

International Nuclear Information System (INIS)

Wu Ya-Min; Chen Guo-Qing; Xue Si-Zhong; Zhu Zhuo-Wei; Ma Chao-Qun

2012-01-01

The intrinsic optical bistability (OB) of graded core-shell granular composites is investigated. The coated particles are made of cores with gradient dielectric function in c (r) = A(r/a) k and nonlinear shells. In view of the exponential distribution of the core dielectric constant, the potential functions of each region are obtained by solving the Maxwell equations, and the mathematical expressions of electric field in the shells and cores are determined. Numerical study reveals that the optical bistable threshold and the threshold width of the composite medium are dependent on the shell thickness, core dielectric exponent, and power function coefficient. The optical bistable width increases with the decreasing shell thickness and the power exponent and with the increasing power function coefficient

Bistable Epigenetic States Explain Age-Dependent Decline in Mesenchymal Stem Cell Heterogeneity.

Science.gov (United States)

Hamidouche, Zahia; Rother, Karen; Przybilla, Jens; Krinner, Axel; Clay, Denis; Hopp, Lydia; Fabian, Claire; Stolzing, Alexandra; Binder, Hans; Charbord, Pierre; Galle, Joerg

2017-03-01

The molecular mechanisms by which heterogeneity, a major characteristic of stem cells, is achieved are yet unclear. We here study the expression of the membrane stem cell antigen-1 (Sca-1) in mouse bone marrow mesenchymal stem cell (MSC) clones. We show that subpopulations with varying Sca-1 expression profiles regenerate the Sca-1 profile of the mother population within a few days. However, after extensive replication in vitro, the expression profiles shift to lower values and the regeneration time increases. Study of the promoter of Ly6a unravels that the expression level of Sca-1 is related to the promoter occupancy by the activating histone mark H3K4me3. We demonstrate that these findings can be consistently explained by a computational model that considers positive feedback between promoter H3K4me3 modification and gene transcription. This feedback implicates bistable epigenetic states which the cells occupy with an age-dependent frequency due to persistent histone (de-)modification. Our results provide evidence that MSC heterogeneity, and presumably that of other stem cells, is associated with bistable epigenetic states and suggest that MSCs are subject to permanent state fluctuations. Stem Cells 2017;35:694-704. © The Authors Stem Cells published by Wiley Periodicals, Inc. on behalf of AlphaMed Press.

Kinetic models of gene expression including non-coding RNAs

Energy Technology Data Exchange (ETDEWEB)

Zhdanov, Vladimir P., E-mail: zhdanov@catalysis.r

2011-03-15

In cells, genes are transcribed into mRNAs, and the latter are translated into proteins. Due to the feedbacks between these processes, the kinetics of gene expression may be complex even in the simplest genetic networks. The corresponding models have already been reviewed in the literature. A new avenue in this field is related to the recognition that the conventional scenario of gene expression is fully applicable only to prokaryotes whose genomes consist of tightly packed protein-coding sequences. In eukaryotic cells, in contrast, such sequences are relatively rare, and the rest of the genome includes numerous transcript units representing non-coding RNAs (ncRNAs). During the past decade, it has become clear that such RNAs play a crucial role in gene expression and accordingly influence a multitude of cellular processes both in the normal state and during diseases. The numerous biological functions of ncRNAs are based primarily on their abilities to silence genes via pairing with a target mRNA and subsequently preventing its translation or facilitating degradation of the mRNA-ncRNA complex. Many other abilities of ncRNAs have been discovered as well. Our review is focused on the available kinetic models describing the mRNA, ncRNA and protein interplay. In particular, we systematically present the simplest models without kinetic feedbacks, models containing feedbacks and predicting bistability and oscillations in simple genetic networks, and models describing the effect of ncRNAs on complex genetic networks. Mathematically, the presentation is based primarily on temporal mean-field kinetic equations. The stochastic and spatio-temporal effects are also briefly discussed.

Optical bistability controlling light with light

CERN Document Server

Gibbs, Hyatt

1985-01-01

Optical Bistability: Controlling Light with Light focuses on optical bistability in nonlinear optical systems. Emphasis is on passive (non-laser) systems that exhibit reversible bistability with input intensity as the hysteresis variable, along with the physics and the potential applications of such systems for nonlinear optical signal processing. This book consists of seven chapters and begins with a historical overview of optical bistability in lasers and passive systems. The next chapter describes steady-state theories of optical bistability, including the Bonifacio-Lugiato model, as we

A Miniature Coupled Bistable Vibration Energy Harvester

International Nuclear Information System (INIS)

Zhu, D; Arthur, D C; Beeby, S P

2014-01-01

This paper reports the design and test of a miniature coupled bistable vibration energy harvester. Operation of a bistable structure largely depends on vibration amplitude rather than frequency, which makes it very promising for wideband vibration energy harvesting applications. A coupled bistable structure consists of a pair of mobile magnets that create two potential wells and thus the bistable phenomenon. It requires lower excitation to trigger bistable operation compared to conventional bistable structures. Based on previous research, this work focused on miniaturisation of the coupled bistable structure for energy harvesting application. The proposed bistable energy harvester is a combination of a Duffing's nonlinear structure and a linear assisting resonator. Experimental results show that the output spectrum of the miniature coupled bistable vibration energy harvester was the superposition of several spectra. It had a higher maximum output power and a much greater bandwidth compared to simply the Duffing's structure without the assisting resonator

Controlling bistability by linear augmentation

International Nuclear Information System (INIS)

Sharma, Pooja Rani; Shrimali, Manish Dev; Prasad, Awadhesh; Feudel, Ulrike

2013-01-01

In many bistable oscillating systems only one of the attractors is desired to possessing certain system performance. We present a method to drive a bistable system to a desired target attractor by annihilating the other one. This shift from bistability to monostability is achieved by augmentation of the nonlinear oscillator with a linear control system. For a proper choice of the control function one of the attractors disappears at a critical coupling strength in an control-induced boundary crisis. This transition from bistability to monostability is demonstrated with two paradigmatic examples, the autonomous Chua oscillator and a neuronal system with a periodic input signal.

Bistable Mechanisms for Space Applications.

Science.gov (United States)

Zirbel, Shannon A; Tolman, Kyler A; Trease, Brian P; Howell, Larry L

2016-01-01

Compliant bistable mechanisms are monolithic devices with two stable equilibrium positions separated by an unstable equilibrium position. They show promise in space applications as nonexplosive release mechanisms in deployment systems, thereby eliminating friction and improving the reliability and precision of those mechanical devices. This paper presents both analytical and numerical models that are used to predict bistable behavior and can be used to create bistable mechanisms in materials not previously feasible for compliant mechanisms. Materials compatible with space applications are evaluated for use as bistable mechanisms and prototypes are fabricated in three different materials. Pin-puller and cutter release mechanisms are proposed as potential space applications.

A novel bistable energy harvesting concept

International Nuclear Information System (INIS)

Scarselli, G; Nicassio, F; Pinto, F; Ciampa, F; Iervolino, O; Meo, M

2016-01-01

Bistable energy harvesting has become a major field of research due to some unique features for converting mechanical energy into electrical power. When properly loaded, bistable structures snap-through from one stable configuration to another, causing large strains and consequently power generation. Moreover, bistable structures can harvest energy across a broad-frequency bandwidth due to their nonlinear characteristics. Despite the fact that snap-through may be triggered regardless of the form or frequency of exciting vibration, the external force must reach a specific snap-through activation threshold value to trigger the transition from one stable state to another. This aspect is a limiting factor for realistic vibration energy harvesting application with bistable devices. This paper presents a novel power harvesting concept for bistable composites based on a ‘lever effect’ aimed at minimising the activation force to cause the snap through by choosing properly the bistable structures’ constraints. The concept was demonstrated with the help of numerical simulation and experimental testing. The results showed that the actuation force is one order of magnitude smaller (3%–6%) than the activation force of conventionally constrained bistable devices. In addition, it was shown that the output voltage was higher than the conventional configuration, leading to a significant increase in power generation. This novel concept could lead to a new generation of more efficient bistable energy harvesters for realistic vibration environments. (paper)

What is refractive optical bistability

International Nuclear Information System (INIS)

Dzhehov, Tomislav

1993-01-01

The basic elements of the theory of refractive optical bistability, assuming mediums with linear absorption are given. Special attention is paid to bistable etalons of semiconductor materials an oxide glasses, since some of them are considered as promising components for optical bistability applications. The design optimization of such devices for minimum switching intensity is analyzed. Computer simulation of the transfer characteristic recording for two InSb etalons is presented. (author)

A bistable mechanism for directional sensing

International Nuclear Information System (INIS)

Beta, C; Amselem, G; Bodenschatz, E

2008-01-01

We present a generic mechanism for directional sensing in eukaryotic cells that is based on bistable dynamics. As the key feature of this modeling approach, the velocity of trigger waves in the bistable sensing system changes its sign across cells that are exposed to an external chemoattractant gradient. This is achieved by combining a two-component activator/inhibitor system with a bistable switch that induces an identical symmetry breaking for arbitrary gradient input signals. A simple kinetic example is designed to illustrate the dynamics of a bistable directional sensing mechanism in numerical simulations

Bistable scattering in graphene-coated dielectric nanowires.

Science.gov (United States)

Li, Rujiang; Wang, Huaping; Zheng, Bin; Dehdashti, Shahram; Li, Erping; Chen, Hongsheng

2017-06-22

In nonlinear plasmonics, the switching threshold of optical bistability is limited by the weak nonlinear responses from the conventional Kerr dielectric media. Considering the giant nonlinear susceptibility of graphene, here we develop a nonlinear scattering model under the mean field approximation and study the bistable scattering in graphene-coated dielectric nanowires based on the semi-analytical solutions. We find that the switching intensities of bistable scattering can be smaller than 1 MW cm -2 at the working frequency. To further decrease the switching intensities, we show that the most important factor that restricts the bistable scattering is the relaxation time of graphene. Our work not only reveals some general characteristics of graphene-based bistable scattering, but also provides a guidance to further applications of optical bistability in the high speed all-optical signal processing.

Optimization of Bistable Viscoelastic Systems

DEFF Research Database (Denmark)

Jensen, Kristian Ejlebjærg; Szabo, Peter; Okkels, Fridolin

2014-01-01

driving pressure corresponding to the point of bistability, such that the effect is enhanced. The point of bistability is, however, not explicitly contained in the solution, so we opt for a heuristic approach based on the dissipation ratio between the asymmetric and unstable symmetric flow solutions. We...... find a design that significantly reduces the driving pressure required for bistability, and furthermore is in agreement with the approach followed by experimental researchers. Furthermore, by comparing the two asymmetric solutions, we succesfully apply the same approach to a problem with two fluids...

A broadband electromagnetic energy harvester with a coupled bistable structure

International Nuclear Information System (INIS)

Zhu, D; Beeby, S P

2013-01-01

This paper investigates a broadband electromagnetic energy harvester with a coupled bistable structure. Both analytical model and experimental results showed that the coupled bistable structure requires lower excitation force to trigger bistable operation than conventional bistable structures. A compact electromagnetic vibration energy harvester with a coupled bistable structure was implemented and tested. It was excited under white noise vibrations. Experimental results showed that the coupled bistable energy harvester can achieve bistable operation with lower excitation amplitude and generate more output power than both conventional bistable and linear energy harvesters under white noise excitation

Diversity and functional properties of bistable pigments.

Science.gov (United States)

Tsukamoto, Hisao; Terakita, Akihisa

2010-11-01

Rhodopsin and related opsin-based pigments, which are photosensitive membrane proteins, have been extensively studied using a wide variety of techniques, with rhodopsin being the most understood G protein-coupled receptor (GPCR). Animals use various opsin-based pigments for vision and a wide variety of non-visual functions. Many functionally varied pigments are roughly divided into two kinds, based on their photoreaction: bistable and monostable pigments. Bistable pigments are thermally stable before and after photo-activation, but monostable pigments are stable only before activation. Here, we review the diversity of bistable pigments and their molecular characteristics. We also discuss the mechanisms underlying different molecular characteristics of bistable and monostable pigments. In addition, the potential of bistable pigments as a GPCR model is proposed.

A modified consumer inkjet for spatiotemporal control of gene expression.

Directory of Open Access Journals (Sweden)

Daniel J Cohen

Full Text Available This paper presents a low-cost inkjet dosing system capable of continuous, two-dimensional spatiotemporal regulation of gene expression via delivery of diffusible regulators to a custom-mounted gel culture of E. coli. A consumer-grade, inkjet printer was adapted for chemical printing; E. coli cultures were grown on 750 microm thick agar embedded in micro-wells machined into commercial compact discs. Spatio-temporal regulation of the lac operon was demonstrated via the printing of patterns of lactose and glucose directly into the cultures; X-Gal blue patterns were used for visual feedback. We demonstrate how the bistable nature of the lac operon's feedback, when perturbed by patterning lactose (inducer and glucose (inhibitor, can lead to coordination of cell expression patterns across a field in ways that mimic motifs seen in developmental biology. Examples of this include sharp boundaries and the generation of traveling waves of mRNA expression. To our knowledge, this is the first demonstration of reaction-diffusion effects in the well-studied lac operon. A finite element reaction-diffusion model of the lac operon is also presented which predicts pattern formation with good fidelity.

Distributed processing in bistable perception

NARCIS (Netherlands)

Knapen, T.H.J.

2007-01-01

A very incisive way of studying visual awareness and the mechanisms that underlie it, it to use bistable perception. In bistable perception, an observer's perceptual state alternates between one interpretation and its mutually exclusive counterpart while the stimulus remains the same. This gives us

Bistability of Cavity Magnon Polaritons

Science.gov (United States)

Wang, Yi-Pu; Zhang, Guo-Qiang; Zhang, Dengke; Li, Tie-Fu; Hu, C.-M.; You, J. Q.

2018-01-01

We report the first observation of the magnon-polariton bistability in a cavity magnonics system consisting of cavity photons strongly interacting with the magnons in a small yttrium iron garnet (YIG) sphere. The bistable behaviors emerged as sharp frequency switchings of the cavity magnon polaritons (CMPs) and related to the transition between states with large and small numbers of polaritons. In our experiment, we align, respectively, the [100] and [110] crystallographic axes of the YIG sphere parallel to the static magnetic field and find very different bistable behaviors (e.g., clockwise and counter-clockwise hysteresis loops) in these two cases. The experimental results are well fitted and explained as being due to the Kerr nonlinearity with either a positive or negative coefficient. Moreover, when the magnetic field is tuned away from the anticrossing point of CMPs, we observe simultaneous bistability of both magnons and cavity photons by applying a drive field on the lower branch.

Bistability and Biofilm Formation in Bacillus subtilis

Science.gov (United States)

Chai, Yunrong; Chu, Frances; Kolter, Roberto; Losick, Richard

2008-01-01

Summary Biofilms of Bacillus subtilis consist of long chains of cells that are held together in bundles by an extracellular matrix of exopolysaccharide and the protein TasA. The exopolysaccharide is produced by enzymes encoded by the epsA-O operon and the gene encoding TasA is located in the yqxM-sipW-tasA operon. Both operons are under the control of the repressor SinR. Derepression is mediated by the antirepressor SinI, which binds to SinR with a 1:1 stoichiometry. Paradoxically, in medium promoting derepression of the matrix operons, the overall concentration of SinR in the culture greatly exceeded that of SinI. We show that under biofilm-promoting conditions sinI, which is under the control of the response regulator Spo0A, was expressed only in a small subpopulation of cells, whereas sinR was expressed in almost all cells. Activation of Spo0A is known to be subject to a bistable switch, and we infer that SinI reaches levels sufficient to trigger matrix production only in the subpopulation of cells in which Spo0A is active. Additionally, evidence suggests that sinI is expressed at intermediate, but not low or high, levels of Spo0A activity, which may explain why certain nutritional conditions are more effective in promoting biofilm formation than others. PMID:18047568

Optical bistability without the rotating wave approximation

Energy Technology Data Exchange (ETDEWEB)

Sharaby, Yasser A., E-mail: Yasser_Sharaby@hotmail.co [Physics Department, Faculty of Applied Sciences, Suez Canal University, Suez (Egypt); Joshi, Amitabh, E-mail: ajoshi@eiu.ed [Department of Physics, Eastern Illinois University, Charleston, IL 61920 (United States); Hassan, Shoukry S., E-mail: Shoukryhassan@hotmail.co [Mathematics Department, College of Science, University of Bahrain, P.O. Box 32038 (Bahrain)

2010-04-26

Optical bistability for two-level atomic system in a ring cavity is investigated outside the rotating wave approximation (RWA) using non-autonomous Maxwell-Bloch equations with Fourier decomposition up to first harmonic. The first harmonic output field component exhibits reversed or closed loop bistability simultaneously with the usual (anti-clockwise) bistability in the fundamental field component.

Optical bistability without the rotating wave approximation

International Nuclear Information System (INIS)

Sharaby, Yasser A.; Joshi, Amitabh; Hassan, Shoukry S.

2010-01-01

Optical bistability for two-level atomic system in a ring cavity is investigated outside the rotating wave approximation (RWA) using non-autonomous Maxwell-Bloch equations with Fourier decomposition up to first harmonic. The first harmonic output field component exhibits reversed or closed loop bistability simultaneously with the usual (anti-clockwise) bistability in the fundamental field component.

Bistable near field and bistable transmittance in 2D composite slab consisting of nonlocal core-Kerr shell inclusions.

Science.gov (United States)

Huang, Yang; Wu, Ya Min; Gao, Lei

2017-01-23

We carry out a theoretical study on optical bistability of near field intensity and transmittance in two-dimensional nonlinear composite slab. This kind of 2D composite is composed of nonlocal metal/Kerr-type dielectric core-shell inclusions randomly embedded in the host medium, and we derivate the nonlinear relation between the field intensity in the shell of inclusions and the incident field intensity with self-consistent mean field approximation. Numerical demonstration has been performed to show the viable parameter space for the bistable near field. We show that nonlocality can provide broader region in geometric parameter space for bistable near field as well as bistable transmittance of the nonlocal composite slab compared to local case. Furthermore, we investigate the bistable transmittance in wavelength spectrum, and find that besides the input intensity, the wavelength operation could as well make the transmittance jump from a high value to a low one. This kind of self-tunable nano-composite slab might have potential application in optical switching devices.

Bistable microelectromechanical actuator

Science.gov (United States)

Fleming, James G.

1999-01-01

A bistable microelectromechanical (MEM) actuator is formed on a substrate and includes a stressed membrane of generally rectangular shape that upon release assumes a curvilinear cross-sectional shape due to attachment at a midpoint to a resilient member and at opposing edges to a pair of elongate supports. The stressed membrane can be electrostatically switched between a pair of mechanical states having mirror-image symmetry, with the MEM actuator remaining in a quiescent state after a programming voltage is removed. The bistable MEM actuator according to various embodiments of the present invention can be used to form a nonvolatile memory element, an optical modulator (with a pair of mirrors supported above the membrane and moving in synchronism as the membrane is switched), a switchable mirror (with a single mirror supported above the membrane at the midpoint thereof) and a latching relay (with a pair of contacts that open and close as the membrane is switched). Arrays of bistable MEM actuators can be formed for applications including nonvolatile memories, optical displays and optical computing.

Bubbling and bistability in two parameter discrete systems

Indian Academy of Sciences (India)

The birth of X *. · is concurrent with the ... for bistability viz. a½, and the higher order bistability points a¾, etc. are marked. The quadrilateral marked as ... The characteristics of 2 parameter 1-d maps that exhibit bubbling/bistability related to their ...

Bistable amphoteric centers in semiconductors

International Nuclear Information System (INIS)

Nikitina, A. G.; Zuev, V. V.

2008-01-01

It is shown that, at thermodynamic equilibrium, the release of charge carriers from the localized states of bistable amphoteric centers into quasi-free states depends on the degree of compensation. This brings about different functional dependences of the concentration of free charge carriers on temperature. It is found that, in uncompensated semiconductors, the concentration of free charge carriers follows the same dependence in the case of bistable amphoteric centers and bistable amphoteric U - centers, although the distributions of charge carriers over the charge states and configurations are different for these types of centers. The results can be used for interpreting various experimental data insufficiently explained in the context of the traditional approach

A broadband electromagnetic energy harvester with a coupled bistable structure

OpenAIRE

Zhu, Dibin; Beeby, Steve

2013-01-01

This paper investigates a broadband electromagnetic energy harvester with a coupled bistable structure. Both analytical model and experimental results showed that the coupled bistable structure requires lower excitation force to trigger bistable operation than conventional bistable structures. A compact electromagnetic vibration energy harvester with a coupled bistable structure was implemented and tested. It was excited under white noise vibrations. Experimental results showed that the coupl...

Convergent Transcription in the Butyrolactone Regulon in Streptomyces coelicolor Confers a Bistable Genetic Switch for Antibiotic Biosynthesis

Science.gov (United States)

Chatterjee, Anushree; Drews, Laurie; Mehra, Sarika; Takano, Eriko; Kaznessis, Yiannis N.; Hu, Wei-Shou

2011-01-01

cis-encoded antisense RNAs (cis asRNA) have been reported to participate in gene expression regulation in both eukaryotic and prokaryotic organisms. Its presence in Streptomyces coelicolor has also been reported recently; however, its role has yet to be fully investigated. Using mathematical modeling we explore the role of cis asRNA produced as a result of convergent transcription in scbA-scbR genetic switch. scbA and scbR gene pair, encoding repressor–amplifier proteins respectively, mediates the synthesis of a signaling molecule, the γ-butyrolactone SCB1 and controls the onset of antibiotic production. Our model considers that transcriptional interference caused by convergent transcription of two opposing RNA polymerases results in fatal collision and transcriptional termination, which suppresses transcription efficiency. Additionally, convergent transcription causes sense and antisense interactions between complementary sequences from opposing strands, rendering the full length transcript inaccessible for translation. We evaluated the role of transcriptional interference and the antisense effect conferred by convergent transcription on the behavior of scbA-scbR system. Stability analysis showed that while transcriptional interference affects the system, it is asRNA that confers scbA-scbR system the characteristics of a bistable switch in response to the signaling molecule SCB1. With its critical role of regulating the onset of antibiotic synthesis the bistable behavior offers this two gene system the needed robustness to be a genetic switch. The convergent two gene system with potential of transcriptional interference is a frequent feature in various genomes. The possibility of asRNA regulation in other such gene-pairs is yet to be examined. PMID:21765930

A Precise Temperature-Responsive Bistable Switch Controlling Yersinia Virulence.

Science.gov (United States)

Nuss, Aaron Mischa; Schuster, Franziska; Roselius, Louisa; Klein, Johannes; Bücker, René; Herbst, Katharina; Heroven, Ann Kathrin; Pisano, Fabio; Wittmann, Christoph; Münch, Richard; Müller, Johannes; Jahn, Dieter; Dersch, Petra

2016-12-01

Different biomolecules have been identified in bacterial pathogens that sense changes in temperature and trigger expression of virulence programs upon host entry. However, the dynamics and quantitative outcome of this response in individual cells of a population, and how this influences pathogenicity are unknown. Here, we address these questions using a thermosensing virulence regulator of an intestinal pathogen (RovA of Yersinia pseudotuberculosis) as a model. We reveal that this regulator is part of a novel thermoresponsive bistable switch, which leads to high- and low-invasive subpopulations within a narrow temperature range. The temperature range in which bistability is observed is defined by the degradation and synthesis rate of the regulator, and is further adjustable via a nutrient-responsive regulator. The thermoresponsive switch is also characterized by a hysteretic behavior in which activation and deactivation occurred on vastly different time scales. Mathematical modeling accurately mirrored the experimental behavior and predicted that the thermoresponsiveness of this sophisticated bistable switch is mainly determined by the thermo-triggered increase of RovA proteolysis. We further observed RovA ON and OFF subpopulations of Y. pseudotuberculosis in the Peyer's patches and caecum of infected mice, and that changes in the RovA ON/OFF cell ratio reduce tissue colonization and overall virulence. This points to a bet-hedging strategy in which the thermoresponsive bistable switch plays a key role in adapting the bacteria to the fluctuating conditions encountered as they pass through the host's intestinal epithelium and suggests novel strategies for the development of antimicrobial therapies.

A Precise Temperature-Responsive Bistable Switch Controlling Yersinia Virulence.

Directory of Open Access Journals (Sweden)

Aaron Mischa Nuss

2016-12-01

Full Text Available Different biomolecules have been identified in bacterial pathogens that sense changes in temperature and trigger expression of virulence programs upon host entry. However, the dynamics and quantitative outcome of this response in individual cells of a population, and how this influences pathogenicity are unknown. Here, we address these questions using a thermosensing virulence regulator of an intestinal pathogen (RovA of Yersinia pseudotuberculosis as a model. We reveal that this regulator is part of a novel thermoresponsive bistable switch, which leads to high- and low-invasive subpopulations within a narrow temperature range. The temperature range in which bistability is observed is defined by the degradation and synthesis rate of the regulator, and is further adjustable via a nutrient-responsive regulator. The thermoresponsive switch is also characterized by a hysteretic behavior in which activation and deactivation occurred on vastly different time scales. Mathematical modeling accurately mirrored the experimental behavior and predicted that the thermoresponsiveness of this sophisticated bistable switch is mainly determined by the thermo-triggered increase of RovA proteolysis. We further observed RovA ON and OFF subpopulations of Y. pseudotuberculosis in the Peyer's patches and caecum of infected mice, and that changes in the RovA ON/OFF cell ratio reduce tissue colonization and overall virulence. This points to a bet-hedging strategy in which the thermoresponsive bistable switch plays a key role in adapting the bacteria to the fluctuating conditions encountered as they pass through the host's intestinal epithelium and suggests novel strategies for the development of antimicrobial therapies.

GABA shapes the dynamics of bistable perception.

Science.gov (United States)

van Loon, Anouk M; Knapen, Tomas; Scholte, H Steven; St John-Saaltink, Elexa; Donner, Tobias H; Lamme, Victor A F

2013-05-06

Sometimes, perception fluctuates spontaneously between two distinct interpretations of a constant sensory input. These bistable perceptual phenomena provide a unique window into the neural mechanisms that create the contents of conscious perception. Models of bistable perception posit that mutual inhibition between stimulus-selective neural populations in visual cortex plays a key role in these spontaneous perceptual fluctuations. However, a direct link between neural inhibition and bistable perception has not yet been established experimentally. Here, we link perceptual dynamics in three distinct bistable visual illusions (binocular rivalry, motion-induced blindness, and structure from motion) to measurements of gamma-aminobutyric acid (GABA) concentrations in human visual cortex (as measured with magnetic resonance spectroscopy) and to pharmacological stimulation of the GABAA receptor by means of lorazepam. As predicted by a model of neural interactions underlying bistability, both higher GABA concentrations in visual cortex and lorazepam administration induced slower perceptual dynamics, as reflected in a reduced number of perceptual switches and a lengthening of percept durations. Thus, we show that GABA, the main inhibitory neurotransmitter, shapes the dynamics of bistable perception. These results pave the way for future studies into the competitive neural interactions across the visual cortical hierarchy that elicit conscious perception. Copyright © 2013 Elsevier Ltd. All rights reserved.

The derivation of a bistable criterion for double V-beam mechanisms

International Nuclear Information System (INIS)

Wu, Cho-Chun; Chen, Rongshun; Lin, Meng-Ju

2013-01-01

This study presents the theoretical derivation of the discriminant D as a structural and material criterion for determining whether bistability can occur in micromechanically bistable mechanisms. When D < 0, the mechanism displays bistable behavior if an appropriate force is applied to push the bistable mechanism, whereas when D > 0, bistable behavior cannot occur. The proposed V-beam bistable mechanism was successfully fabricated with various beam lengths and tilted angles. The experiments conducted in this study validated the theoretical study of bistability. A comparison of the theoretical solutions and experimental results shows good agreement. Results further show that to design a bistable V-beam mechanism, the tilted angle should be larger for the same beam length, whereas the beam length should be longer for the same tilted angle. The developed discriminant D can be used to predict if a bistable mechanism can achieve bistable behavior based on structural sizes and material properties. Consequently, researchers can reduce trial-and-error experiments when designing a bistable mechanism. A V-beam with a larger tilted angle of up to 5° was successfully fabricated to act as a bistable mechanism, compared to a 3.5° tilted angle in existing studies. Consequently, the proposed method has the advantages of shorter beam lengths and smaller device areas. (paper)

Balancing bistable perception during self-motion.

Science.gov (United States)

van Elk, Michiel; Blanke, Olaf

2012-10-01

In two experiments we investigated whether bistable visual perception is influenced by passive own body displacements due to vestibular stimulation. For this we passively rotated our participants around the vertical (yaw) axis while observing different rotating bistable stimuli (bodily or non-bodily) with different ambiguous motion directions. Based on previous work on multimodal effects on bistable perception, we hypothesized that vestibular stimulation should alter bistable perception and that the effects should differ for bodily versus non-bodily stimuli. In the first experiment, it was found that the rotation bias (i.e., the difference between the percentage of time that a CW or CCW rotation was perceived) was selectively modulated by vestibular stimulation: the perceived duration of the bodily stimuli was longer for the rotation direction congruent with the subject's own body rotation, whereas the opposite was true for the non-bodily stimulus (Necker cube). The results found in the second experiment extend the findings from the first experiment and show that these vestibular effects on bistable perception only occur when the axis of rotation of the bodily stimulus matches the axis of passive own body rotation. These findings indicate that the effect of vestibular stimulation on the rotation bias depends on the stimulus that is presented and the rotation axis of the stimulus. Although most studies on vestibular processing have traditionally focused on multisensory signal integration for posture, balance, and heading direction, the present data show that vestibular self-motion influences the perception of bistable bodily stimuli revealing the importance of vestibular mechanisms for visual consciousness.

Coupling between feedback loops in autoregulatory networks affects bistability range, open-loop gain and switching times

International Nuclear Information System (INIS)

Tiwari, Abhinav; Igoshin, Oleg A

2012-01-01

Biochemical regulatory networks governing diverse cellular processes such as stress-response, differentiation and cell cycle often contain coupled feedback loops. We aim at understanding how features of feedback architecture, such as the number of loops, the sign of the loops and the type of their coupling, affect network dynamical performance. Specifically, we investigate how bistability range, maximum open-loop gain and switching times of a network with transcriptional positive feedback are affected by additive or multiplicative coupling with another positive- or negative-feedback loop. We show that a network's bistability range is positively correlated with its maximum open-loop gain and that both quantities depend on the sign of the feedback loops and the type of feedback coupling. Moreover, we find that the addition of positive feedback could decrease the bistability range if we control the basal level in the signal-response curves of the two systems. Furthermore, the addition of negative feedback has the capacity to increase the bistability range if its dissociation constant is much lower than that of the positive feedback. We also find that the addition of a positive feedback to a bistable network increases the robustness of its bistability range, whereas the addition of a negative feedback decreases it. Finally, we show that the switching time for a transition from a high to a low steady state increases with the effective fold change in gene regulation. In summary, we show that the effect of coupled feedback loops on the bistability range and switching times depends on the underlying mechanistic details. (paper)

Steady state statistical correlations predict bistability in reaction motifs.

Science.gov (United States)

Chakravarty, Suchana; Barik, Debashis

2017-03-28

Various cellular decision making processes are regulated by bistable switches that take graded input signals and convert them to binary all-or-none responses. Traditionally, a bistable switch generated by a positive feedback loop is characterized either by a hysteretic signal response curve with two distinct signaling thresholds or by characterizing the bimodality of the response distribution in the bistable region. To identify the intrinsic bistability of a feedback regulated network, here we propose that bistability can be determined by correlating higher order moments and cumulants (≥2) of the joint steady state distributions of two components connected in a positive feedback loop. We performed stochastic simulations of four feedback regulated models with intrinsic bistability and we show that for a bistable switch with variation of the signal dose, the steady state variance vs. covariance adopts a signatory cusp-shaped curve. Further, we find that the (n + 1)th order cross-cumulant vs. nth order cross-cumulant adopts a closed loop structure for at least n = 3. We also propose that our method is capable of identifying systems without intrinsic bistability even though the system may show bimodality in the marginal response distribution. The proposed method can be used to analyze single cell protein data measured at steady state from experiments such as flow cytometry.

Organic bistable light-emitting devices

Science.gov (United States)

Ma, Liping; Liu, Jie; Pyo, Seungmoon; Yang, Yang

2002-01-01

An organic bistable device, with a unique trilayer structure consisting of organic/metal/organic sandwiched between two outmost metal electrodes, has been invented. [Y. Yang, L. P. Ma, and J. Liu, U.S. Patent Pending, U.S. 01/17206 (2001)]. When the device is biased with voltages beyond a critical value (for example 3 V), the device suddenly switches from a high-impedance state to a low-impedance state, with a difference in injection current of more than 6 orders of magnitude. When the device is switched to the low-impedance state, it remains in that state even when the power is off. (This is called "nonvolatile" phenomenon in memory devices.) The high-impedance state can be recovered by applying a reverse bias; therefore, this bistable device is ideal for memory applications. In order to increase the data read-out rate of this type of memory device, a regular polymer light-emitting diode has been integrated with the organic bistable device, such that it can be read out optically. These features make the organic bistable light-emitting device a promising candidate for several applications, such as digital memories, opto-electronic books, and recordable papers.

Space charge effects and electronic bistability

International Nuclear Information System (INIS)

Ruffini, A.; Strumia, F.; Tommasi, O.

1996-01-01

The excitation of metastable states in an atomic beam apparatus by means of electron collision is a widespread technique. The authors have observed a large bistable behaviour in apparatus designed to provide an intense and collimated beam of metastable helium by excitation with orthogonally impinging electrons. This bistable behaviour largely affects the efficiency of the apparatus and is therefore worth of being carefully investigated. The apparatus has an electrode configuration equivalent to that of a tetrode valve with large intergrid distances. The bistability consists in a hysteresis cycle in the curve of the anode current vs. grid voltage. Experimental measurements, supported by a simple theoretical model and by numerical simulation, stress out the crucial role played by space charge effects for the onset of bistability. A comparison with previous observations of this phenomenon is given. Spontaneous current oscillations with various shapes have been recorded in one of the two curves of the hysteresis cycle

Bistability in a laser with injected signal

International Nuclear Information System (INIS)

Dorobantu, I.A.; Vlad, V.I.; Ursu, I.

1987-04-01

A unified description of bistability is given in free running lasers, optical bistable devices, ring lasers and lasers with an injected signal (LIS). A general review of laser instabilities is also presented in the frame of the theory of elementary catastrophes, emphasizing the apparence of higher order catastrophes in the case of a LIS suggesting thus a possibility to devise from first principles the whole hierarchy of laser instabilities. Experimental results on the bistability in the polarisation of LIS are also discussed. (authors)

Gene expression and gene therapy imaging

International Nuclear Information System (INIS)

Rome, Claire; Couillaud, Franck; Moonen, Chrit T.W.

2007-01-01

The fast growing field of molecular imaging has achieved major advances in imaging gene expression, an important element of gene therapy. Gene expression imaging is based on specific probes or contrast agents that allow either direct or indirect spatio-temporal evaluation of gene expression. Direct evaluation is possible with, for example, contrast agents that bind directly to a specific target (e.g., receptor). Indirect evaluation may be achieved by using specific substrate probes for a target enzyme. The use of marker genes, also called reporter genes, is an essential element of MI approaches for gene expression in gene therapy. The marker gene may not have a therapeutic role itself, but by coupling the marker gene to a therapeutic gene, expression of the marker gene reports on the expression of the therapeutic gene. Nuclear medicine and optical approaches are highly sensitive (detection of probes in the picomolar range), whereas MRI and ultrasound imaging are less sensitive and require amplification techniques and/or accumulation of contrast agents in enlarged contrast particles. Recently developed MI techniques are particularly relevant for gene therapy. Amongst these are the possibility to track gene therapy vectors such as stem cells, and the techniques that allow spatiotemporal control of gene expression by non-invasive heating (with MRI guided focused ultrasound) and the use of temperature sensitive promoters. (orig.)

Does visual attention drive the dynamics of bistable perception?

Science.gov (United States)

Dieter, Kevin C; Brascamp, Jan; Tadin, Duje; Blake, Randolph

2016-10-01

How does attention interact with incoming sensory information to determine what we perceive? One domain in which this question has received serious consideration is that of bistable perception: a captivating class of phenomena that involves fluctuating visual experience in the face of physically unchanging sensory input. Here, some investigations have yielded support for the idea that attention alone determines what is seen, while others have implicated entirely attention-independent processes in driving alternations during bistable perception. We review the body of literature addressing this divide and conclude that in fact both sides are correct-depending on the form of bistable perception being considered. Converging evidence suggests that visual attention is required for alternations in the type of bistable perception called binocular rivalry, while alternations during other types of bistable perception appear to continue without requiring attention. We discuss some implications of this differential effect of attention for our understanding of the mechanisms underlying bistable perception, and examine how these mechanisms operate during our everyday visual experiences.

A bistable model of cell polarity.

Directory of Open Access Journals (Sweden)

Matteo Semplice

Full Text Available Ultrasensitivity, as described by Goldbeter and Koshland, has been considered for a long time as a way to realize bistable switches in biological systems. It is not as well recognized that when ultrasensitivity and reinforcing feedback loops are present in a spatially distributed system such as the cell plasmamembrane, they may induce bistability and spatial separation of the system into distinct signaling phases. Here we suggest that bistability of ultrasensitive signaling pathways in a diffusive environment provides a basic mechanism to realize cell membrane polarity. Cell membrane polarization is a fundamental process implicated in several basic biological phenomena, such as differentiation, proliferation, migration and morphogenesis of unicellular and multicellular organisms. We describe a simple, solvable model of cell membrane polarization based on the coupling of membrane diffusion with bistable enzymatic dynamics. The model can reproduce a broad range of symmetry-breaking events, such as those observed in eukaryotic directional sensing, the apico-basal polarization of epithelium cells, the polarization of budding and mating yeast, and the formation of Ras nanoclusters in several cell types.

Perceptual incongruence influences bistability and cortical activation

NARCIS (Netherlands)

Brouwer, G.J.; Tong, F.; Hagoort, P.; van Ee, R.

2009-01-01

We employed a parametric psychophysical design in combination with functional imaging to examine the influence of metric changes in perceptual incongruence on perceptual alternation rates and cortical responses. Subjects viewed a bistable stimulus defined by incongruent depth cues; bistability

GABA shapes the dynamics of bistable perception

NARCIS (Netherlands)

van Loon, A.M.; Knapen, T.; Scholte, H.S.; St. John-Saaltink, E.; Donner, T.H.; Lamme, V.A.F.

2013-01-01

Sometimes, perception fluctuates spontaneously between two distinct interpretations of a constant sensory input. These bistable perceptual phenomena provide a unique window into the neural mechanisms that create the contents of conscious perception. Models of bistable perception posit that mutual

Gene expression

International Nuclear Information System (INIS)

Hildebrand, C.E.; Crawford, B.D.; Walters, R.A.; Enger, M.D.

1983-01-01

We prepared probes for isolating functional pieces of the metallothionein locus. The probes enabled a variety of experiments, eventually revealing two mechanisms for metallothionein gene expression, the order of the DNA coding units at the locus, and the location of the gene site in its chromosome. Once the switch regulating metallothionein synthesis was located, it could be joined by recombinant DNA methods to other, unrelated genes, then reintroduced into cells by gene-transfer techniques. The expression of these recombinant genes could then be induced by exposing the cells to Zn 2+ or Cd 2+ . We would thus take advantage of the clearly defined switching properties of the metallothionein gene to manipulate the expression of other, perhaps normally constitutive, genes. Already, despite an incomplete understanding of how the regulatory switch of the metallothionein locus operates, such experiments have been performed successfully

Temporal nonlocality in bistable perception

Science.gov (United States)

Atmanspacher, Harald; Filk, Thomas

2012-12-01

A novel conceptual framework for theoretical psychology is presented and illustrated for the example of bistable perception. A basic formal feature of this framework is the non-commutativity of operations acting on mental states. A corresponding model for the bistable perception of ambiguous stimuli, the Necker-Zeno model, is sketched and some empirical evidence for it so far is described. It is discussed how a temporal nonlocality of mental states, predicted by the model, can be understood and tested.

Stochastic stabilization of phenotypic States: the genetic bistable switch as a case study.

Science.gov (United States)

Weber, Marc; Buceta, Javier

2013-01-01

We study by means of analytical calculation and stochastic simulations how intrinsic noise modifies the bifurcation diagram of gene regulatory processes that can be effectively described by the Langevin formalism. In a general context, our study raises the intriguing question of how biochemical fluctuations redesign the epigenetic landscape in differentiation processes. We have applied our findings to a general class of regulatory processes that includes the simplest case that displays a bistable behavior and hence phenotypic variability: the genetic auto-activating switch. Thus, we explain why and how the noise promotes the stability of the low-state phenotype of the switch and show that the bistable region is extended when increasing the intensity of the fluctuations. This phenomenology is found in a simple one-dimensional model of the genetic switch as well as in a more detailed model that takes into account the binding of the protein to the promoter region. Altogether, we prescribe the analytical means to understand and quantify the noise-induced modifications of the bifurcation points for a general class of regulatory processes where the genetic bistable switch is included.

Neighboring Genes Show Correlated Evolution in Gene Expression

Science.gov (United States)

Ghanbarian, Avazeh T.; Hurst, Laurence D.

2015-01-01

When considering the evolution of a gene’s expression profile, we commonly assume that this is unaffected by its genomic neighborhood. This is, however, in contrast to what we know about the lack of autonomy between neighboring genes in gene expression profiles in extant taxa. Indeed, in all eukaryotic genomes genes of similar expression-profile tend to cluster, reflecting chromatin level dynamics. Does it follow that if a gene increases expression in a particular lineage then the genomic neighbors will also increase in their expression or is gene expression evolution autonomous? To address this here we consider evolution of human gene expression since the human-chimp common ancestor, allowing for both variation in estimation of current expression level and error in Bayesian estimation of the ancestral state. We find that in all tissues and both sexes, the change in gene expression of a focal gene on average predicts the change in gene expression of neighbors. The effect is highly pronounced in the immediate vicinity (genes increasing their expression in humans tend to avoid nuclear lamina domains and be enriched for the gene activator 5-hydroxymethylcytosine, we conclude that, most probably owing to chromatin level control of gene expression, a change in gene expression of one gene likely affects the expression evolution of neighbors, what we term expression piggybacking, an analog of hitchhiking. PMID:25743543

Optical bistability using quantum interference in V-type atoms

International Nuclear Information System (INIS)

Anton, M A; Calderon, Oscar G

2002-01-01

The behaviour of a V-type three-level atomic system in a ring cavity driven by a coherent field is studied. We consider a V configuration under conditions such that interference between decay channels is important. We find that when quantum interference is taken into account, optical bistability can be realized with a considerable decrease in the threshold intensity and the cooperative parameter. On the other hand, we also include the finite bandwidth of the driving field and study its role in the optical bistable response. It is found that at certain linewidths of the driving field optical bistability is obtained even if the system satisfies the trapping condition and the threshold intensity can be controlled. Furthermore, a change from the optical bistability due to quantum interference to the usual bistable behaviour based on saturation occurs as the driving field linewidth increases

Fundamental role of bistability in optimal homeostatic control

Science.gov (United States)

Wang, Guanyu

2013-03-01

Bistability is a fundamental phenomenon in nature and has a number of fine properties. However, these properties are consequences of bistability at the physiological level, which do not explain why it had to emerge during evolution. Using optimal homeostasis as the first principle and Pontryagin's Maximum Principle as the optimization approach, I find that bistability emerges as an indispensable control mechanism. Because the mathematical model is general and the result is independent of parameters, it is likely that most biological systems use bistability to control homeostasis. Glucose homeostasis represents a good example. It turns out that bistability is the only solution to a dilemma in glucose homeostasis: high insulin efficiency is required for rapid plasma glucose clearance, whereas an insulin sparing state is required to guarantee the brain's safety during fasting. This new perspective can illuminate studies on the twin epidemics of obesity and diabetes and the corresponding intervening strategies. For example, overnutrition and sedentary lifestyle may represent sudden environmental changes that cause the lose of optimality, which may contribute to the marked rise of obesity and diabetes in our generation.

Bistable perception modeled as competing stochastic integrations at two levels.

Science.gov (United States)

Gigante, Guido; Mattia, Maurizio; Braun, Jochen; Del Giudice, Paolo

2009-07-01

We propose a novel explanation for bistable perception, namely, the collective dynamics of multiple neural populations that are individually meta-stable. Distributed representations of sensory input and of perceptual state build gradually through noise-driven transitions in these populations, until the competition between alternative representations is resolved by a threshold mechanism. The perpetual repetition of this collective race to threshold renders perception bistable. This collective dynamics - which is largely uncoupled from the time-scales that govern individual populations or neurons - explains many hitherto puzzling observations about bistable perception: the wide range of mean alternation rates exhibited by bistable phenomena, the consistent variability of successive dominance periods, and the stabilizing effect of past perceptual states. It also predicts a number of previously unsuspected relationships between observable quantities characterizing bistable perception. We conclude that bistable perception reflects the collective nature of neural decision making rather than properties of individual populations or neurons.

Gene Expression Commons: an open platform for absolute gene expression profiling.

Directory of Open Access Journals (Sweden)

Jun Seita

Full Text Available Gene expression profiling using microarrays has been limited to comparisons of gene expression between small numbers of samples within individual experiments. However, the unknown and variable sensitivities of each probeset have rendered the absolute expression of any given gene nearly impossible to estimate. We have overcome this limitation by using a very large number (>10,000 of varied microarray data as a common reference, so that statistical attributes of each probeset, such as the dynamic range and threshold between low and high expression, can be reliably discovered through meta-analysis. This strategy is implemented in a web-based platform named "Gene Expression Commons" (https://gexc.stanford.edu/ which contains data of 39 distinct highly purified mouse hematopoietic stem/progenitor/differentiated cell populations covering almost the entire hematopoietic system. Since the Gene Expression Commons is designed as an open platform, investigators can explore the expression level of any gene, search by expression patterns of interest, submit their own microarray data, and design their own working models representing biological relationship among samples.

Bistable firing properties of soleus motor units in unrestrained rats

DEFF Research Database (Denmark)

EKEN, T.; KIEHN, O.

1989-01-01

of the motoneuron pool by stimulation of la afferents, or inhibition by stimulation of skin afferents. The shifts were not related to gross limb movements. This phenomenon is referred to as a bistable firing pattern. Bistable firing also occurred spontaneously during quiet standing. Typically the firing frequency...... was unchanged or only phasically influenced. These results demonstrate for the first time a bistable firing pattern during postural activity in the intact animal. The firing pattern closely resembles the bistable behaviour described in spinal motoneurons in reduced preparations, where it is due to the presence...... of a plateau potential. This suggests that the bistable firing is unexplained by plateau potentials also in the intact animal....

Triggered Snap-Through of Bistable Shells

Science.gov (United States)

Cai, Yijie; Huang, Shicheng; Trase, Ian; Hu, Nan; Chen, Zi

Elastic bistable shells are common structures in nature and engineering, such as the lobes of the Venus flytrap or the surface of a toy jumping poppers. Despite their ubiquity, the parameters that control the bistability of such structures are not well understood. In this study, we explore how the geometrical features of radially symmetric elastic shells affect the shape and potential energy of a shell's stable states, and how to tune certain parameters in order to generate a snap-through transition from a convex semi-stable state to concave stable state. We fabricated a series of elastic shells with varying geometric parameters out of silicone rubber and measured the resulting potential energy in the semi-stable state. Finite element simulations were also conducted in order to determine the deformation and stress in the shells during snap-through. It was found that the energy of the semi-stable state is controlled by only two geometric parameters and a dimensionless ratio. We also noted two distinct transitions during snap-through, one between monostability and semi-bistability (the state a popper toy is in before it snaps-through and jumps), and a second transition between semi-bistability and true bistability. This work shows that it is possible to use a set of simple parameters to tailor the energy landscape of an elastic shell in order to generate complex trigger motions for their potential use in smart applications. Z.C. acknowledge support from Society in Science-Branco Weiss Fellowship, administered by ETH Zurich.

