DNA-Based Artificial Receptors as Transmembrane Signal Transduction Systems for Protocellular Communication

The ability to reproduce signal transduction and cellular communication in artificial cell systems is significant in synthetic protobiology. Here, we describe an artificial transmembrane signal transduction through low pH-mediated formation of the i-motif and dimerization of DNA-based artificial membrane receptors, which is coupled to the occurrence of fluorescence resonance energy transfer and the activation of G-quadruplex/hemin-mediated fluorescence amplification inside giant unilamellar vesicles. Moreover, an intercellular signal communication model is established when the extravesicular H⁺ input is replaced by coacervate microdroplets, which activate the dimerization of the artificial receptors, and subsequent fluorescence production or polymerization in giant unilamellar vesicles. This study represents a crucial step towards designing artificial signalling systems with environmental response, and provides an opportunity to establish signalling networks in protocell colonies.     

嘈杂小世界网络中的随机共振现象

以双稳态振荡器耦合而成的具有小世界拓扑结构的网络为研究对象,重点研究了该体系在周期弱信号和乘性高斯白噪声的共同作用下,振荡器之间的耦合强度与网络拓扑结构的无序度对于网络动力学行为的影响．结果显示噪声可以诱导产生随机共振现象,在适中的耦合强度下增加体系拓扑的无序度可以使整个体系的随机共振现象得到加强．另外,研究表明体系中存在着一组最优的耦合强度和拓扑无序度,在它们的协同作用下体系能够最有效地检测到外界的弱信号．     

Response Ability to External Signal Enhanced by Biological Spatial Con guration in Coupled Hindmarsh-Rose Neural System

The effect of realistic topology configuration of intercellular connections on the response ability in coupled cell system is numerically investigated by using the Hindmarsh-Rose model. For the proper coupling intensity, we set the control parameter to be near the critical value, and the external stimulus is introduced to the first cell in coupled system. It is found that, on one hand, when the cells are coupled with some proper topological structures, the external stimulus could transmit through the system, and shows better response ability and higher sensitivity. On the other hand, the in uence of topological configuration on the synchronous ability and selection effect of neural system are also discussed. Our results display that the topology of coupled system may play an important role in the process of signal propagation, which could help us to understand the coordinated performance of cells in tissue.     

Pulse-coupled chemical oscillators with time delay

Finger on the pulse: in a system of two pulse-coupled Belousov-Zhabotinsky oscillators, introducing a time delay or increasing the coupling strength brings about novel dynamic features (see picture, the two oscillators are shown in different colors), such as reversal of the roles of excitatory and inhibitory coupling or fast anti-phase oscillation. These features are not observed in diffusively coupled systems, and shed light on how such pulse coupling occurs at synapses.     

Entrainment in a chemical oscillator chain with a pacemaker

Entrainment by a pacemaker was investigated experimentally and numerically in a chain of chemical oscillators using coupled discrete Belousov-Zhabotinsky reaction oscillators. The spontaneous frequency of each oscillator depended on the concentration of catalyst ions. The coupling strengths among the nearest neighbor oscillators were controlled by changing the spacing distance (d) between beads. When the coupling strength was sufficiently strong, the pacemaker entrained other oscillators in the chain. Subsequently, the trigger waves propagating from a pacemaker were observed. The range of trigger wave propagation area, i.e., the number of entrained oscillators, depended on d. Numerical simulation for the system described the experimental results well. Furthermore, photic noise maximized the strength of entrainment at an optimal noise intensity.     

Proton transfer reactions in model condensed-phase environments: Accurate quantum dynamics using the multilayer multiconfiguration time-dependent Hartree approach

The recently proposed multilayer multiconfiguration time-dependent Hartree (ML-MCTDH) approach to evaluating reactive quantum dynamics is applied to two model condensed-phase proton transfer reactions. The models consist of a one-dimensional double-well "system" that is bilinearly coupled to a "bath" of harmonic oscillators parameterized to represent a condensed-phase environment. Numerically exact quantum-mechanical flux correlation functions and thermal rate constants are obtained for a broad range of temperatures and system-bath coupling strengths, thus demonstrating the efficacy of the ML-MCTDH approach. Particular attention is focused on the regime where low temperatures are combined with weak system-bath coupling. Under such conditions it is found that long propagation times are often required and that quantum coherence effects may prevent a rigorous determination of the rate constant.     

