Interaction of NPR1 with basic leucine zipper protein transcription factors that bind sequences required for salicylic acid induction of the PR–1 gene

The Arabidopsis thaliana NPR1 has been shown to be a key regulator of gene expression during the onset of a plant disease-resistance response known as systemic acquired resistance. The npr1 mutant plants fail to respond to systemic acquired resistance-inducing signals such as salicylic acid (SA), or express SA-induced pathogenesis-related (PR) genes. Using NPR1 as bait in a yeast two-hybrid screen, we identified a subclass of transcription factors in the basic leucine zipper protein family (AHBP-1b and TGA6) and showed that they interact specifically in yeast and in vitro with NPR1. Point mutations that abolish the NPR1 function in A. thaliana also impair the interactions between NPR1 and the transcription factors in the yeast two-hybrid assay. Furthermore, a gel mobility shift assay showed that the purified transcription factor protein, AHBP-1b, binds specifically to an SA-responsive promoter element of the A. thaliana PR-1 gene. These data suggest that NPR1 may regulate PR-1 gene expression by interacting with a subclass of basic leucine zipper protein transcription factors.

Relative entropy rate based design for linear hybrid system models

Hybrid system representations have been applied to many challenging modeling situations. In these hybrid system representations, a mixture of continuous and discrete states is used to capture the dominating behavioural features of a nonlinear, possible uncertain, model under approximation. Unfortunately, the problem of how to best design a suitable hybrid system model has not yet been fully addressed. This paper proposes a new joint state measurement relative entropy rate based approach for this design purpose. Design examples and simulation studies are presented which highlight the benefits of our proposed design approaches.

Relative entropy rate based model selection for linear hybrid system filters of uncertain nonlinear systems

Hybrid system representations have been exploited in a number of challenging modelling situations, including situations where the original nonlinear dynamics are too complex (or too imprecisely known) to be directly filtered. Unfortunately, the question of how to best design suitable hybrid system models has not yet been fully addressed, particularly in the situations involving model uncertainty. This paper proposes a novel joint state-measurement relative entropy rate based approach for design of hybrid system filters in the presence of (parameterised) model uncertainty. We also present a design approach suitable for suboptimal hybrid system filters. The benefits of our proposed approaches are illustrated through design examples and simulation studies.

A novel fluorescent probe involving a graphene quantum dot-enzyme hybrid system for the analysis of hydroquinone in the presence of toxic resorcinol and catechol

An efficient method for the analysis of hydroquinone at trace levels in water samples has been developed in the form of a fluorescent probe based on graphene quantum dots (GQDs). The analytical variable, fluorescence quenching, was generated from the formation of benzoquinone intermediates, which formed during the catalytic oxidation of hydroquinone by horseradish peroxidase (HRP). In general, the reaction mechanism involved hydroquinone, as an electron acceptor, which affected the surface state of GQDs via an electron transfer effect. The water-soluble GQDs were directly prepared by the pyrolysis of citric acid and with the use of the mentioned hybrid enzyme system, the detection limit for hydroquinone was as low as 8.4 × 10−8 M. Furthermore, this analysis was almost unaffected by other phenol and quinine compounds, such as phenol, resorcinol and other quinines, and therefore, the developed GQD method produced satisfactory results for the analysis of hydroquinone in several different lake water samples.

Mu in vitro transposition applications in protein engineering

Transposons, mobile genetic elements that are ubiquitous in all living organisms have been used as tools in molecular biology for decades. They have the ability to move into discrete DNA locations with no apparent homology to the target site. The utility of transposons as molecular tools is based on their ability to integrate into various DNA sequences efficiently, producing extensive mutant clone libraries that can be used in various molecular biology applications. Bacteriophage Mu is one of the most useful transposons due to its well-characterized and simple in vitro transposition reaction. This study establishes the properties of the Mu in vitro transposition system as a versatile multipurpose tool in molecular biology. In addition, this study describes Mu-based applications for engineering proteins by random insertional transposon mutagenesis in order to study structure-function relationships in proteins. We initially characterized the properties of the minimal Mu in vitro transposition system. We showed that the Mu transposition system works efficiently and accurately and produces insertions into a wide spectrum of target sites in different DNA molecules. Then, we developed a pentapeptide insertion mutagenesis strategy for inserting random five amino acid cassettes into proteins. These protein variants can be used especially for screening important sites for protein-protein interactions. Also, the system may produce temperature-sensitive variants of the protein of interest. Furthermore, we developed an efficient screening system for high-resolution mapping of protein-protein interfaces with the pentapeptide insertion mutagenesis. This was accomplished by combining the mutagenesis with subsequent yeast two-hybrid screening and PCR-based genetic footprinting. This combination allows the analysis of the whole mutant library en masse, without the need for producing or isolating separate mutant clones, and the protein-protein interfaces can be determined at amino acid accuracy. The system was validated by analysing the interacting region of JFC1 with Rab8A, and we show that the interaction is mediated via the JFC1 Slp homology domain. In addition, we developed a procedure for the production of nested sets of N- and C-terminal deletion variants of proteins with the Mu system. These variants are useful in many functional studies of proteins, especially in mapping regions involved in protein-protein interactions. This methodology was validated by analysing the region in yeast Mso1 involved in an interaction with Sec1. The results of this study show that the Mu in vitro transposition system is versatile for various applicational purposes and can efficiently be adapted to random protein engineering applications for functional studies of proteins.

