scholarly journals Cell adhesion and fluid flow jointly initiate genotype spatial distribution in biofilms

2018 ◽  
Author(s):  
Ricardo Martínez-García ◽  
Carey D. Nadell ◽  
Raimo Hartmann ◽  
Knut Drescher ◽  
Juan A. Bonachela
Keyword(s):  
Fluid Flow ◽  
Cell Adhesion ◽  
Genetic Structure ◽  
Spatial Organization ◽  
Model Development ◽  
Cell Lineage ◽  
Spatial Arrangement ◽  
Complex Interaction ◽  
Global Functioning ◽  
Different Strains

AbstractBiofilms are microbial collectives that occupy a diverse array of surfaces. The function and evolution of biofilms are strongly influenced by the spatial arrangement of different strains and species within them, but how spatiotemporal distributions of different genotypes in biofilm populations originate is still underexplored. Here, we study the origins of biofilm genetic structure by combining model development, numerical simulations, and microfluidic experiments using the human pathogenVibrio cholerae. Using spatial correlation functions to quantify the differences between emergent cell lineage segregation patterns, we find that strong adhesion often, but not always, maximizes the size of clonal cell clusters on flat surfaces. Counterintuitively, our model predicts that, under some conditions, investing in adhesion can reduce rather than increase clonal group size. Our results emphasize that a complex interaction of fluid flow and cell adhesiveness can underlie emergent patterns of biofilm genetic structure. This structure, in turn, has an outsize influence on how biofilm-dwelling populations function and evolve.Author summaryBiofilms are bacterial groups, often attached to surfaces, in which a broad variety of cooperative and competitive interactions typically occur. The spatial organization of different strains and species within biofilm communities strongly influences their global functioning, but little is known about how such structure arises. Combining experiments onV. choleraeand simulations of a cellular automaton, we show that the complex interaction between bacterial traits (cell adhesion) and environmental factors (fluid flow intensity) strongly influences the early origins of biofilm spatial structure. In most cases, we found that highly-adhesive strains form larger clusters than the weakly-adhesive ones. Against intuition, however, we also found the opposite outcome: weakly-adhesive tend to form larger clusters than the highly adhesive ones when flows are weak or the population density of colonizing cells is high.

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.

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 Organizational metrics of interchromatin speckle factor domains: integrative classifier for stem cell adhesion & lineage signaling

2015 ◽  
Vol 7 (4) ◽  
pp. 435-446 ◽  
Author(s):  
Sebastián L. Vega ◽  
Anandika Dhaliwal ◽  
Varun Arvind ◽  
Parth J. Patel ◽  
Nick R. M. Beijer ◽  
...  
Keyword(s):  
Content Analysis ◽  
Stem Cell ◽  
Cell Adhesion ◽  
Nuclear Protein ◽  
Cell Lineage ◽  
Lineage Commitment ◽  
Cell Microenvironment ◽  
Stem Cell Lineage ◽  
High Content Analysis

Timely classification of stem cell lineage commitment in response to cell–microenvironment interactions using high content analysis of sub-nuclear protein organization.

scholarly journals Substrate traits govern the assembly and spatial organization of microbial community engaged in metabolic division of labor

2020 ◽  
Author(s):  
Miaoxiao Wang ◽  
Xiaoli Chen ◽  
Yong Nie ◽  
Xiao-Lei Wu
Keyword(s):  
Microbial Community ◽  
Division Of Labor ◽  
Substrate Concentration ◽  
Spatial Organization ◽  
Microbial Populations ◽  
Mutual Benefit ◽  
Different Strains ◽  
Microbial Systems ◽  
Benefit Allocation ◽  
Natural Communities

