Crackling noise

Crackling noise arises when a system responds to changing external conditions through discrete, impulsive events spanning a broad range of sizes. A wide variety of physical systems exhibiting crackling noise have been studied, from earthquakes on faults to paper crumpling. Because these systems exhibit regular behaviour over a huge range of sizes, their behaviour is likely to be independent of microscopic and macroscopic details, and progress can be made by the use of simple models. The fact that these models and real systems can share the same behaviour on many scales is called universality. We illustrate these ideas by using results for our model of crackling noise in magnets, explaining the use of the renormalization group and scaling collapses, and we highlight some continuing challenges in this still-evolving field.     

Characterization of murine interleukin B by a monoclonal antibody

Interleukin B (IL-B), formerly termed BEF (B-cell-derived enhancing factor) or IL-B4, was originally described as a non-immunoglobulin regulatory factor spontaneously produced by B lymphocytes and B-cell lines that enhances the in vitro antigen-driven antibody response of unfractionated spleen cells stimulated by thymus-dependent antigens. Since then we have examined the function of interleukin B in a number of immune reactions, both in vitro and in vivo, and found that it inhibits the activation of suppressor T lymphocytes. We report here the production of two monoclonal antibodies (mAb) that specifically inhibit interleukin B activity. The use of these mAb in the purification and characterization of IL-B is described. IL-B from both normal and transformed B cells consists of two subunits of similar size and amino-acid composition. The structure of interleukin B and its specific behaviour in biological assay distinguish it from many other known lymphokines.     

From molecular noise to behavioural variability in a single bacterium

The chemotaxis network that governs the motion of Escherichia coli has long been studied to gain a general understanding of signal transduction. Although this pathway is composed of just a few components, it exhibits some essential characteristics of biological complexity, such as adaptation and response to environmental signals. In studying intracellular networks, most experiments and mathematical models have assumed that network properties can be inferred from population measurements. However, this approach masks underlying temporal fluctuations of intracellular signalling events. We have inferred fundamental properties of the chemotaxis network from a noise analysis of behavioural variations in individual bacteria. Here we show that certain properties established by population measurements, such as adapted states, are not conserved at the single-cell level: for timescales ranging from seconds to several minutes, the behaviour of non-stimulated cells exhibit temporal variations much larger than the expected statistical fluctuations. We find that the signalling network itself causes this noise and identify the molecular events that produce it. Small changes in the concentration of one key network component suppress temporal behavioural variability, suggesting that such variability is a selected property of this adaptive system.     

Loss of mouse fibroblast cell response to phorbol esters restored by microinjected protein kinase C

The phorbol esters in addition to being among the most potent mouse skin tumour promoters profoundly affect many different biological systems. It is postulated that they act through activation of protein kinase C, but substantial heterogeneity in their pharmacological and binding behaviour in some systems has caused concern about whether this is their only target. Evidence linking protein kinase C activation with biological responses to the phorbol esters includes similarity in structure-activity relations for binding and response; in vitro phosphorylation of specific proteins by protein kinase C at the same sites at which phorbol ester treatment induces phosphorylation in intact cells; and correlation in certain cell types between down regulation of protein kinase C on chronic phorbol ester treatment and loss of cellular responsiveness to the phorbol ester. Here we report that microinjection of purified protein kinase C into Swiss 3T3 fibroblasts pretreated with the phorbol ester phorbol 12,13-dibutyrate (PDBu) restores the mitogenic response of the cells to PDBu, directly establishing the involvement of protein kinase C in this response.     

Use of behavioural stochastic resonance by paddle fish for feeding

Stochastic resonance is the phenomenon whereby the addition of an optimal level of noise to a weak information-carrying input to certain nonlinear systems can enhance the information content at their outputs. Computer analysis of spike trains has been needed to reveal stochastic resonance in the responses of sensory receptors except for one study on human psychophysics. But is an animal aware of, and can it make use of, the enhanced sensory information from stochastic resonance? Here, we show that stochastic resonance enhances the normal feeding behaviour of paddlefish (Polyodon spathula), which use passive electroreceptors to detect electrical signals from planktonic prey. We demonstrate significant broadening of the spatial range for the detection of plankton when a noisy electric field of optimal amplitude is applied in the water. We also show that swarms of Daphnia plankton are a natural source of electrical noise. Our demonstration of stochastic resonance at the level of a vital animal behaviour, feeding, which has probably evolved for functional success, provides evidence that stochastic resonance in sensory nervous systems is an evolutionary adaptation.     

