scholarly journals Local growth rules can maintain metabolically efficient spatial structure throughout growth

2018 ◽  
Vol 115 (14) ◽  
pp. 3593-3598
Author(s):  
Yipei Guo ◽  
Mikhail Tikhonov ◽  
Michael P. Brenner
Keyword(s):  
Spatial Structure ◽  
Bacterial Communities ◽  
Spatial Organization ◽  
Colony Growth ◽  
Spatial Structures ◽  
Local Growth ◽  
Signaling Mechanisms ◽  
Metabolite Concentrations ◽  
Metabolic Reactions ◽  
Global Objective

A ubiquitous feature of bacterial communities is the existence of spatial structures. These are often coupled to metabolism, whereby the spatial organization can improve chemical reaction efficiency. However, it is not clear whether or how a desired colony configuration, for example, one that optimizes some overall global objective, could be achieved by individual cells that do not have knowledge of their positions or of the states of all other cells. By using a model which consists of cells producing enzymes that catalyze coupled metabolic reactions, we show that simple, local rules can be sufficient for achieving a global, community-level goal. In particular, even though the optimal configuration varies with colony size, we demonstrate that cells regulating their relative enzyme levels based solely on local metabolite concentrations can maintain the desired overall spatial structure during colony growth. We also show that these rules can be very simple and hence easily implemented by cells. Our framework also predicts scenarios where additional signaling mechanisms may be required.

scholarly journals METHODOLOGICAL ASPECTS OF INFLUENCE OF INTANGIBLE FACTORS ON THE SPATIAL STRUCTURE OF THE CITY

2020 ◽  
Vol 4 (157) ◽  
pp. 38-43
Author(s):  
М. Kosmii
Keyword(s):  
Urban Planning ◽  
Spatial Structure ◽  
Rural Areas ◽  
Spatial Organization ◽  
Qualitative Change ◽  
Spatial Structures ◽  
Legal Norms ◽  
Carpathian Region ◽  
The Impact ◽  
The City

The article identifies the main intangible factors that are inherent in the process of transformation of the spatial structure of settlements. On the example of selected objects of the Carpathian region, the basic approaches to the transformation of existing spatial systems, their potential and prospects are demonstrated and defined. Intangible factors are defined as a set of norms, principles and rules of organization of space, which were formed historically in accordance with the needs of man, society, and focus on meeting intangible needs. Their influence on the spatial structure is realized in the form of legislative and regulatory requirements, political-administrative relations and property relations, as well as mental-ethical, historical-cultural, religious-spiritual and aesthetic factors. In this case, if the material is studied both at the theoretical and practical level, the impact of the intangible requires increased attention from theorists and practitioners of architectural and urban planning. Instead, transformation is a process of qualitative change in the space of the city, which is the result of a combination of tangible and intangible factors, and if there is a clear model of development, it can be directed towards achieving harmony. A detailed study of the impact of intangibles on the spatial organization of architectural and urban planning objects was carried out on the example of rural areas of the region, where there are spiritual and pilgrimage centers and historical and cultural centers. To substantiate the presented conclusions, an architectural and urban inventory of objects was carried out; structural surveys were conducted to identify the analyzed interactions; surveys of residents and visitors; project materials, etc. were found. It is substantiated that in some settlements (villages), in the presence of a high intangible component, there is a higher potential for development of the territory and, accordingly, opportunities for the transformation of their architectural space. Proximity to cities is a determining element in determining the level of readiness of selected objects for the transformation of their spatial structures. The key intangible factors of their development are aesthetic and religious-spiritual factors, which in turn contribute to the development of the material and are system-forming in determining the prospects for the development of spatial structures. The only obstacles that exist in the process of transformation of the spatial structure of these objects are political-administrative, legislative and regulatory factors and the lack of proper infrastructure. The lack of clear legal norms and political will makes it impossible to develop these territories, transfers them to the periphery of tourist routes. It is established that the intangible is a determining factor in the organization of a comfortable space for a person. Intangible components, such as spiritual centers (symbols, chapels) can be an element of landscape design and harmoniously complement aesthetic conditions. In rural areas, since the establishment of OTG, objective conditions have been created for the renovation of existing spatial zones and the formation of open public, cultural or educational space, which will be not only an element of branding, but also a source of investment. Keywords: intangible factors, spatial structure, transformation potential, settlements, Carpathian region.

