Travelling waves and pattern formation in a model for fungal development

 Under a variety of conditions, the hyphal density within the expanding outer edge of growing fungal mycelia can be spatially heterogeneous or nearly uniform. We conduct an analysis of a system of reaction-diffusion equations used to model the growth of fungal mycelia and the subsequent development of macroscopic patterns produced by differing hyphal and hence biomass densities. Both local and global results are obtained using analytical and numerical techniques. The emphasis is on qualitative results, including the effects of changes in parameter values on the structure of the solution set. Received 22 November 1995; received in revised form 17 May 1996     

Advances and challenges in programming pattern formation using living cells

Spatial patterning of cell populations is a ubiquitous phenomenon in nature. Patterns occur at various length and time scales and exhibit immense diversity. In addition to offering a deeper understanding of the emergence of patterns in nature, the ability to program synthetic patterns using living cells has the potential for broad applications. To date, however, progress in engineering pattern formation has been hampered by technical challenges. In this Review, we discuss recent advances in programming pattern formation in terms of biological insights, experimental and computational tool development, and potential applications.     

The role of trans-membrane signal transduction in turing-type cellular pattern formation

The Turing mechanism (Phil. Trans. R. Soc. B 237 (1952) 37) for the production of a broken spatial symmetry in an initially homogeneous system of reacting and diffusing substances has attracted much interest as a potential model for certain aspects of morphogenesis (Models of Biological Pattern Formation, Academic Press, London, 1982; Nature 376 (1995) 765) such as pre-patterning in the embryo. The two features necessary for the formation of Turing patterns are short-range autocatalysis and long-range inhibition (Kybernetik 12 (1972) 30) which usually only occur when the diffusion rate of the inhibitor is significantly greater than that of the activator. This observation has sometimes been used to cast doubt on applicability of the Turing mechanism to cellular patterning since many messenger molecules that diffuse between cells do so at more-or-less similar rates. Here we show that Turing-type patterns will be able to robustly form under a wide variety of realistic physiological conditions though plausible mechanisms of intra-cellular chemical communication without relying on differences in diffusion rates. In the mechanism we propose, reactions occur within cells. Signal transduction leads to the production of messenger molecules, which diffuse between cells at approximately equal rates, coupling the reactions occurring in different cells. These mechanisms also suggest how this process can be controlled in a rather precise way by the genetic machinery of the cell.     

群落二维格局分析的两种方法

群落二维空间格局研究能够更好地揭示群落的特征,但在分析方法上有较大的困难。用垂直相交的两条样带在两个方向上同时取样的二维取样法,获得数据,用DCA排序与格局分析相结合的方法,得到群落不同格局规模斑块的长、宽及面积,实现二维格局研究。在亚高山草甸群落格局研究中应用表明,两个方法均是有效的。     

Comparison of methods in analysis of the tree spatial distribution pattern

The L-function based on K-function, the pair-correlation function and the uniform angle index used in analyzing the tree spatial distribution pattern were compared on the basis of the data from 5 actual plots and 30 simulated plots. It was concluded that the pair-correlation function and the uniform angle index were more accurate than the L-function; the uniform angle index was more effective and feasible than the L-function and the pair-correlation function; the uniform angle index has an additional advantage that it could combine qualitative and quantitative analyses by using the distribution diagram of the uniform angle index and the average valueW .     

Comparison of methods in analysis of the tree spatial distribution pattern

The L-function based on K-function, the pair-correlation function and the uniform angle index used in analyzing the tree spatial distribution pattern were compared on the basis of the data from 5 actual plots and 30 simulated plots. It was concluded that the pair-correlation function and the uniform angle index were more accurate than the L-function; the uniform angle index was more effective and feasible than the L-function and the pair-correlation function; the uniform angle index has an additional advantage that it could combine qualitative and quantitative analyses by using the distribution diagram of the uniform angle index and the average valueW .     