Quantum solution of coupled harmonic oscillator systems beyond normal coordinates

Normal coordinates can be defined as orthogonal linear combinations of coordinates that remove the second order couplings in coupled harmonic oscillator systems. In this paper we go further and explore the possibility of using linear although non-orthogonal coordinate transformations to get the quantum solution of coupled systems. The idea is to use as non-orthogonal linear coordinates those which allow us to express the second-order Hamiltonian matrix in a block diagonal form. To illustrate the viability of this treatment, we first apply it to a system of two bilinearly coupled harmonic oscillators which admits analytical exact solutions. The method provides in this case, as an extra mathematical result, the analytical expressions for the eigenvalues of a certain type of symmetrical tridiagonal matrices. Second, we carry out a numerical application to the Barbanis coupled oscillators system, which contains a third order coupling term and cannot be solved in closed form. We demonstrate that the non-orthogonal coordinates used, named oblique coordinates, are much more efficient than normal coordinates to determine the energy levels and eigenfunctions of this system variationally.     

Prediction of protein signal sequences

Newly synthesized proteins have an intrinsic signal sequence, functioning as "address tags" or "zip codes", that is essential for guiding them wherever they are needed. Owing to such a unique function, protein signals have become a crucial tool in finding new drugs or reprogramming cells for gene therapy. However, to effectively use protein signals as a desirable vehicle in the field of proteomics, the first important thing is to find a fast and powerful method to identify the "address tag" or "zip code" entity. Although all signal sequences contain a hydrophobic core region, they show great variation in both overall length and amino acid sequence. It is this variation that makes it possible to deliver thousands of proteins to many different cellular locations by varieties of modes. It is also this variation that makes it very difficult to formulate a general algorithm to predict signal sequences. Nevertheless, various prediction models and algorithms have been developed during the past 17 years. This Review summarizes the development in this area, from the pioneering methods to neural network approaches, and to the sub-site coupling approaches. Meanwhile, the future challenges in this area, as well as some promising avenues for further improving the prediction quality, have been briefly addressed as well.     

Isolation of phosphopeptides using solid phase enrichment

Protein phosphorylations are post-translational protein modifications that are crucial for intercellular signal transduction and the regulation of many cellular events. We describe herein a novel technology utilizing α-diazo functionalized solid phase resins to isolate phosphorylated peptides from non-phosphorylated substrates.     

New bulk liquid membrane oscillator composed of two coupled oscillators with diffusion-mediated physical coupling

A new type of bulk liquid membrane system, which represents the first example of a bulk liquid membrane oscillator characterised by the presence of two coupled oscillators, is described. When the benzyldimethyltetradecylammonium chloride surfactant undergoes an oscillatory mass transfer through a nitromethane liquid membrane, a new liquid layer (phase X) appears between the membrane and the acceptor phase. Kinetic analysis provides evidence that the whole system is composed of two coupled oscillators with diffusion-mediated physical coupling. The first component oscillator (based on nitromethane) of lower frequency delivers the driving material to the second one (phase X-based oscillator) leading to additional higher frequency oscillations. A new molecular mechanism is proposed for interpreting the experimental observations. The results might enhance understanding of intercellular communication in biology, where periodic signalling is more efficient than any other type of signalling mode.     

Effect of gating currents of ion channels on the collective spiking activity of coupled Hodgkin-Huxley neurons

Based on the coupled stochastic Hodgkin-Huxley neurons, we numerically studied the effect of gating currents of ion channels, as well as coupling and the number of neurons, on the collective spiking rate and regularity in the coupled system. It was found, for a given coupling strength and with a relatively large number of neurons, when gating currents are applied, the collective spiking regularity decreases; meanwhile, the collective spiking rate increases, indicating that gating currents can aggravate the desynchronization of the spikings of all neurons. However, gating currents caused hardly any effect in the spiking of any individual neuron of the coupled system. This result, different from the reduction of the spiking rate by gating currents in a single neuron, provides a new insight into the effect of gating currents on the global information processing and signal transduction in real neural systems. Supported by the Science Foundation of Ludong University (Grant Nos. 23140301, L20072805)     