scholarly journals Spatial and Temporal Features of the Growth of a Bacterial Species Colonizing the Zebrafish Gut

mBio ◽  
2014 ◽  
Vol 5 (6) ◽  
Author(s):  
Matthew Jemielita ◽  
Michael J. Taormina ◽  
Adam R. Burns ◽  
Jennifer S. Hampton ◽  
Annah S. Rolig ◽  
...  
Keyword(s):  
Fluorescence Microscopy ◽  
Spatial Structure ◽  
Growth Kinetics ◽  
Spatial Organization ◽  
Temporal Dynamics ◽  
Bacterial Species ◽  
Bacterial Load ◽  
Light Sheet ◽  
Logistic Growth ◽  
Light Sheet Fluorescence Microscopy

ABSTRACTThe vertebrate intestine is home to microbial ecosystems that play key roles in host development and health. Little is known about the spatial and temporal dynamics of these microbial communities, limiting our understanding of fundamental properties, such as their mechanisms of growth, propagation, and persistence. To address this, we inoculated initially germ-free zebrafish larvae with fluorescently labeled strains of anAeromonasspecies, representing an abundant genus in the zebrafish gut. Using light sheet fluorescence microscopy to obtain three-dimensional images spanning the gut, we quantified the entire bacterial load, as founding populations grew from tens to tens of thousands of cells over several hours. The data yield the first ever measurements of the growth kinetics of a microbial species inside a live vertebrate intestine and show dynamics that robustly fit a logistic growth model. Intriguingly, bacteria were nonuniformly distributed throughout the gut, and bacterial aggregates showed considerably higher growth rates than did discrete individuals. The form of aggregate growth indicates intrinsically higher division rates for clustered bacteria, rather than surface-mediated agglomeration onto clusters. Thus, the spatial organization of gut bacteria both relative to the host and to each other impacts overall growth kinetics, suggesting that spatial characterizations will be an important input to predictive models of host-associated microbial community assembly.IMPORTANCEOur intestines are home to vast numbers of microbes that influence many aspects of health and disease. Though we now know a great deal about the constituents of the gut microbiota, we understand very little about their spatial structure and temporal dynamics in humans or in any animal: how microbial populations establish themselves, grow, fluctuate, and persist. To address this, we made use of a model organism, the zebrafish, and a new optical imaging technique, light sheet fluorescence microscopy, to visualize for the first time the colonization of a live, vertebrate gut by specific bacteria with sufficient resolution to quantify the population over a range from a few individuals to tens of thousands of bacterial cells. Our results provide unprecedented measures of bacterial growth kinetics and also show the influence of spatial structure on bacterial populations, which can be revealed only by direct imaging.

scholarly journals Urban spatial structure re-identification as an approach to solving urban transport problem (A case study in Malang)

2018 ◽  
Vol 181 ◽  
pp. 10006
Author(s):  
Dadang Meru Utomo ◽  
Septiana Hariyani
Keyword(s):  
Local Government ◽  
Spatial Structure ◽  
Urban Transport ◽  
Urban Spatial Structure ◽  
Spatial Structures ◽  
Index Method ◽  
Centrality Index ◽  
Effective Result

In an effort to solve the congestion problem, the local government of Malang City has taken various steps. However, unfortunately, the result has not been effective. This shows that the efforts that have been taken so far are sectoral, therefore a more comprehensive approach is needed in order to reach a more effective result. This research aims at re-evaluating the determination of Malang City's urban spatial structure through the delineation of narrower units of area using the centrality index method. The research suggests that urban spatial structures have a very clear pattern of association with congestion locations. It can be concluded that the local government of Malang City needs to put more consideration on evaluating the urban spatial structure to solve the problem of transportation which is ever-growing the in second largest urban area in East Java Province.

scholarly journals Modeling of fungal mycelium growth by fourth-class continuous stochastic cellular automaton with continuously defined growth conditions

