The role of the circadian system in fractal neurophysiological control

Many neurophysiological variables such as heart rate, motor activity, and neural activity are known to exhibit intrinsic fractal fluctuations – similar temporal fluctuation patterns at different time scales. These fractal patterns contain information about health, as many pathological conditions are accompanied by their alteration or absence. In physical systems, such fluctuations are characteristic of critical states on the border between randomness and order, frequently arising from nonlinear feedback interactions between mechanisms operating on multiple scales. Thus, the existence of fractal fluctuations in physiology challenges traditional conceptions of health and disease, suggesting that high levels of integrity and adaptability are marked by complex variability, not constancy, and are properties of a neurophysiological network, not individual components. Despite the subject's theoretical and clinical interest, the neurophysiological mechanisms underlying fractal regulation remain largely unknown. The recent discovery that the circadian pacemaker (suprachiasmatic nucleus) plays a crucial role in generating fractal patterns in motor activity and heart rate sheds an entirely new light on both fractal control networks and the function of this master circadian clock, and builds a bridge between the fields of circadian biology and fractal physiology. In this review, we sketch the emerging picture of the developing interdisciplinary field of fractal neurophysiology by examining the circadian system's role in fractal regulation.     

A numerical algorithm for investigating the role of the motor-cargo linkage in molecular motor-driven transport

We extend the numerical algorithm developed by Wang et al. (2003. J. Theor. Biol. 221, 491-511) for studying biomolecular transport processes to include the linkage that connects molecular motors to their cargo. The new algorithm is used to investigate how the stiffness of the linkage affects the average velocity, effective diffusion coefficient, and randomness parameter. Three different models for molecular motors are considered: (1) a discrete stepping motor (2) a motor moving in a tilted-periodic potential and (3) a motor driven by a flashing potential. We demonstrate that a flexible motor-cargo linkage can make inferences on motor behavior based on measurements of the cargo's position difficult. We also show that even for the case of a tilted-periodic potential there exists an optimal stiffness of the linkage at which transport is maximized. The MATLAB code used in this paper is available at: http://www.unc.edu/approximatelytelston/code/.     

Bivalent Associations in Mus domesticus 2n=40 Spermatocytes. Are They Random?

The establishment of associations between bivalents from Mus domesticus \(2n=40\) spermatocytes is a common phenomenon that shows up during the first prophase of meiotic nuclei. In each nucleus, a seemingly random display of variable size clusters of bivalents in association is observed. These associations originate a particular nuclear architecture and determine the probability of encounters between chromosome domains. Hence, the type of randomness in associations between bivalents has nontrivial consequences. We explore different models for randomness and the associated bivalent probability distributions and find that a simple model based on randomly coloring a subset of vertices of a 6-regular graph provides best agreement with microspreads observations. The notion of randomness is thereby explained in conjunction with the underlying local geometry of the nuclear envelope.     

Voronoi tessellation captures very early clustering of single primary cells as induced by interactions in nascent biofilms

Biofilms dominate microbial life in numerous aquatic ecosystems, and in engineered and medical systems, as well. The formation of biofilms is initiated by single primary cells colonizing surfaces from the bulk liquid. The next steps from primary cells towards the first cell clusters as the initial step of biofilm formation remain relatively poorly studied. Clonal growth and random migration of primary cells are traditionally considered as the dominant processes leading to organized microcolonies in laboratory grown monocultures. Using Voronoi tessellation, we show that the spatial distribution of primary cells colonizing initially sterile surfaces from natural streamwater community deviates from uniform randomness already during the very early colonisation. The deviation from uniform randomness increased with colonisation--despite the absence of cell reproduction--and was even more pronounced when the flow of water above biofilms was multidirectional and shear stress elevated. We propose a simple mechanistic model that captures interactions, such as cell-to-cell signalling or chemical surface conditioning, to simulate the observed distribution patterns. Model predictions match empirical observations reasonably well, highlighting the role of biotic interactions even already during very early biofilm formation despite few and distant cells. The transition from single primary cells to clustering accelerated by biotic interactions rather than by reproduction may be particularly advantageous in harsh environments--the rule rather than the exception outside the laboratory.     

Prediction of microdamage formation using a mineral-collagen composite model of bone

Age-related changes in bone quality are mainly manifested in the reduced toughness. Since the post-yield deformation of bone is realized through microdamage formation (e.g., microcracking and diffuse damage), it is necessary to understand the mechanism of microdamage formation in bone in order to elucidate underlying mechanisms of age-related bone fractures. In this study, a two-dimensional shear lag model was developed to predict stress concentration fields around an initial crack in a mineral-collagen composite. In this model, non-linear elasticity was assumed for the collagen phase, and linear elasticity for the mineral. Based on the pattern of the stress concentration fields, the condition for microdamage formation was discussed. The results of our analyses indicate that: (1) an initial crack formed in mineral phase may cause stress concentration in the adjacent mineral layers; (2) the pattern of stress concentration fields depends not only on the spatial but also mechanical properties of the collagen and mineral phases; (3) the pattern of the stress concentration fields could determine either coalescence or scattering of nano cracks around the initial crack.     