AbstractMetabolic division of labor (MDOL) is widespread in nature, whereby a complex metabolic pathway is shared between different strains within a community for mutual benefit. However, little is known about how communities engaged in MDOL assemble and spatially organize. We hypothesized that when degradation of an organic compound is carried out via MDOL, substrate concentration and its toxicity modulate the benefit allocation between the two microbial populations, thus governing the assembly of this community. We tested this hypothesis by combining individual-based simulations with pattern formation assays using a synthetic microbial community. We found that while the frequency of the first population increases with an increase in substrate concentration, this increase is capped with an upper bound determined by the biotoxicity of the substrate. In addition, our model showed that substrate concentration and its toxicity affect levels of intermixing between strains. These predictions were quantitatively verified using an engineered system composed of two strains degrading salicylate through MDOL. Our results demonstrate that the structure of the microbial communities can be quantitatively predicted from simple environmental factors, such as substrate concentration and its toxicity, which provides novel perspectives on understanding the assembly of natural communities, as well as insights into how to manage artificial microbial systems.

scholarly journals Controlled spatial organization of bacterial clusters reveals cell filamentation is vital for Xylella fastidiosa biofilm formation

2021 ◽  
Author(s):  
Silambarasan Anbumani ◽  
Aldeliane M. da Silva ◽  
Eduarda R. Fischer ◽  
Mariana de Souza e Silva ◽  
Antonio A.G. von Zuben ◽  
...  
Keyword(s):  
Cell Adhesion ◽  
Quorum Sensing ◽  
Biofilm Formation ◽  
Spatial Organization ◽  
Xylella Fastidiosa ◽  
Cell Formation ◽  
Formation Mechanisms ◽  
Cell Morphogenesis ◽  
Cell Clusters ◽  
Filamentous Cell

The morphological plasticity of bacteria to form filamentous cells commonly represents an adaptive strategy induced by stresses. In contrast, for diverse pathogens filamentous cells have been observed during biofilm formation, with function yet to be elucidated. To identify prior hypothesized quorum sensing as trigger of such cell morphogenesis, spatially controlled cell adhesion is pivotal. Here, we demonstrate highly-selective cell adhesion of the biofilm-forming phytopathogen Xylella fastidiosa to gold-patterned SiO2 substrates with well-defined geometries and dimensions. The consequent control of both cell density and distances between cell clusters using these patterns provided evidence of quorum sensing governing filamentous cell formation. While cell morphogenesis is induced by cell cluster density, filamentous cell growth is oriented towards neighboring cell clusters and distance-dependent; large interconnected cell clusters create the early biofilm structural framework. Together, our findings and investigative platform could facilitate therapeutic developments targeting biofilm formation mechanisms of X. fastidiosa and other pathogens.

scholarly journals Three-dimensional electron microscopy of ribosomal chromatin in two higher plants: a cytochemical, immunocytochemical, and in situ hybridization approach.

1991 ◽  
Vol 39 (11) ◽  
pp. 1495-1506 ◽  
Author(s):  
P M Motte ◽  
R Loppes ◽  
M Menager ◽  
R Deltour
Keyword(s):  
Electron Microscopy ◽  
In Situ Hybridization ◽  
Spatial Organization ◽  
Higher Plants ◽  
Three Dimensional ◽  
Spatial Arrangement ◽  
Thin Sections ◽  
Cytoplasmic Dna ◽  
Immunocytochemical Techniques

We report the 3-D arrangement of DNA within the nucleolar subcomponents from two evolutionary distant higher plants, Zea mays and Sinapis alba. These species are particularly convenient to study the spatial organization of plant intranucleolar DNA, since their nucleoli have been previously reconstructed in 3-D from serial ultra-thin sections. We used the osmium ammine-B complex (a specific DNA stain) on thick sections of Lowicryl-embedded root fragments. Immunocytochemical techniques using anti-DNA antibodies and rDNA/rDNA in situ hybridization were also applied on ultra-thin sections. We showed on tilted images that the OA-B stains DNA throughout the whole thickness of the section. In addition, very low quantities of cytoplasmic DNA were stained by this complex, which is now the best DNA stain used in electron microscopy. Within the nucleoli the DNA was localized in the fibrillar centers, where large clumps of dense chromatin were also visible. In the two plant species intranucleolar chromatin forms a complex network with strands partially linked to chromosomal nucleolar-organizing regions identified by in situ hybridization. This study describes for the first time the spatial arrangement of the intranucleolar chromatin in nucleoli of higher plants using high-resolution techniques.