2017 ◽  
Vol 6 (4) ◽  
pp. 98-102
Author(s):  
Anatoliy Sergeevich Shumilov ◽  
Sergey Alexandrovich Blagodatsky
Keyword(s):  
Spatial Structure ◽  
Cellular Automaton ◽  
Colony Growth ◽  
Growth Conditions ◽  
Growth Patterns ◽  
Fungal Mycelium ◽  
Mycelium Growth ◽  
Proposed Model ◽  
Area Unit ◽  
Fungal Colony

The aim of this work was to simulate the growth and spatial structure of the fungal mycelium using a cellular automaton based on the synthesis of various model approaches. The spatial structure of the mycelium is described in the structural submodel of the cellular automaton, which determines the growth rate in the direction of larger resource amount and the number of branches of the mycelium per area unit. The amount of available substrate determines the probability of unidirectional apical growth. Another, biochemical part of the model allows us to describe the rate of transport of resources into the cell, their transport within the mycelium, and also their excretion, and is intended to describe the vertical and horizontal migration in the soil of two nutrients. The proposed model makes it possible to quantitatively describe such a feature of fungal colony growth as more active absorption of resources by external cells, compared to central ones due to separation of transport resources into active and passive resources. The active transport was described using the Michaelis-Menten kinetics. We were able to simulate the stockpiling of surplus resources and their redistribution over the mycelium after the exhaustion of reserves in the external environment, and also to simulate typical growth patterns of mycelial colonies that were observed in experiments published in the literature.

scholarly journals Research of urban agglomerations in the aspect of implementation of the administrative and territorial reform in Ukraine (case study of Kharkiv region)

2019 ◽  
Keyword(s):  
Spatial Structure ◽  
Spatial Organization ◽  
Weighted Average ◽  
Evolutionary Potential ◽  
Statistical Parameters ◽  
Urban Agglomerations ◽  
Territorial Structure

In the modern context of, one of the main tasks in the regional development management is to optimally realize the complex potential of the territories, which requires a comprehensive study of the spatial structure and evolutionary potential of agglomerations of all levels in order to identify disparities in their development, correct imbalances and optimize the spatial organization of the region. The first step to solve this problem is to identify the spatial structure and evaluate the interconnections of agglomerations sequentially, from local to regional level. This is becoming more relevant in the context of administrative and territorial reform in Ukraine. The purpose of this study is to analyze the prospects for the development of urban agglomerations and the organization of the administrative and territorial structure of Kharkiv region in view of the prevailing influence of the city of Kharkiv and the Kharkiv agglomeration. The basic theoretical and methodological starting points of the study of urban agglomerations are presented; their characteristics and parameters of boundary determination were defined. The essence of the method of modeling of integral influence function (IIF modeling) was revealed, the author's research methodology was substantiated. The tendencies of introduction of administrative and territorial reform in Ukraine were analyzed. It was established that Kharkiv region occupies mediocre places in terms of formation of the united territorial communities, there were 23 ones in the oblast (3 of them are city, 12 town, 8 rural ones) by the end of 2019. The scheme for dividing into enlarged districts has not yet been approved. According to different plans / proposals, the existing 27 districts of the oblast should be consolidated into nine, seven, six or four enlarged districts (counties). All of the above proposals were considered by the authors, it is established that the existing projects do not fully cover the main prevailing factors of allocation of competitive districts, do not take into account the role of historically formed system of settlement, spatial-statistical parameters, integral potential of territories, urbanization and agglomeration. The authors performed the IIF modeling and constructed the IIF surface of the weighted average settlement potential of Kharkiv region by the base radius of influence (2, 10, 20, and 30 km), which allowed to determine the features of the Kharkov agglomeration structure and the interaction of the settlements in the region by different radiuses of interaction, primary agglomerations, prospective growth points. On the basis of the obtained results of IIF modeling, the author's model of administrative and territorial division of Kharkiv region into eight enlarged districts was proposed, given the specific features of the settlement system and the correlation of area and population of the modeled administrative and territorial units. The scientifically grounded division of the region into enlarged districts (counties) and stimulation of their development will contribute to the most complete and rational use of the territories potential, increase of economic, human, investment potential, rise of the level and quality of life of the population, etc.

On the Possible Spatial Structures of the β – Amyloid.