GAD67-mediated GABA synthesis and signaling regulate inhibitory synaptic innervation in the visual cortex

The development of GABAergic inhibitory circuits is shaped by neural activity, but the underlying mechanisms are unclear. Here, we demonstrate a novel function of GABA in regulating GABAergic innervation in the adolescent brain, when GABA is mainly known as an inhibitory transmitter. Conditional knockdown of the rate-limiting synthetic enzyme GAD67 in basket interneurons in adolescent visual cortex resulted in cell autonomous deficits in axon branching, perisomatic synapse formation around pyramidal neurons, and complexity of the innervation fields; the same manipulation had little influence on the subsequent maintenance of perisomatic synapses. These effects of GABA deficiency were rescued by suppressing GABA reuptake and by GABA receptor agonists. Germline knockdown of GAD67 but not GAD65 showed similar deficits, suggesting a specific role of GAD67 in the maturation of perisomatic innervation. Since intracellular GABA levels are modulated by neuronal activity, our results implicate GAD67-mediated GABA synthesis in activity-dependent regulation of inhibitory innervation patterns.     

Temporal Changes in Randomness of Bird Communities across Central Europe

Many studies have examined whether communities are structured by random or deterministic processes, and both are likely to play a role, but relatively few studies have attempted to quantify the degree of randomness in species composition. We quantified, for the first time, the degree of randomness in forest bird communities based on an analysis of spatial autocorrelation in three regions of Germany. The compositional dissimilarity between pairs of forest patches was regressed against the distance between them. We then calculated the y-intercept of the curve, i.e. the ‘nugget’, which represents the compositional dissimilarity at zero spatial distance. We therefore assume, following similar work on plant communities, that this represents the degree of randomness in species composition. We then analysed how the degree of randomness in community composition varied over time and with forest management intensity, which we expected to reduce the importance of random processes by increasing the strength of environmental drivers. We found that a high portion of the bird community composition could be explained by chance (overall mean of 0.63), implying that most of the variation in local bird community composition is driven by stochastic processes. Forest management intensity did not consistently affect the mean degree of randomness in community composition, perhaps because the bird communities were relatively insensitive to management intensity. We found a high temporal variation in the degree of randomness, which may indicate temporal variation in assembly processes and in the importance of key environmental drivers. We conclude that the degree of randomness in community composition should be considered in bird community studies, and the high values we find may indicate that bird community composition is relatively hard to predict at the regional scale.     

Mechanotransduction and fibrosis

Scarring and tissue fibrosis represent a significant source of morbidity in the United States. Despite considerable research focused on elucidating the mechanisms underlying cutaneous scar formation, effective clinical therapies are still in the early stages of development. A thorough understanding of the various signaling pathways involved is essential to formulate strategies to combat fibrosis and scarring. While initial efforts focused primarily on the biochemical mechanisms involved in scar formation, more recent research has revealed a central role for mechanical forces in modulating these pathways. Mechanotransduction, which refers to the mechanisms by which mechanical forces are converted to biochemical stimuli, has been closely linked to inflammation and fibrosis and is believed to play a critical role in scarring. This review provides an overview of our current understanding of the mechanisms underlying scar formation, with an emphasis on the relationship between mechanotransduction pathways and their therapeutic implications.     

The role of diffusible molecules in regulating the cellular differentiation of Dictyostelium discoideum

A central problem in developmental biology is to understand how morphogenetic fields are created and how they act to direct regionalized cellular differentiation. This goal is being pursued in organisms as diverse as moulds, worms, flies, frogs and mice. Each organism has evolved its own solution to the challenge of multicellularity but there appear to be common underlying principles and, once pattern formation is fully understood in any system, some general truths seem certain to be revealed. As a non-obligate metazoan, Dictyostelium discoideum has proven a particularly tractable system in which to identify and characterize cellular morphogens. Cyclic AMP and ammonia stimulate prespore cell differentiation and ammonia plays an additional role in repressing terminal cellular differentiation. Differentiation Inducing Factor (DIF) acts to direct prestalk cell differentiation and adenosine may play a synergistic role in repressing prespore cell differentiation. This review summarizes the evidence for these interactions and describes a number of models which show how this small repertoire of diffusible molecules, acting in concert, may direct the formation of a differentiated structure.     