Affinity enrichment of plasma membrane for proteomics analysis

Proteomics analysis of plasma membranes from cells exposed to different extracellular environments is potentially a powerful approach for the identification of membrane-associated proteins responding to these environments. Preparation of high concentration plasma membrane fractions with low contamination from cellular organelles is essential for such studies. Here, we describe an affinity enrichment method, which combines cell surface biotinylation with affinity enrichment by immobilized streptavidin beads, for the isolation of plasma membranes. This method results in a 400-fold enrichment of plasma membrane relative to endoplasmic reticulum, a major contaminant in standard plasma membrane preparations, and dramatically reduces contamination from other cellular organelles. The biotinylation reaction did not interfere with ligand-dependent activation of receptor tyrosine kinases or G-protein coupled receptors, suggesting cell-surface signal transduction machinery remains functional. Membrane fractions prepared by this method should provide excellent starting materials for membrane proteomics analysis such as studies of dynamic trafficking and regulation of signaling molecules or identification of disease-specific membrane markers.     

Capacitive coupling synchronizes autonomous microfluidic oscillators

Even identically designed autonomous microfluidic oscillators have device‐to‐device oscillation variability that arises due to inconsistencies in fabrication, materials, and operation conditions. This work demonstrates, experimentally and theoretically, that with appropriate capacitive coupling these microfluidic oscillators can be synchronized. The size and characteristics of the capacitive coupling needed and the range of input flow rate differences that can be synchronized are also characterized. In addition to device‐to‐device variability, there is also within‐device oscillation noise that arises. An additional advantage of coupling multiple fluidic oscillators together is that the oscillation noise decreases. The ability to synchronize multiple autonomous oscillators is also a first step towards enhancing their usefulness as tools for biochemical research applications where multiplicate experiments with identical temporal‐stimulation conditions are required.     

ORCADIAN OSCILLATORS AND PHOTORECEPTORS IN THE GASTROPOD,APLYSIA*

Abstract— The sea slug, Aplysia, is a useful model system for research on the neurophysiology of circadian integration. The animal contains several circadian oscillators and several photoreceptors. Each eye contains a circadian oscillator as well as photoreceptors. The ocular oscillators can be entrained by extraocular photoreceptors as well as their own ocular photoreceptors. The abdominal ganglion probably contains another oscillator but it has been much more difficult to manipulate in the laboratory than have the oscillators in the eyes. There is also a circadian rhythm in overt behavioral activity. This rhythm is controlled in part by extraocular oscillators and extraocular photoreceptors and in part by the eyes. In exerting their influence on the behavioral rhythm, the eyes appear to act in the capacity of oscillators and not merely as photoreceptors. Although neurons in the retina have neurosecretory morphology, the entire influence of the eyes on the behavioral rhythm appears to be mediated by nerve signals which travel in the optic nerve. As yet there is no evidence to suggest that any two oscillators in Aplysia are internally coupled. There is also no evidence yet for hormonal coupling between photoreceptors and oscillators or between oscillators and rhythmic outputs.     

On-chip photoactivation of heterologously expressed rhodopsin allows kinetic analysis of G-protein signaling by surface plasmon resonance spectroscopy

Surface plasmon resonance spectroscopy allows the study of protein interaction dynamics in real-time. Application of this technique to G-protein coupled receptors, the largest family of receptors involved in signal transduction, has been complicated by their low level of expression and the critical dependence of their native conformation on the hydrophobic transmembrane lipid environment. Here, we investigate and compare three different strategies to immobilize rhodopsin, a prototypical G-protein coupled receptor on a sensor chip surface using antibodies and a lectin for receptor capturing. By further probing of different experimental conditions (pH, detergent type) we identified the optimal factors to maintain rhodopsin in a functional conformation and extended this approach to recombinant rhodopsin that was heterologously expressed in COS cells. Functional operation of rhodopsin on the sensor chip surface was proven by its activation and subsequent light-stimulated G-protein coupling. The influence of these experimental parameters on the association and dissociation kinetics of G-protein receptor coupling was determined. Thereby, we found that the kinetics of G_t interaction were not changed by the strategy of immobilization or the type of detergent. Regeneration of opsin directly on a chip allowed recycling of the immobilized native and recombinant receptor. Thus, the approach provides an experimental framework for choosing the most suitable conditions for the solubilization, immobilization, and for functional tests of rhodopsin on a biosensor surface.     

