scholarly journals Cellular dialogues that enable self-organization of dynamic spatial patterns

2019 ◽  
Author(s):  
Yiteng Dang ◽  
Douwe Grundel ◽  
Hyun Youk
Keyword(s):  
Spatial Patterns ◽  
Cellular Response ◽  
Spatial Organization ◽  
Spatial Arrangement ◽  
Gene Expressions ◽  
Gene Expression Noise ◽  
Expression Noise ◽  
Self Organized ◽  
Stage Order ◽  
Pattern Formations

SummaryCells form spatial patterns by coordinating their gene expressions. How a group of mesoscopic numbers (hundreds-to-thousands) of cells, without pre-defined morphogens and spatial organization, self-organizes spatial patterns remains incompletely understood. Of particular importance are dynamic spatial patterns - such as spiral waves that perpetually move and transmit information over macroscopic length-scales. We developed an open-source, expandable software that can simulate a field of cells communicating with any number of cell-secreted molecules in any manner. With it and a theory developed here, we identified all possible “cellular dialogues” - ways of communicating with two diffusing molecules - and core architectures underlying them that enable diverse, self-organized dynamic spatial patterns that we classified. The patterns form despite widely varying cellular response to the molecules, gene-expression noise, and spatial arrangement and motility of cells. Three-stage, “order-fluctuate-settle” process forms dynamic spatial patterns: cells form long-lived whirlpools of wavelets that, through chaos-like interactions, settle into a dynamic spatial pattern. These results provide a blueprint to help identify missing regulatory links for observed dynamic-pattern formations and in building synthetic tissues.

Computational Micrograph Registration with Sieve Processes

1996 ◽  
Vol 54 ◽  
pp. 440-441
Author(s):  
P.J. Phillips ◽  
J. Huang ◽  
S. M. Dunn
Keyword(s):  
Planar Graph ◽  
Efficient Algorithm ◽  
Spatial Organization ◽  
Spatial Arrangement ◽  
Stereo Image ◽  
Image Model ◽  
Geometric Invariants ◽  
Point Set

In this paper we present an efficient algorithm for automatically finding the correspondence between pairs of stereo micrographs, the key step in forming a stereo image. The computation burden in this problem is solving for the optimal mapping and transformation between the two micrographs. In this paper, we present a sieve algorithm for efficiently estimating the transformation and correspondence.In a sieve algorithm, a sequence of stages gradually reduce the number of transformations and correspondences that need to be examined, i.e., the analogy of sieving through the set of mappings with gradually finer meshes until the answer is found. The set of sieves is derived from an image model, here a planar graph that encodes the spatial organization of the features. In the sieve algorithm, the graph represents the spatial arrangement of objects in the image. The algorithm for finding the correspondence restricts its attention to the graph, with the correspondence being found by a combination of graph matchings, point set matching and geometric invariants.

Caveolin-1, galectin-3 and lipid raft domains in cancer cell signalling

2015 ◽  
Vol 57 ◽  
pp. 189-201 ◽  
Author(s):  
Jay Shankar ◽  
Cecile Boscher ◽  
Ivan R. Nabi
Keyword(s):  
Plasma Membrane ◽  
Lipid Rafts ◽  
Cancer Cell ◽  
Cellular Response ◽  
Spatial Organization ◽  
Essential Feature ◽  
Cell Signalling ◽  
Coated Pits ◽  
Signalling Molecules ◽  
Raft Domains

Spatial organization of the plasma membrane is an essential feature of the cellular response to external stimuli. Receptor organization at the cell surface mediates transmission of extracellular stimuli to intracellular signalling molecules and effectors that impact various cellular processes including cell differentiation, metabolism, growth, migration and apoptosis. Membrane domains include morphologically distinct plasma membrane invaginations such as clathrin-coated pits and caveolae, but also less well-defined domains such as lipid rafts and the galectin lattice. In the present chapter, we will discuss interaction between caveolae, lipid rafts and the galectin lattice in the control of cancer cell signalling.