林木空间分布格局分析方法

采用5块实地调查样地和30块模拟样地,通过基于Ripley K-函数的L-函数、双相关函数和角尺度方法在林木空间分布格局研究中的比较分析,得出如下结论:双相关函数和角尺度在判断的准确性方面优于L-函数;角尺度在有效性和可行性方面比L-函数和双相关函数更强,并且它能利用角尺度分布图和均值同时作定性和定量分析,从而使其优势更加明显。     

Critical conditions for pattern formation and in vitro tubulogenesis driven by cellular traction fields

In vitro angiogenesis assays have shown that tubulogenesis of endothelial cells within biogels, like collagen or fibrin gels, only appears for a critical range of experimental parameter values. These experiments have enabled us to develop and validate a theoretical model in which mechanical interactions of endothelial cells with extracellular matrix influence both active cell migration--haptotaxis--and cellular traction forces. Depending on the number of cells, cell motility and biogel rheological properties, various 2D endothelial patterns can be generated, from non-connected stripe patterns to fully connected networks, which mimic the spatial organization of capillary structures. The model quantitatively and qualitatively reproduces the range of critical values of cell densities and fibrin concentrations for which these cell networks are experimentally observed. We illustrate how cell motility is associated to the self-enhancement of the local traction fields exerted within the biogel in order to produce a pre-patterning of this matrix and subsequent formation of tubular structures, above critical thresholds corresponding to bifurcation points of the mathematical model. The dynamics of this morphogenetic process is discussed in the light of videomicroscopy time lapse sequences of endothelial cells (EAhy926 line) in fibrin gels. Our modeling approach also explains how the progressive appearance and morphology of the cellular networks are modified by gradients of extracellular matrix thickness.     

Mathematical methods for the acquisition of changes in vecps

Procedures such as principal component analysis, autocorrelation and cross-correlation, Fourier analysis, Wiener filtering, which have been used so far for the mathematical analysis of VECP mainly serve purpose of quantization and frequency analysis of signals and the evaluation of their intraindividual and interindividual variability. Although some of the above methods are also employed for the differentiation of VECPs, it seems that methods of primarily comparative character are better suited for the classification of different signal forms. This paper reports on results obtained by multivariate analysis of variance.     

Common methods for cytosine methylation analysis in DNA

The review considers the methods most commonly used to detect DNA methylation, their advantages, potential limitations, and selection for various purposes. A detailed protocol is described for bisulfite treatment, which is used as a preliminary step in the majority of DNA methylation assays.     

Comparison of four simple methods for estimating sexual dimorphism in fossils

Estimating sexual dimorphism in skeletal and dental features of fossil species is difficult when the sex of individuals cannot be reliably determined. Several different methods of estimating dimorphism in this situation have been suggested: extrapolation from coefficients of variation, division of a sample about the mean or median into two subsamples which are then treated as males and females, and finite mixture analysis (specifically for estimating the maximum dimorphism that could be present in a unimodal distribution). The accuracy of none of these methods has been thoroughly investigated and compared in a controlled manner. Such analysis is necessary because the accuracy of all methods is potentially affected by fluctuations in either sample size, sex ratio, or the magnitude of intrasexual variability. Computer modeling experiments show that the mean method is the least sensitive to fluctuations in these parameters and generally provides the best estimates of dimorphism. However, no method can accurately estimate low to moderate levels of dimorphism, particularly if intrasexual variability is high and sex ratios are skewed. © 1994 Wiley-Liss, Inc.     