Self-destructive cooperation mediated by phenotypic noise

In many biological examples of cooperation, individuals that cooperate cannot benefit from the resulting public good. This is especially clear in cases of self-destructive cooperation, where individuals die when helping others. If self-destructive cooperation is genetically encoded, these genes can only be maintained if they are expressed by just a fraction of their carriers, whereas the other fraction benefits from the public good. One mechanism that can mediate this differentiation into two phenotypically different sub-populations is phenotypic noise. Here we show that noisy expression of self-destructive cooperation can evolve if individuals that have a higher probability for self-destruction have, on average, access to larger public goods. This situation, which we refer to as assortment, can arise if the environment is spatially structured. These results provide a new perspective on the significance of phenotypic noise in bacterial pathogenesis: it might promote the formation of cooperative sub-populations that die while preparing the ground for a successful infection. We show experimentally that this model captures essential features of Salmonella typhimurium pathogenesis. We conclude that noisily expressed self-destructive cooperative actions can evolve under conditions of assortment, that self-destructive cooperation is a plausible biological function of phenotypic noise, and that self-destructive cooperation mediated by phenotypic noise could be important in bacterial pathogenesis.     

Universal alignment of hydrogen levels in semiconductors,insulators and solutions

Hydrogen strongly affects the electronic and structural properties of many materials. It can bind to defects or to other impurities, often eliminating their electrical activity: this effect of defect passivation is crucial to the performance of many photovoltaic and electronic devices. A fuller understanding of hydrogen in solids is required to support development of improved hydrogen-storage systems, proton-exchange membranes for fuel cells, and high-permittivity dielectrics for integrated circuits. In chemistry and in biological systems, there have also been many efforts to correlate proton affinity and deprotonation with host properties. Here we report a systematic theoretical study (based on ab initio methods) of hydrogen in a wide range of hosts, which reveals the existence of a universal alignment for the electronic transition level of hydrogen in semiconductors, insulators and even aqueous solutions. This alignment allows the prediction of the electrical activity of hydrogen in any host material once some basic information about the band structure of that host is known. We present a physical explanation that connects the behaviour of hydrogen to the line-up of electronic band structures at heterojunctions.     

Summing up the noise in gene networks

Random fluctuations in genetic networks are inevitable as chemical reactions are probabilistic and many genes, RNAs and proteins are present in low numbers per cell. Such 'noise' affects all life processes and has recently been measured using green fluorescent protein (GFP). Two studies show that negative feedback suppresses noise, and three others identify the sources of noise in gene expression. Here I critically analyse these studies and present a simple equation that unifies and extends both the mathematical and biological perspectives.     

High resolution imaging using scanning ion conductance microscopy with improved distance feedback control

Microscopy is an essential technique for observation on living cells. There is currently great interest in applying scanning probe microscopy to image-living biological cells in their natural environment at the nanometer scale. Scanning ion conductance microscopy is a new form of scanning probe microscopy, which enables non-contact high-resolution imaging of living biological cells. Based on a scanned nanopipette in physiological buffer, the distance feedback control uses the ion current to control the distance between the pipette tip and the sample surface. However, this feedback control has difficulties over slopes on convoluted cell surfaces, which limits its resolution. In this study, we present an improved form of feedback control that removes the contribution of up to the third-order slope from the ion current signal, hence providing a more accurate signal for controlling the distance. We show that this allows faster and lower noise topographic high-resolution imaging.     

Variability and memory of protein levels in human cells

Protein expression is a stochastic process that leads to phenotypic variation among cells. The cell-cell distribution of protein levels in microorganisms has been well characterized but little is known about such variability in human cells. Here, we studied the variability of protein levels in human cells, as well as the temporal dynamics of this variability, and addressed whether cells with higher than average protein levels eventually have lower than average levels, and if so, over what timescale does this mixing occur. We measured fluctuations over time in the levels of 20 endogenous proteins in living human cells, tagged by the gene for yellow fluorescent protein at their chromosomal loci. We found variability with a standard deviation that ranged, for different proteins, from about 15% to 30% of the mean. Mixing between high and low levels occurred for all proteins, but the mixing time was longer than two cell generations (more than 40 h) for many proteins. We also tagged pairs of proteins with two colours, and found that the levels of proteins in the same biological pathway were far more correlated than those of proteins in different pathways. The persistent memory for protein levels that we found might underlie individuality in cell behaviour and could set a timescale needed for signals to affect fully every member of a cell population.     

High resolution imaging using scanning ion conductance microscopy with improved distance feedback control

Microscopy is an essential technique for observation on living cells. There is currently great interest in apply scanning probe microscopy to image living biological cells in their natural environment at the nanometer scale. Scanning ion conductance microscopy is a new form of scanning probe microscopy, which enables non-contact high resolution imaging of living biological cells. Based on a scanned nanopipette in physiological buffer, the distance feedback control uses the ion current to control the distance between the pipette tip and the sample surface. However, this feedback control has difficulties over slopes on convoluted cell surfaces, which limits its resolution. In this study, we present an improved form of feedback control that removes the contribution of up to the third order slope from the ion current signal, hence providing a more accurate signal for controlling the distance. We show that this allows faster and lower noise topographic high resolution imaging.     