2022 ◽  
Vol 7 (1) ◽  
pp. 0-0
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Spatial Structure ◽  
Spatial Models ◽  
Globular Proteins ◽  
Spatial Structures ◽  
Higher Dimensional ◽  
Protein Molecules ◽  
Β Amyloid ◽  
First Time

Spatial models of the β - structures of protein molecules, forming layers of amino acids, in principle, of unlimited length for both antiparallel and parallel conformation have been constructed. It is shown that the simplified flat Pauling models do not reflect the spatial structure of these layers. Using the recently developed theory of higher-dimensional polytopic prismahedrons, models of the volumetric filling of space with amino acid molecules are constructed. The constructed models for the first time mathematically describe the native structures of globular proteins.

scholarly journals Respiratory Heterogeneity Shapes Biofilm Formation and Host Colonization in Uropathogenic Escherichia coli

mBio ◽  
2019 ◽  
Vol 10 (2) ◽  
Author(s):  
Connor J. Beebout ◽  
Allison R. Eberly ◽  
Sabrina H. Werby ◽  
Seth A. Reasoner ◽  
John R. Brannon ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Extracellular Matrix ◽  
Bacterial Communities ◽  
Spatial Organization ◽  
Bet Hedging ◽  
Content Type ◽  
Dna Organization ◽  
Quinol Oxidases ◽  
Biofilm Development ◽  
Biofilm Community

ABSTRACT Biofilms are multicellular bacterial communities encased in a self-secreted extracellular matrix comprised of polysaccharides, proteinaceous fibers, and DNA. Organization of these components lends spatial organization to the biofilm community such that biofilm residents can benefit from the production of common goods while being protected from exogenous insults. Spatial organization is driven by the presence of chemical gradients, such as oxygen. Here we show that two quinol oxidases found in Escherichia coli and other bacteria organize along the biofilm oxygen gradient and that this spatially coordinated expression controls architectural integrity. Cytochrome bd, a high-affinity quinol oxidase required for aerobic respiration under hypoxic conditions, is the most abundantly expressed respiratory complex in the biofilm community. Depletion of the cytochrome bd-expressing subpopulation compromises biofilm complexity by reducing the abundance of secreted extracellular matrix as well as increasing cellular sensitivity to exogenous stresses. Interrogation of the distribution of quinol oxidases in the planktonic state revealed that ∼15% of the population expresses cytochrome bd at atmospheric oxygen concentration, and this population dominates during acute urinary tract infection. These data point toward a bet-hedging mechanism in which heterogeneous expression of respiratory complexes ensures respiratory plasticity of E. coli across diverse host niches. IMPORTANCE Biofilms are multicellular bacterial communities encased in a self-secreted extracellular matrix comprised of polysaccharides, proteinaceous fibers, and DNA. Organization of these components lends spatial organization in the biofilm community. Here we demonstrate that oxygen gradients in uropathogenic Escherichia coli (UPEC) biofilms lead to spatially distinct expression programs for quinol oxidases—components of the terminal electron transport chain. Our studies reveal that the cytochrome bd-expressing subpopulation is critical for biofilm development and matrix production. In addition, we show that quinol oxidases are heterogeneously expressed in planktonic populations and that this respiratory heterogeneity provides a fitness advantage during infection. These studies define the contributions of quinol oxidases to biofilm physiology and suggest the presence of respiratory bet-hedging behavior in UPEC.

Modulation and mechanism of spatial structure for multi-layer cyanate ester resin composites to achieve remarkably increased energy storage density and decreased dielectric loss

2020 ◽  
pp. 002199832095188
Author(s):  
Xiaobao Zhang ◽  
Li Yuan ◽  
Guozheng Liang ◽  
Aijuan Gu
Keyword(s):  
Energy Storage ◽  
Dielectric Loss ◽  
Spatial Structure ◽  
Breakdown Strength ◽  
Layer Structure ◽  
Single Layer ◽  
Cyanate Ester ◽  
Energy Storage Density ◽  
Spatial Structures ◽  
Storage Density