Alteration of nuclear architecture in male germ cells of chromosomally derived subfertile mice

2001 ◽  
Vol 114 (24) ◽  
pp. 4429-4434
Author(s):  
Silvia Garagna ◽  
Maurizio Zuccotti ◽  
Alan Thornhill ◽  
Raul Fernandez-Donoso ◽  
Soledad Berrios ◽  
...  
Keyword(s):  
Sertoli Cells ◽  
Spatial Organization ◽  
Nuclear Architecture ◽  
Spatial Arrangement ◽  
Cell Types ◽  
Condensed State ◽  
Germ Cell Differentiation ◽  
Y Chromosomes ◽  
Dual Colour ◽  
Pachytene Spermatocytes

The mammalian cell nucleus consists of numerous compartments involved in the regular unfolding of processes such as DNA replication and transcription, RNA maturation, protein synthesis and cell division. Knowledge is increasing of the relationships between high-order levels of chromatin organization and its spatial organization, and of how these relationships contribute to the various functions carried out in the nucleus. We have studied the spatial arrangement of mouse telocentric chromosomes 5, 11, 13, 15, 16 and 17, some of their metacentric Robertsonian derivatives, and X and Y chromosomes by whole chromosome painting in male germ (spermatogonia, pachytene spermatocytes and spermatids) and Sertoli cells of homozygous and heterozygous individuals. Using dual-colour fluorescence in situ hybridization we found that these chromosomes occupy specific nuclear territories in each cell type analysed. When chromosomes are present as Robertsonian metacentrics in the heterozygous state, that is, as Robertsonian metacentrics and their homologous telocentrics, differences in their nuclear positions are detectable: heterozygosity regularly produces a change in the nuclear position of one of the two homologous telocentrics in all the cell types studied. In the Robertsonian heterozygotes, the vast majority of the Sertoli cells show the sex chromosomes in a condensed state, whereas they appear decondensed in the Robertsonian homozygotes. As the Robertsonian heterozygosities we studied produce a chromosomally derived impairment of male germ-cell differentiation, we discuss the possibility that changes in chromosome spatial territories may alter some nuclear machinery (e.g., synapsis, differential gene expression) important for the correct unfolding of the meiotic process and for the proper functioning of Sertoli cells.

The Social and Genetic Structure of a Natural Colony of House Mice, Mus musculus, at Healesville WildlifeSanctuary

1983 ◽  
Vol 31 (2) ◽  
pp. 155 ◽  
Author(s):  
GR Singleton
Keyword(s):  
Genetic Structure ◽  
Life Span ◽  
Social Organization ◽  
Turnover Rate ◽  
Spatial Organization ◽  
House Mice ◽  
Genetic Composition ◽  
Short Life ◽  
Short Life Span ◽  
The Social

A 2-year program monitored the spatial organization, genetic structure and turnover rate of an unconfined commensal colony of mice. Four demes (social breeding units) were identified; each usually consisted of one or two males and two or three females. Demes were detected simultaneously in adjoining cages of an aviary (one deme per cage). Movement between demes was rare and the life span of a deme ranged from 2 to 7 months. The adult members of each deme had genotypes compatible to the majority of the young captured in the respective cage of the aviary at the time of residence of the deme. Taken in isolation, these results suggest that social behaviour would have a major impact on the genetic structure of the aviary population. When viewed over the main breeding season, the short life span of a deme and the genetic differences between demes indicate that social organization probably had only a temporary effect on the genetic composition of the aviary population.