Randomness in crystallization of proteins from Staphylococcus aureus

Of many factors affecting protein crystallization, randomness in proteins has been given less attention although highly structured proteins would be at low entropy state. The factors, which impact on protein crystallization, are almost exclusively related to non-random amino acid properties such as physiochemical properties of amino acids. In this study, we used logistic regression and neural network to model the success rate of crystallization of 420 proteins from Staphylococcus aureus with each of non-random and random amino acid properties in order to determine whether randomness in a protein plays a role in the crystallization process. The results show that randomness is indeed involved in the crystallization process, and this rationale would enrich our knowledge on crystallization process and enhance our ability to crystallize more important proteins.     

ERK is involved in the reorganization of somatosensory cortical maps in adult rats submitted to hindlimb unloading

Sensorimotor restriction by a 14-day period of hindlimb unloading (HU) in the adult rat induces a reorganization of topographic maps and receptive fields. However, the underlying mechanisms are still unclear. Interest was turned towards a possible implication of intracellular MAPK signaling pathway since Extracellular-signal-Regulated Kinase 1/2 (ERK1/2) is known to play a significant role in the control of synaptic plasticity. In order to better understand the mechanisms underlying cortical plasticity in adult rats submitted to a sensorimotor restriction, we analyzed the time-course of ERK1/2 activation by immunoblot and of cortical reorganization by electrophysiological recordings, on rats submitted to hindlimb unloading over four weeks. Immunohistochemistry analysis provided evidence that ERK1/2 phosphorylation was increased in layer III neurons of the somatosensory cortex. This increase was transient, and parallel to the changes in hindpaw cortical map area (layer IV). By contrast, receptive fields were progressively enlarged from 7 to 28 days of hindlimb unloading. To determine whether ERK1/2 was involved in cortical remapping, we administered a specific ERK1/2 inhibitor (PD-98059) through osmotic mini-pump in rats hindlimb unloaded for 14 days. Results demonstrate that focal inhibition of ERK1/2 pathway prevents cortical reorganization, but had no effect on receptive fields. These results suggest that ERK1/2 plays a role in the induction of cortical plasticity during hindlimb unloading.     

Cyclin-dependent kinase 5 in synaptic plasticity, learning and memory

Cyclin-dependent kinase 5 (Cdk5) is a serine/threonine kinase with a multitude of functions. Although Cdk5 is widely expressed, it has been studied most extensively in neurons. Since its initial characterization, the fundamental contribution of Cdk5 to an impressive range of neuronal processes has become clear. These phenomena include neural development, dopaminergic function and neurodegeneration. Data from different fields have recently converged to provide evidence for the participation of Cdk5 in synaptic plasticity, learning and memory. In this review, we consider recent data implicating Cdk5 in molecular and cellular mechanisms underlying synaptic plasticity. We relate these findings to its emerging role in learning and memory. Particular attention is paid to the activation of Cdk5 by p25, which enhances hippocampal synaptic plasticity and memory, and suggests formation of p25 as a physiological process regulating synaptic plasticity and memory.     

Encoding of motion in real time by the fly visual system.

Direction-selective cells in the fly visual system that have large receptive fields play a decisive role in encoding the time-dependent optic flow the animal encounters during locomotion. Recent experiments on the computations performed by these cells have highlighted the significance of dendritic integration and have addressed the role of spikes versus graded membrane potential changes in encoding optic flow information. It is becoming increasingly clear that the way optic flow is encoded in real time is constrained both by the computational needs of the animal in visually guided behaviour as well as by the specific properties of the underlying neuronal hardware.     

Prediction of mutations engineered by randomness in H5N1 hemagglutinins of influenza A virus

This is the continuation of our studies on the prediction of mutation engineered by randomness in proteins from influenza A virus. In our previous studies, we have demonstrated that randomness plays a role in engineering mutations because the measures of randomness in protein are different before and after mutations. Thus we built a cause-mutation relationship to count the mutation engineered by randomness, and conducted several concept-initiated studies to predict the mutations in proteins from influenza A virus, which demonstrated the possibility of prediction of mutations along this line of thought. On the other hand, these concept-initiated studies indicate the directions forwards the enhancement of predictability, of which we need to use the neural network instead of logistic regression that was used in those concept-initiated studies to enhance the predictability. In this proof-of-concept study, we attempt to apply the neural network to modeling the cause-mutation relationship to predict the possible mutation positions, and then we use the amino acid mutating probability to predict the would-be-mutated amino acids at predicted positions. The results confirm the possibility of use of internal cause-mutation relationship with neural network model to predict the mutation positions and use of amino acid mutating probability to predict the would-be-mutated amino acids.     