Optimal control simulation of the Deutsch-Jozsa algorithm in a two-dimensional double well coupled to an environment

The quantum Deutsch-Jozsa algorithm is implemented by using vibrational modes of a two-dimensional double well. The laser fields realizing the different gates (NOT, CNOT, and HADAMARD) on the two-qubit space are computed by the multitarget optimal control theory. The stability of the performance index is checked by coupling the system to an environment. Firstly, the two-dimensional subspace is coupled to a small number Nb of oscillators in order to simulate intramolecular vibrational energy redistribution. The complete (2+Nb)D problem is solved by the coupled harmonic adiabatic channel method which allows including coupled modes up to Nb=5. Secondly, the computational subspace is coupled to a continuous bath of oscillators in order to simulate a confined environment expected to be favorable to achieve molecular computing, for instance, molecules confined in matrices or in a fullerene. The spectral density of the bath is approximated by an Ohmic law with a cutoff for some hundreds of cm(-1). The time scale of the bath dynamics (of the order of 10 fs) is then smaller than the relaxation time and the controlled dynamics (2 ps) so that Markovian dissipative dynamics is used.     

Classical and quantum mechanical infrared echoes from resonantly coupled molecular vibrations

The nonlinear response function associated with the infrared vibrational echo is calculated for a quantum mechanical model of resonantly coupled, anharmonic oscillators at zero temperature. The classical mechanical response function is determined from the quantum response function by setting variant Planck's over 2pi-->0, permitting the comparison of the effects of resonant vibrational coupling among an arbitrary number of anharmonic oscillators on quantum and classical vibrational echoes. The quantum response function displays a time dependence that reflects both anharmonicity and resonant coupling, while the classical response function depends on anharmonicity only through a time-independent amplitude, and shows a time dependence controlled only by the resonant coupling. In addition, the classical response function grows without bound in time, a phenomenon associated with the nonlinearity of classical mechanics, and absent in quantum mechanics. This unbounded growth was previously identified in the response function for a system without resonant vibrational energy transfer, and is observed to persist in the presence of resonant coupling among vibrations. Quantitative agreement between classical and quantum response functions is limited to a time scale of duration inversely proportional to the anharmonicity.     

耦合生物细胞体系中噪声诱导钙信号的传递和增强

Dynamics of calcium oscillation in a coupled cell system is discussed. It shows that when one end of the cell chain is perturbed by noise, the signal induced by noise can propagate along a linearly coupled cell chain with considerable enhancement, a rather ordered internal signal can be obtained on the other end, and the signal itself can also be enhanced. The effects of coupling constant, noise intensity and coupling means on the propagation of the signal are investigated. It is found that there exist an optimal coupling constant and noise intensity in favor of the signal propagation. What′s more, a qualitative explanation via the signal and the noise background is given. And the one way coupling is better for the signal propagation and enhancement than for the two way coupling. The results may have important applications in living cell systems, where information is transmitted along a cell chain.     

Logic‐Gate‐Actuated DNA‐Controlled Receptor Assembly for the Programmable Modulation of Cellular Signal Transduction

Programming cells to sense multiple inputs and activate cellular signal transduction cascades is of great interest. Although this goal has been achieved through the engineering of genetic circuits using synthetic biology tools, a nongenetic and generic approach remains highly demanded. Herein, we present an aptamer‐controlled logic receptor assembly for modulating cellular signal transduction. Aptamers were engineered as “robotic arms” to capture target receptors (c‐Met and CD71) and a DNA logic assembly functioned as a computer processor to handle multiple inputs. As a result, the DNA assembly brings c‐Met and CD71 into close proximity, thus interfering with the ligand–receptor interactions of c‐Met and inhibiting its functions. Using this principle, a set of logic gates was created that respond to DNA strands or light irradiation, modulating the c‐Met/HGF signal pathways. This simple modular design provides a robust chemical tool for modulating cellular signal transduction.