Longitudinal magnetic bistability of electroplated wires

International Nuclear Information System (INIS)

Kurlyandskaya, G.V.; Garcia-Miquel, H.; Vazquez, M.; Svalov, A.V.; Vas'kovskiy, V.O.

2002-01-01

Fe 20 Ni 74 Co 6 and Fe 20 Ni 64 Co 16 1 μm thick magnetic tubes electroplated onto Cu 98 Be 2 conductive wire have been investigated in as-deposited state, after heat treatment under longitudinal magnetic field for 1 h at 330 deg. C, and after rf-sputtering deposition of the additional 2 μm Fe 19 Ni 81 layer. Heat treatments and an additional layer deposition modify the shape of hysteresis loops. Magnetically bistable behaviour, observed after the field annealing at a temperature of 330 deg. C, is studied as a function of the length of the samples. This is the first report by our knowledge on the bistable behaviour of the electroplated wires. The bistability of these wires is promising for applications such as tagging or pulse generator applications

Hybrid optoelectronic device with multiple bistable outputs

Energy Technology Data Exchange (ETDEWEB)

Costazo-Caso, Pablo A; Jin Yiye; Gelh, Michael; Granieri, Sergio; Siahmakoun, Azad, E-mail: pcostanzo@ing.unlp.edu.are, E-mail: granieri@rose-hulma.edu, E-mail: siahmako@rose-hulma.edu [Department of Physics and Optical Engineering, Rose-Hulman Institute of Technology, 5500 Wabash Avenue, Terre Haute, IN 47803 (United States)

2011-01-01

Optoelectronic circuits which exhibit optical and electrical bistability with hysteresis behavior are proposed and experimentally demonstrated. The systems are based on semiconductor optical amplifiers (SOA), bipolar junction transistors (BJT), PIN photodiodes (PD) and laser diodes externally modulated with integrated electro-absorption modulators (LD-EAM). The device operates based on two independent phenomena leading to both electrical bistability and optical bistability. The electrical bistability is due to the series connection of two p-i-n structures (SOA, BJT, PD or LD) in reverse bias. The optical bistability is consequence of the quantum confined Stark effect (QCSE) in the multi-quantum well (MQW) structure in the intrinsic region of the device. This effect produces the optical modulation of the transmitted light through the SOA (or reflected from the PD). Finally, because the optical transmission of the SOA (in reverse bias) and the reflected light from the PD are so small, a LD-EAM modulated by the voltage across these devices are employed to obtain a higher output optical power. Experiments show that the maximum switching frequency is in MHz range and the rise/fall times lower than 1 us. The temporal response is mainly limited by the electrical capacitance of the devices and the parasitic inductances of the connecting wires. The effects of these components can be reduced in current integration technologies.

Bistable flow spectral analysis. Repercussions on jet pumps

International Nuclear Information System (INIS)

Gavilan Moreno, C.J.

2011-01-01

Highlights: → The most important thing in this paper, is the spectral characterization of the bistable flow in a Nuclear Power Plant. → This paper goes deeper in the effect of the bistable flow over the jet pump and the induced vibrations. → The jet pump frequencies are very close to natural jet pump frequencies, in the 3rd and 6th mode. - Abstract: There have been many attempts at characterizing and predicting bistable flow in boiling water reactors (BWRs). Nevertheless, in most cases the results have only managed to develop models that analytically reproduce the phenomenon (). Modeling has been forensic in all cases, while the capacity of the model focus on determining the exclusion areas on the recirculation flow map. The bistability process is known by its effects given there is no clear definition of its causal process. In the 1980s, Hitachi technicians () managed to reproduce bistable flow in the laboratory by means of pipe geometry, similar to that which is found in recirculation loops. The result was that the low flow pattern is formed by the appearance of a quasi stationary, helicoidal vortex in the recirculation collector's branches. This vortex creates greater frictional losses than regions without vortices, at the same discharge pressure. Neither the behavior nor the dynamics of these vortices were characterized in this paper. The aim of this paper is to characterize these vortices in such a way as to enable them to provide their own frequencies and their later effect on the jet pumps. The methodology used in this study is similar to the one used previously when analyzing the bistable flow in tube arrays with cross flow (). The method employed makes use of the power spectral density function. What differs is the field of application. We will analyze a Loop B with a bistable flow and compare the high and low flow situations. The same analysis will also be carried out on the loop that has not developed the bistable flow (Loop A) at the same moments

Non-resonant energy harvesting via an adaptive bistable potential

International Nuclear Information System (INIS)

Hosseinloo, Ashkan Haji; Turitsyn, Konstantin

2016-01-01

Narrow bandwidth and easy detuning, inefficiency in broadband and non-stationary excitations, and difficulties in matching a linear harvester’s resonance frequency to low-frequency excitations at small scales, have convinced researchers to investigate nonlinear, and in particular bistable, energy harvesters in recent years. However, bistable harvesters suffer from co-existing low and high energy orbits, and sensitivity to initial conditions, and have recently been proven inefficient when subjected to many real-world random and non-stationary excitations. Here, we propose a novel non-resonant buy-low-sell-high strategy that can significantly improve the harvester’s effectiveness at low frequencies in a much more robust fashion. This strategy could be realized by a passive adaptive bistable system. Simulation results confirm the high effectiveness of the adaptive bistable system following a buy-low-sell-high logic when subjected to harmonic and random non-stationary walking excitations compared to its conventional bistable and linear counterparts. (paper)

Chaos in a new bistable rotating electromechanical system

International Nuclear Information System (INIS)

Tsapla Fotsa, R.; Woafo, P.

2016-01-01

Highlights: • A new electromechanical system with rotating arm and bistable potential energy is studied. • The bistability is generated by the interaction of three permanent magnets, one fixed at the end of the arm and two other fixed at equal distance relative to the central position of the arm. • It exhibits dissipative and Hamiltonian chaos. • Such a bistable electromechanical system can be used as the actuation part of chaotic sieves and mixers. - Abstract: A device consisting of an induction motor activating a rotating rigid arm is designed and comprises a bistable potential due to the presence of three permanent magnets. Its mathematical equations are established and the numerical results both in the absence and in the presence of magnets are compared. The generation of chaotic behavior is achieved using two different external excitations: sinewave and square wave. In the presence of magnets, the system presents periodic and dissipative chaotic dynamics. Approximating the global potential energy to a bistable quartic potential, the Melnikov method is used to derive the conditions for the appearance of Hamiltonian chaos. Such a device can be used for industrial and domestic applications for mixing and sieving activities.

Frontoparietal cortex mediates perceptual transitions in bistable perception.

Science.gov (United States)

Weilnhammer, Veith A; Ludwig, Karin; Hesselmann, Guido; Sterzer, Philipp

2013-10-02

During bistable vision, perception oscillates between two mutually exclusive percepts despite constant sensory input. Greater BOLD responses in frontoparietal cortex have been shown to be associated with endogenous perceptual transitions compared with "replay" transitions designed to closely match bistability in both perceptual quality and timing. It has remained controversial, however, whether this enhanced activity reflects causal influences of these regions on processing at the sensory level or, alternatively, an effect of stimulus differences that result in, for example, longer durations of perceptual transitions in bistable perception compared with replay conditions. Using a rotating Lissajous figure in an fMRI experiment on 15 human participants, we controlled for potential confounds of differences in transition duration and confirmed previous findings of greater activity in frontoparietal areas for transitions during bistable perception. In addition, we applied dynamic causal modeling to identify the neural model that best explains the observed BOLD signals in terms of effective connectivity. We found that enhanced activity for perceptual transitions is associated with a modulation of top-down connectivity from frontal to visual cortex, thus arguing for a crucial role of frontoparietal cortex in perceptual transitions during bistable perception.

A bistable mechanism for chord extension morphing rotors

Science.gov (United States)

Johnson, Terrence; Frecker, Mary; Gandhi, Farhan

2009-03-01

Research efforts have shown that helicopter rotor blade morphing is an effective means to improve flight performance. Previous example of rotor blade morphing include using smart-materials for trailing deflection and rotor blade twist and tip twist, the development of a comfortable airfoil using compliant mechanisms, the use of a Gurney flap for air-flow deflection and centrifugal force actuated device to increase the span of the blade. In this paper we explore the use of a bistable mechanism for rotor morphing, specifically, blade chord extension using a bistable arc. Increasing the chord of the rotor blade is expected to generate more lift-load and improve helicopter performance. Bistable or "snap through" mechanisms have multiple stable equilibrium states and are a novel way to achieve large actuation output stroke. Bistable mechanisms do not require energy input to maintain a stable equilibrium state as both states do not require locking. In this work, we introduce a methodology for the design of bistable arcs for chord morphing using the finite element analysis and pseudo-rigid body model, to study the effect of different arc types, applied loads and rigidity on arc performance.

Bistable microvalve and microcatheter system

Science.gov (United States)

Seward, Kirk Patrick

2003-05-20

A bistable microvalve of shape memory material is operatively connected to a microcatheter. The bistable microvalve includes a tip that can be closed off until it is in the desired position. Once it is in position it can opened and closed. The system uses heat and pressure to open and close the microvalve. The shape memory material will change stiffness and shape when heated above a transition temperature. The shape memory material is adapted to move from a first shape to a second shape, either open or closed, where it can perform a desired function.

Model-based design of bistable cell factories for metabolic engineering.

Science.gov (United States)

Srinivasan, Shyam; Cluett, William R; Mahadevan, Radhakrishnan

2018-04-15

Metabolism can exhibit dynamic phenomena like bistability due to the presence of regulatory motifs like the positive feedback loop. As cell factories, microorganisms with bistable metabolism can have a high and a low product flux at the two stable steady states, respectively. The exclusion of metabolic regulation and network dynamics limits the ability of pseudo-steady state stoichiometric models to detect the presence of bistability, and reliably assess the outcomes of design perturbations to metabolic networks. Using kinetic models of metabolism, we assess the change in the bistable characteristics of the network, and suggest designs based on perturbations to the positive feedback loop to enable the network to produce at its theoretical maximum rate. We show that the most optimal production design in parameter space, for a small bistable metabolic network, may exist at the boundary of the bistable region separating it from the monostable region of low product fluxes. The results of our analysis can be broadly applied to other bistable metabolic networks with similar positive feedback network topologies. This can complement existing model-based design strategies by providing a smaller number of feasible designs that need to be tested in vivo. http://lmse.biozone.utoronto.ca/downloads/. krishna.mahadevan@utoronto.ca. Supplementary data are available at Bioinformatics online.

Application of the Asymptotic Taylor Expansion Method to Bistable Potentials

Directory of Open Access Journals (Sweden)

Okan Ozer

2013-01-01

Full Text Available A recent method called asymptotic Taylor expansion (ATEM is applied to determine the analytical expression for eigenfunctions and numerical results for eigenvalues of the Schrödinger equation for the bistable potentials. Optimal truncation of the Taylor series gives a best possible analytical expression for eigenfunctions and numerical results for eigenvalues. It is shown that the results are obtained by a simple algorithm constructed for a computer system using symbolic or numerical calculation. It is observed that ATEM produces excellent results consistent with the existing literature.

Imaging gene expression in gene therapy

International Nuclear Information System (INIS)

Wiebe, Leonard I.

1997-01-01

Full text. Gene therapy can be used to introduce new genes, or to supplement the function of indigenous genes. At the present time, however, there is non-invasive test to demonstrate efficacy of the gene transfer and expression processes. It has been postulated that scintigraphic imaging can offer unique information on both the site at which the transferred gene is expressed, and the degree of expression, both of which are critical issue for safety and clinical efficacy. Many current studies are based on 'suicide gene therapy' of cancer. Cells modified to express these genes commit metabolic suicide in the presence of an enzyme encoded by the transferred gene and a specifically-convertible pro drug. Pro drug metabolism can lead to selective metabolic trapping, required for scintigraphy. Herpes simplex virus type-1 thymidine kinase (H S V-1 t k + ) has been use for 'suicide' in vivo tumor gene therapy. It has been proposed that radiolabelled nucleosides can be used as radiopharmaceuticals to detect H S V-1 t k + gene expression where the H S V-1 t k + gene serves a reporter or therapeutic function. Animal gene therapy models have been studied using purine-([ 18 F]F H P G; [ 18 F]-A C V), and pyrimidine- ([ 123 / 131 I]I V R F U; [ 124 / 131I ]) antiviral nucleosides. Principles of gene therapy and gene therapy imaging will be reviewed and experimental data for [ 123 / 131I ]I V R F U imaging with the H S V-1 t k + reporter gene will be presented

Bistable Reflective Etalon (BRET)

National Research Council Canada - National Science Library

Shellenbarger, Zane

2003-01-01

This project designed, fabricated, and characterized normal-incidence etalon structures at 1550 nm wavelength operation for application, as bistable elements, to photonic analog-to-digital conversion...

Multistability in Bistable Ferroelectric Materials toward Adaptive Applications

NARCIS (Netherlands)

Ghosh, Anirban; Koster, Gertjan; Rijnders, Augustinus J.H.M.

2016-01-01

Traditionally thermodynamically bistable ferroic materials are used for nonvolatile operations based on logic gates (e.g., in the form of field effect transistors). But, this inherent bistability in these class of materials limits their applicability for adaptive operations. Emulating biological

Development of a Method to Monitor Gene Expression in Single Bacterial Cells During the Interaction With Plants and Use to Study the Expression of the Type III Secretion System in Single Cells of Dickeya dadantii in Potato

Directory of Open Access Journals (Sweden)

Zhouqi Cui

2018-06-01

Full Text Available Dickeya dadantii is a bacterial plant pathogen that causes soft rot disease on a wide range of host plants. The type III secretion system (T3SS is an important virulence factor in D. dadantii. Expression of the T3SS is induced in the plant apoplast or in hrp-inducing minimal medium (hrp-MM, and is repressed in nutrient-rich media. Despite the understanding of induction conditions, how individual cells in a clonal bacterial population respond to these conditions and modulate T3SS expression is not well understood. In our previous study, we reported that in a clonal population, only a small proportion of bacteria highly expressed T3SS genes while the majority of the population did not express T3SS genes under hrp-MM condition. In this study, we developed a method that enabled in situ observation and quantification of gene expression in single bacterial cells in planta. Using this technique, we observed that the expression of the T3SS genes hrpA and hrpN is restricted to a small proportion of D. dadantii cells during the infection of potato. We also report that the expression of T3SS genes is higher at early stages of infection compared to later stages. This expression modulation is achieved through adjusting the ratio of T3SS ON and T3SS OFF cells and the expression intensity of T3SS ON cells. Our findings not only shed light into how bacteria use a bi-stable gene expression manner to modulate an important virulence factor, but also provide a useful tool to study gene expression in individual bacterial cells in planta.

Bistable energy harvesting enhancement with an auxiliary linear oscillator

Science.gov (United States)

Harne, R. L.; Thota, M.; Wang, K. W.

2013-12-01

Recent work has indicated that linear vibrational energy harvesters with an appended degree-of-freedom (DOF) may be advantageous for introducing new dynamic forms to extend the operational bandwidth. Given the additional interest in bistable harvester designs, which exhibit a propitious snap through effect from one stable state to the other, it is a logical extension to explore the influence of an added DOF to a bistable system. However, bistable snap through is not a resonant phenomenon, which tempers the presumption that the dynamics induced by an additional DOF on bistable designs would inherently be beneficial as for linear systems. This paper presents two analytical formulations to assess the fundamental and superharmonic steady-state dynamics of an excited bistable energy harvester to which is attached an auxiliary linear oscillator. From an energy harvesting perspective, the model predicts that the additional linear DOF uniformly amplifies the bistable harvester response magnitude and generated power for excitation frequencies less than the attachment’s resonance while improved power density spans a bandwidth below this frequency. Analyses predict bandwidths having co-existent responses composed of a unique proportion of fundamental and superharmonic dynamics. Experiments validate key analytical predictions and observe the ability for the coupled system to develop an advantageous multi-harmonic interwell response when the initial conditions are insufficient for continuous high-energy orbit at the excitation frequency. Overall, the addition of an auxiliary linear oscillator to a bistable harvester is found to be an effective means of enhancing the energy harvesting performance and robustness.

Determining Physical Mechanisms of Gene Expression Regulation from Single Cell Gene Expression Data

OpenAIRE

Ezer, Daphne; Moignard, Victoria; G?ttgens, Berthold; Adryan, Boris

2016-01-01

Many genes are expressed in bursts, which can contribute to cell-to-cell heterogeneity. It is now possible to measure this heterogeneity with high throughput single cell gene expression assays (single cell qPCR and RNA-seq). These experimental approaches generate gene expression distributions which can be used to estimate the kinetic parameters of gene expression bursting, namely the rate that genes turn on, the rate that genes turn off, and the rate of transcription. We construct a complete ...

Imaging gene expression in gene therapy

Energy Technology Data Exchange (ETDEWEB)

Wiebe, Leonard I. [Alberta Univ., Edmonton (Canada). Noujaim Institute for Pharmaceutical Oncology Research

1997-12-31

Full text. Gene therapy can be used to introduce new genes, or to supplement the function of indigenous genes. At the present time, however, there is non-invasive test to demonstrate efficacy of the gene transfer and expression processes. It has been postulated that scintigraphic imaging can offer unique information on both the site at which the transferred gene is expressed, and the degree of expression, both of which are critical issue for safety and clinical efficacy. Many current studies are based on `suicide gene therapy` of cancer. Cells modified to express these genes commit metabolic suicide in the presence of an enzyme encoded by the transferred gene and a specifically-convertible pro drug. Pro drug metabolism can lead to selective metabolic trapping, required for scintigraphy. Herpes simplex virus type-1 thymidine kinase (H S V-1 t k{sup +}) has been use for `suicide` in vivo tumor gene therapy. It has been proposed that radiolabelled nucleosides can be used as radiopharmaceuticals to detect H S V-1 t k{sup +} gene expression where the H S V-1 t k{sup +} gene serves a reporter or therapeutic function. Animal gene therapy models have been studied using purine-([{sup 18} F]F H P G; [{sup 18} F]-A C V), and pyrimidine- ([{sup 123}/{sup 131} I]I V R F U; [{sup 124}/{sup 131I}]) antiviral nucleosides. Principles of gene therapy and gene therapy imaging will be reviewed and experimental data for [{sup 123}/{sup 131I}]I V R F U imaging with the H S V-1 t k{sup +} reporter gene will be presented

Electrical bistabilities and memory stabilities of nonvolatile bistable devices fabricated utilizing C60 molecules embedded in a polymethyl methacrylate layer

International Nuclear Information System (INIS)

Cho, Sung Hwan; Lee, Dong Ik; Jung, Jae Hun; Kim, Tae Whan

2009-01-01

Current-voltage (I-V) measurements on Al/fullerene (C 60 ) molecules embedded in polymethyl methacrylate/Al devices at 300 K showed a current bistability due to the existence of the C 60 molecules. The on/off ratio of the current bistability for the memory devices was as large as 10 3 . The retention time of the devices was above 2.5 x 10 4 s at room temperature, and cycling endurance tests on these devices indicated that the ON and OFF currents showed no degradation until 50 000 cycles. Carrier transport mechanisms for the nonvolatile bistable devices are described on the basis of the I-V experimental and fitting results.

Oscillations in the bistable regime of neuronal networks.

Science.gov (United States)

Roxin, Alex; Compte, Albert

2016-07-01

Bistability between attracting fixed points in neuronal networks has been hypothesized to underlie persistent activity observed in several cortical areas during working memory tasks. In network models this kind of bistability arises due to strong recurrent excitation, sufficient to generate a state of high activity created in a saddle-node (SN) bifurcation. On the other hand, canonical network models of excitatory and inhibitory neurons (E-I networks) robustly produce oscillatory states via a Hopf (H) bifurcation due to the E-I loop. This mechanism for generating oscillations has been invoked to explain the emergence of brain rhythms in the β to γ bands. Although both bistability and oscillatory activity have been intensively studied in network models, there has not been much focus on the coincidence of the two. Here we show that when oscillations emerge in E-I networks in the bistable regime, their phenomenology can be explained to a large extent by considering coincident SN and H bifurcations, known as a codimension two Takens-Bogdanov bifurcation. In particular, we find that such oscillations are not composed of a stable limit cycle, but rather are due to noise-driven oscillatory fluctuations. Furthermore, oscillations in the bistable regime can, in principle, have arbitrarily low frequency.

Bistable soliton states and switching in doubly inhomogeneously ...

Indian Academy of Sciences (India)

Dec. 2001 physics pp. 969–979. Bistable soliton states and switching in doubly inhomogeneously doped fiber couplers. AJIT KUMAR. Department of Physics, Indian Institute of Technology, Hauz Khas, New Delhi 110 016, India. Abstract. Switching between the bistable soliton states in a doubly and inhomogeneously doped.

Novel piezoelectric bistable oscillator architecture for wideband vibration energy harvesting

International Nuclear Information System (INIS)

Liu, W Q; Badel, A; Formosa, F; Wu, Y P; Agbossou, A

2013-01-01

Bistable vibration energy harvesters are attracting more and more interest because of their capability to scavenge energy over a large frequency band. The bistable effect is usually based on magnetic interaction or buckled beams. This paper presents a novel architecture based on amplified piezoelectric structures. This buckled spring–mass architecture allows the energy of the dynamic mass to be converted into electrical energy in the piezoelectric materials as efficiently as possible. Modeling and design are performed and a normalized expression of the harvester behavior is given. Chirp and band-limited noise excitations are used to evaluate the proposed harvester’s performances. Simulation and experimental results are in good agreement. A method of using a spectrum plot for investigating the interwell motion is presented. The effect of the electric load impedance matching strategy is also studied. Results and comparisons with the literature show that the proposed device combines a large bandwidth and a high power density. (paper)

The Impact of ExoS on Pseudomonas aeruginosa Internalization by Epithelial Cells Is Independent of fleQ and Correlates with Bistability of Type Three Secretion System Gene Expression.

Science.gov (United States)

Kroken, Abby R; Chen, Camille K; Evans, David J; Yahr, Timothy L; Fleiszig, Suzanne M J

2018-05-01

Pseudomonas aeruginosa is internalized into multiple types of epithelial cell in vitro and in vivo and yet is often regarded as an exclusively extracellular pathogen. Paradoxically, ExoS, a type three secretion system (T3SS) effector, has antiphagocytic activities but is required for intracellular survival of P. aeruginosa and its occupation of bleb niches in epithelial cells. Here, we addressed mechanisms for this dichotomy using invasive (ExoS-expressing) P. aeruginosa and corresponding effector-null isogenic T3SS mutants, effector-null mutants of cytotoxic P. aeruginosa with and without ExoS transformation, antibiotic exclusion assays, and imaging using a T3SS-GFP reporter. Except for effector-null PA103, all strains were internalized while encoding ExoS. Intracellular bacteria showed T3SS activation that continued in replicating daughter cells. Correcting the fleQ mutation in effector-null PA103 promoted internalization by >10-fold with or without ExoS. Conversely, mutating fleQ in PAO1 reduced internalization by >10-fold, also with or without ExoS. Effector-null PA103 remained less well internalized than PAO1 matched for fleQ status, but only with ExoS expression, suggesting additional differences between these strains. Quantifying T3SS activation using GFP fluorescence and quantitative reverse transcription-PCR (qRT-PCR) showed that T3SS expression was hyperinducible for strain PA103Δ exoUT versus other isolates and was unrelated to fleQ status. These findings support the principle that P. aeruginosa is not exclusively an extracellular pathogen, with internalization influenced by the relative proportions of T3SS-positive and T3SS-negative bacteria in the population during host cell interaction. These data also challenge current thinking about T3SS effector delivery into host cells and suggest that T3SS bistability is an important consideration in studying P. aeruginosa pathogenesis. IMPORTANCE P. aeruginosa is often referred to as an extracellular

Optical bistability via quantum interference from incoherent pumping and spontaneous emission

International Nuclear Information System (INIS)

Sahrai, M.; Asadpour, S.H.; Sadighi-Bonabi, R.

2011-01-01

We theoretically investigate the optical bistability (OB) in a V-type three-level atomic system confined in a unidirectional ring cavity via incoherent pumping field. It is shown that the threshold of optical bistability can be controlled by the rate of an incoherent pumping field and by interference mechanism arising from the spontaneous emission and incoherent pumping field. We demonstrate that the optical bistability converts to optical multi-stability (OM) by the quantum interference mechanism. - Highlights: → We modulate the optical bistability (OB) in a four-level N-type atomic system. → The threshold of optical bistability can be controlled by the quantum interferences. → OB converts to optical multi-stability (OM) by the quantum interferences. → We discuss the effect of an incoherent pumping field on reduction of OB threshold.

Evaluation of bistable systems versus matched filters in detecting bipolar pulse signals

OpenAIRE

Duan, Fabing; Abbott, Derek; Gao, Qisheng

2004-01-01

This paper presents a thorough evaluation of a bistable system versus a matched filter in detecting bipolar pulse signals. The detectability of the bistable system can be optimized by adding noise, i.e. the stochastic resonance (SR) phenomenon. This SR effect is also demonstrated by approximate statistical detection theory of the bistable system and corresponding numerical simulations. Furthermore, the performance comparison results between the bistable system and the matched filter show that...

Bistable dynamics of a levitated nanoparticle (Presentation Recording)

Science.gov (United States)

Ricci, Francesco; Spasenovic, M.; Rica, Raúl A.; Novotny, Lukas; Quidant, Romain

2015-08-01

Bistable systems are ubiquitous in nature. Classical examples in chemistry and biology include relaxation kinetics in chemical reactions [1] and stochastic resonance processes such as neuron firing [2,3]. Likewise, bistable systems play a key role in signal processing and information handling at the nanoscale, giving rise to intriguing applications such as optical switches [4], coherent signal amplification [5,6] and weak forces detection [5]. The interest and applicability of bistable systems are intimately connected with the complexity of their dynamics, typically due to the presence of a large number of parameters and nonlinearities. Appropriate modeling is therefore challenging. Alternatively, the possibility to experimentally recreate bistable systems in a clean and controlled way has recently become very appealing, but elusive and complicated. With this aim, we combined optical tweezers with a novel active feedback-cooling scheme to develop a well-defined opto-mechanical platform reaching unprecedented performances in terms of Q-factor, frequency stability and force sensitivity [7,8]. Our experimental system consists of a single nanoparticle levitated in high vacuum with optical tweezers, which behaves as a non-linear (Duffing) oscillator under appropriate conditions. Here, we prove it to be an ideal tool for a deep study of bistability. We demonstrate bistability of the nanoparticle by noise activated switching between two oscillation states, discussing our results in terms of a double-well potential model. We also show the flexibility of our system in shaping the potential at will, in order to meet the conditions prescribed by any bistable system that could therefore then be simulated with our setup. References [1] T. Amemiya, T. Ohmori, M. Nakaiwa, T. Yamamoto, and T. Yamaguchi, "Modeling of Nonlinear Chemical Reaction Systems and Two-Parameter Stochastic Resonance," J. Biol. Phys. 25 (1999) 73 [2] F. Moss, L. M. Ward, and W. G. Sannita, "Stochastic

Ground-state kinetics of bistable redox-active donor-acceptor mechanically interlocked molecules.

Science.gov (United States)

Fahrenbach, Albert C; Bruns, Carson J; Li, Hao; Trabolsi, Ali; Coskun, Ali; Stoddart, J Fraser

2014-02-18

The ability to design and confer control over the kinetics of theprocesses involved in the mechanisms of artificial molecular machines is at the heart of the challenge to create ones that can carry out useful work on their environment, just as Nature is wont to do. As one of the more promising forerunners of prototypical artificial molecular machines, chemists have developed bistable redox-active donor-acceptor mechanically interlocked molecules (MIMs) over the past couple of decades. These bistable MIMs generally come in the form of [2]rotaxanes, molecular compounds that constitute a ring mechanically interlocked around a dumbbell-shaped component, or [2]catenanes, which are composed of two mechanically interlocked rings. As a result of their interlocked nature, bistable MIMs possess the inherent propensity to express controllable intramolecular, large-amplitude, and reversible motions in response to redox stimuli. In this Account, we rationalize the kinetic behavior in the ground state for a large assortment of these types of bistable MIMs, including both rotaxanes and catenanes. These structures have proven useful in a variety of applications ranging from drug delivery to molecular electronic devices. These bistable donor-acceptor MIMs can switch between two different isomeric states. The favored isomer, known as the ground-state co-conformation (GSCC) is in equilibrium with the less favored metastable state co-conformation (MSCC). The forward (kf) and backward (kb) rate constants associated with this ground-state equilibrium are intimately connected to each other through the ground-state distribution constant, KGS. Knowing the rate constants that govern the kinetics and bring about the equilibration between the MSCC and GSCC, allows researchers to understand the operation of these bistable MIMs in a device setting and apply them toward the construction of artificial molecular machines. The three biggest influences on the ground-state rate constants arise from

Magnetic-field induced bistability in a quasi-one-dimensional semiconductor microcavity

International Nuclear Information System (INIS)

Zhang, Chuanyi; Zhang, Weifeng

2015-01-01

We theoretically study the magnetic-field induced bistability in a quasi-one-dimensional semiconductor microcavity. A critical magnetic field is obtained, and the bistability appears if a magnetic field is greater than the critical value. For a positive energy detuning of the pump from the bare exciton polaritons, one bistability loop first emerges, then it divides into two loops, and finally one of them vanishes with the increasing magnetic field. This phenomenon originates from the magnetic-field modulated interactions for opposite spins. In the variational process, there are two important effects: one is a logic gate with a small variation of the excitation laser, and the other is a spin texture like skyrmion and this texture is periodic if the energy detuning varies periodically in real space, which is useful for designing the spin-dependent optoelectronic devices. - Highlights: • We study the bistability induced by a magnetic field in a microcavity. • One bistability loop can divide into two, and then the two loops return to one. • A spin texture like skyrmion and logic gate arise in the variation of bistability loop

Two optical bistability domains in composites of metal nanoparticles with nonlinear dielectric core

Energy Technology Data Exchange (ETDEWEB)

Shewamare, Sisay, E-mail: sisayshewa20@yahoo.com [Department of Physics, Addis Ababa University, P.O. Box 1176, Addis Ababa (Ethiopia); Mal' nev, V.N., E-mail: vadimnmalnev@yahoo.com [Department of Physics, Addis Ababa University, P.O. Box 1176, Addis Ababa (Ethiopia)

2012-12-15

It is shown that the local field in metal spherical particles with a dielectric core in an external varying electric field has two maxima at two different frequencies. The second maximum becomes more important with an increment in the metal fraction. Due to the nonlinear dielectric function of the core, the composite of these inclusions may have two optically induced bistability domains at different frequencies. At rather high metal fraction, two bistability domains merge and form one entire bistability domain. The parameters of these domains are studied numerically. The paper focuses on the second bistability domain, which has not been discussed in the literature so far. This domain exists in a comparatively narrow frequency range and its onset fields are lower than those of the first bistability domain. The lowest bistability onset fields are obtained in the entire domain. This peculiarity of the optical induced bistability in the metal composite with small dielectric cores can be attractive for possible applications.

Two optical bistability domains in composites of metal nanoparticles with nonlinear dielectric core

International Nuclear Information System (INIS)

Shewamare, Sisay; Mal'nev, V.N.

2012-01-01

It is shown that the local field in metal spherical particles with a dielectric core in an external varying electric field has two maxima at two different frequencies. The second maximum becomes more important with an increment in the metal fraction. Due to the nonlinear dielectric function of the core, the composite of these inclusions may have two optically induced bistability domains at different frequencies. At rather high metal fraction, two bistability domains merge and form one entire bistability domain. The parameters of these domains are studied numerically. The paper focuses on the second bistability domain, which has not been discussed in the literature so far. This domain exists in a comparatively narrow frequency range and its onset fields are lower than those of the first bistability domain. The lowest bistability onset fields are obtained in the entire domain. This peculiarity of the optical induced bistability in the metal composite with small dielectric cores can be attractive for possible applications.

Activation of Transducin by Bistable Pigment Parapinopsin in the Pineal Organ of Lower Vertebrates.

Science.gov (United States)

Kawano-Yamashita, Emi; Koyanagi, Mitsumasa; Wada, Seiji; Tsukamoto, Hisao; Nagata, Takashi; Terakita, Akihisa

2015-01-01

Pineal organs of lower vertebrates contain several kinds of photosensitive molecules, opsins that are suggested to be involved in different light-regulated physiological functions. We previously reported that parapinopsin is an ultraviolet (UV)-sensitive opsin that underlies hyperpolarization of the pineal photoreceptor cells of lower vertebrates to achieve pineal wavelength discrimination. Although, parapinopsin is phylogenetically close to vertebrate visual opsins, it exhibits a property similar to invertebrate visual opsins and melanopsin: the photoproduct of parapinopsin is stable and reverts to the original dark states, demonstrating the nature of bistable pigments. Therefore, it is of evolutionary interest to identify a phototransduction cascade driven by parapinopsin and to compare it with that in vertebrate visual cells. Here, we showed that parapinopsin is coupled to vertebrate visual G protein transducin in the pufferfish, zebrafish, and lamprey pineal organs. Biochemical analyses demonstrated that parapinopsins activated transducin in vitro in a light-dependent manner, similar to vertebrate visual opsins. Interestingly, transducin activation by parapinopsin was provoked and terminated by UV- and subsequent orange-lights irradiations, respectively, due to the bistable nature of parapinopsin, which could contribute to a wavelength-dependent control of a second messenger level in the cell as a unique optogenetic tool. Immunohistochemical examination revealed that parapinopsin was colocalized with Gt2 in the teleost, which possesses rod and cone types of transducin, Gt1, and Gt2. On the other hand, in the lamprey, which does not possess the Gt2 gene, in situ hybridization suggested that parapinopsin-expressing photoreceptor cells contained Gt1 type transducin GtS, indicating that lamprey parapinopsin may use GtS in place of Gt2. Because it is widely accepted that vertebrate visual opsins having a bleaching nature have evolved from non-bleaching opsins

Optical bistability induced by quantum coherence in a negative index atomic medium

International Nuclear Information System (INIS)

Zhang Hong-Jun; Sun Hui; Li Jin-Ping; Yin Bao-Yin; Guo Hong-Ju

2013-01-01

Bistability behaviors in an optical ring cavity filled with a dense V-type four-level atomic medium are theoretically investigated. It is found that the optical bistability can appear in the negative refraction frequency band, while both the bistability and multi-stability can occur in the positive refraction frequency bands. Therefore, optical bistability can be realized from conventional material to negative index material due to quantum coherence in our scheme. (electromagnetism, optics, acoustics, heat transfer, classical mechanics, and fluid dynamics)

Optical bistability and multistability in polaritonic materials doped with nanoparticles

International Nuclear Information System (INIS)

Wang, Zhiping; Yu, Benli

2014-01-01

We investigate the optical bistability and multistability in polaritonic materials doped with nanoparticles inside an optical ring cavity. It is found that the optical bistability and multistability can be easily controlled by adjusting the corresponding parameters of the system properly. The effect of the dipole–dipole interaction has also been included in the formulation, which leads to interesting phenomena. Our scheme opens up the possibility of controling the optical bistability and multistability in polaritonic materials doped with nanoparticles. (letter)

Dynamic control of a bistable wing under aerodynamic loading

International Nuclear Information System (INIS)

Bilgen, Onur; Arrieta, Andres F; Friswell, Michael I; Hagedorn, Peter

2013-01-01

The aerodynamic evaluation of a dynamic control technique applied to a bistable unsymmetrical cross-ply composite plate with surface bonded piezoelectric actuators is presented. The plate is clamped on one end to form a low-aspect-ratio wing. A previously proposed dynamic control method, utilizing bending resonance in different stable equilibrium positions, is used to induce snap-through between the two equilibrium states. Compared to quasi-static actuation, driving the bistable plate near resonance using surface bonded piezoelectric materials requires, theoretically, a lower peak excitation voltage to achieve snap-through. First, a set of extensive wind tunnel experiments are conducted on the passive bistable wing to understand the change in the dynamic behavior under various aerodynamic conditions. The passive wing demonstrated sufficient bending stiffness to sustain its shape under aerodynamic loading while preserving the desired bistable behavior. Next, by the use of the resonant control technique, the plate is turned into an effectively monostable structure, or alternatively, both stable equilibrium positions can be reached actively from the other stable equilibrium. Dynamic forward and reverse snap-through is demonstrated in the wind tunnel which shows both the effectiveness of the piezoelectric actuation as well as the load carrying capability of both states of the bistable wing. (paper)

Investigation of a bistable dual-stage vibration isolator under harmonic excitation

International Nuclear Information System (INIS)

Yang, Kai; Huang, Hai; Harne, R L; Wang, K W

2014-01-01

This study explores the steady-state performance of a dual-stage vibration isolator, which is configured by a bistable oscillator and a linear oscillator. The potential force of the bistable stage comprises negative linear and positive cubic nonlinear stiffnesses such that the two restoring force contributions may counterbalance to minimize dynamic force transmission. By applying a first-order harmonic balance, it is predicted that the bistable dual-stage isolator may significantly outperform an equivalent pure linear dual-stage isolator. This conclusion is verified through a series of numerical investigations. Following a parametric study, design guidelines are detailed to achieve performance improvements. Then, the ‘valley’ response, which is the special phenomenon of the bistable dual-stage isolator due to the counterbalance of the negative linear and positive nonlinear potential forces, is revealed and quantitatively explained. Numerical studies demonstrate the role of initial conditions, and it is shown that the likelihood of beneficial single periodic valley and intra-well responses for isolation purposes can be increased by greater bistable stage damping. Finally, a bistable dual-stage isolator prototype is developed and tested, and the numerical and experimental results verify the theoretical predictions. (paper)

Linear population allocation by bistable switches in response to transient stimulation.

Science.gov (United States)

Srimani, Jaydeep K; Yao, Guang; Neu, John; Tanouchi, Yu; Lee, Tae Jun; You, Lingchong

2014-01-01

Many cellular decision processes, including proliferation, differentiation, and phenotypic switching, are controlled by bistable signaling networks. In response to transient or intermediate input signals, these networks allocate a population fraction to each of two distinct states (e.g. OFF and ON). While extensive studies have been carried out to analyze various bistable networks, they are primarily focused on responses of bistable networks to sustained input signals. In this work, we investigate the response characteristics of bistable networks to transient signals, using both theoretical analysis and numerical simulation. We find that bistable systems exhibit a common property: for input signals with short durations, the fraction of switching cells increases linearly with the signal duration, allowing the population to integrate transient signals to tune its response. We propose that this allocation algorithm can be an optimal response strategy for certain cellular decisions in which excessive switching results in lower population fitness.

Ground-state thermodynamics of bistable redox-active donor-acceptor mechanically interlocked molecules.

Science.gov (United States)

Fahrenbach, Albert C; Bruns, Carson J; Cao, Dennis; Stoddart, J Fraser

2012-09-18

Fashioned through billions of years of evolution, biological molecular machines, such as ATP synthase, myosin, and kinesin, use the intricate relative motions of their components to drive some of life's most essential processes. Having control over the motions in molecules is imperative for life to function, and many chemists have designed, synthesized, and investigated artificial molecular systems that also express controllable motions within molecules. Using bistable mechanically interlocked molecules (MIMs), based on donor-acceptor recognition motifs, we have sought to imitate the sophisticated nanoscale machines present in living systems. In this Account, we analyze the thermodynamic characteristics of a series of redox-switchable [2]rotaxanes and [2]catenanes. Control and understanding of the relative intramolecular movements of components in MIMs have been vital in the development of a variety of applications of these compounds ranging from molecular electronic devices to drug delivery systems. These bistable donor-acceptor MIMs undergo redox-activated switching between two isomeric states. Under ambient conditions, the dominant translational isomer, the ground-state coconformation (GSCC), is in equilibrium with the less favored translational isomer, the metastable-state coconformation (MSCC). By manipulating the redox state of the recognition site associated with the GSCC, we can stimulate the relative movements of the components in these bistable MIMs. The thermodynamic parameters of model host-guest complexes provide a good starting point to rationalize the ratio of GSCC to MSCC at equilibrium. The bistable [2]rotaxanes show a strong correlation between the relative free energies of model complexes and the ground-state distribution constants (K(GS)). This relationship does not always hold for bistable [2]catenanes, most likely because of the additional steric and electronic constraints present when the two rings are mechanically interlocked with each other

The limiting dynamics of a bistable molecular switch with and without noise.

Science.gov (United States)

Mackey, Michael C; Tyran-Kamińska, Marta

2016-08-01

We consider the dynamics of a population of organisms containing two mutually inhibitory gene regulatory networks, that can result in a bistable switch-like behaviour. We completely characterize their local and global dynamics in the absence of any noise, and then go on to consider the effects of either noise coming from bursting (transcription or translation), or Gaussian noise in molecular degradation rates when there is a dominant slow variable in the system. We show analytically how the steady state distribution in the population can range from a single unimodal distribution through a bimodal distribution and give the explicit analytic form for the invariant stationary density which is globally asymptotically stable. Rather remarkably, the behaviour of the stationary density with respect to the parameters characterizing the molecular behaviour of the bistable switch is qualitatively identical in the presence of noise coming from bursting as well as in the presence of Gaussian noise in the degradation rate. This implies that one cannot distinguish between either the dominant source or nature of noise based on the stationary molecular distribution in a population of cells. We finally show that the switch model with bursting but two dominant slow genes has an asymptotically stable stationary density.

Propagating gene expression fronts in a one-dimensional coupled system of artificial cells

Science.gov (United States)

Tayar, Alexandra M.; Karzbrun, Eyal; Noireaux, Vincent; Bar-Ziv, Roy H.

2015-12-01

Living systems employ front propagation and spatiotemporal patterns encoded in biochemical reactions for communication, self-organization and computation. Emulating such dynamics in minimal systems is important for understanding physical principles in living cells and in vitro. Here, we report a one-dimensional array of DNA compartments in a silicon chip as a coupled system of artificial cells, offering the means to implement reaction-diffusion dynamics by integrated genetic circuits and chip geometry. Using a bistable circuit we programmed a front of protein synthesis propagating in the array as a cascade of signal amplification and short-range diffusion. The front velocity is maximal at a saddle-node bifurcation from a bistable regime with travelling fronts to a monostable regime that is spatially homogeneous. Near the bifurcation the system exhibits large variability between compartments, providing a possible mechanism for population diversity. This demonstrates that on-chip integrated gene circuits are dynamical systems driving spatiotemporal patterns, cellular variability and symmetry breaking.

Bistable behaviour of biexciton population in a dense exciton-biexciton system in semiconductors

International Nuclear Information System (INIS)

Nguyen Ba An.

1986-05-01

The steady state bistable behaviour of biexciton population in a dense exciton-biexciton semiconductor is considered. The intrinsic optical feedback is provided by the recombination mechanism. The exciton-biexciton and biexciton-biexciton interactions play the role of non-linearity responsible for biexciton bistability to occur. The conditions leading to the effect of bistability are obtained and two-parameter phase transition diagrams are drawn for both intensity and frequency bistable phenomena. (author)

Bubbling and bistability in two parameter discrete systems

OpenAIRE

Ambika, G.; Sujatha, N. V.

2000-01-01

We present a graphical analysis of the mechanisms underlying the occurrences of bubbling sequences and bistability regions in the bifurcation scenario of a special class of one dimensional two parameter maps. The main result of the analysis is that whether it is bubbling or bistability is decided by the sign of the third derivative at the inflection point of the map function.

Controllable optical bistability in a three-mode optomechanical system with atom-cavity-mirror couplings

Science.gov (United States)

Chen, Bin; Wang, Xiao-Fang; Yan, Jia-Kai; Zhu, Xiao-Fei; Jiang, Cheng

2018-01-01

We theoretically investigate the optical bistable behavior in a three-mode optomechanical system with atom-cavity-mirror couplings. The effects of the cavity-pump detuning and the pump power on the bistable behavior are discussed detailedly, the impacts of the atom-pump detuning and the atom-cavity coupling strength on the bistability of the system are also explored, and the influences of the cavity-resonator coupling strength and the cavity decay rate are also taken into consideration. The numerical results demonstrate that by tuning these parameters the bistable behavior of the system can be freely switched on or off, and the threshold of the pump power for the bistability as well as the bistable region width can also be effectively controlled. These results can find potential applications in optical bistable switch in the quantum information processing.

Bistable luminescence of trivalent rare-earth ions in crystals

International Nuclear Information System (INIS)

Sole, Jose Garcia; Ramirez O, Maria de la; Rodenas, Airan; Jaque, Daniel; Bausa, Luisa; Bettinelli, Marco; Speghini, Adolfo; Cavalli, Enrico; Ivleva, Lioudmila

2006-01-01

In this work, we have examined three new bistable systems based on the luminescence of three different crystals activated with trivalent rare earth ions. We have focussed our attention on Yb 3+ ions activators, for which the most relevant results are obtained. The first crystal, Sr 0.6 Ba 0.4 Nb 2 O 6 , is a ferroelectric material with a relatively low phase transition temperature (∼370 K), which provides bistability in the luminescence of Yb 3+ ions due to the thermal hysteresis associated with phase transition. The second crystal, LiNbO 3 , provides an intrinsic bistability in the luminescence of Yb 3+ ions, which is driven by changes in the excitation intensity. In the third crystal, NdPO 4 , a new mechanism of excitation intensity driven bistability is obtained when activated with Yb 3+ ions, due to a interplay between the Nd 3+ ↔Yb 3+ energy transfer and back transfer processes

Controllable optical bistability in photonic-crystal one-atom laser

International Nuclear Information System (INIS)

Guo Xiaoyong; Lue Shuchen

2009-01-01

We investigate the property of optical bistability in a photonic-crystal one-atom laser when nonlinear microcavity is present. The physical system consists of a coherently driven two-level light emitter strongly coupled to a high-quality microcavity which is embedded within a photonic crystal and another coherent probing field which has incident into the microcavity. In our case, the microcavity is fabricated by nonlinear material and placed as an impurity in photonic crystal. This study reveals that such a system can exhibit optical bistability. The dependence of threshold value and hysteresis loop on the photonic band gap of the photonic crystal, driving field Rabi frequency and dephasing processes, are studied. Our results clearly illustrate the ability to control optical bistability through suitable photonic-crystal architectures and external coherent driving field, and this study suggests that in a photonic-crystal nonlinear microcavity, the one-atom laser acts as an effective controllable bistable device in the design of all-light digital computing systems in the near future.

Bistable output from a coupled-resonator vertical-cavity laser diode

International Nuclear Information System (INIS)

Fischer, A. J.; Choquette, K. D.; Chow, W. W.; Allerman, A. A.; Geib, K.

2000-01-01

We report a monolithic coupled-resonator vertical-cavity laser with an ion-implanted top cavity and a selectively oxidized bottom cavity which exhibits bistable behavior in the light output versus injection current. Large bistability regions over current ranges as wide as 18 mA have been observed with on/off contrast ratios of greater than 20 dB. The position and width of the bistability region can be varied by changing the bias to the top cavity. Switching between on and off states can be accomplished with changes as small as 250 μW to the electrical power applied to the top cavity. The bistable behavior is the response of the nonlinear susceptibility in the top cavity to the changes in the bottom intracavity laser intensity as the bottom cavity reaches the thermal rollover point

A Redox-Active Bistable Molecular Switch Mounted inside a Metal-Organic Framework.

Science.gov (United States)

Chen, Qishui; Sun, Junling; Li, Peng; Hod, Idan; Moghadam, Peyman Z; Kean, Zachary S; Snurr, Randall Q; Hupp, Joseph T; Farha, Omar K; Stoddart, J Fraser

2016-11-02

We describe the incorporation of a bistable mechanically interlocked molecule (MIM) into a robust Zr-based metal-organic framework (MOF), NU-1000, by employing a post-synthetic functionalization protocol. On average, close to two bistable [2]catenanes can be incorporated per repeating unit of the hexagonal channels of NU-1000. The reversible redox-switching of the bistable [2]catenanes is retained inside the MOF, as evidenced by solid-state UV-vis-NIR reflectance spectroscopy and cyclic voltammetry. This research demonstrates that bistable MIMs are capable of exhibiting robust dynamics inside the nanopores of a MOF.

