The spatial organization of centromeric heterochromatin during normal human lymphopoiesis: evidence for ontogenically determined spatial patterns

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).

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Chromosomal G-dark Bands Determine the Spatial Organization of Centromeric Heterochromatin in the Nucleus

Molecular Biology of the Cell ◽

10.1091/mbc.12.11.3563 ◽

2001 ◽

Vol 12 (11) ◽

pp. 3563-3572 ◽

Cited By ~ 48

Author(s):

Célia Carvalho ◽

Henrique M. Pereira ◽

João Ferreira ◽

Cristina Pina ◽

Denise Mendonça ◽

...

Keyword(s):

Satellite Dna ◽

Spatial Organization ◽

Nuclear Periphery ◽

Three Dimensional ◽

Lymphoid Cells ◽

Spatial Proximity ◽

Centromeric Heterochromatin ◽

Chromosome 11 ◽

Cis Acting ◽

Tight Correlation

Gene expression can be silenced by proximity to heterochromatin blocks containing centromeric α-satellite DNA. This has been shown experimentally through cis-acting chromosome rearrangements resulting in linear genomic proximity, or throughtrans-acting changes resulting in intranuclear spatial proximity. Although it has long been been established that centromeres are nonrandomly distributed during interphase, little is known of what determines the three-dimensional organization of these silencing domains in the nucleus. Here, we propose a model that predicts the intranuclear positioning of centromeric heterochromatin for each individual chromosome. With the use of fluorescence in situ hybridization and confocal microscopy, we show that the distribution of centromeric α-satellite DNA in human lymphoid cells synchronized at G0/G1is unique for most individual chromosomes. Regression analysis reveals a tight correlation between nuclear distribution of centromeric α-satellite DNA and the presence of G-dark bands in the corresponding chromosome. Centromeres surrounded by G-dark bands are preferentially located at the nuclear periphery, whereas centromeres of chromosomes with a lower content of G-dark bands tend to be localized at the nucleolus. Consistent with the model, a t(11; 14) translocation that removes G-dark bands from chromosome 11 causes a repositioning of the centromere, which becomes less frequently localized at the nuclear periphery and more frequently associated with the nucleolus. The data suggest that “chromosomal environment” plays a key role in the intranuclear organization of centromeric heterochromatin. Our model further predicts that facultative heterochromatinization of distinct genomic regions may contribute to cell-type specific patterns of centromere localization.

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Ecological feedback on diffusion dynamics

Royal Society Open Science ◽

10.1098/rsos.181273 ◽

2019 ◽

Vol 6 (2) ◽

pp. 181273 ◽

Cited By ~ 5

Author(s):

Hye Jin Park ◽

Chaitanya S. Gokhale

Keyword(s):

Public Goods ◽

Spatial Patterns ◽

Spatial Organization ◽

Evolutionary Dynamics ◽

Evolutionary Process ◽

Reaction Diffusion ◽

Reaction Diffusion Equations ◽

Public Goods Games ◽

Diffusion Dynamics ◽

Spatially Extended

Spatial patterns are ubiquitous across different scales of organization in ecological systems. Animal coat pattern, spatial organization of insect colonies and vegetation in arid areas are prominent examples from such diverse ecologies. Typically, pattern formation has been described by reaction–diffusion equations, which consider individuals dispersing between subpopulations of a global pool. This framework applied to public goods game nicely showed the endurance of populations via diffusion and generation of spatial patterns. However, how the spatial characteristics, such as diffusion, are related to the eco-evolutionary process as well as the nature of the feedback from evolution to ecology and vice versa, has been so far neglected. We present a thorough analysis of the ecologically driven evolutionary dynamics in a spatially extended version of ecological public goods games. Furthermore, we show how these evolutionary dynamics feed back into shaping the ecology, thus together determining the fate of the system.

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Spatial patterns of a Southern Bell Frog Litoria raniformis population in an agricultural landscape

Pacific Conservation Biology ◽

10.1071/pc070104 ◽

2007 ◽

Vol 13 (2) ◽

pp. 104 ◽

Cited By ~ 4

Author(s):

Skye Wassens ◽

David A. Roshier ◽

Robyn J. Watts ◽

Alistar I. Robertson

Keyword(s):

Spatial Patterns ◽

Spatial Organization ◽

Agricultural Landscape ◽

Spatial Scales ◽

Temporal Changes ◽

Breeding Period ◽

Apparent Location ◽

Ripley’S K ◽

K Function ◽

Flooded Areas

We investigated changes in the spatial organization of individuals within a population of endangered Southern Bell Frogs Litoria raniformis over an eight-month period. Our results identified strong temporal changes in both spatial organization and the apparent location of L. raniformis within the study site. Ripley's K Function analyses showed that the position of individuals relative to one another shifted from random immediately after the study site was flooded (p < 0.005), to strongly clustered at spatial scales between 0-1500 m during the peak breeding period (p < 0.005). The majority of flooded areas were dry by April and May and individuals again became aggregated within the remaining waterbodies.