ЛАНДШАФТНАЯ ОРГАНИЗАЦИЯ БЕРЕГОВОЙ ГЕОСТРУКТУРЫ ОСТРОВА ШКОТА (ЗАЛИВ ПЕТРА ВЕЛИКОГО)

2019 ◽  
Author(s):  
K.S. Ganzei ◽  
V.V. Zharikov ◽  
N.F. Pshenichnikova ◽  
A.M. Lebedev ◽  
A.G. Kiselyova ◽  
...  
Keyword(s):  
Spatial Organization ◽  
Peter The Great Bay ◽  
Spatial Arrangement ◽  
Water Area ◽  
Marine Spatial Planning ◽  
Landscape Approach ◽  
Important Condition ◽  
Statistical Comparison ◽  
Peter The Great ◽  
Comprehensive Study

Важнейшим условием достижения устойчивого развития прибрежноморского природопользования в заливе Петра Великого системы является морское пространственное планирование. Основой для этого является информация о природных комплексах территории и акватории, полученная на основе ландшафтного подхода. Ключевым районом для изучения пространственной организации ландшафтов прибрежных геоструктур стала территория острова Шкота и его подводных склонов. Для наземных ландшафтов было описано 49 наблюдательных пунктов, 4 профиля были заложены для подводных ландшафтов описано 64 наблюдательных пункта, проложено 18 профилей. Выделено 22 вида ландшафтов, из них 16 наземных, 6 подводных. Берега острова сформированы преобладанием абразивноденудационного и абразивного типов. В результате всестороннего изучения показаны особенности пространственной организации воздушных и водных природных комплексов. Особенностью исследуемой территории является экспозиция дифференциации ландшафтов между юговосточной и северозападной частями острова, обусловленная муссонной природой климата. Результаты полевых и картографических работ послужили основой для выбора зон интенсивного, умеренного и ослабленного взаимодействия наземных и подводных ландшафтов. Пространственное расположение зон взаимодействия четко иллюстрируется значительными различиями экспозиции. Результаты статистического сравнения ландшафтов суши и мелководья, окружающего остров, на основе картометрических характеристик указывают на неоднородность геоструктуры острова, обусловленную, прежде всего, сочетанием ландшафтообразующих факторов. The most important condition for achieving sustainable development of coastalmarine environmental management in Peter the Great Bay is marine spatial planning. The basis for this is information about the natural complexes of the territory and water area, obtained based on the landscape approach. The main area for studying the spatial organization of landscapes of coastal geostructures was the territory of the island of Shkota and its underwater slopes. For terrestrial landscapes, 49 observation points were described, 4 profiles were laid 64 observation points were described for underwater landscapes, 18 profiles were laid. 22 species of landscapes have been identified, of which 16 are terrestrial, 6 are underwater. The shores of the island are formed by the predominance of abrasivedenudation and abrasive types. Because of a comprehensive study, features of the spatial organization of air and aquatic natural complexes are shown. A special feature of the study area is the exposure of the differentiation of landscapes between the southeastern and northwestern parts of the island, due to the monsoon nature of the climate. The results of field and cartographic works served as the basis for selecting areas of intense, moderate and weakened interaction of land and underwater landscapes. The spatial arrangement of the interaction zones is clearly illustrated by significant differences in exposure. The results of a statistical comparison of the land and shallow water landscapes surrounding the island, based on the cartometric characteristics, indicate the heterogeneity of the islands geostructure, primarily due to the combination of landscapeforming factors.

scholarly journals A Comparative Analysis of Two Major Approaches for Mapping the Wildland-Urban Interface: A Case Study in California

Land ◽  
2021 ◽  
Vol 10 (7) ◽  
pp. 679
Author(s):  
Avi Bar-Massada
Keyword(s):  
At Risk ◽  
Comparative Analysis ◽  
Spatial Patterns ◽  
Practical Purpose ◽  
Spatial Arrangement ◽  
Spatial Accuracy ◽  
Wildland Urban Interface ◽  
Spatial Correspondence ◽  
Data Requirements

The Wildland Urban Interface (WUI) is where human settlements border or intermingle with undeveloped land, often with multiple detrimental consequences. Therefore, mapping the WUI is required in order to identify areas-at-risk. There are two main WUI mapping methods, the point-based approach and the zonal approach. Both differ in data requirements and may produce considerably different maps, yet they were never compared before. My objective was to systematically compare the point-based and the zonal-based WUI maps of California, and to test the efficacy of a new database of building locations in the context of WUI mapping. I assessed the spatial accuracy of the building database, and then compared the spatial patterns of WUI maps by estimating the effect of multiple ancillary variables on the amount of agreement between maps. I found that the building database is highly accurate and is suitable for WUI mapping. The point-based approach estimated a consistently larger WUI area across California compared to the zonal approach. The spatial correspondence between maps was low-to-moderate, and was significantly affected by building numbers and by their spatial arrangement. The discrepancy between WUI maps suggests that they are not directly comparable within and across landscapes, and that each WUI map should serve a distinct practical purpose.