Unidirectional Transition Waves in Bistable Lattices.

Science.gov (United States)

Nadkarni, Neel; Arrieta, Andres F; Chong, Christopher; Kochmann, Dennis M; Daraio, Chiara

2016-06-17

We present a model system for strongly nonlinear transition waves generated in a periodic lattice of bistable members connected by magnetic links. The asymmetry of the on-site energy wells created by the bistable members produces a mechanical diode that supports only unidirectional transition wave propagation with constant wave velocity. We theoretically justify the cause of the unidirectionality of the transition wave and confirm these predictions by experiments and simulations. We further identify how the wave velocity and profile are uniquely linked to the double-well energy landscape, which serves as a blueprint for transition wave control.

Bistability and self-oscillations effects in a polariton-laser semiconductor microcavity

International Nuclear Information System (INIS)

Cotta, E A; Matinaga, F M

2007-01-01

We report an experimental observation of polaritonic optical bistability of the laser emission in a planar semiconductor microcavity with a 100 0 A GaAs single quantum well in the strong-coupling regime. The bistability curves show crossings that indicate a competition between a Kerr-like effect induced by the polariton population and thermal effects. Associated with the bistability, laser-like emission occurs at the bare cavity mode

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.

Bistable polarization switching in a continuous wave ruby laser

Science.gov (United States)

Lawandy, N. M.; Afzal, R. Sohrab

1988-01-01

Bistability in the output power, polarization state, and mode volume of an argon-ion laser pumped single mode ruby laser at 6943 A has been observed. The laser operates in a radially confined mode which exhibits hysteresis and bistability only when the pump polarization is parallel to the c-axis.

Asymmetric Effects on Escape Rates of Bistable System

International Nuclear Information System (INIS)

Wang Canjun; Mei Dongcheng; Dai Zucheng

2011-01-01

The asymmetric effects on the escape rates from the stable states x ± in the bistable system are analyzed. The results indicate that the multiplicative noise and the additive noise always enhance the particle escape from stable states x ± of bistable. However, the asymmetric parameter r enhances the particle escape from stable state x + , and holds back the particle escape from stable state x - . (general)

Numerical and experimental study of bistable plates for morphing structures

Science.gov (United States)

Nicassio, F.; Scarselli, G.; Avanzini, G.; Del Core, G.

2017-04-01

This study is concerned with the activation energy threshold of bistable composite plates in order to tailor a bistable system for specific aeronautical applications. The aim is to explore potential configurations of the bistable plates and their dynamic behavior for designing novel morphing structure suitable for aerodynamic surfaces and, as a possible further application, for power harvesters. Bistable laminates have two stable mechanical shapes that can withstand aerodynamic loads without additional constraint forces or locking mechanisms. This kind of structures, when properly loaded, snap-through from one stable configuration to another, causing large strains that can also be used for power harvesting scopes. The transition between the stable states of the composite laminate can be triggered, in principle, simply by aerodynamic loads (pilot, disturbance or passive inputs) without the need of servo-activated control systems. Both numerical simulations based on Finite Element models and experimental testing based on different activating forcing spectra are used to validate this concept. The results show that dynamic activation of bistable plates depend on different parameters that need to be carefully managed for their use as aircraft passive wing flaps.

FARO server: Meta-analysis of gene expression by matching gene expression signatures to a compendium of public gene expression data

DEFF Research Database (Denmark)

Manijak, Mieszko P.; Nielsen, Henrik Bjørn

2011-01-01

circumvented by instead matching gene expression signatures to signatures of other experiments. FINDINGS: To facilitate this we present the Functional Association Response by Overlap (FARO) server, that match input signatures to a compendium of 242 gene expression signatures, extracted from more than 1700...... Arabidopsis microarray experiments. CONCLUSIONS: Hereby we present a publicly available tool for robust characterization of Arabidopsis gene expression experiments which can point to similar experimental factors in other experiments. The server is available at http://www.cbs.dtu.dk/services/faro/....

Digital gene expression analysis of gene expression differences within Brassica diploids and allopolyploids.

Science.gov (United States)

Jiang, Jinjin; Wang, Yue; Zhu, Bao; Fang, Tingting; Fang, Yujie; Wang, Youping

2015-01-27

Brassica includes many successfully cultivated crop species of polyploid origin, either by ancestral genome triplication or by hybridization between two diploid progenitors, displaying complex repetitive sequences and transposons. The U's triangle, which consists of three diploids and three amphidiploids, is optimal for the analysis of complicated genomes after polyploidization. Next-generation sequencing enables the transcriptome profiling of polyploids on a global scale. We examined the gene expression patterns of three diploids (Brassica rapa, B. nigra, and B. oleracea) and three amphidiploids (B. napus, B. juncea, and B. carinata) via digital gene expression analysis. In total, the libraries generated between 5.7 and 6.1 million raw reads, and the clean tags of each library were mapped to 18547-21995 genes of B. rapa genome. The unambiguous tag-mapped genes in the libraries were compared. Moreover, the majority of differentially expressed genes (DEGs) were explored among diploids as well as between diploids and amphidiploids. Gene ontological analysis was performed to functionally categorize these DEGs into different classes. The Kyoto Encyclopedia of Genes and Genomes analysis was performed to assign these DEGs into approximately 120 pathways, among which the metabolic pathway, biosynthesis of secondary metabolites, and peroxisomal pathway were enriched. The non-additive genes in Brassica amphidiploids were analyzed, and the results indicated that orthologous genes in polyploids are frequently expressed in a non-additive pattern. Methyltransferase genes showed differential expression pattern in Brassica species. Our results provided an understanding of the transcriptome complexity of natural Brassica species. The gene expression changes in diploids and allopolyploids may help elucidate the morphological and physiological differences among Brassica species.

Perceptual incongruence influences bistability and cortical activation.

Directory of Open Access Journals (Sweden)

Gijs Joost Brouwer

Full Text Available We employed a parametric psychophysical design in combination with functional imaging to examine the influence of metric changes in perceptual incongruence on perceptual alternation rates and cortical responses. Subjects viewed a bistable stimulus defined by incongruent depth cues; bistability resulted from incongruence between binocular disparity and monocular perspective cues that specify different slants (slant rivalry. Psychophysical results revealed that perceptual alternation rates were positively correlated with the degree of perceived incongruence. Functional imaging revealed systematic increases in activity that paralleled the psychophysical results within anterior intraparietal sulcus, prior to the onset of perceptual alternations. We suggest that this cortical activity predicts the frequency of subsequent alternations, implying a putative causal role for these areas in initiating bistable perception. In contrast, areas implicated in form and depth processing (LOC and V3A were sensitive to the degree of slant, but failed to show increases in activity when these cues were in conflict.

Designing a stochastic genetic switch by coupling chaos and bistability.

Science.gov (United States)

Zhao, Xiang; Ouyang, Qi; Wang, Hongli

2015-11-01

In stem cell differentiation, a pluripotent stem cell becomes progressively specialized and generates specific cell types through a series of epigenetic processes. How cells can precisely determine their fate in a fluctuating environment is a currently unsolved problem. In this paper, we suggest an abstract gene regulatory network to describe mathematically the differentiation phenomenon featuring stochasticity, divergent cell fates, and robustness. The network consists of three functional motifs: an upstream chaotic motif, a buffering motif of incoherent feed forward loop capable of generating a pulse, and a downstream motif which is bistable. The dynamic behavior is typically a transient chaos with fractal basin boundaries. The trajectories take transiently chaotic journeys before divergently settling down to the bistable states. The ratio of the probability that the high state is achieved to the probability that the low state is reached can maintain a constant in a population of cells with varied molecular fluctuations. The ratio can be turned up or down when proper parameters are adjusted. The model suggests a possible mechanism for the robustness against fluctuations that is prominently featured in pluripotent cell differentiations and developmental phenomena.

Designing a stochastic genetic switch by coupling chaos and bistability

Energy Technology Data Exchange (ETDEWEB)

Zhao, Xiang [State Key Laboratory for Mesoscopic Physics and School of Physics, Peking University, Beijing 100871 (China); Ouyang, Qi [State Key Laboratory for Mesoscopic Physics and School of Physics, Peking University, Beijing 100871 (China); Center for Quantitative Biology, Peking University, Beijing 100871 (China); The Peking-Tsinghua Center for Life Sciences, Beijing 100871 (China); Wang, Hongli, E-mail: hlwang@pku.edu.cn [State Key Laboratory for Mesoscopic Physics and School of Physics, Peking University, Beijing 100871 (China); Center for Quantitative Biology, Peking University, Beijing 100871 (China)

2015-11-15

In stem cell differentiation, a pluripotent stem cell becomes progressively specialized and generates specific cell types through a series of epigenetic processes. How cells can precisely determine their fate in a fluctuating environment is a currently unsolved problem. In this paper, we suggest an abstract gene regulatory network to describe mathematically the differentiation phenomenon featuring stochasticity, divergent cell fates, and robustness. The network consists of three functional motifs: an upstream chaotic motif, a buffering motif of incoherent feed forward loop capable of generating a pulse, and a downstream motif which is bistable. The dynamic behavior is typically a transient chaos with fractal basin boundaries. The trajectories take transiently chaotic journeys before divergently settling down to the bistable states. The ratio of the probability that the high state is achieved to the probability that the low state is reached can maintain a constant in a population of cells with varied molecular fluctuations. The ratio can be turned up or down when proper parameters are adjusted. The model suggests a possible mechanism for the robustness against fluctuations that is prominently featured in pluripotent cell differentiations and developmental phenomena.

Three gene expression vector sets for concurrently expressing multiple genes in Saccharomyces cerevisiae.

Science.gov (United States)

Ishii, Jun; Kondo, Takashi; Makino, Harumi; Ogura, Akira; Matsuda, Fumio; Kondo, Akihiko

2014-05-01

Yeast has the potential to be used in bulk-scale fermentative production of fuels and chemicals due to its tolerance for low pH and robustness for autolysis. However, expression of multiple external genes in one host yeast strain is considerably labor-intensive due to the lack of polycistronic transcription. To promote the metabolic engineering of yeast, we generated systematic and convenient genetic engineering tools to express multiple genes in Saccharomyces cerevisiae. We constructed a series of multi-copy and integration vector sets for concurrently expressing two or three genes in S. cerevisiae by embedding three classical promoters. The comparative expression capabilities of the constructed vectors were monitored with green fluorescent protein, and the concurrent expression of genes was monitored with three different fluorescent proteins. Our multiple gene expression tool will be helpful to the advanced construction of genetically engineered yeast strains in a variety of research fields other than metabolic engineering. © 2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

The Necker-Zeno model for bistable perception.

Science.gov (United States)

Atmanspacher, Harald; Filk, Thomas

2013-10-01

A novel conceptual framework for theoretical psychology is presented and illustrated for the example of bistable perception. A basic formal feature of this framework is the non-commutativity of operations acting on mental states. A corresponding model for the bistable perception of ambiguous stimuli, the Necker-Zeno model, is sketched and some empirical evidence for it so far is described. It is discussed how a temporal non-locality of mental states, predicted by the model, can be understood and tested. © 2013 Cognitive Science Society, Inc.

Bistable minimum energy structures (BiMES) for binary robotics

International Nuclear Information System (INIS)

Follador, M; Conn, A T; Rossiter, J

2015-01-01

Bistable minimum energy structures (BiMES) are devices derived from the union of the concepts of dielectric elastomer minimum energy structures and bistable systems. This article presents this novel approach to active, elastic and bistable structures. BiMES are based on dielectric elastomer actuators (DEAs), which act as antagonists and provide the actuation for switching between the two equilibrium positions. A central elastic beam is the backbone of the structure and is buckled into the minimum energy configurations by the action of the two DEAs. The theory and the model of the device are presented, and also its fabrication process. BiMES are considered as fundamental units for more complex structures, which are presented and fabricated as proof of concept. Two different ways of combining the multiple units are proposed: a parallel configuration, to make a simple gripper, and a serial configuration, to generate a binary device. The possibility of using the bistable system as a continuous bender actuator, by modulating the actuation voltage of the two DEAs, was also investigated. (paper)

Bistable cholesteric liquid crystal light shutter with multielectrode driving.

Science.gov (United States)

Li, Cheng-Chang; Tseng, Heng-Yi; Pai, Tsung-Wei; Wu, Yu-Ching; Hsu, Wen-Hao; Jau, Hung-Chang; Chen, Chun-Wei; Lin, Tsung-Hsien

2014-08-01

An electrically activated bistable light shutter that exploits polymer-stabilized cholesteric liquid crystal film was developed. Under double-sided three-terminal electrode driving, the device can be bistable and switched between focal conic and homeotropic textures with a uniform in-plane and vertical electrical field. The transparent state with a transmittance of 80% and the opaque/scattering state with a transmittance of 13% can be realized without any optical compensation film, and each can be simply switched to the other by applying a pulse voltage. Also, gray-scale selection can be performed by varying the applied voltage. The designed energy-saving bistable light shutter can be utilized to preserve privacy and control illumination and the flow of energy.

Bistable Topological Insulator with Exciton-Polaritons

Science.gov (United States)

Kartashov, Yaroslav V.; Skryabin, Dmitry V.

2017-12-01

The functionality of many nonlinear and quantum optical devices relies on the effect of optical bistability. Using microcavity exciton-polaritons in a honeycomb arrangement of microcavity pillars, we report the resonance response and bistability of topological edge states. A balance between the pump, loss, and nonlinearity ensures a broad range of dynamical stability and controls the distribution of power between counterpropagating states on the opposite edges of the honeycomb lattice stripe. Tuning energy and polarization of the pump photons, while keeping their momentum constant, we demonstrate control of the propagation direction of the dominant edge state. Our results facilitate the development of practical applications of topological photonics.

Dynamics of a bistable Miura-origami structure

Science.gov (United States)

Fang, Hongbin; Li, Suyi; Ji, Huimin; Wang, K. W.

2017-05-01

Origami-inspired structures and materials have shown extraordinary properties and performances originating from the intricate geometries of folding. However, current state of the art studies have mostly focused on static and quasistatic characteristics. This research performs a comprehensive experimental and analytical study on the dynamics of origami folding through investigating a stacked Miura-Ori (SMO) structure with intrinsic bistability. We fabricate and experimentally investigated a bistable SMO prototype with rigid facets and flexible crease lines. Under harmonic base excitation, the SMO exhibits both intrawell and interwell oscillations. Spectrum analyses reveal that the dominant nonlinearities of SMO are quadratic and cubic, which generate rich dynamics including subharmonic and chaotic oscillations. The identified nonlinearities indicate that a third-order polynomial can be employed to approximate the measured force-displacement relationship. Such an approximation is validated via numerical study by qualitatively reproducing the phenomena observed in the experiments. The dynamic characteristics of the bistable SMO resemble those of a Helmholtz-Duffing oscillator (HDO); this suggests the possibility of applying the established tools and insights of HDO to predict origami dynamics. We also show that the bistability of SMO can be programmed within a large design space via tailoring the crease stiffness and initial stress-free configurations. The results of this research offer a wealth of fundamental insights into the dynamics of origami folding, and provide a solid foundation for developing foldable and deployable structures and materials with embedded dynamic functionalities.

Dynamics of a bistable Miura-origami structure.

Science.gov (United States)

Fang, Hongbin; Li, Suyi; Ji, Huimin; Wang, K W

2017-05-01

Origami-inspired structures and materials have shown extraordinary properties and performances originating from the intricate geometries of folding. However, current state of the art studies have mostly focused on static and quasistatic characteristics. This research performs a comprehensive experimental and analytical study on the dynamics of origami folding through investigating a stacked Miura-Ori (SMO) structure with intrinsic bistability. We fabricate and experimentally investigated a bistable SMO prototype with rigid facets and flexible crease lines. Under harmonic base excitation, the SMO exhibits both intrawell and interwell oscillations. Spectrum analyses reveal that the dominant nonlinearities of SMO are quadratic and cubic, which generate rich dynamics including subharmonic and chaotic oscillations. The identified nonlinearities indicate that a third-order polynomial can be employed to approximate the measured force-displacement relationship. Such an approximation is validated via numerical study by qualitatively reproducing the phenomena observed in the experiments. The dynamic characteristics of the bistable SMO resemble those of a Helmholtz-Duffing oscillator (HDO); this suggests the possibility of applying the established tools and insights of HDO to predict origami dynamics. We also show that the bistability of SMO can be programmed within a large design space via tailoring the crease stiffness and initial stress-free configurations. The results of this research offer a wealth of fundamental insights into the dynamics of origami folding, and provide a solid foundation for developing foldable and deployable structures and materials with embedded dynamic functionalities.

Large scale gene expression meta-analysis reveals tissue-specific, sex-biased gene expression in humans

Directory of Open Access Journals (Sweden)

Benjamin Mayne

2016-10-01

Full Text Available The severity and prevalence of many diseases are known to differ between the sexes. Organ specific sex-biased gene expression may underpin these and other sexually dimorphic traits. To further our understanding of sex differences in transcriptional regulation, we performed meta-analyses of sex biased gene expression in multiple human tissues. We analysed 22 publicly available human gene expression microarray data sets including over 2500 samples from 15 different tissues and 9 different organs. Briefly, by using an inverse-variance method we determined the effect size difference of gene expression between males and females. We found the greatest sex differences in gene expression in the brain, specifically in the anterior cingulate cortex, (1818 genes, followed by the heart (375 genes, kidney (224 genes, colon (218 genes and thyroid (163 genes. More interestingly, we found different parts of the brain with varying numbers and identity of sex-biased genes, indicating that specific cortical regions may influence sexually dimorphic traits. The majority of sex-biased genes in other tissues such as the bladder, liver, lungs and pancreas were on the sex chromosomes or involved in sex hormone production. On average in each tissue, 32% of autosomal genes that were expressed in a sex-biased fashion contained androgen or estrogen hormone response elements. Interestingly, across all tissues, we found approximately two-thirds of autosomal genes that were sex-biased were not under direct influence of sex hormones. To our knowledge this is the largest analysis of sex-biased gene expression in human tissues to date. We identified many sex-biased genes that were not under the direct influence of sex chromosome genes or sex hormones. These may provide targets for future development of sex-specific treatments for diseases.

Bistability of mangrove forests and competition with freshwater plants

Science.gov (United States)

Jiang, Jiang; Fuller, Douglas O; Teh, Su Yean; Zhai, Lu; Koh, Hock Lye; DeAngelis, Donald L.; Sternberg, L.D.S.L.

2015-01-01

Halophytic communities such as mangrove forests and buttonwood hammocks tend to border freshwater plant communities as sharp ecotones. Most studies attribute this purely to underlying physical templates, such as groundwater salinity gradients caused by tidal flux and topography. However, a few recent studies hypothesize that self-reinforcing feedback between vegetation and vadose zone salinity are also involved and create a bistable situation in which either halophytic dominated habitat or freshwater plant communities may dominate as alternative stable states. Here, we revisit the bistability hypothesis and demonstrate the mechanisms that result in bistability. We demonstrate with remote sensing imagery the sharp boundaries between freshwater hardwood hammock communities in southern Florida and halophytic communities such as buttonwood hammocks and mangroves. We further document from the literature how transpiration of mangroves and freshwater plants respond differently to vadose zone salinity, thus altering the salinity through feedback. Using mathematical models, we show how the self-reinforcing feedback, together with physical template, controls the ecotones between halophytic and freshwater communities. Regions of bistability along environmental gradients of salinity have the potential for large-scale vegetation shifts following pulse disturbances such as hurricane tidal surges in Florida, or tsunamis in other regions. The size of the region of bistability can be large for low-lying coastal habitat due to the saline water table, which extends inland due to salinity intrusion. We suggest coupling ecological and hydrologic processes as a framework for future studies.

Inflammation

DEFF Research Database (Denmark)

Holst-Hansen, Thomas

of the cytokine secreting cells will affect the collective dynamical behaviour. By describing cytokine-releasing cells as an excitable medium, we related medium size and density to a transition between a collective excitable and bistable state. Finally, we considered how a single cell model of bistable phenotype...... expression leads to bimodal expression on a population level and how the distribution of phenotype expression is altered by gene copy number variations. We assumed that a positive feedback is responsible for the bistability at the single cell level and show that the position of the feedback relative to gene...

Differential Gene Expression and Aging

Directory of Open Access Journals (Sweden)

Laurent Seroude

2002-01-01

Full Text Available It has been established that an intricate program of gene expression controls progression through the different stages in development. The equally complex biological phenomenon known as aging is genetically determined and environmentally modulated. This review focuses on the genetic component of aging, with a special emphasis on differential gene expression. At least two genetic pathways regulating organism longevity act by modifying gene expression. Many genes are also subjected to age-dependent transcriptional regulation. Some age-related gene expression changes are prevented by caloric restriction, the most robust intervention that slows down the aging process. Manipulating the expression of some age-regulated genes can extend an organism's life span. Remarkably, the activity of many transcription regulatory elements is linked to physiological age as opposed to chronological age, indicating that orderly and tightly controlled regulatory pathways are active during aging.

Bistable responses in bacterial genetic networks: Designs and dynamical consequences

Science.gov (United States)

Tiwari, Abhinav; Ray, J. Christian J.; Narula, Jatin; Igoshin, Oleg A.

2011-01-01

A key property of living cells is their ability to react to stimuli with specific biochemical responses. These responses can be understood through the dynamics of underlying biochemical and genetic networks. Evolutionary design principles have been well studied in networks that display graded responses, with a continuous relationship between input signal and system output. Alternatively, biochemical networks can exhibit bistable responses so that over a range of signals the network possesses two stable steady states. In this review, we discuss several conceptual examples illustrating network designs that can result in a bistable response of the biochemical network. Next, we examine manifestations of these designs in bacterial master-regulatory genetic circuits. In particular, we discuss mechanisms and dynamic consequences of bistability in three circuits: two-component systems, sigma-factor networks, and a multistep phosphorelay. Analyzing these examples allows us to expand our knowledge of evolutionary design principles for networks with bistable responses. PMID:21385588

Polycistronic gene expression in Aspergillus niger.

Science.gov (United States)

Schuetze, Tabea; Meyer, Vera

2017-09-25

Genome mining approaches predict dozens of biosynthetic gene clusters in each of the filamentous fungal genomes sequenced so far. However, the majority of these gene clusters still remain cryptic because they are not expressed in their natural host. Simultaneous expression of all genes belonging to a biosynthetic pathway in a heterologous host is one approach to activate biosynthetic gene clusters and to screen the metabolites produced for bioactivities. Polycistronic expression of all pathway genes under control of a single and tunable promoter would be the method of choice, as this does not only simplify cloning procedures, but also offers control on timing and strength of expression. However, polycistronic gene expression is a feature not commonly found in eukaryotic host systems, such as Aspergillus niger. In this study, we tested the suitability of the viral P2A peptide for co-expression of three genes in A. niger. Two genes descend from Fusarium oxysporum and are essential to produce the secondary metabolite enniatin (esyn1, ekivR). The third gene (luc) encodes the reporter luciferase which was included to study position effects. Expression of the polycistronic gene cassette was put under control of the Tet-On system to ensure tunable gene expression in A. niger. In total, three polycistronic expression cassettes which differed in the position of luc were constructed and targeted to the pyrG locus in A. niger. This allowed direct comparison of the luciferase activity based on the position of the luciferase gene. Doxycycline-mediated induction of the Tet-On expression cassettes resulted in the production of one long polycistronic mRNA as proven by Northern analyses, and ensured comparable production of enniatin in all three strains. Notably, gene position within the polycistronic expression cassette matters, as, luciferase activity was lowest at position one and had a comparable activity at positions two and three. The P2A peptide can be used to express at

Bi-stable optical actuator

Science.gov (United States)

Holdener, Fred R.; Boyd, Robert D.

2000-01-01

The present invention is a bi-stable optical actuator device that is depowered in both stable positions. A bearing is used to transfer motion and smoothly transition from one state to another. The optical actuator device may be maintained in a stable position either by gravity or a restraining device.

Interlinked bistable mechanisms generate robust mitotic transitions.

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Hutter, Lukas H; Rata, Scott; Hochegger, Helfrid; Novák, Béla

2017-10-18

The transitions between phases of the cell cycle have evolved to be robust and switch-like, which ensures temporal separation of DNA replication, sister chromatid separation, and cell division. Mathematical models describing the biochemical interaction networks of cell cycle regulators attribute these properties to underlying bistable switches, which inherently generate robust, switch-like, and irreversible transitions between states. We have recently presented new mathematical models for two control systems that regulate crucial transitions in the cell cycle: mitotic entry and exit, 1 and the mitotic checkpoint. 2 Each of the two control systems is characterized by two interlinked bistable switches. In the case of mitotic checkpoint control, these switches are mutually activating, whereas in the case of the mitotic entry/exit network, the switches are mutually inhibiting. In this Perspective we describe the qualitative features of these regulatory motifs and show that having two interlinked bistable mechanisms further enhances robustness and irreversibility. We speculate that these network motifs also underlie other cell cycle transitions and cellular transitions between distinct biochemical states.

Brain networks underlying bistable perception.

Science.gov (United States)

Baker, Daniel H; Karapanagiotidis, Theodoros; Coggan, David D; Wailes-Newson, Kirstie; Smallwood, Jonathan

2015-10-01

Bistable stimuli, such as the Necker Cube, demonstrate that experience can change in the absence of changes in the environment. Such phenomena can be used to assess stimulus-independent aspects of conscious experience. The current study used resting state functional magnetic resonance imaging (rs-fMRI) to index stimulus-independent changes in neural activity to understand the neural architecture that determines dominance durations during bistable perception (using binocular rivalry and Necker cube stimuli). Anterior regions of the Superior Parietal Lobule (SPL) exhibited robust connectivity with regions of primary sensorimotor cortex. The strength of this region's connectivity with the striatum predicted shorter dominance durations during binocular rivalry, whereas its connectivity to pre-motor cortex predicted longer dominance durations for the Necker Cube. Posterior regions of the SPL, on the other hand, were coupled to associative cortex in the temporal and frontal lobes. The posterior SPL's connectivity to the temporal lobe predicted longer dominance during binocular rivalry. In conjunction with prior work, these data suggest that the anterior SPL contributes to perceptual rivalry through the inhibition of incongruent bottom up information, whereas the posterior SPL influences rivalry by supporting the current interpretation of a bistable stimulus. Our data suggests that the functional connectivity of the SPL with regions of sensory, motor, and associative cortex allows it to regulate the interpretation of the environment that forms the focus of conscious attention at a specific moment in time. Copyright © 2015. Published by Elsevier Inc.

Noise-induced multistability in the regulation of cancer by genes and pseudogenes

Energy Technology Data Exchange (ETDEWEB)

Petrosyan, K. G., E-mail: pkaren@phys.sinica.edu.tw [Institute of Physics, Academia Sinica, Nankang, Taipei 11529, Taiwan (China); Hu, Chin-Kun, E-mail: huck@phys.sinica.edu.tw [Institute of Physics, Academia Sinica, Nankang, Taipei 11529, Taiwan (China); National Center for Theoretical Sciences, National Tsing Hua University, Hsinchu 30013, Taiwan (China); Business School, University of Shanghai for Science and Technology, Shanghai 200093 (China)

2016-07-28

We extend a previously introduced model of stochastic gene regulation of cancer to a nonlinear case having both gene and pseudogene messenger RNAs (mRNAs) self-regulated. The model consists of stochastic Boolean genetic elements and possesses noise-induced multistability (multimodality). We obtain analytical expressions for probabilities for the case of constant but finite number of microRNA molecules which act as a noise source for the competing gene and pseudogene mRNAs. The probability distribution functions display both the global bistability regime as well as even-odd number oscillations for a certain range of model parameters. Statistical characteristics of the mRNA’s level fluctuations are evaluated. The obtained results of the extended model advance our understanding of the process of stochastic gene and pseudogene expressions that is crucial in regulation of cancer.

Feedback-induced bistability of an optically levitated nanoparticle: A Fokker-Planck treatment

Science.gov (United States)

Ge, Wenchao; Rodenburg, Brandon; Bhattacharya, M.

2016-08-01

Optically levitated nanoparticles have recently emerged as versatile platforms for investigating macroscopic quantum mechanics and enabling ultrasensitive metrology. In this paper we theoretically consider two damping regimes of an optically levitated nanoparticle cooled by cavityless parametric feedback. Our treatment is based on a generalized Fokker-Planck equation derived from the quantum master equation presented recently and shown to agree very well with experiment [B. Rodenburg, L. P. Neukirch, A. N. Vamivakas, and M. Bhattacharya, Quantum model of cooling and force sensing with an optically trapped nanoparticle, Optica 3, 318 (2016), 10.1364/OPTICA.3.000318]. For low damping, we find that the resulting Wigner function yields the single-peaked oscillator position distribution and recovers the appropriate energy distribution derived earlier using a classical theory and verified experimentally [J. Gieseler, R. Quidant, C. Dellago, and L. Novotny, Dynamic relaxation of a levitated nanoparticle from a non-equilibrium steady state, Nat. Nano. 9, 358 (2014), 10.1038/nnano.2014.40]. For high damping, in contrast, we predict a double-peaked position distribution, which we trace to an underlying bistability induced by feedback. Unlike in cavity-based optomechanics, stochastic processes play a major role in determining the bistable behavior. To support our conclusions, we present analytical expressions as well as numerical simulations using the truncated Wigner function approach. Our work opens up the prospect of developing bistability-based devices, characterization of phase-space dynamics, and investigation of the quantum-classical transition using levitated nanoparticles.

Regularity, variability and bi-stability in the activity of cerebellar purkinje cells.

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Rokni, Dan; Tal, Zohar; Byk, Hananel; Yarom, Yosef

2009-01-01

Recent studies have demonstrated that the membrane potential of Purkinje cells is bi-stable and that this phenomenon underlies bi-modal simple spike firing. Membrane potential alternates between a depolarized state, that is associated with spontaneous simple spike firing (up state), and a quiescent hyperpolarized state (down state). A controversy has emerged regarding the relevance of bi-stability to the awake animal, yet recordings made from behaving cat Purkinje cells have demonstrated that at least 50% of the cells exhibit bi-modal firing. The robustness of the phenomenon in vitro or in anaesthetized systems on the one hand, and the controversy regarding its expression in behaving animals on the other hand suggest that state transitions are under neuronal control. Indeed, we have recently demonstrated that synaptic inputs can induce transitions between the states and suggested that the role of granule cell input is to control the states of Purkinje cells rather than increase or decrease firing rate gradually. We have also shown that the state of a Purkinje cell does not only affect its firing but also the waveform of climbing fiber-driven complex spikes and the associated calcium influx. These findings call for a reconsideration of the role of Purkinje cells in cerebellar function. In this manuscript we review the recent findings on Purkinje cell bi-stability and add some analyses of its effect on the regularity and variability of Purkinje cell activity.

Regularity, variabilty and bi-stability in the activity of cerebellar Purkinje cells

Directory of Open Access Journals (Sweden)

Dan Rokni

2009-11-01

Full Text Available Recent studies have demonstrated that the membrane potential of Purkinje cells is bi-stable and that this phenomenon underlies bi-modal simple spike firing. Membrane potential alternates between a depolarized state, that is associated with spontaneous simple spike firing (up state, and a quiescent hyperpolarized state (down state. A controversy has emerged regarding the relevance of bi-stability to the awake animal, yet recordings made from behaving cat Purkinje cells have demonstrated that at least 50% of the cells exhibit bi-modal firing. The robustness of the phenomenon in-vitro or in anaesthetized systems on the one hand, and the controversy regarding its expression in behaving animals on the other hand suggest that state transitions are under neuronal control. Indeed, we have recently demonstrated that synaptic inputs can induce transitions between the states and suggested that the role of granule cell input is to control the states of Purkinje cells rather than increase or decrease firing rate gradually. We have also shown that the state of a Purkinje cell does not only affect its firing but also the waveform of climbing fiber-driven complex spikes and the associated calcium influx. These findings call for a reconsideration of the role of Purkinje cells in cerebellar function. In this manuscript we review the recent findings on Purkinje cell bi-stability and add some analyses of its effect on the regularity and variability of Purkinje cell activity.

Two Bistable Switches Govern M Phase Entry.

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Mochida, Satoru; Rata, Scott; Hino, Hirotsugu; Nagai, Takeharu; Novák, Béla

2016-12-19

The abrupt and irreversible transition from interphase to M phase is essential to separate DNA replication from chromosome segregation. This transition requires the switch-like phosphorylation of hundreds of proteins by the cyclin-dependent kinase 1 (Cdk1):cyclin B (CycB) complex. Previous studies have ascribed these switch-like phosphorylations to the auto-activation of Cdk1:CycB through the removal of inhibitory phosphorylations on Cdk1-Tyr15 [1, 2]. The positive feedback in Cdk1 activation creates a bistable switch that makes mitotic commitment irreversible [2-4]. Here, we surprisingly find that Cdk1 auto-activation is dispensable for irreversible, switch-like mitotic entry due to a second mechanism, whereby Cdk1:CycB inhibits its counteracting phosphatase (PP2A:B55). We show that the PP2A:B55-inhibiting Greatwall (Gwl)-endosulfine (ENSA) pathway is both necessary and sufficient for switch-like phosphorylations of mitotic substrates. Using purified components of the Gwl-ENSA pathway in a reconstituted system, we found a sharp Cdk1 threshold for phosphorylation of a luminescent mitotic substrate. The Cdk1 threshold to induce mitotic phosphorylation is distinctly higher than the Cdk1 threshold required to maintain these phosphorylations-evidence for bistability. A combination of mathematical modeling and biochemical reconstitution show that the bistable behavior of the Gwl-ENSA pathway emerges from its mutual antagonism with PP2A:B55. Our results demonstrate that two interlinked bistable mechanisms provide a robust solution for irreversible and switch-like mitotic entry. Copyright © 2016 Elsevier Ltd. All rights reserved.

Analytic descriptions of stochastic bistable systems under force ramp.

Science.gov (United States)

Friddle, Raymond W

2016-05-01

Solving the two-state master equation with time-dependent rates, the ubiquitous driven bistable system, is a long-standing problem that does not permit a complete solution for all driving rates. Here we show an accurate approximation to this problem by considering the system in the control parameter regime. The results are immediately applicable to a diverse range of bistable systems including single-molecule mechanics.

Bistable Microvalve For Use With Microcatheter System

Science.gov (United States)

Seward, Kirk Patrick

2003-12-16

A bistable microvalve of shape memory material is operatively connected to a microcatheter. The bistable microvalve includes a tip that can be closed off until it is in the desired position. Once it is in position it can be opened and closed. The system uses heat and pressure to open and close the microvalve. The shape memory material will change stiffness and shape when heated above a transition temperature. The shape memory material is adapted to move from a first shape to a second shape, either open or closed, where it can perform a desired function.

Noticeable positive Doppler effect on optical bistability in an N-type active Raman gain atomic system

International Nuclear Information System (INIS)

Chang Zeng-Guang; Zhang Jing-Tao; Niu Yue-Ping; Gong Shang-Qing

2012-01-01

We theoretically investigate the Doppler effect on optical bistability in an N-type active Raman gain atomic system inside an optical ring cavity. It is shown that the Doppler effect can greatly enhance the dispersion and thus create the bistable behaviour or greatly increase the bistable region, which has been known as the positive Doppler effect on optical bistability. In addition, we find that a positive Doppler effect can change optical bistability from the hybrid dispersion-gain type to a dispersive type

Multiple Bistability in Quinonoid-Bridged Diiron(II) Complexes: Influence of Bridge Symmetry on Bistable Properties.

Science.gov (United States)

van der Meer, Margarethe; Rechkemmer, Yvonne; Breitgoff, Frauke D; Marx, Raphael; Neugebauer, Petr; Frank, Uta; van Slageren, Joris; Sarkar, Biprajit

2016-11-21

Quinonoid bridges are well-suited for generating dinuclear assemblies that might display various bistable properties. In this contribution we present two diiron(II) complexes where the iron(II) centers are either bridged by the doubly deprotonated form of a symmetrically substituted quinonoid bridge, 2,5-bis[4-(isopropyl)anilino]-1,4-benzoquinone (H 2 L2') with a [O,N,O,N] donor set, or with the doubly deprotonated form of an unsymmetrically substituted quinonoid bridge, 2-[4-(isopropyl)anilino]-5-hydroxy-1,4-benzoquinone (H 2 L5') with a [O,O,O,N] donor set. Both complexes display temperature-induced spin crossover (SCO). The nature of the SCO is strongly dependent on the bridging ligand, with only the complex with the [O,O,O,N] donor set displaying a prominent hysteresis loop of about 55 K. Importantly, only the latter complex also shows a pronounced light-induced spin state change. Furthermore, both complexes can be oxidized to the mixed-valent iron(II)-iron(III) form, and the nature of the bridge determines the Robin and Day classification of these forms. Both complexes have been probed by a battery of electrochemical, spectroscopic, and magnetic methods, and this combined approach is used to shed light on the electronic structures of the complexes and on bistability. The results presented here thus show the potential of using the relatively new class of unsymmetrically substituted bridging quinonoid ligands for generating intriguing bistable properties and for performing site-specific magnetic switching.

Gene expression inference with deep learning.

Science.gov (United States)

Chen, Yifei; Li, Yi; Narayan, Rajiv; Subramanian, Aravind; Xie, Xiaohui

2016-06-15

Large-scale gene expression profiling has been widely used to characterize cellular states in response to various disease conditions, genetic perturbations, etc. Although the cost of whole-genome expression profiles has been dropping steadily, generating a compendium of expression profiling over thousands of samples is still very expensive. Recognizing that gene expressions are often highly correlated, researchers from the NIH LINCS program have developed a cost-effective strategy of profiling only ∼1000 carefully selected landmark genes and relying on computational methods to infer the expression of remaining target genes. However, the computational approach adopted by the LINCS program is currently based on linear regression (LR), limiting its accuracy since it does not capture complex nonlinear relationship between expressions of genes. We present a deep learning method (abbreviated as D-GEX) to infer the expression of target genes from the expression of landmark genes. We used the microarray-based Gene Expression Omnibus dataset, consisting of 111K expression profiles, to train our model and compare its performance to those from other methods. In terms of mean absolute error averaged across all genes, deep learning significantly outperforms LR with 15.33% relative improvement. A gene-wise comparative analysis shows that deep learning achieves lower error than LR in 99.97% of the target genes. We also tested the performance of our learned model on an independent RNA-Seq-based GTEx dataset, which consists of 2921 expression profiles. Deep learning still outperforms LR with 6.57% relative improvement, and achieves lower error in 81.31% of the target genes. D-GEX is available at https://github.com/uci-cbcl/D-GEX CONTACT: xhx@ics.uci.edu Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Controllable optical bistability and multistability in asymmetric double quantum wells via spontaneously generated coherence

Energy Technology Data Exchange (ETDEWEB)

Chen, Yuan; Deng, Li [Department of Applied Physics, East China Jiaotong University, Nanchang, 330013 (China); Chen, Aixi, E-mail: aixichen@ecjtu.jx.cn [Department of Applied Physics, East China Jiaotong University, Nanchang, 330013 (China); Institute for Quantum Computing, University of Waterloo, Ontario N2L 3G1 (Canada)

2015-02-15

We investigate the nonlinear optical phenomena of the optical bistability and multistability via spontaneously generated coherence in an asymmetric double quantum well structure coupled by a weak probe field and a controlling field. It is shown that the threshold and hysteresis cycle of the optical bistability can be conveniently controlled only by adjusting the intensity of the SGC or the controlling field. Moreover, switching between optical bistability and multistability can be achieved. These studies may have practical significance for the preparation of optical bistable switching device.

Controllable optical bistability and multistability in asymmetric double quantum wells via spontaneously generated coherence

International Nuclear Information System (INIS)

Chen, Yuan; Deng, Li; Chen, Aixi

2015-01-01

We investigate the nonlinear optical phenomena of the optical bistability and multistability via spontaneously generated coherence in an asymmetric double quantum well structure coupled by a weak probe field and a controlling field. It is shown that the threshold and hysteresis cycle of the optical bistability can be conveniently controlled only by adjusting the intensity of the SGC or the controlling field. Moreover, switching between optical bistability and multistability can be achieved. These studies may have practical significance for the preparation of optical bistable switching device

Evidence for distinct mechanisms underlying attentional priming and sensory memory for bistable perception.

Science.gov (United States)

Brinkhuis, M A B; Kristjánsson, Á; Brascamp, J W

2015-08-01

Attentional selection in visual search paradigms and perceptual selection in bistable perception paradigms show functional similarities. For example, both are sensitive to trial history: They are biased toward previously selected targets or interpretations. We investigated whether priming by target selection in visual search and sensory memory for bistable perception are related. We did this by presenting two trial types to observers. We presented either ambiguous spheres that rotated over a central axis and could be perceived as rotating in one of two directions, or search displays in which the unambiguously rotating target and distractor spheres closely resembled the two possible interpretations of the ambiguous stimulus. We interleaved both trial types within experiments, to see whether priming by target selection during search trials would affect the perceptual outcome of bistable perception and, conversely, whether sensory memory during bistable perception would affect target selection times during search. Whereas we found intertrial repetition effects among consecutive search trials and among consecutive bistable trials, we did not find cross-paradigm effects. Thus, even though we could ascertain that our experiments robustly elicited processes of both search priming and sensory memory for bistable perception, these same experiments revealed no interaction between the two.

The Independent and Shared Mechanisms of Intrinsic Brain Dynamics: Insights From Bistable Perception

Directory of Open Access Journals (Sweden)

Teng Cao

2018-04-01

Full Text Available In bistable perception, constant input leads to alternating perception. The dynamics of the changing perception reflects the intrinsic dynamic properties of the “unconscious inferential” process in the brain. Under the same condition, individuals differ in how fast they experience the perceptual alternation. In this study, testing many forms of bistable perception in a large number of observers, we investigated the key question of whether there is a general and common mechanism or multiple and independent mechanisms that control the dynamics of the inferential brain. Bistable phenomena tested include binocular rivalry, vase-face, Necker cube, moving plaid, motion induced blindness, biological motion, spinning dancer, rotating cylinder, Lissajous-figure, rolling wheel, and translating diamond. Switching dynamics for each bistable percept was measured in 100 observers. Results show that the switching rates of subsets of bistable percept are highly correlated. The clustering of dynamic properties of some bistable phenomena but not an overall general control of switching dynamics implies that the brain’s inferential processes are both shared and independent – faster in constructing 3D structure from motion does not mean faster in integrating components into an objects.

Take it of leave it : Mechanisms underlying bacterial bistable regulatory networks

NARCIS (Netherlands)

Siebring, Jeroen; Sorg, Robin; Herber, Martijn; Kuipers, Oscar; Filloux, Alain A.M.

2012-01-01

Bistable switches occur in regulatory networks that can exist in two distinct stable states. Such networks allow distinct switching of individual cells. In bacteria these switches coexist with regulatory networks that respond gradually to environmental input. Bistable switches play key roles in high

A bistable switch in dynamic thiodepsipeptide folding and template-directed ligation.

Science.gov (United States)

Mukherjee, Rakesh; Cohen-Luria, Rivka; Wagner, Nathaniel; Ashkenasy, Gonen

2015-10-12

Bistable reaction networks provide living cells with chemically controlled mechanisms for long-term memory storage. Such networks are also often switchable and can be flipped from one state to the other. We target here a major challenge in systems chemistry research, namely developing synthetic, non-enzymatic, networks that mimic such a complex function. Therefore, we describe a dynamic network that depending on initial thiodepsipeptide concentrations leads to one of two distinct steady states. This bistable system is readily switched by applying the appropriate stimuli. The relationship between the reaction network topology and its capacity to invoke bistability is then analyzed by control experiments and theory. We suggest that demonstrating bistable behavior using synthetic networks further highlights their possible role in early evolution, and may shine light on potential utility for novel applications, such as chemical memories. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Scaling of gene expression data allowing the comparison of different gene expression platforms

NARCIS (Netherlands)

van Ruissen, Fred; Schaaf, Gerben J.; Kool, Marcel; Baas, Frank; Ruijter, Jan M.

2008-01-01

Serial analysis of gene expression (SAGE) and microarrays have found a widespread application, but much ambiguity exists regarding the amalgamation of the data resulting from these technologies. Cross-platform utilization of gene expression data from the SAGE and microarray technology could reduce

cis sequence effects on gene expression

Directory of Open Access Journals (Sweden)

Jacobs Kevin

2007-08-01

Full Text Available Abstract Background Sequence and transcriptional variability within and between individuals are typically studied independently. The joint analysis of sequence and gene expression variation (genetical genomics provides insight into the role of linked sequence variation in the regulation of gene expression. We investigated the role of sequence variation in cis on gene expression (cis sequence effects in a group of genes commonly studied in cancer research in lymphoblastoid cell lines. We estimated the proportion of genes exhibiting cis sequence effects and the proportion of gene expression variation explained by cis sequence effects using three different analytical approaches, and compared our results to the literature. Results We generated gene expression profiling data at N = 697 candidate genes from N = 30 lymphoblastoid cell lines for this study and used available candidate gene resequencing data at N = 552 candidate genes to identify N = 30 candidate genes with sufficient variance in both datasets for the investigation of cis sequence effects. We used two additive models and the haplotype phylogeny scanning approach of Templeton (Tree Scanning to evaluate association between individual SNPs, all SNPs at a gene, and diplotypes, with log-transformed gene expression. SNPs and diplotypes at eight candidate genes exhibited statistically significant (p cis sequence effects in our study, respectively. Conclusion Based on analysis of our results and the extant literature, one in four genes exhibits significant cis sequence effects, and for these genes, about 30% of gene expression variation is accounted for by cis sequence variation. Despite diverse experimental approaches, the presence or absence of significant cis sequence effects is largely supported by previously published studies.

Extracting gene expression patterns and identifying co-expressed genes from microarray data reveals biologically responsive processes

Directory of Open Access Journals (Sweden)

Paules Richard S

2007-11-01

Full Text Available Abstract Background A common observation in the analysis of gene expression data is that many genes display similarity in their expression patterns and therefore appear to be co-regulated. However, the variation associated with microarray data and the complexity of the experimental designs make the acquisition of co-expressed genes a challenge. We developed a novel method for Extracting microarray gene expression Patterns and Identifying co-expressed Genes, designated as EPIG. The approach utilizes the underlying structure of gene expression data to extract patterns and identify co-expressed genes that are responsive to experimental conditions. Results Through evaluation of the correlations among profiles, the magnitude of variation in gene expression profiles, and profile signal-to-noise ratio's, EPIG extracts a set of patterns representing co-expressed genes. The method is shown to work well with a simulated data set and microarray data obtained from time-series studies of dauer recovery and L1 starvation in C. elegans and after ultraviolet (UV or ionizing radiation (IR-induced DNA damage in diploid human fibroblasts. With the simulated data set, EPIG extracted the appropriate number of patterns which were more stable and homogeneous than the set of patterns that were determined using the CLICK or CAST clustering algorithms. However, CLICK performed better than EPIG and CAST with respect to the average correlation between clusters/patterns of the simulated data. With real biological data, EPIG extracted more dauer-specific patterns than CLICK. Furthermore, analysis of the IR/UV data revealed 18 unique patterns and 2661 genes out of approximately 17,000 that were identified as significantly expressed and categorized to the patterns by EPIG. The time-dependent patterns displayed similar and dissimilar responses between IR and UV treatments. Gene Ontology analysis applied to each pattern-related subset of co-expressed genes revealed underlying

Revisiting the Lissajous figure as a tool to study bistable perception.

Science.gov (United States)

Weilnhammer, V A; Ludwig, K; Sterzer, P; Hesselmann, G

2014-05-01

During bistable vision perception spontaneously "switches" between two mutually exclusive percepts despite constant sensory input. The endogenous nature of these perceptual transitions has motivated extensive research aimed at the underlying mechanisms, since spontaneous perceptual transitions of bistable stimuli should in principle allow for a dissociation of processes related to sensory stimulation from those related to conscious perception. However, transitions from one conscious percept to another are often not instantaneous, and participants usually report a considerable amount of mixed or unclear percepts. This feature of bistable vision makes it difficult to isolate transition-related visual processes. Here, we revisited an ambiguous depth-from-motion stimulus which was first introduced to experimental psychology more than 80 years ago. This rotating Lissajous figure might prove useful in complementing other bistable stimuli, since its perceptual transitions only occur at critical stimulus configurations and are virtually instantaneous, thus facilitating the construction of a perceptually equivalent replay condition. We found that three parameters of the Lissajous figure - complexity, line width, and rotational speed - differentially modulated its perceptual dominance durations and transition probabilities, thus providing experimenters with a versatile tool to study the perceptual dynamics of bistable vision. Copyright © 2014 Elsevier B.V. All rights reserved.