Overcoming sticky problems of large dielectric loss and poor breakdown strength ( Eb) is prerequisite of actual applications for high dielectric constant polymer composites. Herein, three kinds of multi-layer structure composites with different spatial structures (2MP-CE/CNT, CE/CNT-2MP-CE/CNT, MP-CE/CNT-MP) were prepared based on carbon nanotubes (CNTs), cyanate ester (CE) resin and mica paper (MP). Compared with traditional single-layer CE/CNT composite, multi-layer CE/CNT-2MP-CE/CNT composites, of which the middle layer is two pieces of MPs with a thickness of 60 µm, while both bottom and top layers are CE/CNT composite, simultaneously achieve 105 reduction in dielectric loss and 18.1 times increase in energy storage density ( Ue). Through modulating two sheets of MPs and CE/CNT as top and bottom layer, respectively, 2MP-CE/CNT composite with 60 μm MPs has the largest breakdown strength ( Eb), its Eb and Ue are severally about 7.1 and 19.5 times of those of CE/CNT composite. The relationship and mechanism between spatial structure and integrated performance such as dielectric properties, Eb and Ue of composites were systematically investigated. The attractive integrated performances of CE/CNT-2MP-CE/CNT and 2MP-CE/CNT composites are attributed to their unique composition and spatial structures, which bring special micro-capacitance and interfacial polarization, and thus leading to outstanding performances. Therefore, this investigation provides a strategy for getting desirable performances through building composites with specific spatial structure.

scholarly journals Intercellular adhesion promotes clonal mixing in growing bacterial populations

2018 ◽  
Vol 15 (146) ◽  
pp. 20180406 ◽  
Author(s):  
Anton Kan ◽  
Ilenne Del Valle ◽  
Tim Rudge ◽  
Fernán Federici ◽  
Jim Haseloff
Keyword(s):  
Spatial Organization ◽  
Single Cells ◽  
Computational Modelling ◽  
Colony Growth ◽  
Intercellular Adhesion ◽  
Adhesive Properties ◽  
Bacterial Populations ◽  
Intercellular Interactions ◽  
Solid Media ◽  
Adhesin Protein

Dense bacterial communities, known as biofilms, can have functional spatial organization driven by self-organizing chemical and physical interactions between cells, and their environment. In this work, we investigated intercellular adhesion, a pervasive property of bacteria in biofilms, to identify effects on the internal structure of bacterial colonies. We expressed the self-recognizing ag43 adhesin protein in Escherichia coli to generate adhesion between cells, which caused aggregation in liquid culture and altered microcolony morphology on solid media. We combined the adhesive phenotype with an artificial colony patterning system based on plasmid segregation, which marked clonal lineage domains in colonies grown from single cells. Engineered E. coli were grown to colonies containing domains with varying adhesive properties, and investigated with microscopy, image processing and computational modelling techniques. We found that intercellular adhesion elongated the fractal-like boundary between cell lineages only when both domains within the colony were adhesive, by increasing the rotational motion during colony growth. Our work demonstrates that adhesive intercellular interactions can have significant effects on the spatial organization of bacterial populations, which can be exploited for biofilm engineering. Furthermore, our approach provides a robust platform to study the influence of intercellular interactions on spatial structure in bacterial populations.

scholarly journals The Evolution of Urban Spatial Structure in Brasília: Focusing on the Role of Urban Development Policies

2019 ◽  
Vol 11 (2) ◽  
pp. 553
Author(s):  
Cayo Costa ◽  
Sugie Lee
Keyword(s):  
Urban Planning ◽  
Spatial Structure ◽  
Urban Development ◽  
Spatial Organization ◽  
Driving Forces ◽  
Urban Spatial Structure ◽  
Development Policies ◽  
Governance Processes ◽  
Over Time

Many cities evolve over time, but some are designed from scratch. Brasília is presented as a unique case on urban planning for having been built from figuratively nothing, based on a design concept that was the brainchild of Brazilian urbanist Lucio Costa. The present study aimed to analyze the interrelation between urban planning and spatial structure change over time to understand the role of urban development policies on the spatial organization of Brasília. The study was conducted based on three interrelated aspects: (1) The intentions of the plans, (2) territorial governance, and (3) external conditions. The results showed that the circumstances of territory occupation—characterized by a polycentric development system with dispersed satellite cities economically dependent on Brasília—have been gradually replaced by strategic development policies, mainly influenced by social and political driving forces. Accordingly, this research suggests a reconsideration of the scale of development instrumentations based on a better understanding of the metropolitan area of Brasília as a unique structure by strengthening its interrelations and seeking better coordination of interests and adaptability of governance processes.

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