Reduction in gene expression noise by targeted increase in accessibility at gene loci

2021 ◽  
Vol 118 (42) ◽  
pp. e2018640118
Author(s):  
LaTasha C. R. Fraser ◽  
Ryan J. Dikdan ◽  
Supravat Dey ◽  
Abhyudai Singh ◽  
Sanjay Tyagi
Keyword(s):  
Gene Expression ◽  
Transcription Factors ◽  
Single Molecule ◽  
Single Cells ◽  
Global Changes ◽  
Messenger Rnas ◽  
Histone Acetyl Transferase ◽  
Gene Expression Noise ◽  
Expression Noise ◽  
Eukaryotic Genes

Many eukaryotic genes are expressed in randomly initiated bursts that are punctuated by periods of quiescence. Here, we show that the intermittent access of the promoters to transcription factors through relatively impervious chromatin contributes to this “noisy” transcription. We tethered a nuclease-deficient Cas9 fused to a histone acetyl transferase at the promoters of two endogenous genes in HeLa cells. An assay for transposase-accessible chromatin using sequencing showed that the activity of the histone acetyl transferase altered the chromatin architecture locally without introducing global changes in the nucleus and rendered the targeted promoters constitutively accessible. We measured the gene expression variability from the gene loci by performing single-molecule fluorescence in situ hybridization against mature messenger RNAs (mRNAs) and by imaging nascent mRNA molecules present at active gene loci in single cells. Because of the increased accessibility of the promoter to transcription factors, the transcription from two genes became less noisy, even when the average levels of expression did not change. In addition to providing evidence for chromatin accessibility as a determinant of the noise in gene expression, our study offers a mechanism for controlling gene expression noise which is otherwise unavoidable.

scholarly journals CpG island composition differences are a source of gene expression noise indicative of promoter responsiveness

2018 ◽  
Vol 19 (1) ◽  
Author(s):  
Michael D. Morgan ◽  
John C. Marioni
Keyword(s):  
Gene Expression ◽  
Cpg Island ◽  
Gene Expression Noise ◽  
Expression Noise

scholarly journals A Five Species Cyclically Dominant Evolutionary Game with Fixed Direction: A New Way to Produce Self-Organized Spatial Patterns

Entropy ◽  
2016 ◽  
Vol 18 (8) ◽  
pp. 284 ◽  
Author(s):  
Yibin Kang ◽  
Qiuhui Pan ◽  
Xueting Wang ◽  
Mingfeng He
Keyword(s):  
Spatial Patterns ◽  
Evolutionary Game ◽  
Self Organized ◽  
Fixed Direction

scholarly journals The Nine Forms of the French Riviera: Classifying Urban Fabrics from the Pedestrian Perspective.

2017 ◽  
Author(s):  
Alessandro Araldi ◽  
Giovanni Fusco
Keyword(s):  
Spatial Patterns ◽  
Urban Space ◽  
Metropolitan Area ◽  
Urban Form ◽  
Spatial Organization ◽  
Spatial Relations ◽  
Urban Morphology ◽  
Urban Fabric ◽  
Central Cities ◽  
French Riviera

The Nine Forms of the French Riviera: Classifying Urban Fabrics from the Pedestrian Perspective. Giovanni Fusco, Alessandro Araldi ¹Université Côte-Azur, CNRS, ESPACE - Bd. Eduard Herriot 98. 06200 Nice E-mail: [email protected], [email protected] Keywords: French Riviera, Urban Fabrics, Urban Form Recognition, Geoprocessing Conference topics and scale: Tools of analysis in urban morphology     Recent metropolitan growth produces new kinds of urban fabric, revealing different logics in the organization of urban space, but coexisting with more traditional urban fabrics in central cities and older suburbs. Having an overall view of the spatial patterns of urban fabrics in a vast metropolitan area is paramount for understanding the emerging spatial organization of the contemporary metropolis. The French Riviera is a polycentric metropolitan area of more than 1200 km2 structured around the old coastal cities of Nice, Cannes, Antibes and Monaco. XIX century and early XX century urban growth is now complemented by modern developments and more recent suburban areas. A large-scale analysis of urban fabrics can only be carried out through a new geoprocessing protocol, combining indicators of spatial relations within urban fabrics, geo-statistical analysis and Bayesian data-mining. Applied to the French Riviera, nine families of urban fabrics are identified and correlated to the historical periods of their production. Central cities are thus characterized by the combination of different families of pre-modern, dense, continuous built-up fabrics, as well as by modern discontinuous forms. More interestingly, fringe-belts in Nice and Cannes, as well as the techno-park of Sophia-Antipolis, combine a spinal cord of connective artificial fabrics having sparse specialized buildings, with the already mentioned discontinuous fabrics of modern urbanism. Further forms are identified in the suburban and “rurban” spaces around central cities. The proposed geoprocessing procedure is not intended to supersede traditional expert-base analysis of urban fabric. Rather, it should be considered as a complementary tool for large urban space analysis and as an input for studying urban form relation to socioeconomic phenomena. References   Conzen, M.R.G (1960) Alnwick, Northumberland : A Study in Town-Planning Analysis. (London, George Philip). Conzen, M.P. (2009) “How cities internalize their former urban fringe. A cross-cultural comparison”. Urban Morphology, 13, 29-54. Graff, P. (2014) Une ville d’exception. Nice, dans l'effervescence du 20° siècle. (Serre, Nice). Yamada I., Thill J.C. (2010) “Local indicators of network-constrained clusters in spatial patterns represented by a link attribute.” Annals of the Association of American Geographers, 100(2), 269-285. Levy, A. (1999) “Urban morphology and the problem of modern urban fabric : some questions for research”, Urban Morphology, 3(2), 79-85. Okabe, A. Sugihara, K. (2012) Spatial Analysis along Networks: Statistical and Computational Methods. (John Wiley and sons, UK).