Renal Gene Expression Database (RGED): a relational database of gene expression profiles in kidney disease.

Science.gov (United States)

Zhang, Qingzhou; Yang, Bo; Chen, Xujiao; Xu, Jing; Mei, Changlin; Mao, Zhiguo

2014-01-01

We present a bioinformatics database named Renal Gene Expression Database (RGED), which contains comprehensive gene expression data sets from renal disease research. The web-based interface of RGED allows users to query the gene expression profiles in various kidney-related samples, including renal cell lines, human kidney tissues and murine model kidneys. Researchers can explore certain gene profiles, the relationships between genes of interests and identify biomarkers or even drug targets in kidney diseases. The aim of this work is to provide a user-friendly utility for the renal disease research community to query expression profiles of genes of their own interest without the requirement of advanced computational skills. Website is implemented in PHP, R, MySQL and Nginx and freely available from http://rged.wall-eva.net. http://rged.wall-eva.net. © The Author(s) 2014. Published by Oxford University Press.

Renal Gene Expression Database (RGED): a relational database of gene expression profiles in kidney disease

Science.gov (United States)

Zhang, Qingzhou; Yang, Bo; Chen, Xujiao; Xu, Jing; Mei, Changlin; Mao, Zhiguo

2014-01-01

We present a bioinformatics database named Renal Gene Expression Database (RGED), which contains comprehensive gene expression data sets from renal disease research. The web-based interface of RGED allows users to query the gene expression profiles in various kidney-related samples, including renal cell lines, human kidney tissues and murine model kidneys. Researchers can explore certain gene profiles, the relationships between genes of interests and identify biomarkers or even drug targets in kidney diseases. The aim of this work is to provide a user-friendly utility for the renal disease research community to query expression profiles of genes of their own interest without the requirement of advanced computational skills. Availability and implementation: Website is implemented in PHP, R, MySQL and Nginx and freely available from http://rged.wall-eva.net. Database URL: http://rged.wall-eva.net PMID:25252782

Modulation of gene expression made easy

DEFF Research Database (Denmark)

Solem, Christian; Jensen, Peter Ruhdal

2002-01-01

A new approach for modulating gene expression, based on randomization of promoter (spacer) sequences, was developed. The method was applied to chromosomal genes in Lactococcus lactis and shown to generate libraries of clones with broad ranges of expression levels of target genes. In one example...... that the method can be applied to modulating the expression of native genes on the chromosome. We constructed a series of strains in which the expression of the las operon, containing the genes pfk, pyk, and ldh, was modulated by integrating a truncated copy of the pfk gene. Importantly, the modulation affected...

Dynamics of unidirectionally coupled bistable Henon maps

International Nuclear Information System (INIS)

Sausedo-Solorio, J.M.; Pisarchik, A.N.

2011-01-01

We study dynamics of two bistable Henon maps coupled in a master-slave configuration. In the case of coexistence of two periodic orbits, the slave map evolves into the master map state after transients, which duration determines synchronization time and obeys a -1/2 power law with respect to the coupling strength. This scaling law is almost independent of the map parameter. In the case of coexistence of chaotic and periodic attractors, very complex dynamics is observed, including the emergence of new attractors as the coupling strength is increased. The attractor of the master map always exists in the slave map independently of the coupling strength. For a high coupling strength, complete synchronization can be achieved only for the attractor similar to that of the master map. -- Highlights: → We study dynamics of two bistable Henon maps coupled in a master-slave configuration. → Synchronization time for periodic orbits obeys a -1/2 power law with respect to coupling. → For a high coupling strength, the slave map remains bistable. → Complete synchronization can be achieved only when both maps stay at the same attractor.

The effects of intrinsic noise on the behaviour of bistable cell regulatory systems under quasi-steady state conditions.

Science.gov (United States)

de la Cruz, Roberto; Guerrero, Pilar; Spill, Fabian; Alarcón, Tomás

2015-08-21

We analyse the effect of intrinsic fluctuations on the properties of bistable stochastic systems with time scale separation operating under quasi-steady state conditions. We first formulate a stochastic generalisation of the quasi-steady state approximation based on the semi-classical approximation of the partial differential equation for the generating function associated with the chemical master equation. Such approximation proceeds by optimising an action functional whose associated set of Euler-Lagrange (Hamilton) equations provides the most likely fluctuation path. We show that, under appropriate conditions granting time scale separation, the Hamiltonian can be re-scaled so that the set of Hamilton equations splits up into slow and fast variables, whereby the quasi-steady state approximation can be applied. We analyse two particular examples of systems whose mean-field limit has been shown to exhibit bi-stability: an enzyme-catalysed system of two mutually inhibitory proteins and a gene regulatory circuit with self-activation. Our theory establishes that the number of molecules of the conserved species is order parameters whose variation regulates bistable behaviour in the associated systems beyond the predictions of the mean-field theory. This prediction is fully confirmed by direct numerical simulations using the stochastic simulation algorithm. This result allows us to propose strategies whereby, by varying the number of molecules of the three conserved chemical species, cell properties associated to bistable behaviour (phenotype, cell-cycle status, etc.) can be controlled.

The effects of intrinsic noise on the behaviour of bistable cell regulatory systems under quasi-steady state conditions

Energy Technology Data Exchange (ETDEWEB)

Cruz, Roberto; Alarcón, Tomás de la [Centre de Recerca Matemàtica. Edifici C, Campus de Bellaterra, 08193 Bellaterra (Barcelona) (Spain); Departament de Matemàtiques, Universitat Autònoma de Barcelona, 08193 Bellaterra (Barcelona) (Spain); Guerrero, Pilar [Department of Mathematics, University College London, Gower Street, London WC1E 6BT (United Kingdom); Spill, Fabian [Department of Biomedical Engineering, Boston University, 44 Cummington Street, Boston, Massachusetts 02215 (United States); Department of Mechanical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139 (United States)

2015-08-21

We analyse the effect of intrinsic fluctuations on the properties of bistable stochastic systems with time scale separation operating under quasi-steady state conditions. We first formulate a stochastic generalisation of the quasi-steady state approximation based on the semi-classical approximation of the partial differential equation for the generating function associated with the chemical master equation. Such approximation proceeds by optimising an action functional whose associated set of Euler-Lagrange (Hamilton) equations provides the most likely fluctuation path. We show that, under appropriate conditions granting time scale separation, the Hamiltonian can be re-scaled so that the set of Hamilton equations splits up into slow and fast variables, whereby the quasi-steady state approximation can be applied. We analyse two particular examples of systems whose mean-field limit has been shown to exhibit bi-stability: an enzyme-catalysed system of two mutually inhibitory proteins and a gene regulatory circuit with self-activation. Our theory establishes that the number of molecules of the conserved species is order parameters whose variation regulates bistable behaviour in the associated systems beyond the predictions of the mean-field theory. This prediction is fully confirmed by direct numerical simulations using the stochastic simulation algorithm. This result allows us to propose strategies whereby, by varying the number of molecules of the three conserved chemical species, cell properties associated to bistable behaviour (phenotype, cell-cycle status, etc.) can be controlled.

A review of the recent research on vibration energy harvesting via bistable systems

International Nuclear Information System (INIS)

Harne, R L; Wang, K W

2013-01-01

The investigation of the conversion of vibrational energy into electrical power has become a major field of research. In recent years, bistable energy harvesting devices have attracted significant attention due to some of their unique features. Through a snap-through action, bistable systems transition from one stable state to the other, which could cause large amplitude motion and dramatically increase power generation. Due to their nonlinear characteristics, such devices may be effective across a broad-frequency bandwidth. Consequently, a rapid engagement of research has been undertaken to understand bistable electromechanical dynamics and to utilize the insight for the development of improved designs. This paper reviews, consolidates, and reports on the major efforts and findings documented in the literature. A common analytical framework for bistable electromechanical dynamics is presented, the principal results are provided, the wide variety of bistable energy harvesters are described, and some remaining challenges and proposed solutions are summarized. (topical review)

Controlling the optical bistability and multistability in a two-level pumped-probe system

International Nuclear Information System (INIS)

Mahmoudi, Mohammad; Sahrai, Mostafa; Masoumeh Mousavi, Seyede

2010-01-01

We study the behavior of the optical bistability (OB) and multistability (OM) in a two-level pumped-probe atomic system by means of a unidirectional ring cavity. We show that the optical bistability in a two-level atomic system can be controlled by adjusting the intensity of the pump field and the detuning between two fields. We find that applying the pumping field decreases the threshold of the optical bistability.

A predictive coding account of bistable perception - a model-based fMRI study.

Science.gov (United States)

Weilnhammer, Veith; Stuke, Heiner; Hesselmann, Guido; Sterzer, Philipp; Schmack, Katharina

2017-05-01

In bistable vision, subjective perception wavers between two interpretations of a constant ambiguous stimulus. This dissociation between conscious perception and sensory stimulation has motivated various empirical studies on the neural correlates of bistable perception, but the neurocomputational mechanism behind endogenous perceptual transitions has remained elusive. Here, we recurred to a generic Bayesian framework of predictive coding and devised a model that casts endogenous perceptual transitions as a consequence of prediction errors emerging from residual evidence for the suppressed percept. Data simulations revealed close similarities between the model's predictions and key temporal characteristics of perceptual bistability, indicating that the model was able to reproduce bistable perception. Fitting the predictive coding model to behavioural data from an fMRI-experiment on bistable perception, we found a correlation across participants between the model parameter encoding perceptual stabilization and the behaviourally measured frequency of perceptual transitions, corroborating that the model successfully accounted for participants' perception. Formal model comparison with established models of bistable perception based on mutual inhibition and adaptation, noise or a combination of adaptation and noise was used for the validation of the predictive coding model against the established models. Most importantly, model-based analyses of the fMRI data revealed that prediction error time-courses derived from the predictive coding model correlated with neural signal time-courses in bilateral inferior frontal gyri and anterior insulae. Voxel-wise model selection indicated a superiority of the predictive coding model over conventional analysis approaches in explaining neural activity in these frontal areas, suggesting that frontal cortex encodes prediction errors that mediate endogenous perceptual transitions in bistable perception. Taken together, our current work

A predictive coding account of bistable perception - a model-based fMRI study.

Directory of Open Access Journals (Sweden)

Veith Weilnhammer

2017-05-01

Full Text Available In bistable vision, subjective perception wavers between two interpretations of a constant ambiguous stimulus. This dissociation between conscious perception and sensory stimulation has motivated various empirical studies on the neural correlates of bistable perception, but the neurocomputational mechanism behind endogenous perceptual transitions has remained elusive. Here, we recurred to a generic Bayesian framework of predictive coding and devised a model that casts endogenous perceptual transitions as a consequence of prediction errors emerging from residual evidence for the suppressed percept. Data simulations revealed close similarities between the model's predictions and key temporal characteristics of perceptual bistability, indicating that the model was able to reproduce bistable perception. Fitting the predictive coding model to behavioural data from an fMRI-experiment on bistable perception, we found a correlation across participants between the model parameter encoding perceptual stabilization and the behaviourally measured frequency of perceptual transitions, corroborating that the model successfully accounted for participants' perception. Formal model comparison with established models of bistable perception based on mutual inhibition and adaptation, noise or a combination of adaptation and noise was used for the validation of the predictive coding model against the established models. Most importantly, model-based analyses of the fMRI data revealed that prediction error time-courses derived from the predictive coding model correlated with neural signal time-courses in bilateral inferior frontal gyri and anterior insulae. Voxel-wise model selection indicated a superiority of the predictive coding model over conventional analysis approaches in explaining neural activity in these frontal areas, suggesting that frontal cortex encodes prediction errors that mediate endogenous perceptual transitions in bistable perception. Taken together

Bridging time scales in cellular decision making with a stochastic bistable switch

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Waldherr Steffen

2010-08-01

Full Text Available Abstract Background Cellular transformations which involve a significant phenotypical change of the cell's state use bistable biochemical switches as underlying decision systems. Some of these transformations act over a very long time scale on the cell population level, up to the entire lifespan of the organism. Results In this work, we aim at linking cellular decisions taking place on a time scale of years to decades with the biochemical dynamics in signal transduction and gene regulation, occuring on a time scale of minutes to hours. We show that a stochastic bistable switch forms a viable biochemical mechanism to implement decision processes on long time scales. As a case study, the mechanism is applied to model the initiation of follicle growth in mammalian ovaries, where the physiological time scale of follicle pool depletion is on the order of the organism's lifespan. We construct a simple mathematical model for this process based on experimental evidence for the involved genetic mechanisms. Conclusions Despite the underlying stochasticity, the proposed mechanism turns out to yield reliable behavior in large populations of cells subject to the considered decision process. Our model explains how the physiological time constant may emerge from the intrinsic stochasticity of the underlying gene regulatory network. Apart from ovarian follicles, the proposed mechanism may also be of relevance for other physiological systems where cells take binary decisions over a long time scale.

Energy landscape and dynamics of brain activity during human bistable perception.

Science.gov (United States)

Watanabe, Takamitsu; Masuda, Naoki; Megumi, Fukuda; Kanai, Ryota; Rees, Geraint

2014-08-28

Individual differences in the structure of parietal and prefrontal cortex predict the stability of bistable visual perception. However, the mechanisms linking such individual differences in brain structures to behaviour remain elusive. Here we demonstrate a systematic relationship between the dynamics of brain activity, cortical structure and behaviour underpinning bistable perception. Using fMRI in humans, we find that the activity dynamics during bistable perception are well described as fluctuating between three spatially distributed energy minimums: visual-area-dominant, frontal-area-dominant and intermediate states. Transitions between these energy minimums predicted behaviour, with participants whose brain activity tend to reflect the visual-area-dominant state exhibiting more stable perception and those whose activity transits to frontal-area-dominant states reporting more frequent perceptual switches. Critically, these brain activity dynamics are correlated with individual differences in grey matter volume of the corresponding brain areas. Thus, individual differences in the large-scale dynamics of brain activity link focal brain structure with bistable perception.

Harnessing the bistable composite shells to design a tunable phononic band gap structure

Science.gov (United States)

Li, Yi; Xu, Yanlong

2018-02-01

By proposing a system composed of an array of bistable composite shells immersed in air, we develop a new class of periodic structure to control the propagation of sound. Through numerical investigation, we find that the acoustic band gap of this system can be switched on and off by triggering the snap through deformation of the bistable composite shells. The shape of cross section and filling fraction of unit cell can be altered by different number of bistable composite shells, and they have strong impact on the position and width of the band gap. The proposed concept paves the way of using the bistable structures to design a new class of metamaterials that can be enable to manipulate sound.

Optical bistability in the oscillation of an inhomogeneously broadened quasi-three-level laser

International Nuclear Information System (INIS)

Liu, Junhai; Tian, Xueping

2013-01-01

A theoretical modeling analysis is presented to study the optical bistability exhibited in the oscillation of an inhomogeneously broadened quasi-three-level laser. All the major characteristics of optical bistability depend on two normalized parameters, f and x a , which are defined by f = I sat,a /I sat,m and x a = 2α a0 p a /δ and are related to measurable properties of the laser medium. In comparison with the case of a homogeneously broadened laser, the essential condition for the occurrence of such bistability, f a /(x a + 1), turns out to be the same, whereas the intensities at the up- and down-thresholds are substantially increased and the bistability range is reduced. (paper)

Collective Activity of Many Bistable Assemblies Reproduces Characteristic Dynamics of Multistable Perception.

Science.gov (United States)

Cao, Robin; Pastukhov, Alexander; Mattia, Maurizio; Braun, Jochen

2016-06-29

The timing of perceptual decisions depends on both deterministic and stochastic factors, as the gradual accumulation of sensory evidence (deterministic) is contaminated by sensory and/or internal noise (stochastic). When human observers view multistable visual displays, successive episodes of stochastic accumulation culminate in repeated reversals of visual appearance. Treating reversal timing as a "first-passage time" problem, we ask how the observed timing densities constrain the underlying stochastic accumulation. Importantly, mean reversal times (i.e., deterministic factors) differ enormously between displays/observers/stimulation levels, whereas the variance and skewness of reversal times (i.e., stochastic factors) keep characteristic proportions of the mean. What sort of stochastic process could reproduce this highly consistent "scaling property?" Here we show that the collective activity of a finite population of bistable units (i.e., a generalized Ehrenfest process) quantitatively reproduces all aspects of the scaling property of multistable phenomena, in contrast to other processes under consideration (Poisson, Wiener, or Ornstein-Uhlenbeck process). The postulated units express the spontaneous dynamics of attractor assemblies transitioning between distinct activity states. Plausible candidates are cortical columns, or clusters of columns, as they are preferentially connected and spontaneously explore a restricted repertoire of activity states. Our findings suggests that perceptual representations are granular, probabilistic, and operate far from equilibrium, thereby offering a suitable substrate for statistical inference. Spontaneous reversals of high-level perception, so-called multistable perception, conform to highly consistent and characteristic statistics, constraining plausible neural representations. We show that the observed perceptual dynamics would be reproduced quantitatively by a finite population of distinct neural assemblies, each with

Using gene expression noise to understand gene regulation

NARCIS (Netherlands)

Munsky, B.; Neuert, G.; van Oudenaarden, A.

2012-01-01

Phenotypic variation is ubiquitous in biology and is often traceable to underlying genetic and environmental variation. However, even genetically identical cells in identical environments display variable phenotypes. Stochastic gene expression, or gene expression "noise," has been suggested as a

Kinetic evaluation of photosensitivity in bi-stable variants of chimeric channelrhodopsins.

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Shoko Hososhima

Full Text Available Channelrhodopsin-1 and 2 (ChR1 and ChR2 form cation channels that are gated by light through an unknown mechanism. We tested the DC-gate hypothesis that C167 and D195 are involved in the stabilization of the cation-permeable state of ChRWR/C1C2 which consists of TM1-5 of ChR1 and TM6-7 of ChR2 and ChRFR which consists of TM1-2 of ChR1 and TM3-7 of ChR2. The cation permeable state of each ChRWR and ChRFR was markedly prolonged in the order of several tens of seconds when either C167 or D195 position was mutated to alanine (A. Therefore, the DC-gate function was conserved among these chimeric ChRs. We next investigated the kinetic properties of the ON/OFF response of these bi-stable ChR mutants as they are important in designing the photostimulation protocols for the optogenetic manipulation of neuronal activities. The turning-on rate constant of each photocurrent followed a linear relationship to 0-0.12 mW mm(-2 of blue LED light or to 0-0.33 mW mm(-2 of cyan LED light. Each photocurrent of bi-stable ChR was shut off to the non-conducting state by yellow or orange LED light in a manner dependent on the irradiance. As the magnitude of the photocurrent was mostly determined by the turning-on rate constant and the irradiation time, the minimal irradiance that effectively evoked an action potential (threshold irradiance was decreased with time only if the neuron, which expresses bi-stable ChRs, has a certain large membrane time constant (eg. τm > 20 ms. On the other hand, in another group of neurons, the threshold irradiance was not dependent on the irradiation time. Based on these quantitative data, we would propose that these bi-stable ChRs would be most suitable for enhancing the intrinsic activity of excitatory pyramidal neurons at a minimal magnitude of irradiance.

Reverse bistable effect in ferroelectric liquid crystal devices with ultra-fast switching at low driving voltage.

Science.gov (United States)

Guo, Qi; Zhao, Xiaojin; Zhao, Huijie; Chigrinov, V G

2015-05-15

In this Letter, reverse bistable effect with deep-sub-millisecond switching time is first reported in ferroelectric liquid crystal (FLC) devices using a homogeneous photo-alignment technique. It is indicated by our experimental results that both the anchoring energy and the dielectric property of the FLC's alignment layer is critical for the existence of the reverse bistable effect. In addition, with the derived criteria of the reverse bistable effect, we quantitatively analyze the switching dynamics of the reverse bistable FLC and the transition condition between the traditional bistability and our presented reverse bistability. Moreover, the fabricated FLC device exhibits an ultra-fast switching of ∼160  μs and a high contrast ratio of 1000:1, both of which were measured at a low driving voltage of 11 V. The featured deep-sub-millisecond switching time is really advantageous for our presented reverse bistable FLC devices, which enables a significant quality improvement of the existing optical devices, as well as a wide range of new applications in photonics and display areas.

Characterization of differentially expressed genes using high-dimensional co-expression networks

DEFF Research Database (Denmark)

Coelho Goncalves de Abreu, Gabriel; Labouriau, Rodrigo S.

2010-01-01

We present a technique to characterize differentially expressed genes in terms of their position in a high-dimensional co-expression network. The set-up of Gaussian graphical models is used to construct representations of the co-expression network in such a way that redundancy and the propagation...... that allow to make effective inference in problems with high degree of complexity (e.g. several thousands of genes) and small number of observations (e.g. 10-100) as typically occurs in high throughput gene expression studies. Taking advantage of the internal structure of decomposable graphical models, we...... construct a compact representation of the co-expression network that allows to identify the regions with high concentration of differentially expressed genes. It is argued that differentially expressed genes located in highly interconnected regions of the co-expression network are less informative than...

Regulation of eucaryotic gene expression

Energy Technology Data Exchange (ETDEWEB)

Brent, R.; Ptashne, M.S

1989-05-23

This patent describes a method of regulating the expression of a gene in a eucaryotic cell. The method consists of: providing in the eucaryotic cell, a peptide, derived from or substantially similar to a peptide of a procaryotic cell able to bind to DNA upstream from or within the gene, the amount of the peptide being sufficient to bind to the gene and thereby control expression of the gene.

Non-symmetric bi-stable flow around the Ahmed body

International Nuclear Information System (INIS)

Meile, W.; Ladinek, T.; Brenn, G.; Reppenhagen, A.; Fuchs, A.

2016-01-01

Highlights: • The non-symmetric bi-stable flow around the Ahmed body is investigated experimentally. • Bi-stability, described for symmetric flow by Cadot and co-workers, was found in nonsymmetric flow also. • The flow field randomly switches between two states. • The flow is subject to a spanwise instability identified by Cadot and co-workers for symmetric flow. • Aerodynamic forces fluctuate strongly due to the bi-stability. - Abstract: The flow around the Ahmed body at varying Reynolds numbers under yawing conditions is investigated experimentally. The body geometry belongs to a regime subject to spanwise flow instability identified in symmetric flow by Cadot and co-workers (Grandemange et al., 2013b). Our experiments cover the two slant angles 25° and 35° and Reynolds numbers up to 2.784 × 10"6. Special emphasis lies on the aerodynamics under side wind influence. For the 35° slant angle, forces and moments change significantly with the yawing angle in the range 10° ≤ |β| ≤ 15°. The lift and the pitching moment exhibit strong fluctuations due to bi-stable flow around a critical angle β of ±12.5°, where the pitching moment changes sign. Time series of the forces and moments are studied and explained by PIV measurements in the flow field near the rear of the body.

Optical bistability in Er-Yb codoped phosphate glass microspheres at room temperature

NARCIS (Netherlands)

Warda, Jonathan M.; O'Shea, Danny G.; Shortt, Brian J.; Chormaic, Sile Nic

2007-01-01

We experimentally demonstrate optical bistability in Er(3+)-Yb(3+) phosphate glass microspheres at 295 K. Bistability is associated with both Er(3+) fluorescence and lasing behavior, and chromatic switching. The chromatic switching results from an intrinsic mechanism exploiting the thermal coupling

Stochastic resonance in an asymmetric bistable system driven by multiplicative colored noise and additive white noise

International Nuclear Information System (INIS)

Zhou Bingchang; Xu Wei

2008-01-01

The phenomenon of stochastic resonance (SR) in a bistable system driven by multiplicative colored and additive white noises and a periodic rectangular signal with a constant component is studied by using the unified colored noise approximation and the theory of signal-to-noise (SNR) in the adiabatic limit. The analytic expression of the SNR is obtained for arbitrary signal amplitude without being restricted to small amplitudes. The SNR is a non-monotonic function of intensities of multiplicative colored and additive white noises and correlation time of multiplicative colored noise, so SR exhibits in the bistable system. The effects of potential asymmetry r and correlation time τ of multiplicative colored noise on SNR are opposite. Moreover, It is more sensitive to control SR through adjusting the additive white noise intensity D than adjusting the multiplicative colored noise intensity Q

A Strategy for Magnifying Vibration in High-Energy Orbits of a Bistable Oscillator at Low Excitation Levels

International Nuclear Information System (INIS)

Wang Guang-Qing; Liao Wei-Hsin

2015-01-01

This work focuses on how to maintain a high-energy orbit motion of a bistable oscillator when subjected to a low level excitation. An elastic magnifier (EM) positioned between the base and the bistable oscillator is used to magnify the base vibration displacement to significantly enhance the output characteristics of the bistable oscillator. The dimensionless electromechanical equations of the bistable oscillator with an EM are derived, and the effects of the mass and stiffness ratios between the EM and the bistable oscillator on the output displacement are studied. It is shown that the jump phenomenon occurs at a lower excitation level with increasing the mass and stiffness ratios. With the comparison of the displacement trajectories and the phase portraits obtained from experiments, it is validated that the bistable oscillator with an EM can effectively oscillate in a high-energy orbit and can generate a superior output vibration at a low excitation level as compared with the bistable oscillator without an EM. (paper)

Bistable resistive memory behavior in gelatin-CdTe quantum dot composite film

Science.gov (United States)

Vallabhapurapu, Sreedevi; Rohom, Ashwini; Chaure, N. B.; Du, Shengzhi; Srinivasan, Ananthakrishnan

2018-05-01

Bistable memory behavior has been observed for the first time in gelatin type A thin film dispersed with functionalized CdTe quantum dots. The two terminal device with the polymer nanocomposite layer sandwiched between an indium tin oxide coated glass plate and an aluminium top electrode performs as a bistable resistive random access memory module. Butterfly shaped (O-shaped with a hysteresis in forward and reverse sweeps) current-voltage response is observed in this device. The conduction mechanism leading to the bistable electrical switching has been deduced to be a combination of ohmic and electron hopping.

Bistable laser device with multiple coupled active vertical-cavity resonators

Science.gov (United States)

Fischer, Arthur J.; Choquette, Kent D.; Chow, Weng W.

2003-08-19

A new class of bistable coupled-resonator vertical-cavity semiconductor laser devices has been developed. These bistable laser devices can be switched, either electrically or optically, between lasing and non-lasing states. A switching signal with a power of a fraction of a milliwatt can change the laser output of such a device by a factor of a hundred, thereby enabling a range of optical switching and data encoding applications.

Delay induced stability switch, multitype bistability and chaos in an intraguild predation model.

Science.gov (United States)

Shu, Hongying; Hu, Xi; Wang, Lin; Watmough, James

2015-12-01

In many predator-prey models, delay has a destabilizing effect and induces oscillations; while in many competition models, delay does not induce oscillations. By analyzing a rather simple delayed intraguild predation model, which combines both the predator-prey relation and competition, we show that delay in intraguild predation models promotes very complex dynamics. The delay can induce stability switches exhibiting a destabilizing role as well as a stabilizing role. It is shown that three types of bistability are possible: one stable equilibrium coexists with another stable equilibrium (node-node bistability); one stable equilibrium coexists with a stable periodic solution (node-cycle bistability); one stable periodic solution coexists with another stable periodic solution (cycle-cycle bistability). Numerical simulations suggest that delay can also induce chaos in intraguild predation models.

A novel optic bistable device with very low threshold intensity using photorefractive films

Science.gov (United States)

Wang, Sean X.; Sun, Yuankun; Trivedi, Sudhir B.; Li, Guifang

1994-08-01

Brimrose Corporation of America reports the successful completion of the SBIR Phase I research in low-threshold intensity optical bistable devices using photorefractive nonlinearity. A thin photorefractive film optical bistable device was proposed in the Phase I proposal. The feasibility of this device was theoretically investigated. The theoretical feasibility study formulates the materials requirements in such a kind of configuration for Phase II research. In addition, we have proposed and investigated another configuration of optical bistable devices that do not require advanced photorefractive materials, namely, the self-pumped phase conjugator. We have successfully demonstrated a low-threshold optical bistable operation in a KNSBN:CU crystal. To the best of our knowledge, the threshold of 650 mW/sq. cm is the lowest of its kind to be achieved so far.

Bistable fluidic valve is electrically switched

Science.gov (United States)

Fiet, O.; Salvinski, R. J.

1970-01-01

Bistable control valve is selectively switched by direct application of an electrical field to divert fluid from one output channel to another. Valve is inexpensive, has no moving parts, and operates on fluids which are relatively poor electrical conductors.

Inferring gene expression dynamics via functional regression analysis

Directory of Open Access Journals (Sweden)

Leng Xiaoyan

2008-01-01

Full Text Available Abstract Background Temporal gene expression profiles characterize the time-dynamics of expression of specific genes and are increasingly collected in current gene expression experiments. In the analysis of experiments where gene expression is obtained over the life cycle, it is of interest to relate temporal patterns of gene expression associated with different developmental stages to each other to study patterns of long-term developmental gene regulation. We use tools from functional data analysis to study dynamic changes by relating temporal gene expression profiles of different developmental stages to each other. Results We demonstrate that functional regression methodology can pinpoint relationships that exist between temporary gene expression profiles for different life cycle phases and incorporates dimension reduction as needed for these high-dimensional data. By applying these tools, gene expression profiles for pupa and adult phases are found to be strongly related to the profiles of the same genes obtained during the embryo phase. Moreover, one can distinguish between gene groups that exhibit relationships with positive and others with negative associations between later life and embryonal expression profiles. Specifically, we find a positive relationship in expression for muscle development related genes, and a negative relationship for strictly maternal genes for Drosophila, using temporal gene expression profiles. Conclusion Our findings point to specific reactivation patterns of gene expression during the Drosophila life cycle which differ in characteristic ways between various gene groups. Functional regression emerges as a useful tool for relating gene expression patterns from different developmental stages, and avoids the problems with large numbers of parameters and multiple testing that affect alternative approaches.

Synthetic promoter libraries- tuning of gene expression

DEFF Research Database (Denmark)

Hammer, Karin; Mijakovic, Ivan; Jensen, Peter Ruhdal

2006-01-01

knockout and strong overexpression. However, applications such as metabolic optimization and control analysis necessitate a continuous set of expression levels with only slight increments in strength to cover a specific window around the wildtype expression level of the studied gene; this requirement can......The study of gene function often requires changing the expression of a gene and evaluating the consequences. In principle, the expression of any given gene can be modulated in a quasi-continuum of discrete expression levels but the traditional approaches are usually limited to two extremes: gene...

Adaptive Evolution of Gene Expression in Drosophila.

Science.gov (United States)

Nourmohammad, Armita; Rambeau, Joachim; Held, Torsten; Kovacova, Viera; Berg, Johannes; Lässig, Michael

2017-08-08

Gene expression levels are important quantitative traits that link genotypes to molecular functions and fitness. In Drosophila, population-genetic studies have revealed substantial adaptive evolution at the genomic level, but the evolutionary modes of gene expression remain controversial. Here, we present evidence that adaptation dominates the evolution of gene expression levels in flies. We show that 64% of the observed expression divergence across seven Drosophila species are adaptive changes driven by directional selection. Our results are derived from time-resolved data of gene expression divergence across a family of related species, using a probabilistic inference method for gene-specific selection. Adaptive gene expression is stronger in specific functional classes, including regulation, sensory perception, sexual behavior, and morphology. Moreover, we identify a large group of genes with sex-specific adaptation of expression, which predominantly occurs in males. Our analysis opens an avenue to map system-wide selection on molecular quantitative traits independently of their genetic basis. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

Adaptive Evolution of Gene Expression in Drosophila

Directory of Open Access Journals (Sweden)

Armita Nourmohammad

2017-08-01

Full Text Available Gene expression levels are important quantitative traits that link genotypes to molecular functions and fitness. In Drosophila, population-genetic studies have revealed substantial adaptive evolution at the genomic level, but the evolutionary modes of gene expression remain controversial. Here, we present evidence that adaptation dominates the evolution of gene expression levels in flies. We show that 64% of the observed expression divergence across seven Drosophila species are adaptive changes driven by directional selection. Our results are derived from time-resolved data of gene expression divergence across a family of related species, using a probabilistic inference method for gene-specific selection. Adaptive gene expression is stronger in specific functional classes, including regulation, sensory perception, sexual behavior, and morphology. Moreover, we identify a large group of genes with sex-specific adaptation of expression, which predominantly occurs in males. Our analysis opens an avenue to map system-wide selection on molecular quantitative traits independently of their genetic basis.

Propensity for Bistability of Bursting and Silence in the Leech Heart Interneuron

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Tatiana Dashevskiy

2018-02-01

Full Text Available The coexistence of neuronal activity regimes has been reported under normal and pathological conditions. Such multistability could enhance the flexibility of the nervous system and has many implications for motor control, memory, and decision making. Multistability is commonly promoted by neuromodulation targeting specific membrane ionic currents. Here, we investigated how modulation of different ionic currents could affect the neuronal propensity for bistability. We considered a leech heart interneuron model. It exhibits bistability of bursting and silence in a narrow range of the leak current parameters, conductance (gleak and reversal potential (Eleak. We assessed the propensity for bistability of the model by using bifurcation diagrams. On the diagram (gleak, Eleak, we mapped bursting and silent regimes. For the canonical value of Eleak we determined the range of gleak which supported the bistability. We use this range as an index of propensity for bistability. We investigated how this index was affected by alterations of ionic currents. We systematically changed their conductances, one at a time, and built corresponding bifurcation diagrams in parameter planes of the maximal conductance of a given current and the leak conductance. We found that conductance of only one current substantially affected the index of propensity; the increase of the maximal conductance of the hyperpolarization-activated cationic current increased the propensity index. The second conductance with the strongest effect was the conductance of the low-threshold fast Ca2+ current; its reduction increased the propensity index although the effect was about two times smaller in magnitude. Analyzing the model with both changes applied simultaneously, we found that the diagram (gleak, Eleak showed a progressively expanded area of bistability of bursting and silence.

Bistable traveling waves for a competitive-cooperative system with nonlocal delays

Science.gov (United States)

Tian, Yanling; Zhao, Xiao-Qiang

2018-04-01

This paper is devoted to the study of bistable traveling waves for a competitive-cooperative reaction and diffusion system with nonlocal time delays. The existence of bistable waves is established by appealing to the theory of monotone semiflows and the finite-delay approximations. Then the global stability of such traveling waves is obtained via a squeezing technique and a dynamical systems approach.

Bistability induces episodic spike communication by inhibitory neurons in neuronal networks.

Science.gov (United States)

Kazantsev, V B; Asatryan, S Yu

2011-09-01

Bistability is one of the important features of nonlinear dynamical systems. In neurodynamics, bistability has been found in basic Hodgkin-Huxley equations describing the cell membrane dynamics. When the neuron is clamped near its threshold, the stable rest potential may coexist with the stable limit cycle describing periodic spiking. However, this effect is often neglected in network computations where the neurons are typically reduced to threshold firing units (e.g., integrate-and-fire models). We found that the bistability may induce spike communication by inhibitory coupled neurons in the spiking network. The communication is realized in the form of episodic discharges with synchronous (correlated) spikes during the episodes. A spiking phase map is constructed to describe the synchronization and to estimate basic spike phase locking modes.

Dynamics of interface in three-dimensional anisotropic bistable reaction-diffusion system

International Nuclear Information System (INIS)

He Zhizhu; Liu, Jing

2010-01-01

This paper presents a theoretical investigation of dynamics of interface (wave front) in three-dimensional (3D) reaction-diffusion (RD) system for bistable media with anisotropy constructed by means of anisotropic surface tension. An equation of motion for the wave front is derived to carry out stability analysis of transverse perturbations, which discloses mechanism of pattern formation such as labyrinthine in 3D bistable media. Particularly, the effects of anisotropy on wave propagation are studied. It was found that, sufficiently strong anisotropy can induce dynamical instabilities and lead to breakup of the wave front. With the fast-inhibitor limit, the bistable system can further be described by a variational dynamics so that the boundary integral method is adopted to study the dynamics of wave fronts.

Excitonic optical bistability in n-type doped semiconductors

International Nuclear Information System (INIS)

Nguyen Ba An; Le Thi Cat Tuong

1991-07-01

A resonant monochromatic pump laser generates coherent excitons in an n-type doped semiconductor. Both exciton-exciton and exciton-donor interactions come into play. The former interaction can give rise to the appearance of optical bistability which is heavily influenced by the latter one. When optical bistability occurs at a fixed laser frequency both its holding intensity and hysteresis loop size are shown to decrease with increasing donor concentration. Two possibilities are suggested for experimentally determining one of the two parameters of the system - the exciton-donor coupling constant and the donor concentration, if the other parameter is known beforehand. (author). 36 refs, 2 figs

Bistability Analysis of Excitatory-Inhibitory Neural Networks in Limited-Sustained-Activity Regime

International Nuclear Information System (INIS)

Ni Yun; Wu Liang; Wu Dan; Zhu Shiqun

2011-01-01

Bistable behavior of neuronal complex networks is investigated in the limited-sustained-activity regime when the network is composed of excitatory and inhibitory neurons. The standard stability analysis is performed on the two metastable states separately. Both theoretical analysis and numerical simulations show consistently that the difference between time scales of excitatory and inhibitory populations can influence the dynamical behaviors of the neuronal networks dramatically, leading to the transition from bistable behaviors with memory effects to the collapse of bistable behaviors. These results may suggest one possible neuronal information processing by only tuning time scales. (interdisciplinary physics and related areas of science and technology)

High-resolution bistable nematic liquid crystal device realized on orientational surface patterns

International Nuclear Information System (INIS)

Kim, Jong-Hyun; Yoneya, Makoto; Yokoyama, Hiroshi

2003-01-01

The four-fold symmetry of a checkerboard-like surface alignment consisted of square domains arrived at the macroscopic orientational bistability of nematic liquid crystals. Switching between the two orientations took place with an appropriate electric field. Here the threshold field of bistable switching decreased as temperature increased, and the light could heat only the selected region in the cell including a light-absorbing medium. Irradiating the laser concurrently with an electric field, we addressed a selected region in the alignment pattern without the disturbance of neighboring regions. Extending this process, we realized an extremely fine bistable device of nematic liquid crystal with a pixel size down to about 2 μm

Microscopic observation of zenithal bistable switching in nematic devices with different surface relief structures

International Nuclear Information System (INIS)

Uche, C; Elston, S J; Parry-Jones, L A

2005-01-01

Nematic liquid crystals have been shown to exhibit zenithal electro-optic bistability in devices containing sinusoidal and deformed sinusoidal gratings. Recently it has been shown that zenithal bistable states can also be supported at isolated edges of square gratings. In this paper, we present microscopic observations of bistability in cells containing sinusoidal gratings and long-pitch square gratings. We have also investigated a novel display based on square wells. High frame-rate video microscopy was used to obtain time-sequenced images when the devices were switched with monopolar pulses. These show that zenithal bistable switching can occur by two different processes: (i) domain growth (observed in cells containing sinusoidal gratings) and (ii) homogenous switching (observed in cells containing isolated edges

Reversibly Bistable Flexible Electronics

KAUST Repository

Alfaraj, Nasir

2015-05-01

Introducing the notion of transformational silicon electronics has paved the way for integrating various applications with silicon-based, modern, high-performance electronic circuits that are mechanically flexible and optically semitransparent. While maintaining large-scale production and prototyping rapidity, this flexible and translucent scheme demonstrates the potential to transform conventionally stiff electronic devices into thin and foldable ones without compromising long-term performance and reliability. In this work, we report on the fabrication and characterization of reversibly bistable flexible electronic switches that utilize flexible n-channel metal-oxide-semiconductor field-effect transistors. The transistors are fabricated initially on rigid (100) silicon substrates before they are peeled off. They can be used to control flexible batches of light-emitting diodes, demonstrating both the relative ease of scaling at minimum cost and maximum reliability and the feasibility of integration. The peeled-off silicon fabric is about 25 µm thick. The fabricated devices are transferred to a reversibly bistable flexible platform through which, for example, a flexible smartphone can be wrapped around a user’s wrist and can also be set back to its original mechanical position. Buckling and cyclic bending of such host platforms brings a completely new dimension to the development of flexible electronics, especially rollable displays.

Identifying potential maternal genes of Bombyx mori using digital gene expression profiling

Science.gov (United States)

Xu, Pingzhen

2018-01-01

Maternal genes present in mature oocytes play a crucial role in the early development of silkworm. Although maternal genes have been widely studied in many other species, there has been limited research in Bombyx mori. High-throughput next generation sequencing provides a practical method for gene discovery on a genome-wide level. Herein, a transcriptome study was used to identify maternal-related genes from silkworm eggs. Unfertilized eggs from five different stages of early development were used to detect the changing situation of gene expression. The expressed genes showed different patterns over time. Seventy-six maternal genes were annotated according to homology analysis with Drosophila melanogaster. More than half of the differentially expressed maternal genes fell into four expression patterns, while the expression patterns showed a downward trend over time. The functional annotation of these material genes was mainly related to transcription factor activity, growth factor activity, nucleic acid binding, RNA binding, ATP binding, and ion binding. Additionally, twenty-two gene clusters including maternal genes were identified from 18 scaffolds. Altogether, we plotted a profile for the maternal genes of Bombyx mori using a digital gene expression profiling method. This will provide the basis for maternal-specific signature research and improve the understanding of the early development of silkworm. PMID:29462160

Flexible Bistable Cholesteric Reflective Displays

Science.gov (United States)

Yang, Deng-Ke

2006-03-01

Cholesteric liquid crystals (ChLCs) exhibit two stable states at zero field condition-the reflecting planar state and the nonreflecting focal conic state. ChLCs are an excellent candidate for inexpensive and rugged electronic books and papers. This paper will review the display cell structure,materials and drive schemes for flexible bistable cholesteric (Ch) reflective displays.

Time-Course Gene Set Analysis for Longitudinal Gene Expression Data.

Directory of Open Access Journals (Sweden)

Boris P Hejblum

2015-06-01

Full Text Available Gene set analysis methods, which consider predefined groups of genes in the analysis of genomic data, have been successfully applied for analyzing gene expression data in cross-sectional studies. The time-course gene set analysis (TcGSA introduced here is an extension of gene set analysis to longitudinal data. The proposed method relies on random effects modeling with maximum likelihood estimates. It allows to use all available repeated measurements while dealing with unbalanced data due to missing at random (MAR measurements. TcGSA is a hypothesis driven method that identifies a priori defined gene sets with significant expression variations over time, taking into account the potential heterogeneity of expression within gene sets. When biological conditions are compared, the method indicates if the time patterns of gene sets significantly differ according to these conditions. The interest of the method is illustrated by its application to two real life datasets: an HIV therapeutic vaccine trial (DALIA-1 trial, and data from a recent study on influenza and pneumococcal vaccines. In the DALIA-1 trial TcGSA revealed a significant change in gene expression over time within 69 gene sets during vaccination, while a standard univariate individual gene analysis corrected for multiple testing as well as a standard a Gene Set Enrichment Analysis (GSEA for time series both failed to detect any significant pattern change over time. When applied to the second illustrative data set, TcGSA allowed the identification of 4 gene sets finally found to be linked with the influenza vaccine too although they were found to be associated to the pneumococcal vaccine only in previous analyses. In our simulation study TcGSA exhibits good statistical properties, and an increased power compared to other approaches for analyzing time-course expression patterns of gene sets. The method is made available for the community through an R package.

All-optical bistable logic control based on coupled Tamm plasmons.

Science.gov (United States)

Zhang, Wei Li; Jiang, Yao; Zhu, Ye Yu; Wang, Fen; Rao, Yun Jiang

2013-10-15

A method for realizing low-threshold all-optical bistable logic control is proposed based on Tamm plasmons (TPs), which are formed in an asymmetric dielectric Bragg reflector (DBR)-metal-DBR (ADMD) structure with a layer of Kerr medium embedded. The ADMD structure supports two TPs due to coupling of trapped modes at each metal-DBR interface, generating two dips in the structure's reflection spectrum. Thus, control (i.e., pump) and controlled (i.e., probe) light with wavelengths close to the two dips, respectively, can be imported. It is verified theoretically that, thanks to the enhanced Kerr nonlinearity related to excitation of high-quality TP, bistable switching at very low injection intensity can be initiated by strength or direction variation of the pump. Meanwhile, the probe changes correspondingly with the pump. Thus, all-optical bistable logic operation of the probe can be controlled by the pump.

Low-threshold optical bistability with multilayer graphene-covering Otto configuration

International Nuclear Information System (INIS)

Wang, Hengliang; Wu, Jipeng; Xiang, Yuanjiang; Wen, Shuangchun; Guo, Jun; Jiang, Leyong

2016-01-01

In this paper, we propose a modified Otto configuration to realize tunable and low-threshold optical bistability at terahertz frequencies by attaching multilayer graphene sheets to a nonlinear substrate interface. Our work demonstrates that the threshold of optical bistability can be markedly reduced (three orders of magnitude) by covering the nonlinear substrate with multilayer graphene sheets, due to strong local field enhancement with the excitation of surface plasmons. We present the influences of the Fermi energy of graphene, the incident angle, the thickness of air gap and the relaxation time of graphene on the hysteresis phenomenon and give a way to optimize the surface plasmon resonance, which will enable us to further lower the minimal power requirements for realizing optical bistability due to the strong interaction of light with graphene sheets. These results are promising for realization of terahertz optical switches, optical modulators and logical devices. (paper)

Innovative Energy Harvester Design Using Bistable Mechanism With Compensational Springs In Gravity Field

International Nuclear Information System (INIS)

Vysotskyi, Bogdan; Parrain, Fabien; Lefeuvre, Elie; Aubry, Denis; Gaucher, Philippe

2016-01-01

The purpose of the presented work is to introduce the novel design of electrostatic energy harvester using bistable mechanism with compensational springs in gravity field capable of providing the output of several μW under the excitation of extremely small amplitude (up to 0.2g) and low frequency (10-100Hz). Presented energy harvester uses the bistable hysteresis modification to achieve low-frequency low-amplitude sensibility. It was demonstrated with finite element modelling (FEM) that hysteresis width produced by bistability is changing with a constant linear coefficient as a function of a compensational spring stiffness and thus a device sensitivity could be adjusted to the minimum point for the amplitude of external excitation. Further, highly non-linear bistable double curved beam mechanism assures the high sensitivity in frequencial domain due to the non-defined bandwidth. The equivalent circuit technique is used for simulating the device performance. (paper)

Conditional bistability, a generic cellular mnemonic mechanism for robust and flexible working memory computations.

