Ultrasensitivity in phosphorylation-dephosphorylation cycles with little substrate

Cellular decision-making is driven by dynamic behaviours, such as the preparations for sunrise enabled by circadian rhythms and the choice of cell fates enabled by positive feedback. Such behaviours are often built upon ultrasensitive responses where a linear change in input generates a sigmoidal change in output. Phosphorylation-dephosphorylation cycles are one means to generate ultrasensitivity. Using bioinformatics, we show that in vivo levels of kinases and phosphatases frequently exceed the levels of their corresponding substrates in budding yeast. This result is in contrast to the conditions often required by zero-order ultrasensitivity, perhaps the most well known means for how such cycles become ultrasensitive. We therefore introduce a mechanism to generate ultrasensitivity when numbers of enzymes are higher than numbers of substrates. Our model combines distributive and non-distributive actions of the enzymes with two-stage binding and concerted allosteric transitions of the substrate. We use analytical and numerical methods to calculate the Hill number of the response. For a substrate with [Formula: see text] phosphosites, we find an upper bound of the Hill number of [Formula: see text], and so even systems with a single phosphosite can be ultrasensitive. Two-stage binding, where an enzyme must first bind to a binding site on the substrate before it can access the substrate's phosphosites, allows the enzymes to sequester the substrate. Such sequestration combined with competition for each phosphosite provides an intuitive explanation for the sigmoidal shifts in levels of phosphorylated substrate. Additionally, we find cases for which the response is not monotonic, but shows instead a peak at intermediate levels of input. Given its generality, we expect the mechanism described by our model to often underlay decision-making circuits in eukaryotic cells

The mid-infrared spectrum of the transiting exoplanet HD 209458b

We report the spectroscopic detection of mid-infrared emission from the transiting exoplanet HD 209458b. Using archive data taken with the Spitzer/IRS instrument, we have determined the spectrum of HD 209458b between 7.46 and 15.25 microns. We have used two independent methods to determine the planet spectrum, one differential in wavelength and one absolute, and find the results are in good agreement. Over much of this spectral range, the planet spectrum is consistent with featureless thermal emission. Between 7.5 and 8.5 microns, we find evidence for an unidentified spectral feature. If this spectral modulation is due to absorption, it implies that the dayside vertical temperature profile of the planetary atmosphere is not entirely isothermal. Using the IRS data, we have determined the broad-band eclipse depth to be 0.00315 +/- 0.000315, implying significant redistribution of heat from the dayside to the nightside. This work required development of improved methods for Spitzer/IRS data calibration that increase the achievable absolute calibration precision and dynamic range for observations of bright point sources.Comment: 35 pages, 12 figures, revised version accepted by the Astrophysical Journa

Phase Transitions in Multicomponent String Model

We propose a one-dimensional model of a string decorated with adhesion molecules (stickers) to mimic multicomponent membranes in restricted geometries. The string is bounded by two parallel walls and it interacts with one of them by short range attractive forces while the stickers are attracted by the other wall. The exact solution of the model in the case of infinite wall separation predicts both continuous and discontinuous transitions between phases characterised by low and high concentration of stickers on the string. Our model exhibits also coexistence of these two phases, similarly to models of multicomponent membranes.Comment: letter, 8 pages, 3 figure

Nanoindentation-induced deformation of Ge

The deformation mechanisms of crystalline (100) Ge were studied using nanoindentation, cross sectional transmission electron microscopy (XTEM) and Raman microspectroscopy. For a wide range of indentation conditions using both spherical and pointed indenters, multiple discontinuities were found in the force–displacement curves on loading, but no discontinuities were found on unloading. Raman microspectroscopy, measured from samples which had plastically deformed on loading, showed a spectrum shift from that in pristine Ge, suggesting only residual strain. No evidence (such as extra Raman bands) was found to suggest that any pressure-induced phase transformations had occurred, despite the fact that the material had undergone severe plastic deformation.Selected area diffraction pattern studies of the mechanically damaged regions also confirmed the absence of additional phases. Moreover, XTEM showed that, at low loads, plastic deformation occurs by twinning and dislocation motion. This indicates that the hardness of Gemeasured by indentation is not primarily dominated by phase transformation, rather by the nucleation and propagation of twin bands and/or dislocations

Fractal Electromagnetic Showers

We study the self-similar structure of electromagnetic showers and introduce the notion of the fractal dimension of a shower. Studies underway of showers in various materials and at various energies are presented, and the range over which the fractal scaling behaviour is observed is discussed. Applications to fast shower simulations and identification, particularly in the context of extensive air showers, are also discussed.Comment: Talk to be presented at the XI International Symposium on Very High Energy Cosmic Ray Interaction

EFFECT OF SULPHUR DIOXIDE ON GROWTH, CHLOROPHYLL AND SULPHUR CONTENTS OF TOMATO (SOLANUM LYCOPERSICUM L.)