Brownian motion: absolute negative particle mobility

Noise effects in technological applications, far from being a nuisance, can be exploited with advantage - for example, unavoidable thermal fluctuations have found application in the transport and sorting of colloidal particles and biomolecules. Here we use a microfluidic system to demonstrate a paradoxical migration mechanism in which particles always move in a direction opposite to the net acting force ('absolute negative mobility') as a result of an interplay between thermal noise, a periodic and symmetric microstructure, and a biased alternating-current electric field. This counterintuitive phenomenon could be used for bioanalytical purposes, for example in the separation and fractionation of colloids, biological molecules and cells.     

Common effector processing mediates cell-specific responses to stimuli

The fundamental components of many signalling pathways are common to all cells. However, stimulating or perturbing the intracellular network often causes distinct phenotypes that are specific to a given cell type. This 'cell specificity' presents a challenge in understanding how intracellular networks regulate cell behaviour and an obstacle to developing drugs that treat signalling dysfunctions. Here we apply a systems-modelling approach to investigate how cell-specific signalling events are integrated through effector proteins to cause cell-specific outcomes. We focus on the synergy between tumour necrosis factor and an adenoviral vector as a therapeutically relevant stimulus that induces cell-specific responses. By constructing models that estimate how kinase-signalling events are processed into phenotypes through effector substrates, we find that accurate predictions of cell specificity are possible when different cell types share a common 'effector-processing' mechanism. Partial-least-squares regression models based on common effector processing accurately predict cell-specific apoptosis, chemokine release, gene induction, and drug sensitivity across divergent epithelial cell lines. We conclude that cell specificity originates from the differential activation of kinases and other upstream transducers, which together enable different cell types to use common effectors to generate diverse outcomes. The common processing of network signals by downstream effectors points towards an important cell biological principle, which can be applied to the understanding of cell-specific responses to targeted drug therapies.     

Global organization of metabolic fluxes in the bacterium Escherichia coli

Cellular metabolism, the integrated interconversion of thousands of metabolic substrates through enzyme-catalysed biochemical reactions, is the most investigated complex intracellular web of molecular interactions. Although the topological organization of individual reactions into metabolic networks is well understood, the principles that govern their global functional use under different growth conditions raise many unanswered questions. By implementing a flux balance analysis of the metabolism of Escherichia coli strain MG1655, here we show that network use is highly uneven. Whereas most metabolic reactions have low fluxes, the overall activity of the metabolism is dominated by several reactions with very high fluxes. E. coli responds to changes in growth conditions by reorganizing the rates of selected fluxes predominantly within this high-flux backbone. This behaviour probably represents a universal feature of metabolic activity in all cells, with potential implications for metabolic engineering.     

A silicon neuron.

By combining neurophysiological principles with silicon engineering, we have produced an analog integrated circuit with the functional characteristics of real nerve cells. Because the physics underlying the conductivity of silicon devices and biological membranes is similar, the 'silicon neuron' is able to emulate efficiently the ion currents that cause nerve impulses and control the dynamics of their discharge. It operates in real-time and consumes little power, and many 'neurons' can be fabricated on a single silicon chip. The silicon neuron represents a step towards constructing artificial nervous systems that use more realistic principles of neuronal computation than do existing electronic neuronal networks.     

分块噪声自适应高光谱图像去噪算法研究

高光谱图像在获取过程中容易产生噪音,从而影响了地物空间信息的识别。噪声去除是高光谱图像处理十分必要的步骤。结合低秩矩阵分解理论,在传统奇异值阈值方法的基础上提出基于分块的噪声自适应遥感去噪方法。实验结果证明,该方法运算速度快,并能够有效去除缺失值造成的死线噪声以及高斯噪声,在平均峰值信噪比(MPSNR)和平均结构相似性(MSSIM)上优于Godec算法。     

神经网络的自旋玻璃体模型中的高阶相关

讨论神经网络的自旋玻璃体模型,首先从一个集合选出接近一个初始神经组态的图形,然后假定神经网络动力学中的神经组态,经转换神经元实现这个假设,来自干扰图形的噪声影响许多亚稳态的状况,大数目N的神经元网络存储多个图形,其大小是N个二进制数,对n＝3,网络能量最小,这个能量函数可描述三自旋相关的自旋玻璃体系,在神经元N＝20网络对不同阶进行了比较,推测三神经元相互作用在生物系统中是可实现的。