Science.gov (United States)

Rodriguez, Guillaume; Sarazin, Matthieu; Clemente, Alexandra; Holden, Stephanie; Paz, Jeanne T; Delord, Bruno

2018-04-30

Persistent neural activity, the substrate of working memory, is thought to emerge from synaptic reverberation within recurrent networks. However, reverberation models do not robustly explain fundamental dynamics of persistent activity, including high-spiking irregularity, large intertrial variability, and state transitions. While cellular bistability may contribute to persistent activity, its rigidity appears incompatible with persistent activity labile characteristics. Here, we unravel in a cellular model a form of spike-mediated conditional bistability that is robust, generic and provides a rich repertoire of mnemonic computations. Under asynchronous synaptic inputs of the awakened state, conditional bistability generates spiking/bursting episodes, accounting for the irregularity, variability and state transitions characterizing persistent activity. This mechanism has likely been overlooked because of the sub-threshold input it requires and we predict how to assess it experimentally. Our results suggest a reexamination of the role of intrinsic properties in the collective network dynamics responsible for flexible working memory. SIGNIFICANCE STATEMENT This study unravels a novel form of intrinsic neuronal property, i.e. conditional bistability. We show that, thanks of its conditional character, conditional bistability favors the emergence of flexible and robust forms of persistent activity in PFC neural networks, in opposition to previously studied classical forms of absolute bistability. Specifically, we demonstrate for the first time that conditional bistability 1) is a generic biophysical spike-dependent mechanism of layer V pyramidal neurons in the PFC and that 2) it accounts for essential neurodynamical features for the organisation and flexibility of PFC persistent activity (the large irregularity and intertrial variability of the discharge and its organization under discrete stable states), which remain unexplained in a robust fashion by current models

The rules of gene expression in plants: Organ identity and gene body methylation are key factors for regulation of gene expression in Arabidopsis thaliana

Directory of Open Access Journals (Sweden)

Gutiérrez Rodrigo A

2008-09-01

Full Text Available Abstract Background Microarray technology is a widely used approach for monitoring genome-wide gene expression. For Arabidopsis, there are over 1,800 microarray hybridizations representing many different experimental conditions on Affymetrix™ ATH1 gene chips alone. This huge amount of data offers a unique opportunity to infer the principles that govern the regulation of gene expression in plants. Results We used bioinformatics methods to analyze publicly available data obtained using the ATH1 chip from Affymetrix. A total of 1887 ATH1 hybridizations were normalized and filtered to eliminate low-quality hybridizations. We classified and compared control and treatment hybridizations and determined differential gene expression. The largest differences in gene expression were observed when comparing samples obtained from different organs. On average, ten-fold more genes were differentially expressed between organs as compared to any other experimental variable. We defined "gene responsiveness" as the number of comparisons in which a gene changed its expression significantly. We defined genes with the highest and lowest responsiveness levels as hypervariable and housekeeping genes, respectively. Remarkably, housekeeping genes were best distinguished from hypervariable genes by differences in methylation status in their transcribed regions. Moreover, methylation in the transcribed region was inversely correlated (R2 = 0.8 with gene responsiveness on a genome-wide scale. We provide an example of this negative relationship using genes encoding TCA cycle enzymes, by contrasting their regulatory responsiveness to nitrate and methylation status in their transcribed regions. Conclusion Our results indicate that the Arabidopsis transcriptome is largely established during development and is comparatively stable when faced with external perturbations. We suggest a novel functional role for DNA methylation in the transcribed region as a key determinant

The functional landscape of mouse gene expression

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Zhang Wen

2004-12-01

Full Text Available Abstract Background Large-scale quantitative analysis of transcriptional co-expression has been used to dissect regulatory networks and to predict the functions of new genes discovered by genome sequencing in model organisms such as yeast. Although the idea that tissue-specific expression is indicative of gene function in mammals is widely accepted, it has not been objectively tested nor compared with the related but distinct strategy of correlating gene co-expression as a means to predict gene function. Results We generated microarray expression data for nearly 40,000 known and predicted mRNAs in 55 mouse tissues, using custom-built oligonucleotide arrays. We show that quantitative transcriptional co-expression is a powerful predictor of gene function. Hundreds of functional categories, as defined by Gene Ontology 'Biological Processes', are associated with characteristic expression patterns across all tissues, including categories that bear no overt relationship to the tissue of origin. In contrast, simple tissue-specific restriction of expression is a poor predictor of which genes are in which functional categories. As an example, the highly conserved mouse gene PWP1 is widely expressed across different tissues but is co-expressed with many RNA-processing genes; we show that the uncharacterized yeast homolog of PWP1 is required for rRNA biogenesis. Conclusions We conclude that 'functional genomics' strategies based on quantitative transcriptional co-expression will be as fruitful in mammals as they have been in simpler organisms, and that transcriptional control of mammalian physiology is more modular than is generally appreciated. Our data and analyses provide a public resource for mammalian functional genomics.

Expression of Sox genes in tooth development.

Science.gov (United States)

Kawasaki, Katsushige; Kawasaki, Maiko; Watanabe, Momoko; Idrus, Erik; Nagai, Takahiro; Oommen, Shelly; Maeda, Takeyasu; Hagiwara, Nobuko; Que, Jianwen; Sharpe, Paul T; Ohazama, Atsushi

2015-01-01

Members of the Sox gene family play roles in many biological processes including organogenesis. We carried out comparative in situ hybridization analysis of seventeen sox genes (Sox1-14, 17, 18, 21) during murine odontogenesis from the epithelial thickening to the cytodifferentiation stages. Localized expression of five Sox genes (Sox6, 9, 13, 14 and 21) was observed in tooth bud epithelium. Sox13 showed restricted expression in the primary enamel knots. At the early bell stage, three Sox genes (Sox8, 11, 17 and 21) were expressed in pre-ameloblasts, whereas two others (Sox5 and 18) showed expression in odontoblasts. Sox genes thus showed a dynamic spatio-temporal expression during tooth development.

Bistable optical response of a nanoparticle heterodimer : Mechanism, phase diagram, and switching time

NARCIS (Netherlands)

Nugroho, Bintoro; Iskandar, Alexander; Malyshev, V.A.; Knoester, Jasper

2013-01-01

We conduct a theoretical study of the bistable optical response of a nanoparticle heterodimer comprised of a closely spaced semiconductor quantum dot and a metal nanoparticle. The bistable nature of the response results from the interplay between the quantum dot's optical nonlinearity and its

Possible hysteresis loops of resonatorless optical bistability

International Nuclear Information System (INIS)

Nguyen Ba An; Le Thi Cat Tuong.

1990-05-01

We qualitatively show that hysteresis loops of intrinsic optical bistability phenomena without any additional feedback may be of various shapes including those of a butterfly and a three-winged bow. (author). 15 refs, 4 figs

Profiling Gene Expression in Germinating Brassica Roots.

Science.gov (United States)

Park, Myoung Ryoul; Wang, Yi-Hong; Hasenstein, Karl H

2014-01-01

Based on previously developed solid-phase gene extraction (SPGE) we examined the mRNA profile in primary roots of Brassica rapa seedlings for highly expressed genes like ACT7 (actin7), TUB (tubulin1), UBQ (ubiquitin), and low expressed GLK (glucokinase) during the first day post-germination. The assessment was based on the mRNA load of the SPGE probe of about 2.1 ng. The number of copies of the investigated genes changed spatially along the length of primary roots. The expression level of all genes differed significantly at each sample position. Among the examined genes ACT7 expression was most even along the root. UBQ was highest at the tip and root-shoot junction (RS). TUB and GLK showed a basipetal gradient. The temporal expression of UBQ was highest in the MZ 9 h after primary root emergence and higher than at any other sample position. Expressions of GLK in EZ and RS increased gradually over time. SPGE extraction is the result of oligo-dT and oligo-dA hybridization and the results illustrate that SPGE can be used for gene expression profiling at high spatial and temporal resolution. SPGE needles can be used within two weeks when stored at 4 °C. Our data indicate that gene expression studies that are based on the entire root miss important differences in gene expression that SPGE is able to resolve for example growth adjustments during gravitropism.

Optical nonlinearity and bistability in the bound exciton energy range of CdS

International Nuclear Information System (INIS)

Hoenig, T.; Gutowski, J.

1988-01-01

Under high excitation conditions thick CdS samples show pronounced broad-band nonlinear transmission in the bound exciton region and up to a wavelength of about 515 nm at cryo-temperatures. This behavior is only explainable in a model based on impurity neutralization and bound exciton creation. The suitability of these nonlinearities to yield optical bistability will be shown. Bistable operation is investigated in dependence of crystal thickness, impurity concentration, excitation density, wavelength, and temperature. A strong correlation to acceptor-bound exciton generation is obtained, and the explanation of this bistable operation fits well with that of the above mentioned transmission behavior. (author)

Unstable Expression of Commonly Used Reference Genes in Rat Pancreatic Islets Early after Isolation Affects Results of Gene Expression Studies.

Directory of Open Access Journals (Sweden)

Lucie Kosinová

Full Text Available The use of RT-qPCR provides a powerful tool for gene expression studies; however, the proper interpretation of the obtained data is crucially dependent on accurate normalization based on stable reference genes. Recently, strong evidence has been shown indicating that the expression of many commonly used reference genes may vary significantly due to diverse experimental conditions. The isolation of pancreatic islets is a complicated procedure which creates severe mechanical and metabolic stress leading possibly to cellular damage and alteration of gene expression. Despite of this, freshly isolated islets frequently serve as a control in various gene expression and intervention studies. The aim of our study was to determine expression of 16 candidate reference genes and one gene of interest (F3 in isolated rat pancreatic islets during short-term cultivation in order to find a suitable endogenous control for gene expression studies. We compared the expression stability of the most commonly used reference genes and evaluated the reliability of relative and absolute quantification using RT-qPCR during 0-120 hrs after isolation. In freshly isolated islets, the expression of all tested genes was markedly depressed and it increased several times throughout the first 48 hrs of cultivation. We observed significant variability among samples at 0 and 24 hrs but substantial stabilization from 48 hrs onwards. During the first 48 hrs, relative quantification failed to reflect the real changes in respective mRNA concentrations while in the interval 48-120 hrs, the relative expression generally paralleled the results determined by absolute quantification. Thus, our data call into question the suitability of relative quantification for gene expression analysis in pancreatic islets during the first 48 hrs of cultivation, as the results may be significantly affected by unstable expression of reference genes. However, this method could provide reliable information

Comprehensive analysis of gene expression patterns of hedgehog-related genes

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Baillie David

2006-10-01

Full Text Available Abstract Background The Caenorhabditis elegans genome encodes ten proteins that share sequence similarity with the Hedgehog signaling molecule through their C-terminal autoprocessing Hint/Hog domain. These proteins contain novel N-terminal domains, and C. elegans encodes dozens of additional proteins containing only these N-terminal domains. These gene families are called warthog, groundhog, ground-like and quahog, collectively called hedgehog (hh-related genes. Previously, the expression pattern of seventeen genes was examined, which showed that they are primarily expressed in the ectoderm. Results With the completion of the C. elegans genome sequence in November 2002, we reexamined and identified 61 hh-related ORFs. Further, we identified 49 hh-related ORFs in C. briggsae. ORF analysis revealed that 30% of the genes still had errors in their predictions and we improved these predictions here. We performed a comprehensive expression analysis using GFP fusions of the putative intergenic regulatory sequence with one or two transgenic lines for most genes. The hh-related genes are expressed in one or a few of the following tissues: hypodermis, seam cells, excretory duct and pore cells, vulval epithelial cells, rectal epithelial cells, pharyngeal muscle or marginal cells, arcade cells, support cells of sensory organs, and neuronal cells. Using time-lapse recordings, we discovered that some hh-related genes are expressed in a cyclical fashion in phase with molting during larval development. We also generated several translational GFP fusions, but they did not show any subcellular localization. In addition, we also studied the expression patterns of two genes with similarity to Drosophila frizzled, T23D8.1 and F27E11.3A, and the ortholog of the Drosophila gene dally-like, gpn-1, which is a heparan sulfate proteoglycan. The two frizzled homologs are expressed in a few neurons in the head, and gpn-1 is expressed in the pharynx. Finally, we compare the

Simple Comparative Analyses of Differentially Expressed Gene Lists May Overestimate Gene Overlap.

Science.gov (United States)

Lawhorn, Chelsea M; Schomaker, Rachel; Rowell, Jonathan T; Rueppell, Olav

2018-04-16

Comparing the overlap between sets of differentially expressed genes (DEGs) within or between transcriptome studies is regularly used to infer similarities between biological processes. Significant overlap between two sets of DEGs is usually determined by a simple test. The number of potentially overlapping genes is compared to the number of genes that actually occur in both lists, treating every gene as equal. However, gene expression is controlled by transcription factors that bind to a variable number of transcription factor binding sites, leading to variation among genes in general variability of their expression. Neglecting this variability could therefore lead to inflated estimates of significant overlap between DEG lists. With computer simulations, we demonstrate that such biases arise from variation in the control of gene expression. Significant overlap commonly arises between two lists of DEGs that are randomly generated, assuming that the control of gene expression is variable among genes but consistent between corresponding experiments. More overlap is observed when transcription factors are specific to their binding sites and when the number of genes is considerably higher than the number of different transcription factors. In contrast, overlap between two DEG lists is always lower than expected when the genetic architecture of expression is independent between the two experiments. Thus, the current methods for determining significant overlap between DEGs are potentially confounding biologically meaningful overlap with overlap that arises due to variability in control of expression among genes, and more sophisticated approaches are needed.

Parallel replica dynamics method for bistable stochastic reaction networks: Simulation and sensitivity analysis

Science.gov (United States)

Wang, Ting; Plecháč, Petr

2017-12-01

Stochastic reaction networks that exhibit bistable behavior are common in systems biology, materials science, and catalysis. Sampling of stationary distributions is crucial for understanding and characterizing the long-time dynamics of bistable stochastic dynamical systems. However, simulations are often hindered by the insufficient sampling of rare transitions between the two metastable regions. In this paper, we apply the parallel replica method for a continuous time Markov chain in order to improve sampling of the stationary distribution in bistable stochastic reaction networks. The proposed method uses parallel computing to accelerate the sampling of rare transitions. Furthermore, it can be combined with the path-space information bounds for parametric sensitivity analysis. With the proposed methodology, we study three bistable biological networks: the Schlögl model, the genetic switch network, and the enzymatic futile cycle network. We demonstrate the algorithmic speedup achieved in these numerical benchmarks. More significant acceleration is expected when multi-core or graphics processing unit computer architectures and programming tools such as CUDA are employed.

Flexible Bistable Smectic-A Liquid Crystal Device Using Photolithography and Photoinduced Phase Separation

Directory of Open Access Journals (Sweden)

Yang Lu

2012-01-01

Full Text Available A flexible bistable smectic-A liquid crystal (SmA LC device using pixel-isolated mode was demonstrated, in which SmA LC molecules were isolated in pixels by vertical polymer wall and horizontal polymer layer. The above microstructure was achieved by using ultraviolet (UV photolithography and photoinduced phase separation. The polymer wall was fabricated by photolithography, and then the SmA LC was encapsulated in pixels between polymer wall through UV-induced phase separation, in which the polymer wall acts as supporting structure from mechanical pressure and maintains the cell gap from bending, and the polymer layer acts as adhesive for tight attachment of two substrates. The results demonstrated that all the intrinsic bistable properties of the SmA LC are preserved, and good electrooptical characteristics such as high contrast ratio and excellent stability of the bistable states were characterized. This kind of SmA bistable flexible display has high potential to be used as electronic paper, smart switchable reflective windows, and so forth.

Parallel replica dynamics method for bistable stochastic reaction networks: Simulation and sensitivity analysis.

Science.gov (United States)

Wang, Ting; Plecháč, Petr

2017-12-21

Stochastic reaction networks that exhibit bistable behavior are common in systems biology, materials science, and catalysis. Sampling of stationary distributions is crucial for understanding and characterizing the long-time dynamics of bistable stochastic dynamical systems. However, simulations are often hindered by the insufficient sampling of rare transitions between the two metastable regions. In this paper, we apply the parallel replica method for a continuous time Markov chain in order to improve sampling of the stationary distribution in bistable stochastic reaction networks. The proposed method uses parallel computing to accelerate the sampling of rare transitions. Furthermore, it can be combined with the path-space information bounds for parametric sensitivity analysis. With the proposed methodology, we study three bistable biological networks: the Schlögl model, the genetic switch network, and the enzymatic futile cycle network. We demonstrate the algorithmic speedup achieved in these numerical benchmarks. More significant acceleration is expected when multi-core or graphics processing unit computer architectures and programming tools such as CUDA are employed.

Methods for monitoring multiple gene expression

Energy Technology Data Exchange (ETDEWEB)

Berka, Randy [Davis, CA; Bachkirova, Elena [Davis, CA; Rey, Michael [Davis, CA

2012-05-01

The present invention relates to methods for monitoring differential expression of a plurality of genes in a first filamentous fungal cell relative to expression of the same genes in one or more second filamentous fungal cells using microarrays containing Trichoderma reesei ESTs or SSH clones, or a combination thereof. The present invention also relates to computer readable media and substrates containing such array features for monitoring expression of a plurality of genes in filamentous fungal cells.

Methods for monitoring multiple gene expression

Energy Technology Data Exchange (ETDEWEB)

Berka, Randy; Bachkirova, Elena; Rey, Michael

2013-10-01

The present invention relates to methods for monitoring differential expression of a plurality of genes in a first filamentous fungal cell relative to expression of the same genes in one or more second filamentous fungal cells using microarrays containing Trichoderma reesei ESTs or SSH clones, or a combination thereof. The present invention also relates to computer readable media and substrates containing such array features for monitoring expression of a plurality of genes in filamentous fungal cells.

Bistable flapping of flexible flyers in oscillatory flow

Science.gov (United States)

Huang, Yangyang; Kanso, Eva

2016-11-01

Biological and bio-inspired flyers move by shape actuation. The direct control of shape variables for locomotory purposes is well studied. Less is known about indirect shape actuation via the fluid medium. Here, we consider a flexible Λ-flyer in oscillatory flow that is free to flap and rotate around its fixed apex. We study its motion in the context of the inviscid vortex sheet model. We first analyze symmetric flapping about the vertical axis of gravity. We find that there is a finite value of the flexibility that maximizes both the flapping amplitude and elastic energy storage. Our results show that rather than resonance, the flyer relies on fluidic effects to optimize these two quantities. We then perturb the flyer away from the vertical and analyze its stability. Four distinct types of rolling behavior are identified: mono-stable, bistable, bistable oscillatory rotations and chaotic dynamics. We categorize these types of behavior in terms of the flyer's and flow parameters. In particular, the transition from mono-stable to bistable behavior occurs at a constant value of the product of the flow amplitude and acceleration. This product can be interpreted as the ratio of fluidic drag to gravity, confirming the fluid role in this transition.

Brain mechanisms for simple perception and bistable perception.

Science.gov (United States)

Wang, Megan; Arteaga, Daniel; He, Biyu J

2013-08-27

When faced with ambiguous sensory inputs, subjective perception alternates between the different interpretations in a stochastic manner. Such multistable perception phenomena have intrigued scientists and laymen alike for over a century. Despite rigorous investigations, the underlying mechanisms of multistable perception remain elusive. Recent studies using multivariate pattern analysis revealed that activity patterns in posterior visual areas correlate with fluctuating percepts. However, increasing evidence suggests that vision--and perception at large--is an active inferential process involving hierarchical brain systems. We applied searchlight multivariate pattern analysis to functional magnetic resonance imaging signals across the human brain to decode perceptual content during bistable perception and simple unambiguous perception. Although perceptually reflective activity patterns during simple perception localized predominantly to posterior visual regions, bistable perception involved additionally many higher-order frontoparietal and temporal regions. Moreover, compared with simple perception, both top-down and bottom-up influences were dramatically enhanced during bistable perception. We further studied the intermittent presentation of ambiguous images--a condition that is known to elicit perceptual memory. Compared with continuous presentation, intermittent presentation recruited even more higher-order regions and was accompanied by further strengthened top-down influences but relatively weakened bottom-up influences. Taken together, these results strongly support an active top-down inferential process in perception.

Determinants of human adipose tissue gene expression

DEFF Research Database (Denmark)

Viguerie, Nathalie; Montastier, Emilie; Maoret, Jean-José

2012-01-01

weight maintenance diets. For 175 genes, opposite regulation was observed during calorie restriction and weight maintenance phases, independently of variations in body weight. Metabolism and immunity genes showed inverse profiles. During the dietary intervention, network-based analyses revealed strong...... interconnection between expression of genes involved in de novo lipogenesis and components of the metabolic syndrome. Sex had a marked influence on AT expression of 88 transcripts, which persisted during the entire dietary intervention and after control for fat mass. In women, the influence of body mass index...... on expression of a subset of genes persisted during the dietary intervention. Twenty-two genes revealed a metabolic syndrome signature common to men and women. Genetic control of AT gene expression by cis signals was observed for 46 genes. Dietary intervention, sex, and cis genetic variants independently...

LINE FUSION GENES: a database of LINE expression in human genes

Directory of Open Access Journals (Sweden)

Park Hong-Seog

2006-06-01

Full Text Available Abstract Background Long Interspersed Nuclear Elements (LINEs are the most abundant retrotransposons in humans. About 79% of human genes are estimated to contain at least one segment of LINE per transcription unit. Recent studies have shown that LINE elements can affect protein sequences, splicing patterns and expression of human genes. Description We have developed a database, LINE FUSION GENES, for elucidating LINE expression throughout the human gene database. We searched the 28,171 genes listed in the NCBI database for LINE elements and analyzed their structures and expression patterns. The results show that the mRNA sequences of 1,329 genes were affected by LINE expression. The LINE expression types were classified on the basis of LINEs in the 5' UTR, exon or 3' UTR sequences of the mRNAs. Our database provides further information, such as the tissue distribution and chromosomal location of the genes, and the domain structure that is changed by LINE integration. We have linked all the accession numbers to the NCBI data bank to provide mRNA sequences for subsequent users. Conclusion We believe that our work will interest genome scientists and might help them to gain insight into the implications of LINE expression for human evolution and disease. Availability http://www.primate.or.kr/line

Metastable and bistable defects in silicon

International Nuclear Information System (INIS)

Mukashev, Bulat N; Abdullin, Kh A; Gorelkinskii, Yurii V

2000-01-01

Existing data on the properties and structure of metastable and bistable defects in silicon are analyzed. Primary radiation-induced defects (vacancies, self-interstitial atoms, and Frenkel pairs), complexes of oxygen, carbon, hydrogen, and other impurity atoms and defects with negative correlation energy are considered. (reviews of topical problems)

Global expression differences and tissue specific expression differences in rice evolution result in two contrasting types of differentially expressed genes

KAUST Repository

Horiuchi, Youko

2015-12-23

Background Since the development of transcriptome analysis systems, many expression evolution studies characterized evolutionary forces acting on gene expression, without explicit discrimination between global expression differences and tissue specific expression differences. However, different types of gene expression alteration should have different effects on an organism, the evolutionary forces that act on them might be different, and different types of genes might show different types of differential expression between species. To confirm this, we studied differentially expressed (DE) genes among closely related groups that have extensive gene expression atlases, and clarified characteristics of different types of DE genes including the identification of regulating loci for differential expression using expression quantitative loci (eQTL) analysis data. Results We detected differentially expressed (DE) genes between rice subspecies in five homologous tissues that were verified using japonica and indica transcriptome atlases in public databases. Using the transcriptome atlases, we classified DE genes into two types, global DE genes and changed-tissues DE genes. Global type DE genes were not expressed in any tissues in the atlas of one subspecies, however changed-tissues type DE genes were expressed in both subspecies with different tissue specificity. For the five tissues in the two japonica-indica combinations, 4.6 ± 0.8 and 5.9 ± 1.5 % of highly expressed genes were global and changed-tissues DE genes, respectively. Changed-tissues DE genes varied in number between tissues, increasing linearly with the abundance of tissue specifically expressed genes in the tissue. Molecular evolution of global DE genes was rapid, unlike that of changed-tissues DE genes. Based on gene ontology, global and changed-tissues DE genes were different, having no common GO terms. Expression differences of most global DE genes were regulated by cis-eQTLs. Expression

Social Regulation of Gene Expression in Threespine Sticklebacks.

Directory of Open Access Journals (Sweden)

Anna K Greenwood

Full Text Available Identifying genes that are differentially expressed in response to social interactions is informative for understanding the molecular basis of social behavior. To address this question, we described changes in gene expression as a result of differences in the extent of social interactions. We housed threespine stickleback (Gasterosteus aculeatus females in either group conditions or individually for one week, then measured levels of gene expression in three brain regions using RNA-sequencing. We found that numerous genes in the hindbrain/cerebellum had altered expression in response to group or individual housing. However, relatively few genes were differentially expressed in either the diencephalon or telencephalon. The list of genes upregulated in fish from social groups included many genes related to neural development and cell adhesion as well as genes with functions in sensory signaling, stress, and social and reproductive behavior. The list of genes expressed at higher levels in individually-housed fish included several genes previously identified as regulated by social interactions in other animals. The identified genes are interesting targets for future research on the molecular mechanisms of normal social interactions.

Controlling steady-state and dynamical properties of atomic optical bistability

CERN Document Server

Joshi, Amitabh

2012-01-01

This book provides a comprehensive introduction to the theoretical and experimental studies of atomic optical bistability and multistability, and their dynamical properties in systems with two- and three-level inhomogeneously-broadened atoms inside an optical cavity. By making use of the modified linear absorption and dispersion, as well as the greatly enhanced nonlinearity in the three-level electromagnetically induced transparency system, the optical bistablity and efficient all-optical switching can be achieved at relatively low laser powers, which can be well controlled and manipulated. Un

A constructive approach to gene expression dynamics

International Nuclear Information System (INIS)

Ochiai, T.; Nacher, J.C.; Akutsu, T.

2004-01-01

Recently, experiments on mRNA abundance (gene expression) have revealed that gene expression shows a stationary organization described by a scale-free distribution. Here we propose a constructive approach to gene expression dynamics which restores the scale-free exponent and describes the intermediate state dynamics. This approach requires only one assumption: Markov property

Large Out-of-Plane Displacement Bistable Electromagnetic Microswitch on a Single Wafer.

Science.gov (United States)

Miao, Xiaodan; Dai, Xuhan; Huang, Yi; Ding, Guifu; Zhao, Xiaolin

2016-05-05

This paper presents a bistable microswitch fully batch-fabricated on a single glass wafer, comprising of a microactuator, a signal transformer, a microspring and a permanent magnet. The bistable mechanism of the microswitch with large displacement of 160 μm depends on the balance of the magnetic force and elastic force. Both the magnetic force and elastic force were optimized by finite-element simulation to predict the reliable of the device. The prototype was fabricated and characterized. By utilizing thick laminated photoresist sacrificial layer, the large displacement was obtained to ensure the insulation of the microswitch. The testing results show that the microswitch realized the bistable mechanism at a 3-5 V input voltage and closed in 0.96 ms, which verified the simulation.

Configurational rearrangements of bistable centers in covalent semiconductors - phase transitions of the second type

International Nuclear Information System (INIS)

Ivanyukovich, V.A.; Karas', V.I.; Lomako, V.M.

1989-01-01

A new radiation configurational-bistable defect diffring from the known similar defects by the fact that it possessestemperature inversion of states is detected in gallium arsenide. Configurational-bistable rearrangements are shown to be considered as phase transitions of the second type

Stably Expressed Genes Involved in Basic Cellular Functions.

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Kejian Wang

Full Text Available Stably Expressed Genes (SEGs whose expression varies within a narrow range may be involved in core cellular processes necessary for basic functions. To identify such genes, we re-analyzed existing RNA-Seq gene expression profiles across 11 organs at 4 developmental stages (from immature to old age in both sexes of F344 rats (n = 4/group; 320 samples. Expression changes (calculated as the maximum expression / minimum expression for each gene of >19000 genes across organs, ages, and sexes ranged from 2.35 to >109-fold, with a median of 165-fold. The expression of 278 SEGs was found to vary ≤4-fold and these genes were significantly involved in protein catabolism (proteasome and ubiquitination, RNA transport, protein processing, and the spliceosome. Such stability of expression was further validated in human samples where the expression variability of the homologous human SEGs was significantly lower than that of other genes in the human genome. It was also found that the homologous human SEGs were generally less subject to non-synonymous mutation than other genes, as would be expected of stably expressed genes. We also found that knockout of SEG homologs in mouse models was more likely to cause complete preweaning lethality than non-SEG homologs, corroborating the fundamental roles played by SEGs in biological development. Such stably expressed genes and pathways across life-stages suggest that tight control of these processes is important in basic cellular functions and that perturbation by endogenous (e.g., genetics or exogenous agents (e.g., drugs, environmental factors may cause serious adverse effects.

Lithium ions induce prestalk-associated gene expression and inhibit prespore gene expression in Dictyostelium discoideum

NARCIS (Netherlands)

Peters, Dorien J.M.; Lookeren Campagne, Michiel M. van; Haastert, Peter J.M. van; Spek, Wouter; Schaap, Pauline

1989-01-01

We investigated the effect of Li+ on two types of cyclic AMP-regulated gene expression and on basal and cyclic AMP-stimulated inositol 1,4,5-trisphosphate (Ins(1,4,5)P3) levels. Li+ effectively inhibits cyclic AMP-induced prespore gene expression, half-maximal inhibition occurring at about 2mM-LiCl.

MicroRNA-Mediated Positive Feedback Loop and Optimized Bistable Switch in a Cancer Network Involving miR-17-92

Science.gov (United States)

Li, Yichen; Li, Yumin; Zhang, Hui; Chen, Yong

2011-01-01

MicroRNAs (miRNAs) are small, noncoding RNAs that play an important role in many key biological processes, including development, cell differentiation, the cell cycle and apoptosis, as central post-transcriptional regulators of gene expression. Recent studies have shown that miRNAs can act as oncogenes and tumor suppressors depending on the context. The present work focuses on the physiological significance of miRNAs and their role in regulating the switching behavior. We illustrate an abstract model of the Myc/E2F/miR-17-92 network presented by Aguda et al. (2008), which is composed of coupling between the E2F/Myc positive feedback loops and the E2F/Myc/miR-17-92 negative feedback loop. By systematically analyzing the network in close association with plausible experimental parameters, we show that, in the presence of miRNAs, the system bistability emerges from the system, with a bistable switch and a one-way switch presented by Aguda et al. instead of a single one-way switch. Moreover, the miRNAs can optimize the switching process. The model produces a diverse array of response-signal behaviors in response to various potential regulating scenarios. The model predicts that this transition exists, one from cell death or the cancerous phenotype directly to cell quiescence, due to the existence of miRNAs. It was also found that the network involving miR-17-92 exhibits high noise sensitivity due to a positive feedback loop and also maintains resistance to noise from a negative feedback loop. PMID:22022595

Bistability, electric potentials and sensor behaviour in an enzymatic reaction system

International Nuclear Information System (INIS)

Malchow, H.; Felber, F.

1987-07-01

A special ionic enzyme kinetics in a continuously stirred flow reactor which is membrane coupled to a reservoir is considered starting from a general expression for the substrate dependence of enzymatic reaction rates including pH effects. Both bistability of the reaction and electric potentials between the interior and exterior of the reactor can be observed having regard to mass and charge conservation as well as global electroneutrality. The sudden jumps at critical concentration values from one stable solution branch to the other on a hysteresis loop are supposed to be the basic action principle of a non-equilibrium concentration threshold sensor. (author). 38 refs, 3 figs

Bistable diverter valve in microfluidics

Czech Academy of Sciences Publication Activity Database

Tesař, Václav; Bandulasena, H.C.H.

2011-01-01

Roč. 50, č. 5 (2011), s. 1225-1233 ISSN 0723-4864 R&D Projects: GA ČR GA101/07/1499; GA AV ČR IAA200760705 Institutional research plan: CEZ:AV0Z20760514 Keywords : fluidics * bistable diverter valves * pressure-driven microfluidics Subject RIV: BK - Fluid Dynamics Impact factor: 1.735, year: 2011 http://www.springerlink.com/content/x4907p1908151522/

Experimental chaotic quantification in bistable vortex induced vibration systems

Science.gov (United States)

Huynh, B. H.; Tjahjowidodo, T.

2017-02-01

The study of energy harvesting by means of vortex induced vibration systems has been initiated a few years ago and it is considered to be potential as a low water current energy source. The energy harvester is realized by exposing an elastically supported blunt structure under water flow. However, it is realized that the system will only perform at a limited operating range (water flow) that is attributed to the resonance phenomenon that occurs only at a frequency that corresponds to the fluid flow. An introduction of nonlinear elements seems to be a prominent solution to overcome the problem. Among many nonlinear elements, a bistable spring is known to be able to improve the harvested power by a vortex induced vibrations (VIV) based energy converter at the low velocity water flows. However, it is also observed that chaotic vibrations will occur at different operating ranges that will erratically diminish the harvested power and cause a difficulty in controlling the system that is due to the unpredictability in motions of the VIV structure. In order to design a bistable VIV energy converter with improved harvested power and minimum negative effect of chaotic vibrations, the bifurcation map of the system for varying governing parameters is highly on demand. In this study, chaotic vibrations of a VIV energy converter enhanced by a bistable stiffness element are quantified in a wide range of the governing parameters, i.e. damping and bistable gap. Chaotic vibrations of the bistable VIV energy converter are simulated by utilization of a wake oscillator model and quantified based on the calculation of the Lyapunov exponent. Ultimately, a series of experiments of the system in a water tunnel, facilitated by a computer-based force-feedback testing platform, is carried out to validate the existence of chaotic responses. The main challenge in dealing with experimental data is in distinguishing chaotic response from noise-contaminated periodic responses as noise will smear

Validation of commonly used reference genes for sleep-related gene expression studies

Directory of Open Access Journals (Sweden)

Castro Rosa MRPS

2009-05-01

Full Text Available Abstract Background Sleep is a restorative process and is essential for maintenance of mental and physical health. In an attempt to understand the complexity of sleep, multidisciplinary strategies, including genetic approaches, have been applied to sleep research. Although quantitative real time PCR has been used in previous sleep-related gene expression studies, proper validation of reference genes is currently lacking. Thus, we examined the effect of total or paradoxical sleep deprivation (TSD or PSD on the expression stability of the following frequently used reference genes in brain and blood: beta-actin (b-actin, beta-2-microglobulin (B2M, glyceraldehyde-3-phosphate dehydrogenase (GAPDH, and hypoxanthine guanine phosphoribosyl transferase (HPRT. Results Neither TSD nor PSD affected the expression stability of all tested genes in both tissues indicating that b-actin, B2M, GAPDH and HPRT are appropriate reference genes for the sleep-related gene expression studies. In order to further verify these results, the relative expression of brain derived neurotrophic factor (BDNF and glycerol-3-phosphate dehydrogenase1 (GPD1 was evaluated in brain and blood, respectively. The normalization with each of four reference genes produced similar pattern of expression in control and sleep deprived rats, but subtle differences in the magnitude of expression fold change were observed which might affect the statistical significance. Conclusion This study demonstrated that sleep deprivation does not alter the expression stability of commonly used reference genes in brain and blood. Nonetheless, the use of multiple reference genes in quantitative RT-PCR is required for the accurate results.

Stochastic gene expression in Arabidopsis thaliana.

Science.gov (United States)

Araújo, Ilka Schultheiß; Pietsch, Jessica Magdalena; Keizer, Emma Mathilde; Greese, Bettina; Balkunde, Rachappa; Fleck, Christian; Hülskamp, Martin

2017-12-14

Although plant development is highly reproducible, some stochasticity exists. This developmental stochasticity may be caused by noisy gene expression. Here we analyze the fluctuation of protein expression in Arabidopsis thaliana. Using the photoconvertible KikGR marker, we show that the protein expressions of individual cells fluctuate over time. A dual reporter system was used to study extrinsic and intrinsic noise of marker gene expression. We report that extrinsic noise is higher than intrinsic noise and that extrinsic noise in stomata is clearly lower in comparison to several other tissues/cell types. Finally, we show that cells are coupled with respect to stochastic protein expression in young leaves, hypocotyls and roots but not in mature leaves. Our data indicate that stochasticity of gene expression can vary between tissues/cell types and that it can be coupled in a non-cell-autonomous manner.

Plasmon-modulated bistable four-wave mixing signals from a metal nanoparticle-monolayer MoS2 nanoresonator hybrid system

Science.gov (United States)

Li, Jian-Bo; Tan, Xiao-Long; Ma, Jin-Hong; Xu, Si-Qin; Kuang, Zhi-Wei; Liang, Shan; Xiao, Si; He, Meng-Dong; Kim, Nam-Chol; Luo, Jian-Hua; Chen, Li-Qun

2018-06-01

We present a study for the impact of exciton-phonon and exciton-plasmon interactions on bistable four-wave mixing (FWM) signals in a metal nanoparticle (MNP)-monolayer MoS2 nanoresonator hybrid system. Via tracing the FWM response we predict that, depending on the excitation conditions and the system parameters, such a system exhibits ‘U-shaped’ bistable FWM signals. We also map out bistability phase diagrams within the system’s parameter space. Especially, we show that compared with the exciton-phonon interaction, a strong exciton-plasmon interaction plays a dominant role in the generation of optical bistability, and the bistable region will be greatly broadened by shortening the distance between the MNP and the monolayer MoS2 nanoresonator. In the weak exciton-plasmon coupling regime, the impact of exciton-phonon interaction on optical bistability will become obvious. The scheme proposed may be used for building optical switches and logic-gate devices for optical computing and quantum information processing.

Plasmon-modulated bistable four-wave mixing signals from a metal nanoparticle-monolayer MoS2 nanoresonator hybrid system.

Science.gov (United States)

Li, Jian-Bo; Tan, Xiao-Long; Ma, Jin-Hong; Xu, Si-Qin; Kuang, Zhi-Wei; Liang, Shan; Xiao, Si; He, Meng-Dong; Kim, Nam-Chol; Luo, Jian-Hua; Chen, Li-Qun

2018-06-22

We present a study for the impact of exciton-phonon and exciton-plasmon interactions on bistable four-wave mixing (FWM) signals in a metal nanoparticle (MNP)-monolayer MoS 2 nanoresonator hybrid system. Via tracing the FWM response we predict that, depending on the excitation conditions and the system parameters, such a system exhibits 'U-shaped' bistable FWM signals. We also map out bistability phase diagrams within the system's parameter space. Especially, we show that compared with the exciton-phonon interaction, a strong exciton-plasmon interaction plays a dominant role in the generation of optical bistability, and the bistable region will be greatly broadened by shortening the distance between the MNP and the monolayer MoS 2 nanoresonator. In the weak exciton-plasmon coupling regime, the impact of exciton-phonon interaction on optical bistability will become obvious. The scheme proposed may be used for building optical switches and logic-gate devices for optical computing and quantum information processing.

Deriving Trading Rules Using Gene Expression Programming

Directory of Open Access Journals (Sweden)

Adrian VISOIU

2011-01-01

Full Text Available This paper presents how buy and sell trading rules are generated using gene expression programming with special setup. Market concepts are presented and market analysis is discussed with emphasis on technical analysis and quantitative methods. The use of genetic algorithms in deriving trading rules is presented. Gene expression programming is applied in a form where multiple types of operators and operands are used. This gives birth to multiple gene contexts and references between genes in order to keep the linear structure of the gene expression programming chromosome. The setup of multiple gene contexts is presented. The case study shows how to use the proposed gene setup to derive trading rules encoded by Boolean expressions, using a dataset with the reference exchange rates between the Euro and the Romanian leu. The conclusions highlight the positive results obtained in deriving useful trading rules.

Using PCR to Target Misconceptions about Gene Expression

Directory of Open Access Journals (Sweden)

Leslie K. Wright

2013-02-01

Full Text Available We present a PCR-based laboratory exercise that can be used with first- or second-year biology students to help overcome common misconceptions about gene expression. Biology students typically do not have a clear understanding of the difference between genes (DNA and gene expression (mRNA/protein and often believe that genes exist in an organism or cell only when they are expressed. This laboratory exercise allows students to carry out a PCR-based experiment designed to challenge their misunderstanding of the difference between genes and gene expression. Students first transform E. coli with an inducible GFP gene containing plasmid and observe induced and un-induced colonies. The following exercise creates cognitive dissonance when actual PCR results contradict their initial (incorrect predictions of the presence of the GFP gene in transformed cells. Field testing of this laboratory exercise resulted in learning gains on both knowledge and application questions on concepts related to genes and gene expression.

Excitonic bistabilities, instabilities and chaos in laser-pumped semiconductor

International Nuclear Information System (INIS)

Nguyen Ba An; Nguyen Trung Dan; Hoang Xuan Nguyen

1992-07-01

The Hurwitz criteria are used for a stability analysis of the steady state excitonic optical bistability curves in a semiconductor pumped by an external laser resonant with the exciton level. Besides the middle branch of the bistability curves which is unstable in the sense of the linear stability theory, we have found other domains of instability in the upper and lower branches of the steady state curves. Numerical results show that a possible route to chaos in the photon-exciton system is period-doubling self-oscillation process. The influence of the presence of free carriers that coexist with the excitons is also discussed. (author). 16 refs, 6 figs

Bulk chirality effect for symmetric bistable switching of liquid crystals on topologically self-patterned degenerate anchoring surface.

Science.gov (United States)

Park, Min-Kyu; Joo, Kyung-Il; Kim, Hak-Rin

2017-06-26

We demonstrate a bistable switching liquid crystal (LC) mode utilizing a topologically self-structured dual-groove surface for degenerated easy axes of LC anchoring. In our study, the effect of the bulk elastic distortion of the LC directors on the bistable anchoring surface is theoretically analyzed for balanced bistable states based on a free energy diagram. By adjusting bulk LC chirality, we developed ideally symmetric and stable bistable anchoring and switching properties, which can be driven by a low in-plane pulsed field of about 0.7 V/µm. The fabricated device has a contrast ratio of 196:1.

Influence of Fano interference and incoherent processes on optical bistability in a four-level quantum dot nanostructure

International Nuclear Information System (INIS)

Hossein Asadpour, Seyyed; Solookinejad, G; Panahi, M; Ahmadi Sangachin, E

2016-01-01

Role of Fano interference and incoherent pumping field on optical bistability in a four-level designed InGaN/GaN quantum dot nanostructure embedded in a unidirectional ring cavity are analyzed. It is found that intensity threshold of optical bistability can be manipulated by Fano interference. It is shown that incoherent pumping fields make the threshold of optical bistability behave differently by Fano interference. Moreover, in the presence of Fano interference the medium becomes phase-dependent. Therefore, the relative phase of applied fields can affect the behaviors of optical bistability and intensity threshold can be controlled easily. (paper)

Differential gene expression during Trypanosoma cruzi metacyclogenesis

Directory of Open Access Journals (Sweden)

Marco Aurelio Krieger

1999-09-01

Full Text Available The transformation of epimastigotes into metacyclic trypomastigotes involves changes in the pattern of expressed genes, resulting in important morphological and functional differences between these developmental forms of Trypanosoma cruzi. In order to identify and characterize genes involved in triggering the metacyclogenesis process and in conferring to metacyclic trypomastigotes their stage specific biological properties, we have developed a method allowing the isolation of genes specifically expressed when comparing two close related cell populations (representation of differential expression or RDE. The method is based on the PCR amplification of gene sequences selected by hybridizing and subtracting the populations in such a way that after some cycles of hybridization-amplification genes specific to a given population are highly enriched. The use of this method in the analysis of differential gene expression during T. cruzi metacyclogenesis (6 hr and 24 hr of differentiation and metacyclic trypomastigotes resulted in the isolation of several clones from each time point. Northern blot analysis showed that some genes are transiently expressed (6 hr and 24 hr differentiating cells, while others are present in differentiating cells and in metacyclic trypomastigotes. Nucleotide sequencing of six clones characterized so far showed that they do not display any homology to gene sequences available in the GeneBank.

Conditional gene expression in the mouse using a Sleeping Beauty gene-trap transposon

Directory of Open Access Journals (Sweden)

Hackett Perry B

2006-06-01

Full Text Available Abstract Background Insertional mutagenesis techniques with transposable elements have been popular among geneticists studying model organisms from E. coli to Drosophila and, more recently, the mouse. One such element is the Sleeping Beauty (SB transposon that has been shown in several studies to be an effective insertional mutagen in the mouse germline. SB transposon vector studies have employed different functional elements and reporter molecules to disrupt and report the expression of endogenous mouse genes. We sought to generate a transposon system that would be capable of reporting the expression pattern of a mouse gene while allowing for conditional expression of a gene of interest in a tissue- or temporal-specific pattern. Results Here we report the systematic development and testing of a transposon-based gene-trap system incorporating the doxycycline-repressible Tet-Off (tTA system that is capable of activating the expression of genes under control of a Tet response element (TRE promoter. We demonstrate that the gene trap system is fully functional in vitro by introducing the "gene-trap tTA" vector into human cells by transposition and identifying clones that activate expression of a TRE-luciferase transgene in a doxycycline-dependent manner. In transgenic mice, we mobilize gene-trap tTA vectors, discover parameters that can affect germline mobilization rates, and identify candidate gene insertions to demonstrate the in vivo functionality of the vector system. We further demonstrate that the gene-trap can act as a reporter of endogenous gene expression and it can be coupled with bioluminescent imaging to identify genes with tissue-specific expression patterns. Conclusion Akin to the GAL4/UAS system used in the fly, we have made progress developing a tool for mutating and revealing the expression of mouse genes by generating the tTA transactivator in the presence of a secondary TRE-regulated reporter molecule. A vector like the gene

Analysis of multiplex gene expression maps obtained by voxelation

Directory of Open Access Journals (Sweden)

Smith Desmond J

2009-04-01

Full Text Available Abstract Background Gene expression signatures in the mammalian brain hold the key to understanding neural development and neurological disease. Researchers have previously used voxelation in combination with microarrays for acquisition of genome-wide atlases of expression patterns in the mouse brain. On the other hand, some work has been performed on studying gene functions, without taking into account the location information of a gene's expression in a mouse brain. In this paper, we present an approach for identifying the relation between gene expression maps obtained by voxelation and gene functions. Results To analyze the dataset, we chose typical genes as queries and aimed at discovering similar gene groups. Gene similarity was determined by using the wavelet features extracted from the left and right hemispheres averaged gene expression maps, and by the Euclidean distance between each pair of feature vectors. We also performed a multiple clustering approach on the gene expression maps, combined with hierarchical clustering. Among each group of similar genes and clusters, the gene function similarity was measured by calculating the average gene function distances in the gene ontology structure. By applying our methodology to find similar genes to certain target genes we were able to improve our understanding of gene expression patterns and gene functions. By applying the clustering analysis method, we obtained significant clusters, which have both very similar gene expression maps and very similar gene functions respectively to their corresponding gene ontologies. The cellular component ontology resulted in prominent clusters expressed in cortex and corpus callosum. The molecular function ontology gave prominent clusters in cortex, corpus callosum and hypothalamus. The biological process ontology resulted in clusters in cortex, hypothalamus and choroid plexus. Clusters from all three ontologies combined were most prominently expressed in

Analysis of multiplex gene expression maps obtained by voxelation.

Science.gov (United States)

An, Li; Xie, Hongbo; Chin, Mark H; Obradovic, Zoran; Smith, Desmond J; Megalooikonomou, Vasileios

2009-04-29

Gene expression signatures in the mammalian brain hold the key to understanding neural development and neurological disease. Researchers have previously used voxelation in combination with microarrays for acquisition of genome-wide atlases of expression patterns in the mouse brain. On the other hand, some work has been performed on studying gene functions, without taking into account the location information of a gene's expression in a mouse brain. In this paper, we present an approach for identifying the relation between gene expression maps obtained by voxelation and gene functions. To analyze the dataset, we chose typical genes as queries and aimed at discovering similar gene groups. Gene similarity was determined by using the wavelet features extracted from the left and right hemispheres averaged gene expression maps, and by the Euclidean distance between each pair of feature vectors. We also performed a multiple clustering approach on the gene expression maps, combined with hierarchical clustering. Among each group of similar genes and clusters, the gene function similarity was measured by calculating the average gene function distances in the gene ontology structure. By applying our methodology to find similar genes to certain target genes we were able to improve our understanding of gene expression patterns and gene functions. By applying the clustering analysis method, we obtained significant clusters, which have both very similar gene expression maps and very similar gene functions respectively to their corresponding gene ontologies. The cellular component ontology resulted in prominent clusters expressed in cortex and corpus callosum. The molecular function ontology gave prominent clusters in cortex, corpus callosum and hypothalamus. The biological process ontology resulted in clusters in cortex, hypothalamus and choroid plexus. Clusters from all three ontologies combined were most prominently expressed in cortex and corpus callosum. The experimental

A comparative gene expression database for invertebrates

Directory of Open Access Journals (Sweden)

Ormestad Mattias

2011-08-01

Full Text Available Abstract Background As whole genome and transcriptome sequencing gets cheaper and faster, a great number of 'exotic' animal models are emerging, rapidly adding valuable data to the ever-expanding Evo-Devo field. All these new organisms serve as a fantastic resource for the research community, but the sheer amount of data, some published, some not, makes detailed comparison of gene expression patterns very difficult to summarize - a problem sometimes even noticeable within a single lab. The need to merge existing data with new information in an organized manner that is publicly available to the research community is now more necessary than ever. Description In order to offer a homogenous way of storing and handling gene expression patterns from a variety of organisms, we have developed the first web-based comparative gene expression database for invertebrates that allows species-specific as well as cross-species gene expression comparisons. The database can be queried by gene name, developmental stage and/or expression domains. Conclusions This database provides a unique tool for the Evo-Devo research community that allows the retrieval, analysis and comparison of gene expression patterns within or among species. In addition, this database enables a quick identification of putative syn-expression groups that can be used to initiate, among other things, gene regulatory network (GRN projects.