A densitometrical method for the study of pattern formation in a ciliateChilodonella

Summary An easy and sensitive method is reported here for testing the similarities of individual patterns by photographically transforming maps of these patterns to given, deductively chosen conventions involving constant distances between selected reference points. A cumulative map is produced by loading all landmarks from a set of individual maps on to one sheet of paper. The use of various a priori conventions results in variable cumulative maps, which are then optically transformed on an analog digital converter, with additional input for optical picture processing. The densitometrical maps thus obtained may be compared as to the cumulative degree of areas of maximal and minimal density of landmarks. The best conventions are those that yield the map with the most contrast.Maps of spatial patterns of the sites of contractile vacuole pore (CVP) primordia in an early stage of divisional morphogenesis of the ciliateChilodonella steini were compared after four different transformations and adjustments of the same set of individual maps. The best focusing of the sites of CVP differentiation was achieved by use of the postoral axis, defined by the center of the oral apparatus and the posterior end of the cell as the scaling parameter. The composite domain map obtained by optical transformation of this cumulative map could distinguish the specific CVP territories observed in earlier work (Kaczanowska 1981). These results confirm earlier findings that indicated the site of the oral apparatus is an important reference point in CVP primordia positioning. They also strongly suggest the existence of an overriding scaling factor governing the positioning of sites of differentiation in both dimensions of the developmental field. The method of superposition and scaling of pattern maps is generally applicable to situations in which pattern elements appear at discrete points on a flat surface.     

喷气燃料中污染微生物检测方法概况

微生物污染不仅降解喷气燃料,还严重威胁储存和飞行安全.喷气燃料中污染微生物的检测是有效治理微生物污染的前提.基于此,本文将喷气燃料中污染微生物检测方法分为传统法、分析生物学法以及分子生物学方法,并对三种方法优缺点进行了详细介绍.最后对喷气燃料中污染微生物检测方法进行了展望.     

Analysis of breathing via optoelectronic systems: comparison of four methods for computing breathing volumes and thoraco-abdominal motion pattern

Breathing parameters can be measured by motion capture systems by placing photo-reflective markers on the chest wall. A computational model is mandatory to compute the breathing volume and to calculate temporal and kinematical features by the gathered markers trajectories. Despite different methods based on different geometrical approaches can be adopted to compute volumes, no information about their differences in the respiratory evaluation are available. This study investigated the performances of four methods (conventional, prism-based, convex hull with boundary condition, based on Delaunay triangulation) using an optoelectronic motion capture system, on twelve healthy participants during 30 s of breathing. Temporal trends of volume traces, tidal volume values, and breathing durations were compared between methods and spirometry (used as reference instrument). Additionally, thoraco-abdominal motion patterns were compared between methods by analysing the compartmental contributions and their variability. Results shows comparable similarities between the volume traces obtained using spirometry, prism-based and conventional methods. Prism-based and convex hull with boundary condition methods show lower bias in tidal volumes estimation up to 0.06 L, compared to the conventional and Delaunay triangulation methods. Prism-based method shows maximum differences of 30 mL in the comparison of compartmental contributions to the total volume, by resulting in a maximum deviation of 1.6% in the percentage contribution analysis. In conclusion, our finding demonstrated the accuracy of the non-invasive MoCap-based breathing analysis with the prism-based method tested. Data provided in this study will lead researchers and clinicians in the computational method choice for temporal and volumetric breathing analysis.     

Comparison of the accuracy of semiempirical and some DFT methods for predicting heats of formation

A comparison is made of the relative accuracy of some NDDO semiempirical methods and the DFT functionals LYP and PW91 using both double and triple zeta basis sets. The comparison is between the calculated heat of formation and that reported in the NIST database.Electronic Supplementary Material Parameters for the tailored method are available in the supplementary material; these are suitable for use with MOPAC2002. All raw data (experimental heats of formation, geometries, total energies and heats of formation for the various methods, etc.) are also provided in CAChe format. Supplementary material is available for this article if you access the article at . A link in the frame on the left on that page takes you directly to the supplementary material.     

农业生态系统可持续发展趋势度的评价方法研究

在对农业生态系统时间演替过程分析的基础上,以评价指标年际变异性、评价指标的时间发展斜率变化率和评价指标的初如阈值水平为评价领域,提出了可持续发展趋势度的概念。并以德清县为例进行了案例分析,结果表明该县的可持续度为0.657,属中上水平。