基于不同零模型的点格局分析

在种群空间格局研究中,定量分析格局及其形成过程已成为生态学家的主要目标。在量化分析的众多方法中,点格局分析是最常用的方法,而在选择零模型时,完全空间随机模型以外的复杂零模型很少使用,实际上,这些零模型可能有助于认识格局的内在特征。为此,我们在研究实例中,选择完全空间随机模型(complete spatial randomness)、泊松聚块模型(Poisson cluster process)和嵌套双聚块模型(nested double-cluster process)对典型草原处于不同恢复演替阶段的羊草(Leymus chinensis)种群空间格局进行了分析。结果发现:完全空间随机模型仅能检测种群在不同尺度下的格局类型;而通过泊松聚块模型和嵌套双聚块模型检验表明,在恢复演替的初期阶段,羊草种群在小尺度范围内偏离泊松聚块模型,而在整个取样范围内完全符合嵌套双聚块模型;随着恢复演替时间的推移,在恢复演替的后期,在整个取样尺度上,羊草种群与泊松聚块模型相吻合。这是很有意义的生态学现象。这一实例表明在应用点格局分析种群空间格局时,仅通过完全空间随机模型的检验来分析格局特征,或许很难论证复杂的生态过程,而选择一些完全空间随机模型以外的较复杂的零模型,可能发现一些有价值的生态学现象,对揭示格局掩盖下的内在机制有所裨益。     

On the role of subthreshold dynamics in neuronal signaling

The role of subthreshold dynamics in neuronal signaling is examined using periodic pulse train stimulation of the Fitzhugh-Nagumo (FN) model of nerve membrane excitability and results from the squid giant axon as an experimental data base. For a broad range of stimulus conditions the first pulse in a pulse train elicited an action potential, whereas all subsequent pulses elicited subthreshold responses, both in the axon and in the FN model. These results are not well described by the Hodgkin and Huxley 1952 model. Various different patterns of subthreshold responses, including chaotic dynamics, can be observed in both systems-the FN model and the axon-depending upon stimulus conditions. For some conditions action potentials are occasionally interspersed among the subthreshold events with randomly occurring interspike intervals. The randomness is directly attributable to the underlying subthreshold chaos-deterministic chaos-rather than to a stochastic noise source. We conclude that this mechanism may contribute to multimodal interspike interval histograms which have been observed from individual neurons throughout the nervous system.     

Specificity of cortical synaptic connectivity: Emphasis on perspectives gained from quantitative electron microscopy

This report traces the historical development of concepts regarding the specificity of synaptic connectivity in the cerebral cortex as viewed primarily from the perspective of electron microscopy. The occurrence of stereotypical patterns of connection (e.g., contrasting synaptic patterns on the surfaces of spiny vs. non-spiny neurons, the general consistency with which axonal pathways impinge on and originate within specific cortical areas and layers, triadic synaptic relationships) implies that cortical connectivity is highly structured. The high degree of order characterizing many aspects of cortical organization is mirrored by an equally ordered arrangement of synaptic connections between specific types of neurons. This observation is based on quantitative electron microscopic studies of synapses between identified neurons and from the results of correlative anatomical/electrophysiological investigations. The recognition of recurring synaptic patterns and responses between specific neurons has generated increased support for the notion of specificity of synaptic connections at the expense of randomness, but the role of specificity in cortical function is an unresolved question. At the core of cortical processing lie myriad possibilities for computation provided by the wealth of synaptic connections involving each cortical neuron. Specificity, by limiting possibilities for connection, can impose an order on synaptic interactions even as processes of dynamic selection or synaptic remodeling ensure the constant formation and dissolution of cortical circuits. These operations make maximal use of the richness of cortical synaptic connections to produce a highly flexible system, irrespective of the degree of randomness or specificity that obtains for cortical wiring at any particular time.     

The effects of pulsed electromagnetic fields on the cellular activity of SaOS-2 cells

Although pulsed electromagnetic fields (PEMFs) have been used for treatments of nonunion bone fracture healing for more than three decades, the underlying cellular mechanism of bone formation promoted by PEMFs is still unclear. It has been observed that a series of parameters such as pulse shape and frequency should be carefully controlled to achieve effective treatments. In this article, the effects of PEMFs with repetitive pulse burst waveform on the cellular activity of SaOS-2 osteoblast-like cells were investigated. In particular, cell proliferation and mineralization due to the imposed PEMFs were assessed through direct cell counts, the MTT assay, tissue nonspecific alkaline phosphatase (ALP) and Alizarin Red S (ARS) staining. PEMF stimulation with repetitive pulse burst waveform did not affect metabolic activity and cell number. However, the ALP activity of SaOS-2 cells and mineral nodule formation increased significantly after PEMF stimulation. These observations suggest that repetitive pulse burst PEMF does not affect cellular metabolism; however, it may play a role in the enhancement of SaOS-2 cell mineralization. We are currently investigating cellular responses under different PEMF waveforms and Western blots for protein expression of bone mineralization specific proteins.