Determinants of genetic structure of the Sub-Saharan parasitic wasp Cotesia sesamiae

2017 ◽  
Author(s):  
Antoine Branca ◽  
Bruno Le Ru ◽  
Paul-André Calatayud ◽  
Julius Obonyo ◽  
Boaz Muzyoka ◽  
...  
Keyword(s):  
Biological Control ◽  
Life History ◽  
Genetic Structure ◽  
Parasitic Wasp ◽  
Sub Saharan Africa ◽  
Host Specialization ◽  
Life History Strategies ◽  
Cotesia Sesamiae ◽  
Sub Saharan ◽  
Different Strains

AbstractParasitoid life style represents one of the most diversified life history strategies on earth. There are however very few studies on the variables associated with intraspecific diversity of parasitoid insects, especially regarding the relationship with spatial, biotic and abiotic ecological factors. Cotesia sesamiae is a Sub-Saharan stenophagous parasitic wasp that parasitizes several African stemborer species with variable developmental success. The different host-specialized populations are infected with different strains of Wolbachia, an endosymbiotic bacterium widespread in arthropods that is known for impacting life history traits notably reproduction, and consequently species distribution. In this study, first we analyzed the genetic structure of C. sesamiae across Sub-Saharan Africa, using 8 microsatellite markers, and 3 clustering software. We identified five major population clusters across Sub-Saharan Africa, which probably originated in East African Rift region and expanded throughout Africa in relation to host genus and abiotic factors such as climatic classifications. Using laboratory lines, we estimated the incompatibility between the different strains of Wolbachia infecting C. sesamiae. We observed an incompatibility between Wolbachia strains was asymmetric; expressed in one direction only. Based on these results, we assessed the relationships between direction of gene flow and Wolbachia infections in the genetic clusters. We found that Wolbachia-induced reproductive incompatibility was less influential than host specialization in the genetic structure. Both Wolbachia and host were more influential than geography and current climatic conditions. These results are discussed in the context of African biogeography, and co-evolution between Wolbachia, virus parasitoid and host, in the perspective of improving biological control efficiency through a better knowledge of the biodiversity of biological control agents.

Frequencies in vibrating wood – Does cell organization matter?

IAWA Journal ◽  
2019 ◽  
Vol 40 (1) ◽  
pp. 124-142
Author(s):  
Oliver Dünisch
Keyword(s):  
Spatial Organization ◽  
Ring Width ◽  
Spatial Arrangement ◽  
Cell Types ◽  
Dominant Frequency ◽  
Fast Fourier Transformation ◽  
Frequency Spectra ◽  
Laser Sensors ◽  
Vibrating Plates ◽  
Dominant Frequencies

ABSTRACT The relationship between the spatial organization of different cell types, of the xylem rays, and of the tree rings and the frequencies in vibrating softwoods and hardwoods was studied under controlled conditions. In total, the frequencies in 1007 standardized vibrating plates from 16 softwoods and 74 hardwoods were analysed using high resolution laser sensors (accuracy ± 0.02 μm, sampling frequency 30 kHz) for vibration measurements. Overlapping frequencies within the frequency spectra were identified by means of Fast Fourier Transformation analysis. With regard to the number of distinct frequencies within the spectra, four different vibration types were identified: type 1–one dominant frequency within the frequency spectra; type 2-two dominant frequencies within the frequency spectra; type 3-three dominant frequencies within the frequency spectra; type 4-no dominant frequencies within the frequency spectra. The presence of distinct frequencies was correlated with a highly organized spatial arrangement of tracheids in softwoods, with a storied arrangement of the xylem rays in hardwoods, and with low variation in tree-ring width in both softwoods and hardwoods. The grid size for repetition in these xylem structures influenced the frequencies of the vibrating wood in absolute numbers. The results indicate that the analysis of the anatomical structure of the wood can contribute to the grading of timber for its vibration characteristics, which is of special interest for the selection of resonance wood for musical instruments.

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