Buckled nano rod - a two state system: quantum effects on its dynamics

We consider a suspended elastic rod under longitudinal compression. The compression can be used to adjust potential energy for transverse displacements from the harmonic to the double well regime. The two minima in potential energy curve describe two possible buckled states. Using transition state theory (TST) we have calculated the rate of conversion from one state to other. If the strain epsilon = 4 epsilon c the simple TST rate diverges. We suggest a method to correct this divergence for quantum calculations. We also find that zero point energy contributions can be quite large so that single mode calculations can lead to large errors in the rate.

Symmetry-breaking transition in a two-level system coupled to an Ohmic bath: A squeezed-state approach

Displaced squeezed states are proposed as variational ground states for phonons (Bose fields) coupled to two-level systems (spin systems). We have investigated the zero-temperature phase diagram for the localization-delocalization transition of a tunneling particle interacting with an Ohmic heat bath. Our results are compared with known existing approximate treatments. A modified phase diagram using the displaced squeezed state is presented.

Optimal control of a stochastic hybrid system with discounted cost

We address the optimal control problem of a very general stochastic hybrid system with both autonomous and impulsive jumps. The planning horizon is infinite and we use the discounted-cost criterion for performance evaluation. Under certain assumptions, we show the existence of an optimal control. We then derive the quasivariational inequalities satisfied by the value function and establish well-posedness. Finally, we prove the usual verification theorem of dynamic programming.

The onset of oscillatory Marangoni convection in a two-layer system of conducting fluid in the presence of a uniform magnetic field

A combination of numerical and analytical techniques is used to analyse the effect of magnetic field and encapsulated layer on the onset of oscillatory Marangoni instability in a two layer system. Oscillatory Marangoni instability is possible for a deformed free surface only when the system is heated from above. It is observed that the existence of a second layer has a positive effect on Marangoni overstability with magnetic field whereas it has an opposite effect without magnetic field.

Subnatural linewidth in a strongly-driven degenerate two-level system

We observe linewidths below the natural linewidth for a probe laser on a degenerate two-level F -> F' transition, when the same transition is driven by a strong control laser. We take advantage of the fact that each level of the transition is made of multiple magnetic sublevels, and use the phenomenon of electromagnetically induced transparency (EIT) or absorption ( EIA) in multilevel systems. Optical pumping by the control laser redistributes the population so that only a few sublevels contribute to the probe absorption, an explanation which is verified by a density-matrix analysis of the relevant sublevels. We observe more than a factor of 3 reduction in linewidth in the D(2) line of Rb in room-temperature vapor. Such subnatural features vastly increase the scope of applications of EIT, such as high-resolution spectroscopy and tighter locking of lasers to atomic transitions, since it is not always possible to find a suitable third level. (C) 2011 Elsevier B.V. All rights reserved.

Rv1027c-Rv1028c encode functional KdpDE two - Component system in Mycobacterium tuberculosis

In Mycobacterium tuberculosis Rv1027c-Rv1028c genes are predicted to encode KdpDE two component system, which is highly conserved across all bacterial species. Here, we show that the system is functionally active and KdpD sensor kinase undergoes autophosphorylation and transfers phosphoryl group to KdpE, response regulator protein. We identified His(642) and Asp(52) as conserved phosphorylation sites in KdpD and KdpE respectively and by SPR analysis confirmed the physical interaction between them. KdpD was purified with prebound divalent ions and their importance in phosphorylation was established using protein refolding and ion chelation approaches. Genetically a single transcript encoded both KdpD and KdpE proteins. Overall, we report that M. tuberculosis KdpDE system operates like a canonical two component system. (C) 2014 Elsevier Inc. All rights reserved.

Observation of coherent population trapping in a V-type two-electron system

We observe coherent population trapping (CPT) in a two-electron atom-Yb-174-using the S-1(0), F= 0 -> P-3(1), F `= 1 transition. CPT is not possible for such a transition according to one-electron theory because the magnetic sublevels form a V-type system, but in a two-electron atom like Yb, the interaction of the electrons transforms the level structure into a V-type system, which allows the formation of a dark state and hence the observation of CPT. Since the two levels involved are degenerate, we use a magnetic field to lift the degeneracy. The single fluorescence dip then splits into five dips-the central unshifted one corresponds to coherent population oscillation, while the outer four are due to CPT. The linewidth of the CPT resonance is about 300 kHz and is limited by the natural linewidth of the excited state, which is to be expected because the excited state is involved in the formation of the dark state.

Linear Stability Analysis of Convection in Two-Layer System with an Evaporating Vapor-Liquid Interface

Classical theories have successfully provided an explanation for convection in a liquid layer heated from below without evaporation. However, these theories are inadequate to account for the convective instabilities in an evaporating liquid layer, especially in the case when it is cooled from below. In the present paper, we study the onset of Marangoni convection in a liquid layer being overlain by a vapor layer.A new two-sided model is put forward instead of the one-sided model in previous studies. Marangoni-Bénard instabilities in evaporating liquid thin layers are investigated with a linear instability analysis. We define a new evaporation Biot number, which is different from that in previous studies and discuss the influences of reference evaporating velocity and evaporation Biot number on the vapor-liquid system. At the end, we explain why the instability occurs even when an evaporating liquid layer is cooled from below.

The interaction of two pairs of solitary waves in a two-fluid system

This paper deals with the interaction of solitary waves in a two-fluid system which consistsof two superimposed incompressible inviscid fluids with a free surface and a horizontal rigidbottom. Under the assumption of shallow water wave, we first derive the basic equationssuitable for the model considered, a generalized form of the Boussinesq equations, then usingthe PLK method and the reductive perturbation method, obtain the second-order approximatesolution for the head-on collision between two pairs of interface and surface solitary waves,and give their maximum amplitudes during the collision and the nonuniform phase shiftsafter the collision which lead to the distortion of the wave profiles.