Genetic Variants Contribute to Gene Expression Variability in Humans

Science.gov (United States)

Hulse, Amanda M.; Cai, James J.

2013-01-01

Expression quantitative trait loci (eQTL) studies have established convincing relationships between genetic variants and gene expression. Most of these studies focused on the mean of gene expression level, but not the variance of gene expression level (i.e., gene expression variability). In the present study, we systematically explore genome-wide association between genetic variants and gene expression variability in humans. We adapt the double generalized linear model (dglm) to simultaneously fit the means and the variances of gene expression among the three possible genotypes of a biallelic SNP. The genomic loci showing significant association between the variances of gene expression and the genotypes are termed expression variability QTL (evQTL). Using a data set of gene expression in lymphoblastoid cell lines (LCLs) derived from 210 HapMap individuals, we identify cis-acting evQTL involving 218 distinct genes, among which 8 genes, ADCY1, CTNNA2, DAAM2, FERMT2, IL6, PLOD2, SNX7, and TNFRSF11B, are cross-validated using an extra expression data set of the same LCLs. We also identify ∼300 trans-acting evQTL between >13,000 common SNPs and 500 randomly selected representative genes. We employ two distinct scenarios, emphasizing single-SNP and multiple-SNP effects on expression variability, to explain the formation of evQTL. We argue that detecting evQTL may represent a novel method for effectively screening for genetic interactions, especially when the multiple-SNP influence on expression variability is implied. The implication of our results for revealing genetic mechanisms of gene expression variability is discussed. PMID:23150607

Correction of gene expression data

DEFF Research Database (Denmark)

Darbani Shirvanehdeh, Behrooz; Stewart, C. Neal, Jr.; Noeparvar, Shahin

2014-01-01

This report investigates for the first time the potential inter-treatment bias source of cell number for gene expression studies. Cell-number bias can affect gene expression analysis when comparing samples with unequal total cellular RNA content or with different RNA extraction efficiencies....... For maximal reliability of analysis, therefore, comparisons should be performed at the cellular level. This could be accomplished using an appropriate correction method that can detect and remove the inter-treatment bias for cell-number. Based on inter-treatment variations of reference genes, we introduce...

Gene expression in colorectal cancer

DEFF Research Database (Denmark)

Birkenkamp-Demtroder, Karin; Christensen, Lise Lotte; Olesen, Sanne Harder

2002-01-01

Understanding molecular alterations in colorectal cancer (CRC) is needed to define new biomarkers and treatment targets. We used oligonucleotide microarrays to monitor gene expression of about 6,800 known genes and 35,000 expressed sequence tags (ESTs) on five pools (four to six samples in each...... pool) of total RNA from left-sided sporadic colorectal carcinomas. We compared normal tissue to carcinoma tissue from Dukes' stages A-D (noninvasive to distant metastasis) and identified 908 known genes and 4,155 ESTs that changed remarkably from normal to tumor tissue. Based on intensive filtering 226...

Multiscale Embedded Gene Co-expression Network Analysis.

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Won-Min Song

2015-11-01

Full Text Available Gene co-expression network analysis has been shown effective in identifying functional co-expressed gene modules associated with complex human diseases. However, existing techniques to construct co-expression networks require some critical prior information such as predefined number of clusters, numerical thresholds for defining co-expression/interaction, or do not naturally reproduce the hallmarks of complex systems such as the scale-free degree distribution of small-worldness. Previously, a graph filtering technique called Planar Maximally Filtered Graph (PMFG has been applied to many real-world data sets such as financial stock prices and gene expression to extract meaningful and relevant interactions. However, PMFG is not suitable for large-scale genomic data due to several drawbacks, such as the high computation complexity O(|V|3, the presence of false-positives due to the maximal planarity constraint, and the inadequacy of the clustering framework. Here, we developed a new co-expression network analysis framework called Multiscale Embedded Gene Co-expression Network Analysis (MEGENA by: i introducing quality control of co-expression similarities, ii parallelizing embedded network construction, and iii developing a novel clustering technique to identify multi-scale clustering structures in Planar Filtered Networks (PFNs. We applied MEGENA to a series of simulated data and the gene expression data in breast carcinoma and lung adenocarcinoma from The Cancer Genome Atlas (TCGA. MEGENA showed improved performance over well-established clustering methods and co-expression network construction approaches. MEGENA revealed not only meaningful multi-scale organizations of co-expressed gene clusters but also novel targets in breast carcinoma and lung adenocarcinoma.

Multiscale Embedded Gene Co-expression Network Analysis.

Science.gov (United States)

Song, Won-Min; Zhang, Bin

2015-11-01

Gene co-expression network analysis has been shown effective in identifying functional co-expressed gene modules associated with complex human diseases. However, existing techniques to construct co-expression networks require some critical prior information such as predefined number of clusters, numerical thresholds for defining co-expression/interaction, or do not naturally reproduce the hallmarks of complex systems such as the scale-free degree distribution of small-worldness. Previously, a graph filtering technique called Planar Maximally Filtered Graph (PMFG) has been applied to many real-world data sets such as financial stock prices and gene expression to extract meaningful and relevant interactions. However, PMFG is not suitable for large-scale genomic data due to several drawbacks, such as the high computation complexity O(|V|3), the presence of false-positives due to the maximal planarity constraint, and the inadequacy of the clustering framework. Here, we developed a new co-expression network analysis framework called Multiscale Embedded Gene Co-expression Network Analysis (MEGENA) by: i) introducing quality control of co-expression similarities, ii) parallelizing embedded network construction, and iii) developing a novel clustering technique to identify multi-scale clustering structures in Planar Filtered Networks (PFNs). We applied MEGENA to a series of simulated data and the gene expression data in breast carcinoma and lung adenocarcinoma from The Cancer Genome Atlas (TCGA). MEGENA showed improved performance over well-established clustering methods and co-expression network construction approaches. MEGENA revealed not only meaningful multi-scale organizations of co-expressed gene clusters but also novel targets in breast carcinoma and lung adenocarcinoma.

On the functional relevance of frontal cortex for passive and voluntarily controlled bistable vision.

Science.gov (United States)

de Graaf, Tom A; de Jong, Maartje C; Goebel, Rainer; van Ee, Raymond; Sack, Alexander T

2011-10-01

In bistable vision, one constant ambiguous stimulus leads to 2 alternating conscious percepts. This perceptual switching occurs spontaneously but can also be influenced through voluntary control. Neuroimaging studies have reported that frontal regions are activated during spontaneous perceptual switches, leading some researchers to suggest that frontal regions causally induce perceptual switches. But the opposite also seems possible: frontal activations may themselves be caused by spontaneous switches. Classically implicated in attentional processes, these same regions are also candidates for the origins of voluntary control over bistable vision. Here too, it remains unknown whether frontal cortex is actually functionally relevant. It is even possible that spontaneous perceptual switches and voluntarily induced switches are mediated by the same top-down mechanisms. To directly address these issues, we here induced "virtual lesions," with transcranial magnetic stimulation, in frontal, parietal, and 2 lower level visual cortices using an established ambiguous structure-from-motion stimulus. We found that dorsolateral prefrontal cortex was causally relevant for voluntary control over perceptual switches. In contrast, we failed to find any evidence for an active role of frontal cortex in passive bistable vision. Thus, it seems the same pathway used for willed top-down modulation of bistable vision is not used during passive bistable viewing.

Controlling the optical bistability and transmission coefficient in a four-level atomic medium

International Nuclear Information System (INIS)

Asadpour, Seyyed Hossein; Eslami-Majd, Abdullah

2012-01-01

A novel four level atomic configuration is proposed for controlling the optical bistability and transmission coefficient with application on all-optical switching. Two circularly polarized components from a weak linearly-polarized probe beam are interacted separately by two transitions of this medium. A coherent coupling field has derived another atomic transition. It is demonstrated that the transmission coefficient of two orthogonally polarized beams at different frequencies can be achieved by adjusting the magnitude of the external magnetic field. It is found that the threshold of the optical bistability can be controlled by magnitude of the external magnetic field. Also, it is shown that optical bistability can be converted to optical multistability by switching the two orthogonally polarized beams. - Highlights: ► An inverted Y-type four level atomic system is proposed. ► Transmission coefficient can be controlled by a novel interesting parameter. ► Optical bistability and multistability can be achieved via external magnetic field. ► It is shown that our proposed model is suitable for all optical switching application.

Vascular Gene Expression: A Hypothesis

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Angélica Concepción eMartínez-Navarro

2013-07-01

Full Text Available The phloem is the conduit through which photoassimilates are distributed from autotrophic to heterotrophic tissues and is involved in the distribution of signaling molecules that coordinate plant growth and responses to the environment. Phloem function depends on the coordinate expression of a large array of genes. We have previously identified conserved motifs in upstream regions of the Arabidopsis genes, encoding the homologs of pumpkin phloem sap mRNAs, displaying expression in vascular tissues. This tissue-specific expression in Arabidopsis is predicted by the overrepresentation of GA/CT-rich motifs in gene promoters. In this work we have searched for common motifs in upstream regions of the homologous genes from plants considered to possess a primitive vascular tissue (a lycophyte, as well as from others that lack a true vascular tissue (a bryophyte, and finally from chlorophytes. Both lycophyte and bryophyte display motifs similar to those found in Arabidopsis with a significantly low E-value, while the chlorophytes showed either a different conserved motif or no conserved motif at all. These results suggest that these same genes are expressed coordinately in non- vascular plants; this coordinate expression may have been one of the prerequisites for the development of conducting tissues in plants. We have also analyzed the phylogeny of conserved proteins that may be involved in phloem function and development. The presence of CmPP16, APL, FT and YDA in chlorophytes suggests the recruitment of ancient regulatory networks for the development of the vascular tissue during evolution while OPS is a novel protein specific to vascular plants.

GSEH: A Novel Approach to Select Prostate Cancer-Associated Genes Using Gene Expression Heterogeneity.

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Kim, Hyunjin; Choi, Sang-Min; Park, Sanghyun

2018-01-01

When a gene shows varying levels of expression among normal people but similar levels in disease patients or shows similar levels of expression among normal people but different levels in disease patients, we can assume that the gene is associated with the disease. By utilizing this gene expression heterogeneity, we can obtain additional information that abets discovery of disease-associated genes. In this study, we used collaborative filtering to calculate the degree of gene expression heterogeneity between classes and then scored the genes on the basis of the degree of gene expression heterogeneity to find "differentially predicted" genes. Through the proposed method, we discovered more prostate cancer-associated genes than 10 comparable methods. The genes prioritized by the proposed method are potentially significant to biological processes of a disease and can provide insight into them.

Durable bistable auxetics made of rigid solids

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Shang, Xiao; Liu, Lu; Rafsanjani, Ahmad; Pasini, Damiano

2018-02-01

Bistable Auxetic Metamaterials (BAMs) are a class of monolithic perforated periodic structures with negative Poisson's ratio. Under tension, a BAM can expand and reach a second state of equilibrium through a globally large shape transformation that is ensured by the flexibility of its elastomeric base material. However, if made from a rigid polymer, or metal, BAM ceases to function due to the inevitable rupture of its ligaments. The goal of this work is to extend the unique functionality of the original kirigami architecture of BAM to a rigid solid base material. We use experiments and numerical simulations to assess performance, bistability and durability of rigid BAMs at 10,000 cycles. Geometric maps are presented to elucidate the role of the main descriptors of BAM architecture. The proposed design enables the realization of BAM from a large palette of materials, including elastic-perfectly plastic materials and potentially brittle materials.

The evolution of gene expression in primates

OpenAIRE

Tashakkori Ghanbarian, Avazeh

2015-01-01

The evolution of a gene’s expression profile is commonly assumed to be independent of its genomic neighborhood. This is, however, in contrast to what we know about the lack of autonomy between expression of neighboring genes in extant taxa. Indeed, in all eukaryotic genomes, genes of similar expression-profile tend to cluster, reflecting chromatin level dynamics. Does it follow that if a gene increases expression in a particular lineage then the genomic neighbors will also increase in their e...

Emergence of switch-like behavior in a large family of simple biochemical networks.

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Dan Siegal-Gaskins

2011-05-01

Full Text Available Bistability plays a central role in the gene regulatory networks (GRNs controlling many essential biological functions, including cellular differentiation and cell cycle control. However, establishing the network topologies that can exhibit bistability remains a challenge, in part due to the exceedingly large variety of GRNs that exist for even a small number of components. We begin to address this problem by employing chemical reaction network theory in a comprehensive in silico survey to determine the capacity for bistability of more than 40,000 simple networks that can be formed by two transcription factor-coding genes and their associated proteins (assuming only the most elementary biochemical processes. We find that there exist reaction rate constants leading to bistability in ∼90% of these GRN models, including several circuits that do not contain any of the TF cooperativity commonly associated with bistable systems, and the majority of which could only be identified as bistable through an original subnetwork-based analysis. A topological sorting of the two-gene family of networks based on the presence or absence of biochemical reactions reveals eleven minimal bistable networks (i.e., bistable networks that do not contain within them a smaller bistable subnetwork. The large number of previously unknown bistable network topologies suggests that the capacity for switch-like behavior in GRNs arises with relative ease and is not easily lost through network evolution. To highlight the relevance of the systematic application of CRNT to bistable network identification in real biological systems, we integrated publicly available protein-protein interaction, protein-DNA interaction, and gene expression data from Saccharomyces cerevisiae, and identified several GRNs predicted to behave in a bistable fashion.

Revisiting bistability in the lysis/lysogeny circuit of bacteriophage lambda.

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Michael Bednarz

Full Text Available The lysis/lysogeny switch of bacteriophage lambda serves as a paradigm for binary cell fate decision, long-term maintenance of cellular state and stimulus-triggered switching between states. In the literature, the system is often referred to as "bistable." However, it remains unclear whether this term provides an accurate description or is instead a misnomer. Here we address this question directly. We first quantify transcriptional regulation governing lysogenic maintenance using a single-cell fluorescence reporter. We then use the single-cell data to derive a stochastic theoretical model for the underlying regulatory network. We use the model to predict the steady states of the system and then validate these predictions experimentally. Specifically, a regime of bistability, and the resulting hysteretic behavior, are observed. Beyond the steady states, the theoretical model successfully predicts the kinetics of switching from lysogeny to lysis. Our results show how the physics-inspired concept of bistability can be reliably used to describe cellular phenotype, and how an experimentally-calibrated theoretical model can have accurate predictive power for cell-state switching.

Single coil bistable, bidirectional micromechanical actuator

Science.gov (United States)

Tabat, Ned; Guckel, Henry

1998-09-15

Micromechanical actuators capable of bidirectional and bistable operation can be formed on substrates using lithographic processing techniques. Bistable operation of the microactuator is obtained using a single coil and a magnetic core with a gap. A plunger having two magnetic heads is supported for back and forth linear movement with respect to the gap in the magnetic core, and is spring biased to a neutral position in which the two heads are on each side of the gap in the core. The single electrical coil is coupled to the core and is provided with electrical current to attract one of the heads toward the core by reluctance action to drive the plunger to a limit of travel in one direction. The current is then cut off and the plunger returns by spring action toward the gap, whereafter the current is reapplied to the coil to attract the other head of the plunger by reluctance action to drive the plunger to its other limit of travel. This process can be repeated at a time when switching of the actuator is required.

Reduced expression of Autographa californica nucleopolyhedrovirus ORF34, an essential gene, enhances heterologous gene expression

International Nuclear Information System (INIS)

Salem, Tamer Z.; Zhang, Fengrui; Thiem, Suzanne M.

2013-01-01

Autographa californica multiple nucleopolyhedrovirus ORF34 is part of a transcriptional unit that includes ORF32, encoding a viral fibroblast growth factor (FGF) and ORF33. We identified ORF34 as a candidate for deletion to improve protein expression in the baculovirus expression system based on enhanced reporter gene expression in an RNAi screen of virus genes. However, ORF34 was shown to be an essential gene. To explore ORF34 function, deletion (KO34) and rescue bacmids were constructed and characterized. Infection did not spread from primary KO34 transfected cells and supernatants from KO34 transfected cells could not infect fresh Sf21 cells whereas the supernatant from the rescue bacmids transfection could recover the infection. In addition, budded viruses were not observed in KO34 transfected cells by electron microscopy, nor were viral proteins detected from the transfection supernatants by western blots. These demonstrate that ORF34 is an essential gene with a possible role in infectious virus production.

Reduced expression of Autographa californica nucleopolyhedrovirus ORF34, an essential gene, enhances heterologous gene expression

Energy Technology Data Exchange (ETDEWEB)

Salem, Tamer Z. [Department of Entomology, Michigan State University, East Lansing, MI 48824 (United States); Department of Microbial Molecular Biology, AGERI, Agricultural Research Center, Giza 12619 (Egypt); Division of Biomedical Sciences, Zewail University, Zewail City of Science and Technology, Giza 12588 (Egypt); Zhang, Fengrui [Department of Entomology, Michigan State University, East Lansing, MI 48824 (United States); Thiem, Suzanne M., E-mail: smthiem@msu.edu [Department of Entomology, Michigan State University, East Lansing, MI 48824 (United States); Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824 (United States)

2013-01-20

Autographa californica multiple nucleopolyhedrovirus ORF34 is part of a transcriptional unit that includes ORF32, encoding a viral fibroblast growth factor (FGF) and ORF33. We identified ORF34 as a candidate for deletion to improve protein expression in the baculovirus expression system based on enhanced reporter gene expression in an RNAi screen of virus genes. However, ORF34 was shown to be an essential gene. To explore ORF34 function, deletion (KO34) and rescue bacmids were constructed and characterized. Infection did not spread from primary KO34 transfected cells and supernatants from KO34 transfected cells could not infect fresh Sf21 cells whereas the supernatant from the rescue bacmids transfection could recover the infection. In addition, budded viruses were not observed in KO34 transfected cells by electron microscopy, nor were viral proteins detected from the transfection supernatants by western blots. These demonstrate that ORF34 is an essential gene with a possible role in infectious virus production.

Widespread ectopic expression of olfactory receptor genes

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Yanai Itai

2006-05-01

Full Text Available Abstract Background Olfactory receptors (ORs are the largest gene family in the human genome. Although they are expected to be expressed specifically in olfactory tissues, some ectopic expression has been reported, with special emphasis on sperm and testis. The present study systematically explores the expression patterns of OR genes in a large number of tissues and assesses the potential functional implication of such ectopic expression. Results We analyzed the expression of hundreds of human and mouse OR transcripts, via EST and microarray data, in several dozens of human and mouse tissues. Different tissues had specific, relatively small OR gene subsets which had particularly high expression levels. In testis, average expression was not particularly high, and very few highly expressed genes were found, none corresponding to ORs previously implicated in sperm chemotaxis. Higher expression levels were more common for genes with a non-OR genomic neighbor. Importantly, no correlation in expression levels was detected for human-mouse orthologous pairs. Also, no significant difference in expression levels was seen between intact and pseudogenized ORs, except for the pseudogenes of subfamily 7E which has undergone a human-specific expansion. Conclusion The OR superfamily as a whole, show widespread, locus-dependent and heterogeneous expression, in agreement with a neutral or near neutral evolutionary model for transcription control. These results cannot reject the possibility that small OR subsets might play functional roles in different tissues, however considerable care should be exerted when offering a functional interpretation for ectopic OR expression based only on transcription information.

Identification of Human HK Genes and Gene Expression Regulation Study in Cancer from Transcriptomics Data Analysis

Science.gov (United States)

Zhang, Zhang; Liu, Jingxing; Wu, Jiayan; Yu, Jun

2013-01-01

The regulation of gene expression is essential for eukaryotes, as it drives the processes of cellular differentiation and morphogenesis, leading to the creation of different cell types in multicellular organisms. RNA-Sequencing (RNA-Seq) provides researchers with a powerful toolbox for characterization and quantification of transcriptome. Many different human tissue/cell transcriptome datasets coming from RNA-Seq technology are available on public data resource. The fundamental issue here is how to develop an effective analysis method to estimate expression pattern similarities between different tumor tissues and their corresponding normal tissues. We define the gene expression pattern from three directions: 1) expression breadth, which reflects gene expression on/off status, and mainly concerns ubiquitously expressed genes; 2) low/high or constant/variable expression genes, based on gene expression level and variation; and 3) the regulation of gene expression at the gene structure level. The cluster analysis indicates that gene expression pattern is higher related to physiological condition rather than tissue spatial distance. Two sets of human housekeeping (HK) genes are defined according to cell/tissue types, respectively. To characterize the gene expression pattern in gene expression level and variation, we firstly apply improved K-means algorithm and a gene expression variance model. We find that cancer-associated HK genes (a HK gene is specific in cancer group, while not in normal group) are expressed higher and more variable in cancer condition than in normal condition. Cancer-associated HK genes prefer to AT-rich genes, and they are enriched in cell cycle regulation related functions and constitute some cancer signatures. The expression of large genes is also avoided in cancer group. These studies will help us understand which cell type-specific patterns of gene expression differ among different cell types, and particularly for cancer. PMID:23382867

Coupling-induced oscillations in nonhomogeneous, overdamped, bistable systems

International Nuclear Information System (INIS)

Hernandez, Mayra; In, Visarath; Longhini, Patrick; Palacios, Antonio; Bulsara, Adi; Kho, Andy

2008-01-01

Coupling-induced oscillations in a homogeneous network of overdamped bistable systems have been previously studied both theoretically and experimentally for a system of N (odd) elements, unidirectionally coupled in a ring topology. In this work, we extend the analysis of this system to include a network of nonhomogeneous elements with respect to the parameter that controls the topology of the potential function and the bistability of each element. In particular, we quantify the effects of the nonhomogeneity on the onset of oscillations and the response of the network to external (assumed to be constant and very small) perturbations, using our (recently developed) coupled core fluxgate magnetometer as a representative system. The potential applications of this work include signal detection and characterization for a large class of sensor systems

Coupling-induced oscillations in nonhomogeneous, overdamped, bistable systems

Energy Technology Data Exchange (ETDEWEB)

Hernandez, Mayra [Nonlinear Dynamical Systems Group, Department of Mathematics and Statistics, San Diego State University, San Diego, CA 92182 (United States)], E-mail: mayra.alina@yahoo.com; In, Visarath [Space and Naval Warfare Systems Center, Code 71730, 53560 Hull Street, San Diego, CA 92152-5001 (United States)], E-mail: visarath.in@navy.mil; Longhini, Patrick [Space and Naval Warfare Systems Center, Code 71730, 53560 Hull Street, San Diego, CA 92152-5001 (United States)], E-mail: longhini@navy.mil; Palacios, Antonio [Nonlinear Dynamical Systems Group, Department of Mathematics and Statistics, San Diego State University, San Diego, CA 92182 (United States)], E-mail: palacios@euler.sdsu.edu; Bulsara, Adi [Space and Naval Warfare Systems Center, Code 71730, 53560 Hull Street, San Diego, CA 92152-5001 (United States)], E-mail: bulsara@spawar.navy.mil; Kho, Andy [Space and Naval Warfare Systems Center, Code 71730, 53560 Hull Street, San Diego, CA 92152-5001 (United States)], E-mail: kho@spawar.navy.mil

2008-06-09

Coupling-induced oscillations in a homogeneous network of overdamped bistable systems have been previously studied both theoretically and experimentally for a system of N (odd) elements, unidirectionally coupled in a ring topology. In this work, we extend the analysis of this system to include a network of nonhomogeneous elements with respect to the parameter that controls the topology of the potential function and the bistability of each element. In particular, we quantify the effects of the nonhomogeneity on the onset of oscillations and the response of the network to external (assumed to be constant and very small) perturbations, using our (recently developed) coupled core fluxgate magnetometer as a representative system. The potential applications of this work include signal detection and characterization for a large class of sensor systems.

Dynamics and bistability in a reduced model of the lac operon

Science.gov (United States)

Yildirim, Necmettin; Santillán, Moisés; Horike, Daisuke; Mackey, Michael C.

2004-06-01

It is known that the lac operon regulatory pathway is capable of showing bistable behavior. This is an important complex feature, arising from the nonlinearity of the involved mechanisms, which is essential to understand the dynamic behavior of this molecular regulatory system. To find which of the mechanisms involved in the regulation of the lac operon is the origin of bistability, we take a previously published model which accounts for the dynamics of mRNA, lactose, allolactose, permease and β-galactosidase involvement and simplify it by ignoring permease dynamics (assuming a constant permease concentration). To test the behavior of the reduced model, three existing sets of data on β-galactosidase levels as a function of time are simulated and we obtain a reasonable agreement between the data and the model predictions. The steady states of the reduced model were numerically and analytically analyzed and it was shown that it may indeed display bistability, depending on the extracellular lactose concentration and growth rate.

A computational role for bistability and traveling waves in motor cortex

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Stewart eHeitmann

2012-09-01

Full Text Available Adaptive changes in behavior require rapid changes in brain states yet the brain must also remain stable. We investigated two neural mechanisms for evoking rapid transitions between spatiotemporal synchronization patterns of beta oscillations (13--30Hz in motor cortex. Cortex was modeled as a sheet of neural oscillators that were spatially coupled using a center-surround connection topology. Manipulating the inhibitory surround was found to evoke reliable transitions between synchronous oscillation patterns and traveling waves. These transitions modulated the simulated local field potential in agreement with physiological observations in humans. Intermediate levels of surround inhibition were also found to produce bistable coupling topologies that supported both waves and synchrony. State-dependent perturbation between bistable states produced very rapid transitions but were less reliable. We surmise that motor cortex may thus employ state-dependent computation to achieve very rapid changes between bistable motor states when the demand for speed exceeds the demand for accuracy.

Dynamic association rules for gene expression data analysis.

Science.gov (United States)

Chen, Shu-Chuan; Tsai, Tsung-Hsien; Chung, Cheng-Han; Li, Wen-Hsiung

2015-10-14

The purpose of gene expression analysis is to look for the association between regulation of gene expression levels and phenotypic variations. This association based on gene expression profile has been used to determine whether the induction/repression of genes correspond to phenotypic variations including cell regulations, clinical diagnoses and drug development. Statistical analyses on microarray data have been developed to resolve gene selection issue. However, these methods do not inform us of causality between genes and phenotypes. In this paper, we propose the dynamic association rule algorithm (DAR algorithm) which helps ones to efficiently select a subset of significant genes for subsequent analysis. The DAR algorithm is based on association rules from market basket analysis in marketing. We first propose a statistical way, based on constructing a one-sided confidence interval and hypothesis testing, to determine if an association rule is meaningful. Based on the proposed statistical method, we then developed the DAR algorithm for gene expression data analysis. The method was applied to analyze four microarray datasets and one Next Generation Sequencing (NGS) dataset: the Mice Apo A1 dataset, the whole genome expression dataset of mouse embryonic stem cells, expression profiling of the bone marrow of Leukemia patients, Microarray Quality Control (MAQC) data set and the RNA-seq dataset of a mouse genomic imprinting study. A comparison of the proposed method with the t-test on the expression profiling of the bone marrow of Leukemia patients was conducted. We developed a statistical way, based on the concept of confidence interval, to determine the minimum support and minimum confidence for mining association relationships among items. With the minimum support and minimum confidence, one can find significant rules in one single step. The DAR algorithm was then developed for gene expression data analysis. Four gene expression datasets showed that the proposed

Gene expression in periodontal tissues following treatment

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Eisenacher Martin

2008-07-01

Full Text Available Abstract Background In periodontitis, treatment aimed at controlling the periodontal biofilm infection results in a resolution of the clinical and histological signs of inflammation. Although the cell types found in periodontal tissues following treatment have been well described, information on gene expression is limited to few candidate genes. Therefore, the aim of the study was to determine the expression profiles of immune and inflammatory genes in periodontal tissues from sites with severe chronic periodontitis following periodontal therapy in order to identify genes involved in tissue homeostasis. Gingival biopsies from 12 patients with severe chronic periodontitis were taken six to eight weeks following non-surgical periodontal therapy, and from 11 healthy controls. As internal standard, RNA of an immortalized human keratinocyte line (HaCaT was used. Total RNA was subjected to gene expression profiling using a commercially available microarray system focusing on inflammation-related genes. Post-hoc confirmation of selected genes was done by Realtime-PCR. Results Out of the 136 genes analyzed, the 5% most strongly expressed genes compared to healthy controls were Interleukin-12A (IL-12A, Versican (CSPG-2, Matrixmetalloproteinase-1 (MMP-1, Down syndrome critical region protein-1 (DSCR-1, Macrophage inflammatory protein-2β (Cxcl-3, Inhibitor of apoptosis protein-1 (BIRC-1, Cluster of differentiation antigen 38 (CD38, Regulator of G-protein signalling-1 (RGS-1, and Finkel-Biskis-Jinkins murine osteosarcoma virus oncogene (C-FOS; the 5% least strongly expressed genes were Receptor-interacting Serine/Threonine Kinase-2 (RIP-2, Complement component 3 (C3, Prostaglandin-endoperoxide synthase-2 (COX-2, Interleukin-8 (IL-8, Endothelin-1 (EDN-1, Plasminogen activator inhibitor type-2 (PAI-2, Matrix-metalloproteinase-14 (MMP-14, and Interferon regulating factor-7 (IRF-7. Conclusion Gene expression profiles found in periodontal tissues following

Gene expression profiles in skeletal muscle after gene electrotransfer

DEFF Research Database (Denmark)

Hojman, Pernille; Zibert, John R; Gissel, Hanne

2007-01-01

BACKGROUND: Gene transfer by electroporation (DNA electrotransfer) to muscle results in high level long term transgenic expression, showing great promise for treatment of e.g. protein deficiency syndromes. However little is known about the effects of DNA electrotransfer on muscle fibres. We have...... caused down-regulation of structural proteins e.g. sarcospan and catalytic enzymes. Injection of DNA induced down-regulation of intracellular transport proteins e.g. sentrin. The effects on muscle fibres were transient as the expression profiles 3 weeks after treatment were closely related......) followed by a long low voltage pulse (LV, 100 V/cm, 400 ms); a pulse combination optimised for efficient and safe gene transfer. Muscles were transfected with green fluorescent protein (GFP) and excised at 4 hours, 48 hours or 3 weeks after treatment. RESULTS: Differentially expressed genes were...

Internal optical bistability of quasi-two-dimensional semiconductor nanoheterostructures

Science.gov (United States)

Derevyanchuk, Oleksandr V.; Kramar, Natalia K.; Kramar, Valeriy M.

2018-01-01

We represent the results of numerical computations of the frequency and temperature domains of possible realization of internal optical bistability in flat quasi-two-dimensional semiconductor nanoheterostructures with a single quantum well (i.e., nanofilms). Particular computations have been made for a nanofilm of layered semiconductor PbI2 embedded in dielectric medium, i.e. ethylene-methacrylic acid (E-MAA) copolymer. It is shown that an increase in the nanofilm's thickness leads to a long-wave shift of the frequency range of the manifestation the phenomenon of bistability, to increase the size of the hysteresis loop, as well as to the expansion of the temperature interval at which the realization of this phenomenon is possible.

Comparative gene expression between two yeast species

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Guan Yuanfang

2013-01-01

Full Text Available Abstract Background Comparative genomics brings insight into sequence evolution, but even more may be learned by coupling sequence analyses with experimental tests of gene function and regulation. However, the reliability of such comparisons is often limited by biased sampling of expression conditions and incomplete knowledge of gene functions across species. To address these challenges, we previously systematically generated expression profiles in Saccharomyces bayanus to maximize functional coverage as compared to an existing Saccharomyces cerevisiae data repository. Results In this paper, we take advantage of these two data repositories to compare patterns of ortholog expression in a wide variety of conditions. First, we developed a scalable metric for expression divergence that enabled us to detect a significant correlation between sequence and expression conservation on the global level, which previous smaller-scale expression studies failed to detect. Despite this global conservation trend, between-species gene expression neighborhoods were less well-conserved than within-species comparisons across different environmental perturbations, and approximately 4% of orthologs exhibited a significant change in co-expression partners. Furthermore, our analysis of matched perturbations collected in both species (such as diauxic shift and cell cycle synchrony demonstrated that approximately a quarter of orthologs exhibit condition-specific expression pattern differences. Conclusions Taken together, these analyses provide a global view of gene expression patterns between two species, both in terms of the conditions and timing of a gene's expression as well as co-expression partners. Our results provide testable hypotheses that will direct future experiments to determine how these changes may be specified in the genome.

An analytical approach to bistable biological circuit discrimination using real algebraic geometry.

Science.gov (United States)

Siegal-Gaskins, Dan; Franco, Elisa; Zhou, Tiffany; Murray, Richard M

2015-07-06

Biomolecular circuits with two distinct and stable steady states have been identified as essential components in a wide range of biological networks, with a variety of mechanisms and topologies giving rise to their important bistable property. Understanding the differences between circuit implementations is an important question, particularly for the synthetic biologist faced with determining which bistable circuit design out of many is best for their specific application. In this work we explore the applicability of Sturm's theorem--a tool from nineteenth-century real algebraic geometry--to comparing 'functionally equivalent' bistable circuits without the need for numerical simulation. We first consider two genetic toggle variants and two different positive feedback circuits, and show how specific topological properties present in each type of circuit can serve to increase the size of the regions of parameter space in which they function as switches. We then demonstrate that a single competitive monomeric activator added to a purely monomeric (and otherwise monostable) mutual repressor circuit is sufficient for bistability. Finally, we compare our approach with the Routh-Hurwitz method and derive consistent, yet more powerful, parametric conditions. The predictive power and ease of use of Sturm's theorem demonstrated in this work suggest that algebraic geometric techniques may be underused in biomolecular circuit analysis.

Interplay of Multisensory Processing, Attention, and Consciousness as Revealed by Bistable Figures

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Su-Ling Yeh

2011-10-01

Full Text Available We examined the novel crossmodal semantic congruency effect on bistable figures in which a static stimulus gives rise to two competing percepts that alternate over time. Participants viewed the bistable figure “my wife or my mother-in-law” while listening to the voice of an old woman or a young lady speaking in an unfamiliar language. They had to report whether they saw the old woman, the young lady, or a mixed percept. Robust crossmodal semantic congruency effects in the measures of the first percept and the predominance duration were observed. The possibilities that the participants simply responded to, and/or that they fixed at the location in favor of, the percept congruent with the sound that they happened to hear were ruled out. When the participants were instructed to maintain their attention to a specific view, a strong top-down modulation on the perception of bistable figure was observed, although the audiovisual semantic congruency effect still remained. These results thus demonstrate that top-down attention (ie,, selection and/or voluntary control modulates the audiovisual semantic congruency effect. As the alternating percepts in bistable figures indicate competition for conscious perception, this study has important implications for the multifaceted interactions between multisensory processing, attention, and consciousness.

Interactive visualization of gene regulatory networks with associated gene expression time series data

NARCIS (Netherlands)

Westenberg, M.A.; Hijum, van S.A.F.T.; Lulko, A.T.; Kuipers, O.P.; Roerdink, J.B.T.M.; Linsen, L.; Hagen, H.; Hamann, B.

2008-01-01

We present GENeVis, an application to visualize gene expression time series data in a gene regulatory network context. This is a network of regulator proteins that regulate the expression of their respective target genes. The networks are represented as graphs, in which the nodes represent genes,

Serial analysis of gene expression (SAGE)

NARCIS (Netherlands)

van Ruissen, Fred; Baas, Frank

2007-01-01

In 1995, serial analysis of gene expression (SAGE) was developed as a versatile tool for gene expression studies. SAGE technology does not require pre-existing knowledge of the genome that is being examined and therefore SAGE can be applied to many different model systems. In this chapter, the SAGE

An Interactive Database of Cocaine-Responsive Gene Expression

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Willard M. Freeman

2002-01-01

Full Text Available The postgenomic era of large-scale gene expression studies is inundating drug abuse researchers and many other scientists with findings related to gene expression. This information is distributed across many different journals, and requires laborious literature searches. Here, we present an interactive database that combines existing information related to cocaine-mediated changes in gene expression in an easy-to-use format. The database is limited to statistically significant changes in mRNA or protein expression after cocaine administration. The Flash-based program is integrated into a Web page, and organizes changes in gene expression based on neuroanatomical region, general function, and gene name. Accompanying each gene is a description of the gene, links to the original publications, and a link to the appropriate OMIM (Online Mendelian Inheritance in Man entry. The nature of this review allows for timely modifications and rapid inclusion of new publications, and should help researchers build second-generation hypotheses on the role of gene expression changes in the physiology and behavior of cocaine abuse. Furthermore, this method of organizing large volumes of scientific information can easily be adapted to assist researchers in fields outside of drug abuse.

CDX2 gene expression in acute lymphoblastic leukemia

International Nuclear Information System (INIS)

Arnaoaut, H.H.; Mokhtar, D.A.; Samy, R.M.; Omar, Sh.A.; Khames, S.A.

2014-01-01

CDX genes are classically known as regulators of axial elongation during early embryogenesis. An unsuspected role for CDX genes has been revealed during hematopoietic development. The CDX gene family member CDX2 belongs to the most frequent aberrantly expressed proto-oncogenes in human acute leukemias and is highly leukemogenic in experimental models. We used reversed transcriptase polymerase chain reaction (RT-PCR) to determine the expression level of CDX2 gene in 30 pediatric patients with acute lymphoblastic leukemia (ALL) at diagnosis and 30 healthy volunteers. ALL patients were followed up to detect minimal residual disease (MRD) on days 15 and 42 of induction. We found that CDX2 gene was expressed in 50% of patients and not expressed in controls. Associations between gene expression and different clinical and laboratory data of patients revealed no impact on different findings. With follow up, we could not confirm that CDX2 expression had a prognostic significance.

Identification of reference genes in human myelomonocytic cells for gene expression studies in altered gravity.

Science.gov (United States)

Thiel, Cora S; Hauschild, Swantje; Tauber, Svantje; Paulsen, Katrin; Raig, Christiane; Raem, Arnold; Biskup, Josefine; Gutewort, Annett; Hürlimann, Eva; Unverdorben, Felix; Buttron, Isabell; Lauber, Beatrice; Philpot, Claudia; Lier, Hartwin; Engelmann, Frank; Layer, Liliana E; Ullrich, Oliver

2015-01-01

Gene expression studies are indispensable for investigation and elucidation of molecular mechanisms. For the process of normalization, reference genes ("housekeeping genes") are essential to verify gene expression analysis. Thus, it is assumed that these reference genes demonstrate similar expression levels over all experimental conditions. However, common recommendations about reference genes were established during 1 g conditions and therefore their applicability in studies with altered gravity has not been demonstrated yet. The microarray technology is frequently used to generate expression profiles under defined conditions and to determine the relative difference in expression levels between two or more different states. In our study, we searched for potential reference genes with stable expression during different gravitational conditions (microgravity, normogravity, and hypergravity) which are additionally not altered in different hardware systems. We were able to identify eight genes (ALB, B4GALT6, GAPDH, HMBS, YWHAZ, ABCA5, ABCA9, and ABCC1) which demonstrated no altered gene expression levels in all tested conditions and therefore represent good candidates for the standardization of gene expression studies in altered gravity.

Inferring gene networks from discrete expression data

KAUST Repository

Zhang, L.

2013-07-18

The modeling of gene networks from transcriptional expression data is an important tool in biomedical research to reveal signaling pathways and to identify treatment targets. Current gene network modeling is primarily based on the use of Gaussian graphical models applied to continuous data, which give a closedformmarginal likelihood. In this paper,we extend network modeling to discrete data, specifically data from serial analysis of gene expression, and RNA-sequencing experiments, both of which generate counts of mRNAtranscripts in cell samples.We propose a generalized linear model to fit the discrete gene expression data and assume that the log ratios of the mean expression levels follow a Gaussian distribution.We restrict the gene network structures to decomposable graphs and derive the graphs by selecting the covariance matrix of the Gaussian distribution with the hyper-inverse Wishart priors. Furthermore, we incorporate prior network models based on gene ontology information, which avails existing biological information on the genes of interest. We conduct simulation studies to examine the performance of our discrete graphical model and apply the method to two real datasets for gene network inference. © The Author 2013. Published by Oxford University Press. All rights reserved.

Reference Gene Screening for Analyzing Gene Expression Across Goat Tissue

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Yu Zhang

2013-12-01

Full Text Available Real-time quantitative PCR (qRT-PCR is one of the important methods for investigating the changes in mRNA expression levels in cells and tissues. Selection of the proper reference genes is very important when calibrating the results of real-time quantitative PCR. Studies on the selection of reference genes in goat tissues are limited, despite the economic importance of their meat and dairy products. We used real-time quantitative PCR to detect the expression levels of eight reference gene candidates (18S, TBP, HMBS, YWHAZ, ACTB, HPRT1, GAPDH and EEF1A2 in ten tissues types sourced from Boer goats. The optimal reference gene combination was selected according to the results determined by geNorm, NormFinder and Bestkeeper software packages. The analyses showed that tissue is an important variability factor in genes expression stability. When all tissues were considered, 18S, TBP and HMBS is the optimal reference combination for calibrating quantitative PCR analysis of gene expression from goat tissues. Dividing data set by tissues, ACTB was the most stable in stomach, small intestine and ovary, 18S in heart and spleen, HMBS in uterus and lung, TBP in liver, HPRT1 in kidney and GAPDH in muscle. Overall, this study provided valuable information about the goat reference genes that can be used in order to perform a proper normalisation when relative quantification by qRT-PCR studies is undertaken.

Studying the Complex Expression Dependences between Sets of Coexpressed Genes

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Mario Huerta

2014-01-01

Full Text Available Organisms simplify the orchestration of gene expression by coregulating genes whose products function together in the cell. The use of clustering methods to obtain sets of coexpressed genes from expression arrays is very common; nevertheless there are no appropriate tools to study the expression networks among these sets of coexpressed genes. The aim of the developed tools is to allow studying the complex expression dependences that exist between sets of coexpressed genes. For this purpose, we start detecting the nonlinear expression relationships between pairs of genes, plus the coexpressed genes. Next, we form networks among sets of coexpressed genes that maintain nonlinear expression dependences between all of them. The expression relationship between the sets of coexpressed genes is defined by the expression relationship between the skeletons of these sets, where this skeleton represents the coexpressed genes with a well-defined nonlinear expression relationship with the skeleton of the other sets. As a result, we can study the nonlinear expression relationships between a target gene and other sets of coexpressed genes, or start the study from the skeleton of the sets, to study the complex relationships of activation and deactivation between the sets of coexpressed genes that carry out the different cellular processes present in the expression experiments.

Gene expression of the mismatch repair gene MSH2 in primary colorectal cancer

DEFF Research Database (Denmark)

Jensen, Lars Henrik; Kuramochi, Hidekazu; Crüger, Dorthe Gylling

2011-01-01

promoter was only detected in 14 samples and only at a low level with no correlation to gene expression. MSH2 gene expression was not a prognostic factor for overall survival in univariate or multivariate analysis. The gene expression of MSH2 is a potential quantitative marker ready for further clinical...

A CW Gunn diode bistable switching element.

Science.gov (United States)

Hurtado, M.; Rosenbaum, F. J.

1972-01-01

Experiments with a current-controlled bistable switching element using a CW Gunn diode are reported. Switching rates of the order of 10 MHz have been obtained. Switching is initiated by current pulses of short duration (5-10 ns). Rise times of the order of several nanoseconds could be obtained.

The relationship among gene expression, the evolution of gene dosage, and the rate of protein evolution.

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Jean-François Gout

2010-05-01

Full Text Available The understanding of selective constraints affecting genes is a major issue in biology. It is well established that gene expression level is a major determinant of the rate of protein evolution, but the reasons for this relationship remain highly debated. Here we demonstrate that gene expression is also a major determinant of the evolution of gene dosage: the rate of gene losses after whole genome duplications in the Paramecium lineage is negatively correlated to the level of gene expression, and this relationship is not a byproduct of other factors known to affect the fate of gene duplicates. This indicates that changes in gene dosage are generally more deleterious for highly expressed genes. This rule also holds for other taxa: in yeast, we find a clear relationship between gene expression level and the fitness impact of reduction in gene dosage. To explain these observations, we propose a model based on the fact that the optimal expression level of a gene corresponds to a trade-off between the benefit and cost of its expression. This COSTEX model predicts that selective pressure against mutations changing gene expression level or affecting the encoded protein should on average be stronger in highly expressed genes and hence that both the frequency of gene loss and the rate of protein evolution should correlate negatively with gene expression. Thus, the COSTEX model provides a simple and common explanation for the general relationship observed between the level of gene expression and the different facets of gene evolution.

Noise minimization in eukaryotic gene expression.

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Hunter B Fraser

2004-06-01

Full Text Available All organisms have elaborate mechanisms to control rates of protein production. However, protein production is also subject to stochastic fluctuations, or "noise." Several recent studies in Saccharomyces cerevisiae and Escherichia coli have investigated the relationship between transcription and translation rates and stochastic fluctuations in protein levels, or more generally, how such randomness is a function of intrinsic and extrinsic factors. However, the fundamental question of whether stochasticity in protein expression is generally biologically relevant has not been addressed, and it remains unknown whether random noise in the protein production rate of most genes significantly affects the fitness of any organism. We propose that organisms should be particularly sensitive to variation in the protein levels of two classes of genes: genes whose deletion is lethal to the organism and genes that encode subunits of multiprotein complexes. Using an experimentally verified model of stochastic gene expression in S. cerevisiae, we estimate the noise in protein production for nearly every yeast gene, and confirm our prediction that the production of essential and complex-forming proteins involves lower levels of noise than does the production of most other genes. Our results support the hypothesis that noise in gene expression is a biologically important variable, is generally detrimental to organismal fitness, and is subject to natural selection.

Noise minimization in eukaryotic gene expression

Energy Technology Data Exchange (ETDEWEB)

Fraser, Hunter B.; Hirsh, Aaron E.; Giaever, Guri; Kumm, Jochen; Eisen, Michael B.

2004-01-15

All organisms have elaborate mechanisms to control rates of protein production. However, protein production is also subject to stochastic fluctuations, or noise. Several recent studies in Saccharomyces cerevisiae and Escherichia coli have investigated the relationship between transcription and translation rates and stochastic fluctuations in protein levels, or more generally, how such randomness is a function of intrinsic and extrinsic factors. However, the fundamental question of whether stochasticity in protein expression is generally biologically relevant has not been addressed, and it remains unknown whether random noise in the protein production rate of most genes significantly affects the fitness of any organism. We propose that organisms should be particularly sensitive to variation in the protein levels of two classes of genes: genes whose deletion is lethal to the organism and genes that encode subunits of multiprotein complexes. Using an experimentally verified model of stochastic gene expression in S. cerevisiae, we estimate the noise in protein production for nearly every yeast gene, and confirm our prediction that the production of essential and complex-forming proteins involves lower levels of noise than does the production of most other genes. Our results support the hypothesis that noise in gene expression is a biologically important variable, is generally detrimental to organismal fitness, and is subject to natural selection.

Noise minimization in eukaryotic gene expression

International Nuclear Information System (INIS)

Fraser, Hunter B.; Hirsh, Aaron E.; Giaever, Guri; Kumm, Jochen; Eisen, Michael B.