The direct toxic effect of atmospheric pollutant such as sulphur dioxide on plants has been well documented. It is essentially a potent phytotoxic gas and its toxicity to plant is manifested in typical chronic or acute foliar symptom injury. The mode and extent of damage caused by this pollutant to tomato has not been precisely and systematically studied. Under such circumstances, the present investigation was undertaken under simulating condition to find out the possible extent of adaptability of tomato in SO2 emission of our state. The effect of varying levels of sulphur dioxide (0.25, 0.5 and 1.0 ppm) fumigated for 1 hour, 2 hours and 3 hours under simulated conditions on tomato revealed that the important traits like leaf number, leaf area, fresh weight, dry weight and chlorophyll content in leaves were adversely affected, the latter treatment (SO2 1.0 ppm with 3 hours exposure) being more uninnocuous in this regards. However, no significant variation was seen amongst the treatments in respect of tissue fresh and dry weight when compared with that of control (ambient SO2). On the other hand, sulphur content in tissues increase progressively with increasing levels of SO2 and time of fumigation and the variation observed within treatments was significant to each other. It is suggested that the lowest concentration of SO2 (0.25 ppm) used in this study is more than sufficient to bring about a significant changes in most of the parameters studied

Optimal squeezing, pure states, and amplification of squeezing in resonance fluorescence

It is shown that 100% squeezed output can be produced in the resonance fluorescence from a coherently driven two-level atom interacting with a squeezed vacuum. This is only possible for $N=1/8$ squeezed input, and is associated with a pure atomic state, i.e., a completely polarized state. The quadrature for which optimal squeezing occurs depends on the squeezing phase $\Phi ,$ the Rabi frequency $\Omega ,$ and the atomic detuning $\Delta$. Pure states are described for arbitrary $\Phi ,$ not just $\Phi =0$ or $\pi$ as in previous work. For small values of $N,$ there may be a greater degree of squeezing in the output field than the input - i.e., we have squeezing amplification.Comment: 6 pages & 7 figures, Submitted to Phys. Rev.

Accurate prediction of gene feedback circuit behavior from component properties

A basic assumption underlying synthetic biology is that analysis of genetic circuit elements, such as regulatory proteins and promoters, can be used to understand and predict the behavior of circuits containing those elements. To test this assumption, we used time‐lapse fluorescence microscopy to quantitatively analyze two autoregulatory negative feedback circuits. By measuring the gene regulation functions of the corresponding repressor–promoter interactions, we accurately predicted the expression level of the autoregulatory feedback loops, in molecular units. This demonstration that quantitative characterization of regulatory elements can predict the behavior of genetic circuits supports a fundamental requirement of synthetic biology

Low temperature exposure of root system and inflorescence affected flowering and fruit set in 'Chardonnay' grapevines (Vitis vinifera)

The mechanisms by which low temperature affects flowering and fruit set of grapevines are poorly understood, as is the specific response of the grapevine root system and inflorescence to low temperature effects that reduce fruit set. This study aimed to determine the responses of the root system and inflorescence of the grapevine 'Chardonnay' to low temperature (10 °C) during flowering, and considered the possible mechanisms of low temperature effects on those parts. Temperature treatments of 10 °C or 20 °C were imposed to potted 'Chardonnay' grapevines in a glasshouse for up to two weeks during the early stages of flowering. When the root system alone was exposed to 10 °C (with the rest of the plant at 20 °C) during flowering, the number of attached berries and percentage fruit set were significantly reduced by 50 % than when the root system alone was exposed to 20 °C. Whereas, exposure of the inflorescence alone to 10 °C (with the rest of the plant at 20 °C) delayed flowering, allowed rachis to grow longer, and increased both the number of attached berries (from 22 to 62 per vine) and fruit set (from 8 % to 20 %), than when the inflorescence alone was exposed to 20 °C. This study will enhance our understanding of the possible mechanisms of low temperature effects on grapevine fruit set and productivity.

Charge transfer and coherence dynamics of tunnelling system coupled to a harmonic oscillator

We study the transition probability and coherence of a two-site system, interacting with an oscillator. Both properties depend on the initial preparation. The oscillator is prepared in a thermal state and, even though it cannot be considered as an extended bath, it produces decoherence because of the large number of states involved in the dynamics. In the case in which the oscillator is intially displaced a coherent dynamics of change entangled with oscillator modes takes place. Coherency is however degraded as far as the oscillator mass increases producing a increasingly large recoherence time. Calculations are carried on by exact diagonalization and compared with two semiclassical approximations. The role of the quantum effects are highlighted in the long-time dynamics, where semiclassical approaches give rise to a dissipative behaviour. Moreover, we find that the oscillator dynamics has to be taken into account, even in a semiclassical approximation, in order to reproduce a thermally activated enhancement of the transition probability