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Proof-of-concept for the detection of early osteoarthritis pathology by endomicroscopy

10.1101/734368 ◽

2019 ◽

Author(s):

Mathäus Tschaikowsky ◽

Sofia Brander ◽

Bizan N. Balzer ◽

Bernd Rolauffs ◽

Thorsten Hugel

Keyword(s):

Articular Cartilage ◽

Spatial Patterns ◽

Spatial Organization ◽

Degenerative Joint Disease ◽

Optical Methods ◽

Joint Disease ◽

Confocal Laser Endomicroscopy ◽

Confocal Laser ◽

Proof Of Concept ◽

Early Oa

AbstractOsteoarthritis (OA) is a degenerative joint disease and the leading cause of global disability. Clinical trials to date have been unable to pinpoint early and potentially reversible disease states with current clinical technology and hence disease-modifying OA drug candidates cannot be tested early in the disease. To overcome this obstacle, we correlate articular cartilage stiffness changes and cellular spatial organization. The former is a well-understood and functionally relevant OA pathology, while the latter allows discriminating between healthy vs early OA, based on distinct cellular spatial patterns. We demonstrated that an extensive loss of atomic force microscopy-detected stiffness can be seen in cartilage tissues with spatial patterns exhibiting the earliest identifiable OA. In addition, the translation of commercially available clinically usable probe-based confocal laser-endomicroscopy allows us to detect these early OA spatial patterns. This study resolves a major clinical trial obstacle by presenting the proof-of-concept that early OA pathology can be detected by already available clinical technology.One Sentence SummaryWe report a correlation between articular cartilage surface nanoscale stiffness and chondrocyte spatial organization; using this correlation enables early pathology detection by currently available clinical optical methods.

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Do vegetation patch spatial patterns disrupt the spatial organization of plant species?

Ecological Complexity ◽

10.1016/j.ecocom.2008.10.015 ◽

2009 ◽

Vol 6 (2) ◽

pp. 197-207 ◽

Cited By ~ 18

Author(s):

C.L. Alados ◽

T. Navarro ◽

B. Komac ◽

V. Pascual ◽

F. Martinez ◽

...

Keyword(s):

Plant Species ◽

Spatial Patterns ◽

Spatial Organization ◽

Vegetation Patch

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Using Remote Sensing to Identify Drivers behind Spatial Patterns in the Bio-physical Properties of a Saltmarsh Pioneer

Remote Sensing ◽

10.3390/rs11050511 ◽

2019 ◽

Vol 11 (5) ◽

pp. 511

Author(s):

B. Oteman ◽

E.P. Morris ◽

G. Peralta ◽

T.J. Bouma ◽

D. van der Wal

Keyword(s):

Salt Marsh ◽

Spatial Patterns ◽

Salt Marshes ◽

Spatial Organization ◽

Minor Effect ◽

Surface Reflectance ◽

Area Index ◽

Flood Duration ◽

Wave Forcing ◽

Flooding Duration

Recently, spatial organization in salt marshes was shown to contain vital information on system resilience. However, in salt marshes, it remains poorly understood what shaping processes regulate spatial patterns in soil or vegetation properties that can be detected in the surface reflectance signal. In this case study we compared the effect on surface reflectance of four major shaping processes: Flooding duration, wave forcing, competition, and creek formation. We applied the ProSail model to a pioneering salt marsh species (Spartina anglica) to identify through which vegetation and soil properties these processes affected reflectance, and used in situ reflectance data at the leaf and canopy scale and satellite data on the canopy scale to identify the spatial patterns in the biophysical characteristics of this salt marsh pioneer in spring. Our results suggest that the spatial patterns in the pioneer zone of the studied salt marsh are mainly caused by the effect of flood duration. Flood duration explained over three times as much of the variation in canopy properties as wave forcing, competition, or creek influence. It particularly affects spatial patterns through canopy properties, especially the leaf area index, while leaf characteristics appear to have a relatively minor effect on reflectance.

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Tree-line changes along the Andes: implications of spatial patterns and dynamics

Philosophical Transactions of the Royal Society B Biological Sciences ◽

10.1098/rstb.2006.1986 ◽

2006 ◽

Vol 362 (1478) ◽

pp. 263-272 ◽

Cited By ~ 51

Author(s):

Kenneth R Young ◽

Blanca León

Keyword(s):

Spatial Patterns ◽

Tree Growth ◽

Spatial Organization ◽

Morphological Plasticity ◽

Landscape Patterns ◽

Research Approach ◽

Tree Line ◽

Climate Fluctuations ◽

The Andes ◽

Species Specific

The Andes provide an extensive latitudinal and topographical framework for studying the factors that control the spatial patterns of forests (timberlines) and their species components expressed through the presence of tree growth forms (tree lines). Despite consistent overall similarities in landscape patterns, many processes must be unique, given the dramatic differences in species richness and biophysical constraints along the Andes. In all cases evaluated to date, morphological plasticity is a common trait of plant species that dominate at tree lines. In fact, many changes observed can be related to species-specific traits. Physiological limitations on tree growth form only explain species limits, while disturbances and cyclical climate fluctuations interact to affect many landscape patterns. Over long periods of time, tree lines provide unique habitats and perhaps opportunities for speciation. Understanding the spatial organization of tree-line dynamics is one viable research approach for evaluating the likely past fluxes and possible future changes.

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Cellular dialogues that enable self-organization of dynamic spatial patterns

10.1101/717595 ◽

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.

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Regional Development: Clusters and Districts

10.1093/oxfordhb/9780199546992.003.0025 ◽

2009 ◽

Author(s):

Philip McCann

Keyword(s):

Regional Development ◽

Spatial Patterns ◽

Spatial Organization ◽

Economies Of Scale ◽

Industrial Districts ◽

Transactions Costs ◽

Industrial Activity ◽

Current Trends ◽

Spatial Grouping ◽

The Relationship

This article first makes some clarifications regarding the terminology we use and assumptions we make, simply for expositional purposes. It then outlines the basic tenets of the concept of agglomeration and industrial districts, highlighting the mechanisms by which the spatial grouping of activities and the generation of localized economies of scale may be related. It reviews the various hypotheses which are evident in the literature concerning the relationship between the spatial organization of industrial activity and the spatial patterns of innovation. It explains the current trends in thought about these relationships, pointing out the recent popularity of the concept of a cluster. It then investigates the various notions of clusters and industrial districts from a transactions costs perspective, and provides an assessment of the insights generated from these cluster arguments.

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