2004-01-01

All organisms have elaborate mechanisms to control rates of protein production. However, protein production is also subject to stochastic fluctuations, or noise. Several recent studies in Saccharomyces cerevisiae and Escherichia coli have investigated the relationship between transcription and translation rates and stochastic fluctuations in protein levels, or more generally, how such randomness is a function of intrinsic and extrinsic factors. However, the fundamental question of whether stochasticity in protein expression is generally biologically relevant has not been addressed, and it remains unknown whether random noise in the protein production rate of most genes significantly affects the fitness of any organism. We propose that organisms should be particularly sensitive to variation in the protein levels of two classes of genes: genes whose deletion is lethal to the organism and genes that encode subunits of multiprotein complexes. Using an experimentally verified model of stochastic gene expression in S. cerevisiae, we estimate the noise in protein production for nearly every yeast gene, and confirm our prediction that the production of essential and complex-forming proteins involves lower levels of noise than does the production of most other genes. Our results support the hypothesis that noise in gene expression is a biologically important variable, is generally detrimental to organismal fitness, and is subject to natural selection

Stability estimation of autoregulated genes under Michaelis-Menten-type kinetics

Science.gov (United States)

Arani, Babak M. S.; Mahmoudi, Mahdi; Lahti, Leo; González, Javier; Wit, Ernst C.

2018-06-01

Feedback loops are typical motifs appearing in gene regulatory networks. In some well-studied model organisms, including Escherichia coli, autoregulated genes, i.e., genes that activate or repress themselves through their protein products, are the only feedback interactions. For these types of interactions, the Michaelis-Menten (MM) formulation is a suitable and widely used approach, which always leads to stable steady-state solutions representative of homeostatic regulation. However, in many other biological phenomena, such as cell differentiation, cancer progression, and catastrophes in ecosystems, one might expect to observe bistable switchlike dynamics in the case of strong positive autoregulation. To capture this complex behavior we use the generalized family of MM kinetic models. We give a full analysis regarding the stability of autoregulated genes. We show that the autoregulation mechanism has the capability to exhibit diverse cellular dynamics including hysteresis, a typical characteristic of bistable systems, as well as irreversible transitions between bistable states. We also introduce a statistical framework to estimate the kinetics parameters and probability of different stability regimes given observational data. Empirical data for the autoregulated gene SCO3217 in the SOS system in Streptomyces coelicolor are analyzed. The coupling of a statistical framework and the mathematical model can give further insight into understanding the evolutionary mechanisms toward different cell fates in various systems.

Heat dissipation and information flow for delayed bistable Langevin systems near coherence resonance.

Science.gov (United States)

Xiao, Tiejun

2016-11-01

In this paper, stochastic thermodynamics of delayed bistable Langevin systems near coherence resonance is discussed. We calculate the heat dissipation rate and the information flow of a delayed bistable Langevin system under various noise intensities. Both the heat dissipation rate and the information flow are found to be bell-shaped functions of the noise intensity, which implies that coherence resonance manifests itself in the thermodynamic properties.

Positive selection on gene expression in the human brain

DEFF Research Database (Denmark)

Khaitovich, Philipp; Tang, Kun; Franz, Henriette

2006-01-01

Recent work has shown that the expression levels of genes transcribed in the brains of humans and chimpanzees have changed less than those of genes transcribed in other tissues [1] . However, when gene expression changes are mapped onto the evolutionary lineage in which they occurred, the brain...... shows more changes than other tissues in the human lineage compared to the chimpanzee lineage [1] , [2] and [3] . There are two possible explanations for this: either positive selection drove more gene expression changes to fixation in the human brain than in the chimpanzee brain, or genes expressed...... in the brain experienced less purifying selection in humans than in chimpanzees, i.e. gene expression in the human brain is functionally less constrained. The first scenario would be supported if genes that changed their expression in the brain in the human lineage showed more selective sweeps than other genes...

A minimal model of burst-noise induced bistability.

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Johannes Falk

Full Text Available We investigate the influence of intrinsic noise on stable states of a one-dimensional dynamical system that shows in its deterministic version a saddle-node bifurcation between monostable and bistable behaviour. The system is a modified version of the Schlögl model, which is a chemical reaction system with only one type of molecule. The strength of the intrinsic noise is varied without changing the deterministic description by introducing bursts in the autocatalytic production step. We study the transitions between monostable and bistable behavior in this system by evaluating the number of maxima of the stationary probability distribution. We find that changing the size of bursts can destroy and even induce saddle-node bifurcations. This means that a bursty production of molecules can qualitatively change the dynamics of a chemical reaction system even when the deterministic description remains unchanged.

A stochastic approach to multi-gene expression dynamics

International Nuclear Information System (INIS)

Ochiai, T.; Nacher, J.C.; Akutsu, T.

2005-01-01

In the last years, tens of thousands gene expression profiles for cells of several organisms have been monitored. Gene expression is a complex transcriptional process where mRNA molecules are translated into proteins, which control most of the cell functions. In this process, the correlation among genes is crucial to determine the specific functions of genes. Here, we propose a novel multi-dimensional stochastic approach to deal with the gene correlation phenomena. Interestingly, our stochastic framework suggests that the study of the gene correlation requires only one theoretical assumption-Markov property-and the experimental transition probability, which characterizes the gene correlation system. Finally, a gene expression experiment is proposed for future applications of the model

Assays for noninvasive imaging of reporter gene expression

International Nuclear Information System (INIS)

Gambhir, S.S.; Barrio, J.R.; Herschman, H.R.; Phelps, M.E.

1999-01-01

Repeated, noninvasive imaging of reporter gene expression is emerging as a valuable tool for monitoring the expression of genes in animals and humans. Monitoring of organ/cell transplantation in living animals and humans, and the assessment of environmental, behavioral, and pharmacologic modulation of gene expression in transgenic animals should soon be possible. The earliest clinical application is likely to be monitoring human gene therapy in tumors transduced with the herpes simplex virus type 1 thymidine kinase (HSV1-tk) suicide gene. Several candidate assays for imaging reporter gene expression have been studied, utilizing cytosine deaminase (CD), HSV1-tk, and dopamine 2 receptor (D2R) as reporter genes. For the HSV1-tk reporter gene, both uracil nucleoside derivatives (e.g., 5-iodo-2'-fluoro-2'-deoxy-1-β-D-arabinofuranosyl-5-iodouracil [FIAU] labeled with 124 I, 131 I ) and acycloguanosine derivatives {e.g., 8-[ 18 F]fluoro-9-[[2-hydroxy-1-(hydroxymethyl)ethoxy]methyl]guanine (8-[ 18 F]-fluoroganciclovir) ([ 18 F]FGCV), 9-[(3-[ 18 F]fluoro-1-hydroxy-2-propoxy)methyl]guanine ([ 18 F]FHPG)} have been investigated as reporter probes. For the D2R reporter gene, a derivative of spiperone {3-(2'-[ 18 F]-Fluoroethyl)spiperone ([ 18 F]FESP)} has been used with positron emission tomography (PET) imaging. In this review, the principles and specific assays for imaging reporter gene expression are presented and discussed. Specific examples utilizing adenoviral-mediated delivery of a reporter gene as well as tumors expressing reporter genes are discussed

PRAME gene expression profile in medulloblastoma

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Tânia Maria Vulcani-Freitas

2011-02-01

Full Text Available Medulloblastoma is the most common malignant tumors of central nervous system in the childhood. The treatment is severe, harmful and, thus, has a dismal prognosis. As PRAME is present in various cancers, including meduloblastoma, and has limited expression in normal tissues, this antigen can be an ideal vaccine target for tumor immunotherapy. In order to find a potential molecular target, we investigated PRAME expression in medulloblastoma fragments and we compare the results with the clinical features of each patient. Analysis of gene expression was performed by real-time quantitative PCR from 37 tumor samples. The Mann-Whitney test was used to analysis the relationship between gene expression and clinical characteristics. Kaplan-Meier curves were used to evaluate survival. PRAME was overexpressed in 84% samples. But no statistical association was found between clinical features and PRAME overexpression. Despite that PRAME gene could be a strong candidate for immunotherapy since it is highly expressed in medulloblastomas.

Optical bistability of optical fiber ring doped by Erbium and quantum dots

International Nuclear Information System (INIS)

Safari, S.; Tofighi, S.; Bahrampour, A.; Sajad, B.; Shahshahani, F.

2012-01-01

In this paper, theoretical analysis of the steady state behavior of the optical bistability in an optical fiber ring doped by Erbium and quantum dots is presented. The up and down switching power is calculated and the dependence of the switching power on different fiber ring parameters is investigated. The switching power for this type of optical bistability device is obtained much lower than the fiber ring which its half length is doped by Erbium ion.

Systematic identification of human housekeeping genes possibly useful as references in gene expression studies.

Science.gov (United States)

Caracausi, Maria; Piovesan, Allison; Antonaros, Francesca; Strippoli, Pierluigi; Vitale, Lorenza; Pelleri, Maria Chiara

2017-09-01

The ideal reference, or control, gene for the study of gene expression in a given organism should be expressed at a medium‑high level for easy detection, should be expressed at a constant/stable level throughout different cell types and within the same cell type undergoing different treatments, and should maintain these features through as many different tissues of the organism. From a biological point of view, these theoretical requirements of an ideal reference gene appear to be best suited to housekeeping (HK) genes. Recent advancements in the quality and completeness of human expression microarray data and in their statistical analysis may provide new clues toward the quantitative standardization of human gene expression studies in biology and medicine, both cross‑ and within‑tissue. The systematic approach used by the present study is based on the Transcriptome Mapper tool and exploits the automated reassignment of probes to corresponding genes, intra‑ and inter‑sample normalization, elaboration and representation of gene expression values in linear form within an indexed and searchable database with a graphical interface recording quantitative levels of expression, expression variability and cross‑tissue width of expression for more than 31,000 transcripts. The present study conducted a meta‑analysis of a pool of 646 expression profile data sets from 54 different human tissues and identified actin γ 1 as the HK gene that best fits the combination of all the traditional criteria to be used as a reference gene for general use; two ribosomal protein genes, RPS18 and RPS27, and one aquaporin gene, POM121 transmembrane nucleporin C, were also identified. The present study provided a list of tissue‑ and organ‑specific genes that may be most suited for the following individual tissues/organs: Adipose tissue, bone marrow, brain, heart, kidney, liver, lung, ovary, skeletal muscle and testis; and also provides in these cases a representative

Bistable enhanced total reflection in Kretschmann configuration containing a saturable gain medium.

Science.gov (United States)

Zhou, Haichun; Guo, Jie; Xu, Kun; Li, Zhe; Tang, Junqi; Man, Shiqing

2018-03-05

The reflection of a TM-polarized light beam from a Kretschmann configuration with a saturable gain medium is investigated theoretically. Here, the dielectric constant of the gain medium is described by a classical Lorentzian oscillator model. When surface plasmon polaritons are effectively excited in this structure, it is demonstrated that the curves of enhanced total reflection (ETR) show different shaped hysteresis loops associated with optical bistability owing to gain saturation effect. The effects of the angle of incidence, the thickness of metal film, and the value of small-signal gain on bistable ETR are discussed in detail in a homogeneously broadened (HB) gain medium at line center. Analogous results can also be obtained in an inhomogeneously broadened (inHB) gain medium, while the two switch thresholds and the width of optical bistability hysteresis in an inHB gain medium are significantly different from those in a HB gain medium.

SIGNATURE: A workbench for gene expression signature analysis

Directory of Open Access Journals (Sweden)

Chang Jeffrey T

2011-11-01

Full Text Available Abstract Background The biological phenotype of a cell, such as a characteristic visual image or behavior, reflects activities derived from the expression of collections of genes. As such, an ability to measure the expression of these genes provides an opportunity to develop more precise and varied sets of phenotypes. However, to use this approach requires computational methods that are difficult to implement and apply, and thus there is a critical need for intelligent software tools that can reduce the technical burden of the analysis. Tools for gene expression analyses are unusually difficult to implement in a user-friendly way because their application requires a combination of biological data curation, statistical computational methods, and database expertise. Results We have developed SIGNATURE, a web-based resource that simplifies gene expression signature analysis by providing software, data, and protocols to perform the analysis successfully. This resource uses Bayesian methods for processing gene expression data coupled with a curated database of gene expression signatures, all carried out within a GenePattern web interface for easy use and access. Conclusions SIGNATURE is available for public use at http://genepattern.genome.duke.edu/signature/.

Mining gene expression data of multiple sclerosis.

Directory of Open Access Journals (Sweden)

Pi Guo

Full Text Available Microarray produces a large amount of gene expression data, containing various biological implications. The challenge is to detect a panel of discriminative genes associated with disease. This study proposed a robust classification model for gene selection using gene expression data, and performed an analysis to identify disease-related genes using multiple sclerosis as an example.Gene expression profiles based on the transcriptome of peripheral blood mononuclear cells from a total of 44 samples from 26 multiple sclerosis patients and 18 individuals with other neurological diseases (control were analyzed. Feature selection algorithms including Support Vector Machine based on Recursive Feature Elimination, Receiver Operating Characteristic Curve, and Boruta algorithms were jointly performed to select candidate genes associating with multiple sclerosis. Multiple classification models categorized samples into two different groups based on the identified genes. Models' performance was evaluated using cross-validation methods, and an optimal classifier for gene selection was determined.An overlapping feature set was identified consisting of 8 genes that were differentially expressed between the two phenotype groups. The genes were significantly associated with the pathways of apoptosis and cytokine-cytokine receptor interaction. TNFSF10 was significantly associated with multiple sclerosis. A Support Vector Machine model was established based on the featured genes and gave a practical accuracy of ∼86%. This binary classification model also outperformed the other models in terms of Sensitivity, Specificity and F1 score.The combined analytical framework integrating feature ranking algorithms and Support Vector Machine model could be used for selecting genes for other diseases.

Evolution of the bi-stable wake of a square-back automotive shape

Science.gov (United States)

Pavia, Giancarlo; Passmore, Martin; Sardu, Costantino

2018-01-01

Square-back shapes are popular in the automotive market for their high level of practicality. These geometries, however, are usually characterised by high drag and their wake dynamics present aspects, such as the coexistence of a long-time bi-stable behaviour and short-time global fluctuating modes that are not fully understood. In the present paper, the unsteady behaviour of the wake of a generic square-back car geometry is characterised with an emphasis on identifying the causal relationship between the different dynamic modes in the wake. The study is experimental, consisting of balance, pressure, and stereoscopic PIV measurements. Applying wavelet and cross-wavelet transforms to the balance data, a quasi-steady correlation is demonstrated between the forces and bi-stable modes. This is investigated by applying proper orthogonal decomposition to the pressure and velocity data sets and a new structure is proposed for each bi-stable state, consisting of a hairpin vortex that originates from one of the two model's vertical trailing edges and bends towards the opposite side as it merges into a single streamwise vortex downstream. The wake pumping motion is also identified and for the first time linked with the motion of the bi-stable vortical structure in the streamwise direction, resulting in out-of-phase pressure variations between the two vertical halves of the model base. A phase-averaged low-order model is also proposed that provides a comprehensive description of the mechanisms of the switch between the bi-stable states. It is demonstrated that, during the switch, the wake becomes laterally symmetric and, at this point, the level of interaction between the recirculating structures and the base reaches a minimum, yielding, for this geometry, a 7% reduction of the base drag compared to the time-averaged result.

Bistable behavior of the lac operon in E. coli when induced with a mixture of lactose and TMG

Directory of Open Access Journals (Sweden)

Orlando Díaz-Hernández

2010-07-01

Full Text Available In this work we investigate multistability in the lac operon of Escherichia coli when it is induced by a mixture of lactose and the non-metabolizable thiomethyl galactoside (TMG. In accordance with previously published experimental results and computer simulations, our simulations predict that: (1 when the system is induced by TMG, the system shows a discernible bistable behavior while, (2 when the system is induced by lactose, bistability does not disappear but excessively high concentrations of lactose would be required to observe it. Finally, our simulation results predict that when a mixture of lactose and TMG is used, the bistability region in the extracellular glucose concentration vs. extracellular lactose concentration parameter space changes in such a way that the model predictions regarding bistability could be tested experimentally. These experiments could help to solve a recent controversy regarding the existence of bistability in the lac operon under natural conditions.

Bistable behavior of the lac operon in E. coli when induced with a mixture of lactose and TMG.

Science.gov (United States)

Díaz-Hernández, Orlando; Santillán, Moisés

2010-01-01

In this work we investigate multistability in the lac operon of Escherichia coli when it is induced by a mixture of lactose and the non-metabolizable thiomethyl galactoside (TMG). In accordance with previously published experimental results and computer simulations, our simulations predict that: (1) when the system is induced by TMG, the system shows a discernible bistable behavior while, (2) when the system is induced by lactose, bistability does not disappear but excessively high concentrations of lactose would be required to observe it. Finally, our simulation results predict that when a mixture of lactose and TMG is used, the bistability region in the extracellular glucose concentration vs. extracellular lactose concentration parameter space changes in such a way that the model predictions regarding bistability could be tested experimentally. These experiments could help to solve a recent controversy regarding the existence of bistability in the lac operon under natural conditions.

Experimental Analysis of a Coupled Energy Harvesting System with Monostable and Bistable Configuration

International Nuclear Information System (INIS)

Hoffmann, D; Folkmer, B; Manoli, Y

2014-01-01

In this paper we present experimental results from an energy harvesting system with two coupled energy harvesters. The energy conversion mechanism of the two coupled energy harvesters is based on the electromagnetic principle. The coupling is generated by two magnets in a repulsive arrangement. In this manner a bistable configuration can be obtained if the gap between the magnets is sufficiently small. We demonstrate that the total power output can be increased in comparison to a linear reference system, if specific conditions are fulfilled. In this respect, the highest power output occurs in the nonlinear region of a monostable system configuration, mostly near the transition to a bistable configuration. On the other hand, the results also indicate, that a bistable operating mode does not necessarily enhance the power output of the coupled system

Topical Meeting on Optical Bistability Held at Rochester, New York on 15-17 June 1983.

Science.gov (United States)

1983-01-01

ThB16-1 SELF-BEATING INSTABILITIES IN BISTABLE DEVICES J.A. MARTIN-PEREDA .. M.A. MURIEL DEPARTAMENTO DE ELECTRONICA CUANTICA E.T.S. ING...OPTICAL BISTABLL SYSTEMS J.A. MARTIN PEREDA M.A. MURIEL ; DEPARTAMENIO DE ELECTRONICA CUANTICA E.T.S. ING. TELLCOMUNICACION UNIVERSIDAD POLITECNICA DE

An Optically Driven Bistable Janus Rotor with Patterned Metal Coatings.

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Zong, Yiwu; Liu, Jing; Liu, Rui; Guo, Honglian; Yang, Mingcheng; Li, Zhiyuan; Chen, Ke

2015-11-24

Bistable rotation is realized for a gold-coated Janus colloidal particle in an infrared optical trap. The metal coating on the Janus particles are patterned by sputtering gold on a monolayer of closely packed polystyrene particles. The Janus particle is observed to stably rotate in an optical trap. Both the direction and the rate of rotation can be experimentally controlled. Numerical calculations reveal that the bistable rotation is the result of spontaneous symmetry breaking induced by the uneven curvature of the coating patterns on the Janus sphere. Our results thus provide a simple method to construct large quantities of fully functional rotary motors for nano- or microdevices.

Mathematical modeling of Myosin induced bistability of Lamellipodial fragments.

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Hirsch, S; Manhart, A; Schmeiser, C

2017-01-01

For various cell types and for lamellipodial fragments on flat surfaces, externally induced and spontaneous transitions between symmetric nonmoving states and polarized migration have been observed. This behavior is indicative of bistability of the cytoskeleton dynamics. In this work, the Filament Based Lamellipodium Model (FBLM), a two-dimensional, anisotropic, two-phase continuum model for the dynamics of the actin filament network in lamellipodia, is extended by a new description of actin-myosin interaction. For appropriately chosen parameter values, the resulting model has bistable dynamics with stable states showing the qualitative features observed in experiments. This is demonstrated by numerical simulations and by an analysis of a strongly simplified version of the FBLM with rigid filaments and planar lamellipodia at the cell front and rear.

Plasticity-Related Gene Expression During Eszopiclone-Induced Sleep.

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Gerashchenko, Dmitry; Pasumarthi, Ravi K; Kilduff, Thomas S

2017-07-01

Experimental evidence suggests that restorative processes depend on synaptic plasticity changes in the brain during sleep. We used the expression of plasticity-related genes to assess synaptic plasticity changes during drug-induced sleep. We first characterized sleep induced by eszopiclone in mice during baseline conditions and during the recovery from sleep deprivation. We then compared the expression of 18 genes and two miRNAs critically involved in synaptic plasticity in these mice. Gene expression was assessed in the cerebral cortex and hippocampus by the TaqMan reverse transcription polymerase chain reaction and correlated with sleep parameters. Eszopiclone reduced the latency to nonrapid eye movement (NREM) sleep and increased NREM sleep amounts. Eszopiclone had no effect on slow wave activity (SWA) during baseline conditions but reduced the SWA increase during recovery sleep (RS) after sleep deprivation. Gene expression analyses revealed three distinct patterns: (1) four genes had higher expression either in the cortex or hippocampus in the group of mice with increased amounts of wakefulness; (2) a large proportion of plasticity-related genes (7 out of 18 genes) had higher expression during RS in the cortex but not in the hippocampus; and (3) six genes and the two miRNAs showed no significant changes across conditions. Even at a relatively high dose (20 mg/kg), eszopiclone did not reduce the expression of plasticity-related genes during RS period in the cortex. These results indicate that gene expression associated with synaptic plasticity occurs in the cortex in the presence of a hypnotic medication. © Sleep Research Society 2017. Published by Oxford University Press on behalf of the Sleep Research Society. All rights reserved. For permissions, please e-mail journals.permissions@oup.com.

Evaluation of suitable reference genes for gene expression studies in bovine muscular tissue

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Dunner Susana

2008-09-01

Full Text Available Abstract Background Real-time reverse transcriptase quantitative polymerase chain reaction (real-time RTqPCR is a technique used to measure mRNA species copy number as a way to determine key genes involved in different biological processes. However, the expression level of these key genes may vary among tissues or cells not only as a consequence of differential expression but also due to different factors, including choice of reference genes to normalize the expression levels of the target genes; thus the selection of reference genes is critical for expression studies. For this purpose, ten candidate reference genes were investigated in bovine muscular tissue. Results The value of stability of ten candidate reference genes included in three groups was estimated: the so called 'classical housekeeping' genes (18S, GAPDH and ACTB, a second set of genes used in expression studies conducted on other tissues (B2M, RPII, UBC and HMBS and a third set of novel genes (SF3A1, EEF1A2 and CASC3. Three different statistical algorithms were used to rank the genes by their stability measures as produced by geNorm, NormFinder and Bestkeeper. The three methods tend to agree on the most stably expressed genes and the least in muscular tissue. EEF1A2 and HMBS followed by SF3A1, ACTB, and CASC3 can be considered as stable reference genes, and B2M, RPII, UBC and GAPDH would not be appropriate. Although the rRNA-18S stability measure seems to be within the range of acceptance, its use is not recommended because its synthesis regulation is not representative of mRNA levels. Conclusion Based on geNorm algorithm, we propose the use of three genes SF3A1, EEF1A2 and HMBS as references for normalization of real-time RTqPCR in muscle expression studies.

Investigation of bistable perception with the "silhouette spinner": sit still, spin the dancer with your will.

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Liu, Chao-Hsuan; Tzeng, Ovid J L; Hung, Daisy L; Tseng, Philip; Juan, Chi-Hung

2012-05-01

Many studies have used static and non-biologically related stimuli to investigate bistable perception and found that the percept is usually dominated by their intrinsic nature with some influence of voluntary control from the viewer. Here we used a dynamic stimulus of a rotating human body, the silhouette spinner illusion, to investigate how the viewers' intentions may affect their percepts. In two experiments, we manipulated observer intention (active or passive), fixation position (body or feet), and spinning velocity (fast, medium, or slow). Our results showed that the normalized alternating rate between two bistable percepts was greater when (1) participants actively attempted to switch percepts, (2) when participants fixated at the spinner's feet rather than the body, inducing as many as 25 switches of the bistable percepts within 1 min, and (3) when they watched the spinner at high velocity. These results suggest that a dynamic biologically-bistable percept can be quickly alternated by the viewers' intention. Furthermore, the higher alternating rate in the feet condition compared to the body condition suggests a role for biological meaningfulness in determining bistable percepts, where 'biologically plausible' interpretations are favored by the visual system. Copyright © 2012 Elsevier Ltd. All rights reserved.

Expression profiling identifies genes involved in emphysema severity

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Bowman Rayleen V

2009-09-01

Full Text Available Abstract Chronic obstructive pulmonary disease (COPD is a major public health problem. The aim of this study was to identify genes involved in emphysema severity in COPD patients. Gene expression profiling was performed on total RNA extracted from non-tumor lung tissue from 30 smokers with emphysema. Class comparison analysis based on gas transfer measurement was performed to identify differentially expressed genes. Genes were then selected for technical validation by quantitative reverse transcriptase-PCR (qRT-PCR if also represented on microarray platforms used in previously published emphysema studies. Genes technically validated advanced to tests of biological replication by qRT-PCR using an independent test set of 62 lung samples. Class comparison identified 98 differentially expressed genes (p p Gene expression profiling of lung from emphysema patients identified seven candidate genes associated with emphysema severity including COL6A3, SERPINF1, ZNHIT6, NEDD4, CDKN2A, NRN1 and GSTM3.

Decoupling Linear and Nonlinear Associations of Gene Expression

KAUST Repository

Itakura, Alan

2013-05-01

The FANTOM consortium has generated a large gene expression dataset of different cell lines and tissue cultures using the single-molecule sequencing technology of HeliscopeCAGE. This provides a unique opportunity to investigate novel associations between gene expression over time and different cell types. Here, we create a MatLab wrapper for a powerful and computationally intensive set of statistics known as Maximal Information Coefficient, and then calculate this statistic for a large, comprehensive dataset containing gene expression of a variety of differentiating tissues. We then distinguish between linear and nonlinear associations, and then create gene association networks. Following this analysis, we are then able to identify clusters of linear gene associations that then associate nonlinearly with other clusters of linearity, providing insight to much more complex connections between gene expression patterns than previously anticipated.

Decoupling Linear and Nonlinear Associations of Gene Expression

KAUST Repository

Itakura, Alan

2013-01-01

The FANTOM consortium has generated a large gene expression dataset of different cell lines and tissue cultures using the single-molecule sequencing technology of HeliscopeCAGE. This provides a unique opportunity to investigate novel associations between gene expression over time and different cell types. Here, we create a MatLab wrapper for a powerful and computationally intensive set of statistics known as Maximal Information Coefficient, and then calculate this statistic for a large, comprehensive dataset containing gene expression of a variety of differentiating tissues. We then distinguish between linear and nonlinear associations, and then create gene association networks. Following this analysis, we are then able to identify clusters of linear gene associations that then associate nonlinearly with other clusters of linearity, providing insight to much more complex connections between gene expression patterns than previously anticipated.

Genetic architecture of gene expression in the chicken

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Stanley Dragana

2013-01-01

Full Text Available Abstract Background The annotation of many genomes is limited, with a large proportion of identified genes lacking functional assignments. The construction of gene co-expression networks is a powerful approach that presents a way of integrating information from diverse gene expression datasets into a unified analysis which allows inferences to be drawn about the role of previously uncharacterised genes. Using this approach, we generated a condition-free gene co-expression network for the chicken using data from 1,043 publically available Affymetrix GeneChip Chicken Genome Arrays. This data was generated from a diverse range of experiments, including different tissues and experimental conditions. Our aim was to identify gene co-expression modules and generate a tool to facilitate exploration of the functional chicken genome. Results Fifteen modules, containing between 24 and 473 genes, were identified in the condition-free network. Most of the modules showed strong functional enrichment for particular Gene Ontology categories. However, a few showed no enrichment. Transcription factor binding site enrichment was also noted. Conclusions We have demonstrated that this chicken gene co-expression network is a useful tool in gene function prediction and the identification of putative novel transcription factors and binding sites. This work highlights the relevance of this methodology for functional prediction in poorly annotated genomes such as the chicken.

Anticipating regime shifts in gene expression: The case of an autoactivating positive feedback loop

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Sharma, Yogita; Dutta, Partha Sharathi; Gupta, A. K.

2016-03-01

Considerable evidence suggests that anticipating sudden shifts from one state to another in bistable dynamical systems is a challenging task; examples include ecosystems, financial markets, and complex diseases. In this paper, we investigate the effects of additive, multiplicative, and cross-correlated stochastic perturbations on determining the regime shifts in a bistable gene regulatory system, which gives rise to two distinct states of low and high concentrations of protein. We obtain the stationary probability density and mean first-passage time of the system. We show that increasing the additive (multiplicative) noise intensity induces a regime shift from a low (high) to a high (low) protein concentration state. However, an increase in the cross-correlation intensity always induces regime shifts from a high to a low protein concentration state. For both bifurcation-induced (often called the tipping point) and noise-induced (called stochastic switching) regime shifts, we further explore the robustness of recently developed critical-down-based early warning signal (EWS) indicators (e.g., rising variance and lag-1 autocorrelation) on our simulated time-series data. We identify that using EWS indicators, prediction of an impending bifurcation-induced regime shift is relatively easier than that of a noise-induced regime shift in the considered system. Moreover, the success of EWS indicators also strongly depends upon the nature of the noise.

Bayesian assignment of gene ontology terms to gene expression experiments

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Sykacek, P.

2012-01-01

Motivation: Gene expression assays allow for genome scale analyses of molecular biological mechanisms. State-of-the-art data analysis provides lists of involved genes, either by calculating significance levels of mRNA abundance or by Bayesian assessments of gene activity. A common problem of such approaches is the difficulty of interpreting the biological implication of the resulting gene lists. This lead to an increased interest in methods for inferring high-level biological information. A common approach for representing high level information is by inferring gene ontology (GO) terms which may be attributed to the expression data experiment. Results: This article proposes a probabilistic model for GO term inference. Modelling assumes that gene annotations to GO terms are available and gene involvement in an experiment is represented by a posterior probabilities over gene-specific indicator variables. Such probability measures result from many Bayesian approaches for expression data analysis. The proposed model combines these indicator probabilities in a probabilistic fashion and provides a probabilistic GO term assignment as a result. Experiments on synthetic and microarray data suggest that advantages of the proposed probabilistic GO term inference over statistical test-based approaches are in particular evident for sparsely annotated GO terms and in situations of large uncertainty about gene activity. Provided that appropriate annotations exist, the proposed approach is easily applied to inferring other high level assignments like pathways. Availability: Source code under GPL license is available from the author. Contact: peter.sykacek@boku.ac.at PMID:22962488

Bayesian assignment of gene ontology terms to gene expression experiments.

Science.gov (United States)

Sykacek, P

2012-09-15

Gene expression assays allow for genome scale analyses of molecular biological mechanisms. State-of-the-art data analysis provides lists of involved genes, either by calculating significance levels of mRNA abundance or by Bayesian assessments of gene activity. A common problem of such approaches is the difficulty of interpreting the biological implication of the resulting gene lists. This lead to an increased interest in methods for inferring high-level biological information. A common approach for representing high level information is by inferring gene ontology (GO) terms which may be attributed to the expression data experiment. This article proposes a probabilistic model for GO term inference. Modelling assumes that gene annotations to GO terms are available and gene involvement in an experiment is represented by a posterior probabilities over gene-specific indicator variables. Such probability measures result from many Bayesian approaches for expression data analysis. The proposed model combines these indicator probabilities in a probabilistic fashion and provides a probabilistic GO term assignment as a result. Experiments on synthetic and microarray data suggest that advantages of the proposed probabilistic GO term inference over statistical test-based approaches are in particular evident for sparsely annotated GO terms and in situations of large uncertainty about gene activity. Provided that appropriate annotations exist, the proposed approach is easily applied to inferring other high level assignments like pathways. Source code under GPL license is available from the author. peter.sykacek@boku.ac.at.

Gene expression profile data for mouse facial development

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Sonia M. Leach

2017-08-01

Full Text Available This article contains data related to the research articles "Spatial and Temporal Analysis of Gene Expression during Growth and Fusion of the Mouse Facial Prominences" (Feng et al., 2009 [1] and “Systems Biology of facial development: contributions of ectoderm and mesenchyme” (Hooper et al., 2017 In press [2]. Embryonic mammalian craniofacial development is a complex process involving the growth, morphogenesis, and fusion of distinct facial prominences into a functional whole. Aberrant gene regulation during this process can lead to severe craniofacial birth defects, including orofacial clefting. As a means to understand the genes involved in facial development, we had previously dissected the embryonic mouse face into distinct prominences: the mandibular, maxillary or nasal between E10.5 and E12.5. The prominences were then processed intact, or separated into ectoderm and mesenchyme layers, prior analysis of RNA expression using microarrays (Feng et al., 2009, Hooper et al., 2017 in press [1,2]. Here, individual gene expression profiles have been built from these datasets that illustrate the timing of gene expression in whole prominences or in the separated tissue layers. The data profiles are presented as an indexed and clickable list of the genes each linked to a graphical image of that gene׳s expression profile in the ectoderm, mesenchyme, or intact prominence. These data files will enable investigators to obtain a rapid assessment of the relative expression level of any gene on the array with respect to time, tissue, prominence, and expression trajectory.

Integrated olfactory receptor and microarray gene expression databases

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Crasto Chiquito J

2007-06-01

Full Text Available Abstract Background Gene expression patterns of olfactory receptors (ORs are an important component of the signal encoding mechanism in the olfactory system since they determine the interactions between odorant ligands and sensory neurons. We have developed the Olfactory Receptor Microarray Database (ORMD to house OR gene expression data. ORMD is integrated with the Olfactory Receptor Database (ORDB, which is a key repository of OR gene information. Both databases aim to aid experimental research related to olfaction. Description ORMD is a Web-accessible database that provides a secure data repository for OR microarray experiments. It contains both publicly available and private data; accessing the latter requires authenticated login. The ORMD is designed to allow users to not only deposit gene expression data but also manage their projects/experiments. For example, contributors can choose whether to make their datasets public. For each experiment, users can download the raw data files and view and export the gene expression data. For each OR gene being probed in a microarray experiment, a hyperlink to that gene in ORDB provides access to genomic and proteomic information related to the corresponding olfactory receptor. Individual ORs archived in ORDB are also linked to ORMD, allowing users access to the related microarray gene expression data. Conclusion ORMD serves as a data repository and project management system. It facilitates the study of microarray experiments of gene expression in the olfactory system. In conjunction with ORDB, ORMD integrates gene expression data with the genomic and functional data of ORs, and is thus a useful resource for both olfactory researchers and the public.

Gene expression analysis of flax seed development

Science.gov (United States)

2011-01-01

Background Flax, Linum usitatissimum L., is an important crop whose seed oil and stem fiber have multiple industrial applications. Flax seeds are also well-known for their nutritional attributes, viz., omega-3 fatty acids in the oil and lignans and mucilage from the seed coat. In spite of the importance of this crop, there are few molecular resources that can be utilized toward improving seed traits. Here, we describe flax embryo and seed development and generation of comprehensive genomic resources for the flax seed. Results We describe a large-scale generation and analysis of expressed sequences in various tissues. Collectively, the 13 libraries we have used provide a broad representation of genes active in developing embryos (globular, heart, torpedo, cotyledon and mature stages) seed coats (globular and torpedo stages) and endosperm (pooled globular to torpedo stages) and genes expressed in flowers, etiolated seedlings, leaves, and stem tissue. A total of 261,272 expressed sequence tags (EST) (GenBank accessions LIBEST_026995 to LIBEST_027011) were generated. These EST libraries included transcription factor genes that are typically expressed at low levels, indicating that the depth is adequate for in silico expression analysis. Assembly of the ESTs resulted in 30,640 unigenes and 82% of these could be identified on the basis of homology to known and hypothetical genes from other plants. When compared with fully sequenced plant genomes, the flax unigenes resembled poplar and castor bean more than grape, sorghum, rice or Arabidopsis. Nearly one-fifth of these (5,152) had no homologs in sequences reported for any organism, suggesting that this category represents genes that are likely unique to flax. Digital analyses revealed gene expression dynamics for the biosynthesis of a number of important seed constituents during seed development. Conclusions We have developed a foundational database of expressed sequences and collection of plasmid clones that comprise

Gene expression analysis of flax seed development

Directory of Open Access Journals (Sweden)

Sharpe Andrew

2011-04-01

Full Text Available Abstract Background Flax, Linum usitatissimum L., is an important crop whose seed oil and stem fiber have multiple industrial applications. Flax seeds are also well-known for their nutritional attributes, viz., omega-3 fatty acids in the oil and lignans and mucilage from the seed coat. In spite of the importance of this crop, there are few molecular resources that can be utilized toward improving seed traits. Here, we describe flax embryo and seed development and generation of comprehensive genomic resources for the flax seed. Results We describe a large-scale generation and analysis of expressed sequences in various tissues. Collectively, the 13 libraries we have used provide a broad representation of genes active in developing embryos (globular, heart, torpedo, cotyledon and mature stages seed coats (globular and torpedo stages and endosperm (pooled globular to torpedo stages and genes expressed in flowers, etiolated seedlings, leaves, and stem tissue. A total of 261,272 expressed sequence tags (EST (GenBank accessions LIBEST_026995 to LIBEST_027011 were generated. These EST libraries included transcription factor genes that are typically expressed at low levels, indicating that the depth is adequate for in silico expression analysis. Assembly of the ESTs resulted in 30,640 unigenes and 82% of these could be identified on the basis of homology to known and hypothetical genes from other plants. When compared with fully sequenced plant genomes, the flax unigenes resembled poplar and castor bean more than grape, sorghum, rice or Arabidopsis. Nearly one-fifth of these (5,152 had no homologs in sequences reported for any organism, suggesting that this category represents genes that are likely unique to flax. Digital analyses revealed gene expression dynamics for the biosynthesis of a number of important seed constituents during seed development. Conclusions We have developed a foundational database of expressed sequences and collection of plasmid

Traveling and Pinned Fronts in Bistable Reaction-Diffusion Systems on Networks

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Kouvaris, Nikos E.; Kori, Hiroshi; Mikhailov, Alexander S.

2012-01-01

Traveling fronts and stationary localized patterns in bistable reaction-diffusion systems have been broadly studied for classical continuous media and regular lattices. Analogs of such non-equilibrium patterns are also possible in networks. Here, we consider traveling and stationary patterns in bistable one-component systems on random Erdös-Rényi, scale-free and hierarchical tree networks. As revealed through numerical simulations, traveling fronts exist in network-organized systems. They represent waves of transition from one stable state into another, spreading over the entire network. The fronts can furthermore be pinned, thus forming stationary structures. While pinning of fronts has previously been considered for chains of diffusively coupled bistable elements, the network architecture brings about significant differences. An important role is played by the degree (the number of connections) of a node. For regular trees with a fixed branching factor, the pinning conditions are analytically determined. For large Erdös-Rényi and scale-free networks, the mean-field theory for stationary patterns is constructed. PMID:23028746

Supplementary Material for: Global expression differences and tissue specific expression differences in rice evolution result in two contrasting types of differentially expressed genes

KAUST Repository

Horiuchi, Youko; Harushima, Yoshiaki; Fujisawa, Hironori; Mochizuki, Takako; Fujita, Masahiro; Ohyanagi, Hajime; Kurata, Nori

2015-01-01

Abstract Background Since the development of transcriptome analysis systems, many expression evolution studies characterized evolutionary forces acting on gene expression, without explicit discrimination between global expression differences and tissue specific expression differences. However, different types of gene expression alteration should have different effects on an organism, the evolutionary forces that act on them might be different, and different types of genes might show different types of differential expression between species. To confirm this, we studied differentially expressed (DE) genes among closely related groups that have extensive gene expression atlases, and clarified characteristics of different types of DE genes including the identification of regulating loci for differential expression using expression quantitative loci (eQTL) analysis data. Results We detected differentially expressed (DE) genes between rice subspecies in five homologous tissues that were verified using japonica and indica transcriptome atlases in public databases. Using the transcriptome atlases, we classified DE genes into two types, global DE genes and changed-tissues DE genes. Global type DE genes were not expressed in any tissues in the atlas of one subspecies, however changed-tissues type DE genes were expressed in both subspecies with different tissue specificity. For the five tissues in the two japonica-indica combinations, 4.6 ± 0.8 and 5.9 ± 1.5 % of highly expressed genes were global and changed-tissues DE genes, respectively. Changed-tissues DE genes varied in number between tissues, increasing linearly with the abundance of tissue specifically expressed genes in the tissue. Molecular evolution of global DE genes was rapid, unlike that of changed-tissues DE genes. Based on gene ontology, global and changed-tissues DE genes were different, having no common GO terms. Expression differences of most global DE genes were regulated by cis

Optical bistability in a single-sided cavity coupled to a quantum channel

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Payravi, M.; Solookinejad, Gh; Jabbari, M.; Nafar, M.; Ahmadi Sangachin, E.

2018-06-01

In this paper, we discuss the long wavelength optical reflection and bistable behavior of an InGaN/GaN quantum dot nanostructure coupled to a single-sided cavity. It is found that due to the presence of a strong coupling field, the reflection coefficient can be controlled at long wavelength, which is essential for adjusting the threshold of reflected optical bistability. Moreover, the phase shift features of the reflection pulse inside an electromagnetically induced transparency window are also discussed.

Toward Singlet-Triplet Bistable Nonalternant Kekulé Hydrocarbons: Azulene-to-Naphthalene Rearrangement.

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Das, Soumyajit; Wu, Jishan

2015-12-04

Recent developments of open-shell singlet diradicaloids motivated the search for stable singlet-triplet bistable nonalternant polycyclic hydrocarbons. During the synthesis of this type of molecule, such as the dibenzo-cyclohepta[def]fluorene 3, an unexpected azulene-to-naphthalene rearrangement was observed at room temperature, which resulted in new nonalternant hydrocarbons 8a/8b with a closed-shell singlet ground state. These studies provided insight into the unique chemistry of azulene and challenges for the synthesis of singlet-triplet bistable polycyclic hydrocarbons.

Identification of suitable reference genes for gene expression studies of shoulder instability.

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Mariana Ferreira Leal

Full Text Available Shoulder instability is a common shoulder injury, and patients present with plastic deformation of the glenohumeral capsule. Gene expression analysis may be a useful tool for increasing the general understanding of capsule deformation, and reverse-transcription quantitative polymerase chain reaction (RT-qPCR has become an effective method for such studies. Although RT-qPCR is highly sensitive and specific, it requires the use of suitable reference genes for data normalization to guarantee meaningful and reproducible results. In the present study, we evaluated the suitability of a set of reference genes using samples from the glenohumeral capsules of individuals with and without shoulder instability. We analyzed the expression of six commonly used reference genes (ACTB, B2M, GAPDH, HPRT1, TBP and TFRC in the antero-inferior, antero-superior and posterior portions of the glenohumeral capsules of cases and controls. The stability of the candidate reference gene expression was determined using four software packages: NormFinder, geNorm, BestKeeper and DataAssist. Overall, HPRT1 was the best single reference gene, and HPRT1 and B2M composed the best pair of reference genes from different analysis groups, including simultaneous analysis of all tissue samples. GenEx software was used to identify the optimal number of reference genes to be used for normalization and demonstrated that the accumulated standard deviation resulting from the use of 2 reference genes was similar to that resulting from the use of 3 or more reference genes. To identify the optimal combination of reference genes, we evaluated the expression of COL1A1. Although the use of different reference gene combinations yielded variable normalized quantities, the relative quantities within sample groups were similar and confirmed that no obvious differences were observed when using 2, 3 or 4 reference genes. Consequently, the use of 2 stable reference genes for normalization, especially

The interplay of multiple feedback loops with post-translational kinetics results in bistability of mycobacterial stress response

International Nuclear Information System (INIS)

Tiwari, Abhinav; Igoshin, Oleg A; Balázsi, Gábor; Gennaro, Maria Laura

2010-01-01

Bacterial persistence is the phenomenon in which a genetically identical fraction of a bacterial population can survive exposure to stress by reduction or cessation of growth. Persistence in mycobacteria has been recently linked to a stress-response network, consisting of the MprA/MprB two-component system and alternative sigma factor σ E . This network contains multiple positive transcriptional feedback loops which may give rise to bistability, making it a good candidate for controlling the mycobacterial persistence switch. To analyze the possibility of bistability, we develop a method that involves decoupling of the network into transcriptional and post-translational interaction modules. As a result we reduce the dimensionality of the dynamical system and independently analyze input–output relations in the two modules to formulate a necessary condition for bistability in terms of their logarithmic gains. We show that neither the positive autoregulation in the MprA/MprB network nor the σ E -mediated transcriptional feedback is sufficient to induce bistability in a biochemically realistic parameter range. Nonetheless, inclusion of the post-translational regulation of σ E by RseA increases the effective cooperativity of the system, resulting in bistability that is robust to parameter variation. We predict that overexpression or deletion of RseA, the key element controlling the ultrasensitive response, can eliminate bistability

Bistable switches control memory and plasticity in cellular differentiation

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Wang, Lei; Walker, Brandon L.; Iannaccone, Stephen; Bhatt, Devang; Kennedy, Patrick J.; Tse, William T.

2009-01-01

Development of stem and progenitor cells into specialized tissues in multicellular organisms involves a series of cell fate decisions. Cellular differentiation in higher organisms is generally considered irreversible, and the idea of developmental plasticity in postnatal tissues is controversial. Here, we show that inhibition of mitogen-activated protein kinase (MAPK) in a human bone marrow stromal cell-derived myogenic subclone suppresses their myogenic ability and converts them into satellite cell-like precursors that respond to osteogenic stimulation. Clonal analysis of the induced osteogenic response reveals ultrasensitivity and an “all-or-none” behavior, hallmarks of a bistable switch mechanism with stochastic noise. The response demonstrates cellular memory, which is contingent on the accumulation of an intracellular factor and can be erased by factor dilution through cell divisions or inhibition of protein synthesis. The effect of MAPK inhibition also exhibits memory and appears to be controlled by another bistable switch further upstream that determines cell fate. Once the memory associated with osteogenic differentiation is erased, the cells regain their myogenic ability. These results support a model of cell fate decision in which a network of bistable switches controls inducible production of lineage-specific differentiation factors. A competitive balance between these factors determines cell fate. Our work underscores the dynamic nature of cellular differentiation and explains mechanistically the dual properties of stability and plasticity associated with the process. PMID:19366677

Detecting microRNA activity from gene expression data

LENUS (Irish Health Repository)

Madden, Stephen F

2010-05-18

Abstract Background MicroRNAs (miRNAs) are non-coding RNAs that regulate gene expression by binding to the messenger RNA (mRNA) of protein coding genes. They control gene expression by either inhibiting translation or inducing mRNA degradation. A number of computational techniques have been developed to identify the targets of miRNAs. In this study we used predicted miRNA-gene interactions to analyse mRNA gene expression microarray data to predict miRNAs associated with particular diseases or conditions. Results Here we combine correspondence analysis, between group analysis and co-inertia analysis (CIA) to determine which miRNAs are associated with differences in gene expression levels in microarray data sets. Using a database of miRNA target predictions from TargetScan, TargetScanS, PicTar4way PicTar5way, and miRanda and combining these data with gene expression levels from sets of microarrays, this method produces a ranked list of miRNAs associated with a specified split in samples. We applied this to three different microarray datasets, a papillary thyroid carcinoma dataset, an in-house dataset of lipopolysaccharide treated mouse macrophages, and a multi-tissue dataset. In each case we were able to identified miRNAs of biological importance. Conclusions We describe a technique to integrate gene expression data and miRNA target predictions from multiple sources.

Detecting microRNA activity from gene expression data.

LENUS (Irish Health Repository)

Madden, Stephen F

2010-01-01

BACKGROUND: MicroRNAs (miRNAs) are non-coding RNAs that regulate gene expression by binding to the messenger RNA (mRNA) of protein coding genes. They control gene expression by either inhibiting translation or inducing mRNA degradation. A number of computational techniques have been developed to identify the targets of miRNAs. In this study we used predicted miRNA-gene interactions to analyse mRNA gene expression microarray data to predict miRNAs associated with particular diseases or conditions. RESULTS: Here we combine correspondence analysis, between group analysis and co-inertia analysis (CIA) to determine which miRNAs are associated with differences in gene expression levels in microarray data sets. Using a database of miRNA target predictions from TargetScan, TargetScanS, PicTar4way PicTar5way, and miRanda and combining these data with gene expression levels from sets of microarrays, this method produces a ranked list of miRNAs associated with a specified split in samples. We applied this to three different microarray datasets, a papillary thyroid carcinoma dataset, an in-house dataset of lipopolysaccharide treated mouse macrophages, and a multi-tissue dataset. In each case we were able to identified miRNAs of biological importance. CONCLUSIONS: We describe a technique to integrate gene expression data and miRNA target predictions from multiple sources.