scholarly journals Are Distribution Patterns Correlated with Plant Traits?

2021 ◽  
Author(s):  
◽  
Benjamin Magana-Rodriguez
Keyword(s):  
Life History ◽  
Leaf Area ◽  
Spatial Patterns ◽  
Life History Traits ◽  
Multiple Scales ◽  
Spatial Scales ◽  
Regional Scale ◽  
Distribution Patterns ◽  
Spatial Arrangement ◽  
Scaling Relationship

<p>The current crisis in loss of biodiversity requires rapid action. Knowledge of species' distribution patterns across scales is of high importance in determining their current status. However, species display many different distribution patterns on multiple scales. A positive relationship between regional (broad-scale) distribution and local abundance (fine-scale) of species is almost a constant pattern in macroecology. Nevertheless interspecific relationships typically contain much scatter. For example, species that possess high local abundance and narrow ranges, or species that are widespread, but locally rare. One way to describe these spatial features of distribution patterns is by analysing the scaling properties of occupancy (e.g., aggregation) in combination with knowledge of the processes that are generating the specific spatial pattern (e.g., reproduction, dispersal, and colonisation). The main goal of my research was to investigate if distribution patterns correlate with plant life-history traits across multiple scales. First, I compared the performance of five empirical models for their ability to describe the scaling relationship of occupancy in two datasets from Molesworth Station, New Zealand. Secondly, I analysed the association between spatial patterns and life history traits at two spatial scales in an assemblage of 46 grassland species in Molesworth Station. The spatial arrangement was quantified using the parameter k from the Negative Binomial Distribution (NBD). Finally, I investigated the same association between spatial patterns and life-history traits across local, regional and national scales, focusing in one of the most diverse families of plant species in New Zealand, the Veronica sect. Hebe (Plantaginaceae). The spatial arrangement was investigated using the mass fractal dimension. Cross-species correlations and phylogenetically independent contrasts were used to investigate the relationships between plant life-history traits and spatial patterns on both data bases. There was no superior occupancy-area model overall for describing the scaling relationship, however the results showed that a variety of occupancy-area models can be fit to different data sets at diverse spatial scales using nonlinear regression. Additionally, here I showed that it is possible to deduce and extrapolate information on occupancy at fine scales from coarse-scale data. For the 46 plantassemblage in Molesworth Station, Specific leaf area (SLA) exhibits a positive association with aggregation in cross-species analysis, while leaf area showed a negative association, and dispersule mass a positive correlation with degree of aggregation in phylogenetic contrast analysis at a local-scale (20 × 20 m resolution). Plant height was the only life-history trait that was associated with degree of aggregation at a regional-scale (100 × 60 mresolution). For the Veronica sect. Hebe dataset, leaf area showed a positive correlation with aggregation while specific leaf area showed a negative correlation with aggregation at a fine local-scale (2.5-60 m resolution). Inflorescence length, breeding system and leaf area showed a negative correlation with degree of aggregation at a regional-scale (2.5-20 km resolution). Height was positively associated with aggregation at national-scale (20-100 km resolution). Although life-history traits showed low predictive ability in explaining aggregation throughout this thesis, there was a general pattern about which processes and traits were important at different scales. At local scales traits related to dispersal and completion such as SLA , leaf area, dispersule mass and the presence of structures in seeds for dispersal, were important; while at regional scales traits related to reproduction such as breeding system, inflorescence length and traits related to dispersal (seed mass) were significant. At national scales only plant height was important in predicting aggregation. Here, it was illustrated how the parameters of these scaling models capture an important aspect of spatial pattern that can be related to other macroecological relationships and the life-history traits of species. This study shows that when several scales of analysis are considered, we can improve our understanding about the factors that are related to species' distribution patterns.</p>

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