Gene expression results in lipopolysaccharide-stimulated monocytes depend significantly on the choice of reference genes

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Øvstebø Reidun

2010-05-01

Full Text Available Abstract Background Gene expression in lipopolysaccharide (LPS-stimulated monocytes is mainly studied by quantitative real-time reverse transcription PCR (RT-qPCR using GAPDH (glyceraldehyde 3-phosphate dehydrogenase or ACTB (beta-actin as reference gene for normalization. Expression of traditional reference genes has been shown to vary substantially under certain conditions leading to invalid results. To investigate whether traditional reference genes are stably expressed in LPS-stimulated monocytes or if RT-qPCR results are dependent on the choice of reference genes, we have assessed and evaluated gene expression stability of twelve candidate reference genes in this model system. Results Twelve candidate reference genes were quantified by RT-qPCR in LPS-stimulated, human monocytes and evaluated using the programs geNorm, Normfinder and BestKeeper. geNorm ranked PPIB (cyclophilin B, B2M (beta-2-microglobulin and PPIA (cyclophilin A as the best combination for gene expression normalization in LPS-stimulated monocytes. Normfinder suggested TBP (TATA-box binding protein and B2M as the best combination. Compared to these combinations, normalization using GAPDH alone resulted in significantly higher changes of TNF-α (tumor necrosis factor-alpha and IL10 (interleukin 10 expression. Moreover, a significant difference in TNF-α expression between monocytes stimulated with equimolar concentrations of LPS from N. meningitides and E. coli, respectively, was identified when using the suggested combinations of reference genes for normalization, but stayed unrecognized when employing a single reference gene, ACTB or GAPDH. Conclusions Gene expression levels in LPS-stimulated monocytes based on RT-qPCR results differ significantly when normalized to a single gene or a combination of stably expressed reference genes. Proper evaluation of reference gene stabiliy is therefore mandatory before reporting RT-qPCR results in LPS-stimulated monocytes.

Differentially expressed genes in iron-induced prion protein conversion

International Nuclear Information System (INIS)

Kim, Minsun; Kim, Eun-hee; Choi, Bo-Ran; Woo, Hee-Jong

2016-01-01

The conversion of the cellular prion protein (PrP C ) to the protease-resistant isoform is the key event in chronic neurodegenerative diseases, including transmissible spongiform encephalopathies (TSEs). Increased iron in prion-related disease has been observed due to the prion protein-ferritin complex. Additionally, the accumulation and conversion of recombinant PrP (rPrP) is specifically derived from Fe(III) but not Fe(II). Fe(III)-mediated PK-resistant PrP (PrP res ) conversion occurs within a complex cellular environment rather than via direct contact between rPrP and Fe(III). In this study, differentially expressed genes correlated with prion degeneration by Fe(III) were identified using Affymetrix microarrays. Following Fe(III) treatment, 97 genes were differentially expressed, including 85 upregulated genes and 12 downregulated genes (≥1.5-fold change in expression). However, Fe(II) treatment produced moderate alterations in gene expression without inducing dramatic alterations in gene expression profiles. Moreover, functional grouping of identified genes indicated that the differentially regulated genes were highly associated with cell growth, cell maintenance, and intra- and extracellular transport. These findings showed that Fe(III) may influence the expression of genes involved in PrP folding by redox mechanisms. The identification of genes with altered expression patterns in neural cells may provide insights into PrP conversion mechanisms during the development and progression of prion-related diseases. - Highlights: • Differential genes correlated with prion degeneration by Fe(III) were identified. • Genes were identified in cell proliferation and intra- and extracellular transport. • In PrP degeneration, redox related genes were suggested. • Cbr2, Rsad2, Slc40a1, Amph and Mvd were expressed significantly.

Regulation of meiotic gene expression in plants

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Adele eZhou

2014-08-01

Full Text Available With the recent advances in genomics and sequencing technologies, databases of transcriptomes representing many cellular processes have been built. Meiotic transcriptomes in plants have been studied in Arabidopsis thaliana, rice (Oryza sativa, wheat (Triticum aestivum, petunia (Petunia hybrida, sunflower (Helianthus annuus, and maize (Zea mays. Studies in all organisms, but particularly in plants, indicate that a very large number of genes are expressed during meiosis, though relatively few of them seem to be required for the completion of meiosis. In this review, we focus on gene expression at the RNA level and analyze the meiotic transcriptome datasets and explore expression patterns of known meiotic genes to elucidate how gene expression could be regulated during meiosis. We also discuss mechanisms, such as chromatin organization and non-coding RNAs, that might be involved in the regulation of meiotic transcription patterns.

Evaluating the consistency of gene sets used in the analysis of bacterial gene expression data

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Tintle Nathan L

2012-08-01

Full Text Available Abstract Background Statistical analyses of whole genome expression data require functional information about genes in order to yield meaningful biological conclusions. The Gene Ontology (GO and Kyoto Encyclopedia of Genes and Genomes (KEGG are common sources of functionally grouped gene sets. For bacteria, the SEED and MicrobesOnline provide alternative, complementary sources of gene sets. To date, no comprehensive evaluation of the data obtained from these resources has been performed. Results We define a series of gene set consistency metrics directly related to the most common classes of statistical analyses for gene expression data, and then perform a comprehensive analysis of 3581 Affymetrix® gene expression arrays across 17 diverse bacteria. We find that gene sets obtained from GO and KEGG demonstrate lower consistency than those obtained from the SEED and MicrobesOnline, regardless of gene set size. Conclusions Despite the widespread use of GO and KEGG gene sets in bacterial gene expression data analysis, the SEED and MicrobesOnline provide more consistent sets for a wide variety of statistical analyses. Increased use of the SEED and MicrobesOnline gene sets in the analysis of bacterial gene expression data may improve statistical power and utility of expression data.

Kerr nonlinearity and plasmonic bistability in graphene nanoribbons

DEFF Research Database (Denmark)

Christensen, Thomas; Yan, Wei; Jauho, Antti-Pekka

2015-01-01

due to field enhancement, and the total nonlinearity is significantly affected by the field inhomogeneity of the plasmonic excitation. Finally, we discuss the emergence of a plasmonic bistability which exists for energies red-shifted relative to the linear resonance. Our results offer insights...

Identifying key genes in rheumatoid arthritis by weighted gene co-expression network analysis.

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Ma, Chunhui; Lv, Qi; Teng, Songsong; Yu, Yinxian; Niu, Kerun; Yi, Chengqin

2017-08-01

This study aimed to identify rheumatoid arthritis (RA) related genes based on microarray data using the WGCNA (weighted gene co-expression network analysis) method. Two gene expression profile datasets GSE55235 (10 RA samples and 10 healthy controls) and GSE77298 (16 RA samples and seven healthy controls) were downloaded from Gene Expression Omnibus database. Characteristic genes were identified using metaDE package. WGCNA was used to find disease-related networks based on gene expression correlation coefficients, and module significance was defined as the average gene significance of all genes used to assess the correlation between the module and RA status. Genes in the disease-related gene co-expression network were subject to functional annotation and pathway enrichment analysis using Database for Annotation Visualization and Integrated Discovery. Characteristic genes were also mapped to the Connectivity Map to screen small molecules. A total of 599 characteristic genes were identified. For each dataset, characteristic genes in the green, red and turquoise modules were most closely associated with RA, with gene numbers of 54, 43 and 79, respectively. These genes were enriched in totally enriched in 17 Gene Ontology terms, mainly related to immune response (CD97, FYB, CXCL1, IKBKE, CCR1, etc.), inflammatory response (CD97, CXCL1, C3AR1, CCR1, LYZ, etc.) and homeostasis (C3AR1, CCR1, PLN, CCL19, PPT1, etc.). Two small-molecule drugs sanguinarine and papaverine were predicted to have a therapeutic effect against RA. Genes related to immune response, inflammatory response and homeostasis presumably have critical roles in RA pathogenesis. Sanguinarine and papaverine have a potential therapeutic effect against RA. © 2017 Asia Pacific League of Associations for Rheumatology and John Wiley & Sons Australia, Ltd.

Evaluation of Appropriate Reference Genes for Gene Expression Normalization during Watermelon Fruit Development.

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Qiusheng Kong

Full Text Available Gene expression analysis in watermelon (Citrullus lanatus fruit has drawn considerable attention with the availability of genome sequences to understand the regulatory mechanism of fruit development and to improve its quality. Real-time quantitative reverse-transcription PCR (qRT-PCR is a routine technique for gene expression analysis. However, appropriate reference genes for transcript normalization in watermelon fruits have not been well characterized. The aim of this study was to evaluate the appropriateness of 12 genes for their potential use as reference genes in watermelon fruits. Expression variations of these genes were measured in 48 samples obtained from 12 successive developmental stages of parthenocarpic and fertilized fruits of two watermelon genotypes by using qRT-PCR analysis. Considering the effects of genotype, fruit setting method, and developmental stage, geNorm determined clathrin adaptor complex subunit (ClCAC, β-actin (ClACT, and alpha tubulin 5 (ClTUA5 as the multiple reference genes in watermelon fruit. Furthermore, ClCAC alone or together with SAND family protein (ClSAND was ranked as the single or two best reference genes by NormFinder. By using the top-ranked reference genes to normalize the transcript abundance of phytoene synthase (ClPSY1, a good correlation between lycopene accumulation and ClPSY1 expression pattern was observed in ripening watermelon fruit. These validated reference genes will facilitate the accurate measurement of gene expression in the studies on watermelon fruit biology.

Evaluation of Appropriate Reference Genes for Gene Expression Normalization during Watermelon Fruit Development.

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Kong, Qiusheng; Yuan, Jingxian; Gao, Lingyun; Zhao, Liqiang; Cheng, Fei; Huang, Yuan; Bie, Zhilong

2015-01-01

Gene expression analysis in watermelon (Citrullus lanatus) fruit has drawn considerable attention with the availability of genome sequences to understand the regulatory mechanism of fruit development and to improve its quality. Real-time quantitative reverse-transcription PCR (qRT-PCR) is a routine technique for gene expression analysis. However, appropriate reference genes for transcript normalization in watermelon fruits have not been well characterized. The aim of this study was to evaluate the appropriateness of 12 genes for their potential use as reference genes in watermelon fruits. Expression variations of these genes were measured in 48 samples obtained from 12 successive developmental stages of parthenocarpic and fertilized fruits of two watermelon genotypes by using qRT-PCR analysis. Considering the effects of genotype, fruit setting method, and developmental stage, geNorm determined clathrin adaptor complex subunit (ClCAC), β-actin (ClACT), and alpha tubulin 5 (ClTUA5) as the multiple reference genes in watermelon fruit. Furthermore, ClCAC alone or together with SAND family protein (ClSAND) was ranked as the single or two best reference genes by NormFinder. By using the top-ranked reference genes to normalize the transcript abundance of phytoene synthase (ClPSY1), a good correlation between lycopene accumulation and ClPSY1 expression pattern was observed in ripening watermelon fruit. These validated reference genes will facilitate the accurate measurement of gene expression in the studies on watermelon fruit biology.

Novel gene sets improve set-level classification of prokaryotic gene expression data.

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Holec, Matěj; Kuželka, Ondřej; Železný, Filip

2015-10-28

Set-level classification of gene expression data has received significant attention recently. In this setting, high-dimensional vectors of features corresponding to genes are converted into lower-dimensional vectors of features corresponding to biologically interpretable gene sets. The dimensionality reduction brings the promise of a decreased risk of overfitting, potentially resulting in improved accuracy of the learned classifiers. However, recent empirical research has not confirmed this expectation. Here we hypothesize that the reported unfavorable classification results in the set-level framework were due to the adoption of unsuitable gene sets defined typically on the basis of the Gene ontology and the KEGG database of metabolic networks. We explore an alternative approach to defining gene sets, based on regulatory interactions, which we expect to collect genes with more correlated expression. We hypothesize that such more correlated gene sets will enable to learn more accurate classifiers. We define two families of gene sets using information on regulatory interactions, and evaluate them on phenotype-classification tasks using public prokaryotic gene expression data sets. From each of the two gene-set families, we first select the best-performing subtype. The two selected subtypes are then evaluated on independent (testing) data sets against state-of-the-art gene sets and against the conventional gene-level approach. The novel gene sets are indeed more correlated than the conventional ones, and lead to significantly more accurate classifiers. The novel gene sets are indeed more correlated than the conventional ones, and lead to significantly more accurate classifiers. Novel gene sets defined on the basis of regulatory interactions improve set-level classification of gene expression data. The experimental scripts and other material needed to reproduce the experiments are available at http://ida.felk.cvut.cz/novelgenesets.tar.gz.

Differential neutrophil gene expression in early bovine pregnancy

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Kizaki Keiichiro

2013-02-01

Full Text Available Abstract Background In food production animals, especially cattle, the diagnosis of gestation is important because the timing of gestation directly affects the running of farms. Various methods have been used to detect gestation, but none of them are ideal because of problems with the timing of detection or the accuracy, simplicity, or cost of the method. A new method for detecting gestation, which involves assessing interferon-tau (IFNT-stimulated gene expression in peripheral blood leukocytes (PBL, was recently proposed. PBL fractionation methods were used to examine whether the expression profiles of various PBL populations could be used as reliable diagnostic markers of bovine gestation. Methods PBL were collected on days 0 (just before artificial insemination, 7, 14, 17, 21, and 28 of gestation. The gene expression levels of the PBL were assessed with microarray analysis and/or quantitative real-time reverse transcription (q PCR. PBL fractions were collected by flow cytometry or density gradient cell separation using Histopaque 1083 or Ficoll-Conray solutions. The expression levels of four IFNT-stimulated genes, interferon-stimulated protein 15 kDa (ISG15, myxovirus-resistance (MX 1 and 2, and 2′-5′-oligoadenylate synthetase (OAS1, were then analyzed in each fraction through day 28 of gestation using qPCR. Results Microarray analysis detected 72 and 28 genes in whole PBL that were significantly higher on days 14 and 21 of gestation, respectively, than on day 0. The upregulated genes included IFNT-stimulated genes. The expression levels of these genes increased with the progression of gestation until day 21. In flow cytometry experiments, on day 14 the expression levels of all of the genes were significantly higher in the granulocyte fraction than in the other fractions. Their expression gradually decreased through day 28 of gestation. Strong correlations were observed between the expression levels of the four genes in the granulocyte

Electrical bistabilities and memory mechanisms of nonvolatile organic bistable devices based on exfoliated muscovite-type mica nanoparticle/poly(methylmethacrylate) nanocomposites

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Lim, Won Gyu; Lee, Dea Uk; Na, Han Gil; Kim, Hyoun Woo; Kim, Tae Whan

2018-02-01

Organic bistable devices (OBDs) with exfoliated mica nanoparticles (NPs) embedded into an insulating poly(methylmethacrylate) (PMMA) layer were fabricated by using a spin-coating method. Current-voltage (I-V) curves for the Al/PMMA/exfoliated mica NP/PMMA/indium-tin-oxide/glass devices at 300 K showed a clockwise current hysteresis behavior due to the existence of the exfoliated muscovite-type mica NPs, which is an essential feature for bistable devices. Write-read-erase-read data showed that the OBDs had rewritable nonvolatile memories and an endurance number of ON/OFF switching for the OBDs of 102 cycles. An ON/OFF ratio of 1 × 103 was maintained for retention times larger than 1 × 104 s. The memory mechanisms of the fabricated OBDs were described by using the trapping and the tunneling processes within a PMMA active layer containing exfoliated muscovite-type mica NPs on the basis of the energy band diagram and the I-V curves.

Validation of suitable reference genes for quantitative gene expression analysis in Panax ginseng

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Meizhen eWang

2016-01-01

Full Text Available Reverse transcription-qPCR (RT-qPCR has become a popular method for gene expression studies. Its results require data normalization by housekeeping genes. No single gene is proved to be stably expressed under all experimental conditions. Therefore, systematic evaluation of reference genes is necessary. With the aim to identify optimum reference genes for RT-qPCR analysis of gene expression in different tissues of Panax ginseng and the seedlings grown under heat stress, we investigated the expression stability of eight candidate reference genes, including elongation factor 1-beta (EF1-β, elongation factor 1-gamma (EF1-γ, eukaryotic translation initiation factor 3G (IF3G, eukaryotic translation initiation factor 3B (IF3B, actin (ACT, actin11 (ACT11, glyceraldehyde-3-phosphate dehydrogenase (GAPDH and cyclophilin ABH-like protein (CYC, using four widely used computational programs: geNorm, Normfinder, BestKeeper, and the comparative ΔCt method. The results were then integrated using the web-based tool RefFinder. As a result, EF1-γ, IF3G and EF1-β were the three most stable genes in different tissues of P. ginseng, while IF3G, ACT11 and GAPDH were the top three-ranked genes in seedlings treated with heat. Using three better reference genes alone or in combination as internal control, we examined the expression profiles of MAR, a multiple function-associated mRNA-like non-coding RNA (mlncRNA in P. ginseng. Taken together, we recommended EF1-γ/IF3G and IF3G/ACT11 as the suitable pair of reference genes for RT-qPCR analysis of gene expression in different tissues of P. ginseng and the seedlings grown under heat stress, respectively. The results serve as a foundation for future studies on P. ginseng functional genomics.

Bistable out-of-plane stress-mismatched thermally actuated bilayer devices with large deflection

International Nuclear Information System (INIS)

Goessling, B A; Lucas, T M; Moiseeva, E V; Aebersold, J W; Harnett, C K

2011-01-01

In this paper, we explore microfabricated bistable actuators released as thin films from a silicon wafer. The actuators are based on a serpentine design where two cantilevers are coupled at the tips by a thin-film bar. These devices are parameterized by two lengths: cantilever length and the length of the coupling bar. These two dimensions are systematically varied to study the effect of design parameters on bistability. The three-dimensional devices have extremely large deflection (hundreds of microns rather than tens of microns for most planar microactuators of similar size) and are thermally actuated out of the plane of the wafer by applying a bias across either the left or right side of the serpentine. The bistability of these devices is evaluated using electron and optical microscopy. Potential applications include non-volatile mechanical memory, optical shutters, and reconfigurable antenna elements

The effects of nongenetic memory on population level sensitivity to stress

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Adams, Rhys; Nevozhay, Dmitry; van Itallie, Elizabeth; Bennett, Matthew; Balazsi, Gabor

2011-03-01

While gene expression is often thought of as a unidirectional determinant of cellular fitness, recent studies have shown how growth retardation due to protein expression can affect gene expression levels in single cells. We developed two yeast strains carrying a drug resistance protein under the control of different synthetic gene constructs, one of which was monostable, while the other was bistable. The gene expression of these cell populations was tuned using a molecular inducer so that their respective means and noises were identical, while their nongenetic memory properties were different. We tested the sensitivity of these two cell population distributions to the antibiotic zeocin. We found that the gene expression distributions of bistable cell populations were sensitive to stressful environments, while the gene expression distribution of monostable cells were nearly unchanged by stress. We conclude that cell populations with high nongenetic memory are more adaptable to their environment. This work was funded by the National Institutes of Health through the NIH Director's New Innovator Award Program, 1-DP2- OD006481-01.

Identification of differentially expressed genes in flax (Linum usitatissimum L.) under saline-alkaline stress by digital gene expression.

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Yu, Ying; Huang, Wengong; Chen, Hongyu; Wu, Guangwen; Yuan, Hongmei; Song, Xixia; Kang, Qinghua; Zhao, Dongsheng; Jiang, Weidong; Liu, Yan; Wu, Jianzhong; Cheng, Lili; Yao, Yubo; Guan, Fengzhi

2014-10-01

The salinization and alkalization of soil are widespread environmental problems, and alkaline salt stress is more destructive than neutral salt stress. Therefore, understanding the mechanism of plant tolerance to saline-alkaline stress has become a major challenge. However, little attention has been paid to the mechanism of plant alkaline salt tolerance. In this study, gene expression profiling of flax was analyzed under alkaline-salt stress (AS2), neutral salt stress (NSS) and alkaline stress (AS) by digital gene expression. Three-week-old flax seedlings were placed in 25 mM Na2CO3 (pH11.6) (AS2), 50mM NaCl (NSS) and NaOH (pH11.6) (AS) for 18 h. There were 7736, 1566 and 454 differentially expressed genes in AS2, NSS and AS compared to CK, respectively. The GO category gene enrichment analysis revealed that photosynthesis was particularly affected in AS2, carbohydrate metabolism was particularly affected in NSS, and the response to biotic stimulus was particularly affected in AS. We also analyzed the expression pattern of five categories of genes including transcription factors, signaling transduction proteins, phytohormones, reactive oxygen species proteins and transporters under these three stresses. Some key regulatory gene families involved in abiotic stress, such as WRKY, MAPKKK, ABA, PrxR and ion channels, were differentially expressed. Compared with NSS and AS, AS2 triggered more differentially expressed genes and special pathways, indicating that the mechanism of AS2 was more complex than NSS and AS. To the best of our knowledge, this was the first transcriptome analysis of flax in response to saline-alkaline stress. These data indicate that common and diverse features of saline-alkaline stress provide novel insights into the molecular mechanisms of plant saline-alkaline tolerance and offer a number of candidate genes as potential markers of tolerance to saline-alkaline stress. Copyright © 2014 Elsevier B.V. All rights reserved.

A silicon-nanowire memory driven by optical gradient force induced bistability

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Dong, B. [School of Electrical and Electronic Engineering, Nanyang Technological University, Singapore 639798 (Singapore); Institute of Microelectronics, A*STAR (Agency for Science, Technology and Research), Singapore 117685 (Singapore); Cai, H., E-mail: caih@ime.a-star.edu.sg; Gu, Y. D.; Kwong, D. L. [Institute of Microelectronics, A*STAR (Agency for Science, Technology and Research), Singapore 117685 (Singapore); Chin, L. K.; Ng, G. I.; Ser, W. [School of Electrical and Electronic Engineering, Nanyang Technological University, Singapore 639798 (Singapore); Huang, J. G. [School of Electrical and Electronic Engineering, Nanyang Technological University, Singapore 639798 (Singapore); Institute of Microelectronics, A*STAR (Agency for Science, Technology and Research), Singapore 117685 (Singapore); School of Mechanical Engineering, Xi' an Jiaotong University, Xi' an 710049 (China); Yang, Z. C. [School of Electronics Engineering and Computer Science, Peking University, Beijing 100871 (China); Liu, A. Q., E-mail: eaqliu@ntu.edu.sg [School of Electrical and Electronic Engineering, Nanyang Technological University, Singapore 639798 (Singapore); School of Electronics Engineering and Computer Science, Peking University, Beijing 100871 (China)

2015-12-28

In this paper, a bistable optical-driven silicon-nanowire memory is demonstrated, which employs ring resonator to generate optical gradient force over a doubly clamped silicon-nanowire. Two stable deformation positions of a doubly clamped silicon-nanowire represent two memory states (“0” and “1”) and can be set/reset by modulating the light intensity (<3 mW) based on the optical force induced bistability. The time response of the optical-driven memory is less than 250 ns. It has applications in the fields of all optical communication, quantum computing, and optomechanical circuits.

The effect of magnetic field on bistability in 1D photonic crystal doped by magnetized plasma and coupled nonlinear defects

International Nuclear Information System (INIS)

Mehdian, H.; Mohammadzahery, Z.; Hasanbeigi, A.

2014-01-01

In this work, we study the defect mode and bistability behavior of 1-D photonic band gap structure with magnetized plasma and coupled nonlinear defects. The transfer matrix method has been employed to investigate the magnetic field effect on defect mode frequency and bistability threshold. The obtained results show that the frequency of defect mode and bistability threshold can be altered, without changing the structure of the photonic multilayer. Therefore, the bistability behavior of the subjected structure in the presence of magnetized plasma can be utilized in manufacturing wide frequency range devices

A hierarchical stochastic model for bistable perception.

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Stefan Albert

2017-11-01

Full Text Available Viewing of ambiguous stimuli can lead to bistable perception alternating between the possible percepts. During continuous presentation of ambiguous stimuli, percept changes occur as single events, whereas during intermittent presentation of ambiguous stimuli, percept changes occur at more or less regular intervals either as single events or bursts. Response patterns can be highly variable and have been reported to show systematic differences between patients with schizophrenia and healthy controls. Existing models of bistable perception often use detailed assumptions and large parameter sets which make parameter estimation challenging. Here we propose a parsimonious stochastic model that provides a link between empirical data analysis of the observed response patterns and detailed models of underlying neuronal processes. Firstly, we use a Hidden Markov Model (HMM for the times between percept changes, which assumes one single state in continuous presentation and a stable and an unstable state in intermittent presentation. The HMM captures the observed differences between patients with schizophrenia and healthy controls, but remains descriptive. Therefore, we secondly propose a hierarchical Brownian model (HBM, which produces similar response patterns but also provides a relation to potential underlying mechanisms. The main idea is that neuronal activity is described as an activity difference between two competing neuronal populations reflected in Brownian motions with drift. This differential activity generates switching between the two conflicting percepts and between stable and unstable states with similar mechanisms on different neuronal levels. With only a small number of parameters, the HBM can be fitted closely to a high variety of response patterns and captures group differences between healthy controls and patients with schizophrenia. At the same time, it provides a link to mechanistic models of bistable perception, linking the group

A hierarchical stochastic model for bistable perception.

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Albert, Stefan; Schmack, Katharina; Sterzer, Philipp; Schneider, Gaby

2017-11-01

Viewing of ambiguous stimuli can lead to bistable perception alternating between the possible percepts. During continuous presentation of ambiguous stimuli, percept changes occur as single events, whereas during intermittent presentation of ambiguous stimuli, percept changes occur at more or less regular intervals either as single events or bursts. Response patterns can be highly variable and have been reported to show systematic differences between patients with schizophrenia and healthy controls. Existing models of bistable perception often use detailed assumptions and large parameter sets which make parameter estimation challenging. Here we propose a parsimonious stochastic model that provides a link between empirical data analysis of the observed response patterns and detailed models of underlying neuronal processes. Firstly, we use a Hidden Markov Model (HMM) for the times between percept changes, which assumes one single state in continuous presentation and a stable and an unstable state in intermittent presentation. The HMM captures the observed differences between patients with schizophrenia and healthy controls, but remains descriptive. Therefore, we secondly propose a hierarchical Brownian model (HBM), which produces similar response patterns but also provides a relation to potential underlying mechanisms. The main idea is that neuronal activity is described as an activity difference between two competing neuronal populations reflected in Brownian motions with drift. This differential activity generates switching between the two conflicting percepts and between stable and unstable states with similar mechanisms on different neuronal levels. With only a small number of parameters, the HBM can be fitted closely to a high variety of response patterns and captures group differences between healthy controls and patients with schizophrenia. At the same time, it provides a link to mechanistic models of bistable perception, linking the group differences to

Improved gene expression signature of testicular carcinoma in situ

DEFF Research Database (Denmark)

Almstrup, Kristian; Leffers, Henrik; Lothe, Ragnhild A

2007-01-01

on global gene expression in testicular CIS have been previously published. We have merged the two data sets on CIS samples (n = 6) and identified the shared gene expression signature in relation to expression in normal testis. Among the top-20 highest expressed genes, one-third was transcription factors...... development' were significantly altered and could collectively affect cellular pathways like the WNT signalling cascade, which thus may be disrupted in testicular CIS. The merged CIS data from two different microarray platforms, to our knowledge, provide the most precise CIS gene expression signature to date....

The gsdf gene locus harbors evolutionary conserved and clustered genes preferentially expressed in fish previtellogenic oocytes.

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Gautier, Aude; Le Gac, Florence; Lareyre, Jean-Jacques

2011-02-01

The gonadal soma-derived factor (GSDF) belongs to the transforming growth factor-β superfamily and is conserved in teleostean fish species. Gsdf is specifically expressed in the gonads, and gene expression is restricted to the granulosa and Sertoli cells in trout and medaka. The gsdf gene expression is correlated to early testis differentiation in medaka and was shown to stimulate primordial germ cell and spermatogonia proliferation in trout. In the present study, we show that the gsdf gene localizes to a syntenic chromosomal fragment conserved among vertebrates although no gsdf-related gene is detected on the corresponding genomic region in tetrapods. We demonstrate using quantitative RT-PCR that most of the genes localized in the synteny are specifically expressed in medaka gonads. Gsdf is the only gene of the synteny with a much higher expression in the testis compared to the ovary. In contrast, gene expression pattern analysis of the gsdf surrounding genes (nup54, aff1, klhl8, sdad1, and ptpn13) indicates that these genes are preferentially expressed in the female gonads. The tissue distribution of these genes is highly similar in medaka and zebrafish, two teleostean species that have diverged more than 110 million years ago. The cellular localization of these genes was determined in medaka gonads using the whole-mount in situ hybridization technique. We confirm that gsdf gene expression is restricted to Sertoli and granulosa cells in contact with the premeiotic and meiotic cells. The nup54 gene is expressed in spermatocytes and previtellogenic oocytes. Transcripts corresponding to the ovary-specific genes (aff1, klhl8, and sdad1) are detected only in previtellogenic oocytes. No expression was detected in the gonocytes in 10 dpf embryos. In conclusion, we show that the gsdf gene localizes to a syntenic chromosomal fragment harboring evolutionary conserved genes in vertebrates. These genes are preferentially expressed in previtelloogenic oocytes, and thus, they

Selection of reference genes for quantitative gene expression normalization in flax (Linum usitatissimum L.

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Neutelings Godfrey

2010-04-01

Full Text Available Abstract Background Quantitative real-time PCR (qRT-PCR is currently the most accurate method for detecting differential gene expression. Such an approach depends on the identification of uniformly expressed 'housekeeping genes' (HKGs. Extensive transcriptomic data mining and experimental validation in different model plants have shown that the reliability of these endogenous controls can be influenced by the plant species, growth conditions and organs/tissues examined. It is therefore important to identify the best reference genes to use in each biological system before using qRT-PCR to investigate differential gene expression. In this paper we evaluate different candidate HKGs for developmental transcriptomic studies in the economically-important flax fiber- and oil-crop (Linum usitatissimum L. Results Specific primers were designed in order to quantify the expression levels of 20 different potential housekeeping genes in flax roots, internal- and external-stem tissues, leaves and flowers at different developmental stages. After calculations of PCR efficiencies, 13 HKGs were retained and their expression stabilities evaluated by the computer algorithms geNorm and NormFinder. According to geNorm, 2 Transcriptional Elongation Factors (TEFs and 1 Ubiquitin gene are necessary for normalizing gene expression when all studied samples are considered. However, only 2 TEFs are required for normalizing expression in stem tissues. In contrast, NormFinder identified glyceraldehyde-3-phosphate dehydrogenase (GADPH as the most stably expressed gene when all samples were grouped together, as well as when samples were classed into different sub-groups. qRT-PCR was then used to investigate the relative expression levels of two splice variants of the flax LuMYB1 gene (homologue of AtMYB59. LuMYB1-1 and LuMYB1-2 were highly expressed in the internal stem tissues as compared to outer stem tissues and other samples. This result was confirmed with both ge

Selection of reference genes for quantitative gene expression normalization in flax (Linum usitatissimum L.).

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Huis, Rudy; Hawkins, Simon; Neutelings, Godfrey

2010-04-19

Quantitative real-time PCR (qRT-PCR) is currently the most accurate method for detecting differential gene expression. Such an approach depends on the identification of uniformly expressed 'housekeeping genes' (HKGs). Extensive transcriptomic data mining and experimental validation in different model plants have shown that the reliability of these endogenous controls can be influenced by the plant species, growth conditions and organs/tissues examined. It is therefore important to identify the best reference genes to use in each biological system before using qRT-PCR to investigate differential gene expression. In this paper we evaluate different candidate HKGs for developmental transcriptomic studies in the economically-important flax fiber- and oil-crop (Linum usitatissimum L). Specific primers were designed in order to quantify the expression levels of 20 different potential housekeeping genes in flax roots, internal- and external-stem tissues, leaves and flowers at different developmental stages. After calculations of PCR efficiencies, 13 HKGs were retained and their expression stabilities evaluated by the computer algorithms geNorm and NormFinder. According to geNorm, 2 Transcriptional Elongation Factors (TEFs) and 1 Ubiquitin gene are necessary for normalizing gene expression when all studied samples are considered. However, only 2 TEFs are required for normalizing expression in stem tissues. In contrast, NormFinder identified glyceraldehyde-3-phosphate dehydrogenase (GADPH) as the most stably expressed gene when all samples were grouped together, as well as when samples were classed into different sub-groups.qRT-PCR was then used to investigate the relative expression levels of two splice variants of the flax LuMYB1 gene (homologue of AtMYB59). LuMYB1-1 and LuMYB1-2 were highly expressed in the internal stem tissues as compared to outer stem tissues and other samples. This result was confirmed with both geNorm-designated- and Norm

Modeling bistable behaviors in morphing structures through finite element simulations.

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Guo, Qiaohang; Zheng, Huang; Chen, Wenzhe; Chen, Zi

2014-01-01

Bistable structures, exemplified by the Venus flytrap and slap bracelets, can transit between different configurations upon certain external stimulation. Here we study, through three-dimensional finite element simulations, the bistable behaviors in elastic plates in the absence of terminate loads, but with pre-strains in one (or both) of the two composite layers. Both the scenarios with and without a given geometric mis-orientation angle are investigated, the results of which are consistent with recent theoretical and experimental studies. This work can open ample venues for programmable designs of plant/shell structures with large deformations, with applications in designing bio-inspired robotics for biomedical research and morphing/deployable structures in aerospace engineering.

Stochastic resonance and MFPT in an asymmetric bistable system driven by correlated multiplicative colored noise and additive white noise

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Shi, Pei-Ming; Li, Qun; Han, Dong-Ying

2017-06-01

This paper investigates a new asymmetric bistable model driven by correlated multiplicative colored noise and additive white noise. The mean first-passage time (MFPT) and the signal-to-noise ratio (SNR) as the indexes of evaluating the model are researched. Based on the two-state theory and the adiabatic approximation theory, the expressions of MFPT and SNR have been obtained for the asymmetric bistable system driven by a periodic signal, correlated multiplicative colored noise and additive noise. Simulation results show that it is easier to generate stochastic resonance (SR) to adjust the intensity of correlation strength λ. Meanwhile, the decrease of asymmetric coefficient r2 and the increase of noise intensity are beneficial to realize the transition between the two steady states in the system. At the same time, the twice SR phenomena can be observed by adjusting additive white noise and correlation strength. The influence of asymmetry of potential function on the MFPTs in two different directions is different.

Spatial waves of advance with bistable dynamics: cytoplasmic and genetic analogues of Allee effects.

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Barton, N H; Turelli, Michael

2011-09-01

Unlike unconditionally advantageous "Fisherian" variants that tend to spread throughout a species range once introduced anywhere, "bistable" variants, such as chromosome translocations, have two alternative stable frequencies, absence and (near) fixation. Analogous to populations with Allee effects, bistable variants tend to increase locally only once they become sufficiently common, and their spread depends on their rate of increase averaged over all frequencies. Several proposed manipulations of insect populations, such as using Wolbachia or "engineered underdominance" to suppress vector-borne diseases, produce bistable rather than Fisherian dynamics. We synthesize and extend theoretical analyses concerning three features of their spatial behavior: rate of spread, conditions to initiate spread from a localized introduction, and wave stopping caused by variation in population densities or dispersal rates. Unlike Fisherian variants, bistable variants tend to spread spatially only for particular parameter combinations and initial conditions. Wave initiation requires introduction over an extended region, while subsequent spatial spread is slower than for Fisherian waves and can easily be halted by local spatial inhomogeneities. We present several new results, including robust sufficient conditions to initiate (and stop) spread, using a one-parameter cubic approximation applicable to several models. The results have both basic and applied implications.

The Medicago truncatula gene expression atlas web server

Directory of Open Access Journals (Sweden)

Tang Yuhong

2009-12-01

Full Text Available Abstract Background Legumes (Leguminosae or Fabaceae play a major role in agriculture. Transcriptomics studies in the model legume species, Medicago truncatula, are instrumental in helping to formulate hypotheses about the role of legume genes. With the rapid growth of publically available Affymetrix GeneChip Medicago Genome Array GeneChip data from a great range of tissues, cell types, growth conditions, and stress treatments, the legume research community desires an effective bioinformatics system to aid efforts to interpret the Medicago genome through functional genomics. We developed the Medicago truncatula Gene Expression Atlas (MtGEA web server for this purpose. Description The Medicago truncatula Gene Expression Atlas (MtGEA web server is a centralized platform for analyzing the Medicago transcriptome. Currently, the web server hosts gene expression data from 156 Affymetrix GeneChip® Medicago genome arrays in 64 different experiments, covering a broad range of developmental and environmental conditions. The server enables flexible, multifaceted analyses of transcript data and provides a range of additional information about genes, including different types of annotation and links to the genome sequence, which help users formulate hypotheses about gene function. Transcript data can be accessed using Affymetrix probe identification number, DNA sequence, gene name, functional description in natural language, GO and KEGG annotation terms, and InterPro domain number. Transcripts can also be discovered through co-expression or differential expression analysis. Flexible tools to select a subset of experiments and to visualize and compare expression profiles of multiple genes have been implemented. Data can be downloaded, in part or full, in a tabular form compatible with common analytical and visualization software. The web server will be updated on a regular basis to incorporate new gene expression data and genome annotation, and is accessible

A gene co-expression network in whole blood of schizophrenia patients is independent of antipsychotic-use and enriched for brain-expressed genes.

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Simone de Jong

Full Text Available Despite large-scale genome-wide association studies (GWAS, the underlying genes for schizophrenia are largely unknown. Additional approaches are therefore required to identify the genetic background of this disorder. Here we report findings from a large gene expression study in peripheral blood of schizophrenia patients and controls. We applied a systems biology approach to genome-wide expression data from whole blood of 92 medicated and 29 antipsychotic-free schizophrenia patients and 118 healthy controls. We show that gene expression profiling in whole blood can identify twelve large gene co-expression modules associated with schizophrenia. Several of these disease related modules are likely to reflect expression changes due to antipsychotic medication. However, two of the disease modules could be replicated in an independent second data set involving antipsychotic-free patients and controls. One of these robustly defined disease modules is significantly enriched with brain-expressed genes and with genetic variants that were implicated in a GWAS study, which could imply a causal role in schizophrenia etiology. The most highly connected intramodular hub gene in this module (ABCF1, is located in, and regulated by the major histocompatibility (MHC complex, which is intriguing in light of the fact that common allelic variants from the MHC region have been implicated in schizophrenia. This suggests that the MHC increases schizophrenia susceptibility via altered gene expression of regulatory genes in this network.

Clustering based gene expression feature selection method: A computational approach to enrich the classifier efficiency of differentially expressed genes

KAUST Repository

Abusamra, Heba

2016-07-20

The native nature of high dimension low sample size of gene expression data make the classification task more challenging. Therefore, feature (gene) selection become an apparent need. Selecting a meaningful and relevant genes for classifier not only decrease the computational time and cost, but also improve the classification performance. Among different approaches of feature selection methods, however most of them suffer from several problems such as lack of robustness, validation issues etc. Here, we present a new feature selection technique that takes advantage of clustering both samples and genes. Materials and methods We used leukemia gene expression dataset [1]. The effectiveness of the selected features were evaluated by four different classification methods; support vector machines, k-nearest neighbor, random forest, and linear discriminate analysis. The method evaluate the importance and relevance of each gene cluster by summing the expression level for each gene belongs to this cluster. The gene cluster consider important, if it satisfies conditions depend on thresholds and percentage otherwise eliminated. Results Initial analysis identified 7120 differentially expressed genes of leukemia (Fig. 15a), after applying our feature selection methodology we end up with specific 1117 genes discriminating two classes of leukemia (Fig. 15b). Further applying the same method with more stringent higher positive and lower negative threshold condition, number reduced to 58 genes have be tested to evaluate the effectiveness of the method (Fig. 15c). The results of the four classification methods are summarized in Table 11. Conclusions The feature selection method gave good results with minimum classification error. Our heat-map result shows distinct pattern of refines genes discriminating between two classes of leukemia.

A deep auto-encoder model for gene expression prediction.

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Xie, Rui; Wen, Jia; Quitadamo, Andrew; Cheng, Jianlin; Shi, Xinghua

2017-11-17

Gene expression is a key intermediate level that genotypes lead to a particular trait. Gene expression is affected by various factors including genotypes of genetic variants. With an aim of delineating the genetic impact on gene expression, we build a deep auto-encoder model to assess how good genetic variants will contribute to gene expression changes. This new deep learning model is a regression-based predictive model based on the MultiLayer Perceptron and Stacked Denoising Auto-encoder (MLP-SAE). The model is trained using a stacked denoising auto-encoder for feature selection and a multilayer perceptron framework for backpropagation. We further improve the model by introducing dropout to prevent overfitting and improve performance. To demonstrate the usage of this model, we apply MLP-SAE to a real genomic datasets with genotypes and gene expression profiles measured in yeast. Our results show that the MLP-SAE model with dropout outperforms other models including Lasso, Random Forests and the MLP-SAE model without dropout. Using the MLP-SAE model with dropout, we show that gene expression quantifications predicted by the model solely based on genotypes, align well with true gene expression patterns. We provide a deep auto-encoder model for predicting gene expression from SNP genotypes. This study demonstrates that deep learning is appropriate for tackling another genomic problem, i.e., building predictive models to understand genotypes' contribution to gene expression. With the emerging availability of richer genomic data, we anticipate that deep learning models play a bigger role in modeling and interpreting genomics.

Positron emission tomography imaging of gene expression

International Nuclear Information System (INIS)

Tang Ganghua

2001-01-01

The merging of molecular biology and nuclear medicine is developed into molecular nuclear medicine. Positron emission tomography (PET) of gene expression in molecular nuclear medicine has become an attractive area. Positron emission tomography imaging gene expression includes the antisense PET imaging and the reporter gene PET imaging. It is likely that the antisense PET imaging will lag behind the reporter gene PET imaging because of the numerous issues that have not yet to be resolved with this approach. The reporter gene PET imaging has wide application into animal experimental research and human applications of this approach will likely be reported soon

Manually operatable on-chip bistable pneumatic microstructures for microfluidic manipulations.

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Chen, Arnold; Pan, Tingrui

2014-09-07

Bistable microvalves are of particular interest because of their distinct nature of requiring energy consumption only during the transition between the open and closed states. This characteristic can be highly advantageous in reducing the number of external inputs and the complexity of control circuitries since microfluidic devices as contemporary lab-on-a-chip platforms are transferring from research settings to low-resource environments with high integrability and a small form factor. In this paper, we first present manually operatable, on-chip bistable pneumatic microstructures (BPMs) for microfluidic manipulation. The structural design and operation of the BPM devices can be readily integrated into any pneumatically powered microfluidic network consisting of pneumatic and fluidic channels. It is mainly composed of a vacuum activation chamber (VAC) and a pressure release chamber (PRC), of which users have direct control through finger pressing to switch either to the bistable vacuum state (VS) or the atmospheric state (AS). We have integrated multiple BPM devices into a 4-to-1 microfluidic multiplexor to demonstrate on-chip digital flow switching from different sources. Furthermore, we have shown its clinical relevance in a point-of-care diagnostic chip that processes blood samples to identify the distinct blood types (A/B/O) on-chip.

Understanding gene expression in coronary artery disease through ...

Indian Academy of Sciences (India)

Understanding gene expression in coronary artery disease through global profiling, network analysis and independent validation of key candidate genes. Prathima ... Table 2. Differentially expressed genes in CAD compared to age and gender matched controls. .... Regulation of nuclear pre-mRNA domain containing 1A.

Gene expression profile of pulpitis.

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Galicia, J C; Henson, B R; Parker, J S; Khan, A A

2016-06-01

The cost, prevalence and pain associated with endodontic disease necessitate an understanding of the fundamental molecular aspects of its pathogenesis. This study was aimed to identify the genetic contributors to pulpal pain and inflammation. Inflamed pulps were collected from patients diagnosed with irreversible pulpitis (n=20). Normal pulps from teeth extracted for various reasons served as controls (n=20). Pain level was assessed using a visual analog scale (VAS). Genome-wide microarray analysis was performed using Affymetrix GeneTitan Multichannel Instrument. The difference in gene expression levels were determined by the significance analysis of microarray program using a false discovery rate (q-value) of 5%. Genes involved in immune response, cytokine-cytokine receptor interaction and signaling, integrin cell surface interactions, and others were expressed at relatively higher levels in the pulpitis group. Moreover, several genes known to modulate pain and inflammation showed differential expression in asymptomatic and mild pain patients (⩾30 mm on VAS) compared with those with moderate to severe pain. This exploratory study provides a molecular basis for the clinical diagnosis of pulpitis. With an enhanced understanding of pulpal inflammation, future studies on treatment and management of pulpitis and on pain associated with it can have a biological reference to bridge treatment strategies with pulpal biology.

Cellular variability of RpoS expression underlies subpopulation activation of an integrative and conjugative element.

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Ryo Miyazaki

Full Text Available Conjugative transfer of the integrative and conjugative element ICEclc in the bacterium Pseudomonas knackmussii is the consequence of a bistable decision taken in some 3% of cells in a population during stationary phase. Here we study the possible control exerted by the stationary phase sigma factor RpoS on the bistability decision. The gene for RpoS in P. knackmussii B13 was characterized, and a loss-of-function mutant was produced and complemented. We found that, in absence of RpoS, ICEclc transfer rates and activation of two key ICEclc promoters (P(int and P(inR decrease significantly in cells during stationary phase. Microarray and gene reporter analysis indicated that the most direct effect of RpoS is on P(inR, whereas one of the gene products from the P(inR-controlled operon (InrR transmits activation to P(int and other ICEclc core genes. Addition of a second rpoS copy under control of its native promoter resulted in an increase of the proportion of cells expressing the P(int and P(inR promoters to 18%. Strains in which rpoS was replaced by an rpoS-mcherry fusion showed high mCherry fluorescence of individual cells that had activated P(int and P(inR, whereas a double-copy rpoS-mcherry-containing strain displayed twice as much mCherry fluorescence. This suggested that high RpoS levels are a prerequisite for an individual cell to activate P(inR and thus ICEclc transfer. Double promoter-reporter fusions confirmed that expression of P(inR is dominated by extrinsic noise, such as being the result of cellular variability in RpoS. In contrast, expression from P(int is dominated by intrinsic noise, indicating it is specific to the ICEclc transmission cascade. Our results demonstrate how stochastic noise levels of global transcription factors can be transduced to a precise signaling cascade in a subpopulation of cells leading to ICE activation.

Mel-18, a mammalian Polycomb gene, regulates angiogenic gene expression of endothelial cells.

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Jung, Ji-Hye; Choi, Hyun-Jung; Maeng, Yong-Sun; Choi, Jung-Yeon; Kim, Minhyung; Kwon, Ja-Young; Park, Yong-Won; Kim, Young-Myeong; Hwang, Daehee; Kwon, Young-Guen

2010-10-01

Mel-18 is a mammalian homolog of Polycomb group (PcG) genes. Microarray analysis revealed that Mel-18 expression was induced during endothelial progenitor cell (EPC) differentiation and correlates with the expression of EC-specific protein markers. Overexpression of Mel-18 promoted EPC differentiation and angiogenic activity of ECs. Accordingly, silencing Mel-18 inhibited EC migration and tube formation in vitro. Gene expression profiling showed that Mel-18 regulates angiogenic genes including kinase insert domain receptor (KDR), claudin 5, and angiopoietin-like 2. Our findings demonstrate, for the first time, that Mel-18 plays a significant role in the angiogenic function of ECs by regulating endothelial gene expression. Copyright © 2010 Elsevier Inc. All rights reserved.