scholarly journals Morphometrics of complex cell shapes: Lobe Contribution Elliptic Fourier Analysis (LOCO-EFA)

2017 ◽  
Author(s):  
Yara E. Sánchez-Corrales ◽  
Matthew Hartley ◽  
Jop van Rooij ◽  
Athanasius F. M. Marée ◽  
Verônica A. Grieneisen
Keyword(s):  
Fourier Analysis ◽  
In Silico ◽  
Cell Shape ◽  
Complex Cell ◽  
Elliptic Fourier Analysis ◽  
Pavement Cells ◽  
Highly Sensitive ◽  
Cell Shapes ◽  
Summary Statement ◽  
Novel Method

AbstractQuantifying cell morphology is fundamental to the statistical study of cell populations, and can help us unravel mechanisms underlying cell and tissue morphogenesis. Current methods, however, require extensive human intervention, are highly sensitive to parameter choice, or produce metrics that are difficult to interpret biologically. We therefore developed a novel method, Lobe Contribution Elliptical Fourier Analysis (LOCO-EFA), which generates from digitalised cell outlines meaningful descriptors that can be directly matched to morphological features. We show that LOCO-EFA provides a tool to phenotype efficiently and objectively populations of cells by applying it to the complex shaped pavement cells of Arabidopsis thaliana wild type and speechless leaves. To further validate our method, we analysed computer-generated tissues, where cell shape can be specified in a controlled manner. LOCO-EFA quantifies deviations between the specified shape that an individual in silico cell takes up when in isolation and the resultant shape when they are allowed to interact within a confluent tissue, thereby assessing the role of cell-cell interactions on population cell shape distributions.Summary statementNovel method (LOCO-EFA) quantifies complex cell shapes, extracting meaningful biological features such as protrusion number and amplitude; here shown for plant pavement cells and validated on in silico tissues.

scholarly journals Morphometrics of complex cell shapes: lobe contribution elliptic Fourier analysis (LOCO-EFA)

Development ◽  
2018 ◽  
Vol 145 (6) ◽  
pp. dev156778 ◽  
Author(s):  
Yara E. Sánchez-Corrales ◽  
Matthew Hartley ◽  
Jop van Rooij ◽  
Athanasius F.M. Marée ◽  
Verônica A. Grieneisen
Keyword(s):  
Fourier Analysis ◽  
Complex Cell ◽  
Elliptic Fourier Analysis ◽  
Cell Shapes

scholarly journals Of puzzles and pavements: a quantitative exploration of leaf epidermal cell shape

2018 ◽  
Author(s):  
Róza V. Vőfély ◽  
Joseph Gallagher ◽  
Grace D. Pisano ◽  
Madelaine Bartlett ◽  
Siobhan A. Braybrook
Keyword(s):  
Aspect Ratio ◽  
Cell Shape ◽  
Molecular Mechanisms ◽  
Vascular Plant ◽  
Plant Morphology ◽  
Pavement Cell ◽  
Pavement Cells ◽  
Stomatal Complexes ◽  
Leaf Epidermal Cell ◽  
Cell Shapes

SummaryThe epidermal cells of leaves lend themselves readily to observation and display many shapes and types: tabular pavement cells, complex trichomes, and stomatal complexes1. Pavement cells fromZea mays(maize) andArabidopsis thaliana(arabidopsis) both have highly undulate anticlinal walls and are held as representative of monocots and eudicots, respectively. In these two model species, we have a nuanced understanding of the molecular mechanisms that generate undulating pavement cell shape2–9. This model-system dominance has led to two common assumptions: first, that particular plant lineages are characterized by particular pavement cell shapes; and second, that undulatory pavement cell shapes are common enough to be model shapes. To test these assumptions, we quantified pavement cell shape in the leaves of 278 vascular plant taxa and assessed cell shape metrics across large taxonomic groups. We settled on two metrics that described cell shape diversity well in this dataset: aspect ratio (degree of cell elongation) and solidity (a proxy for margin undulation). We found that pavement cells in the monocots tended to have weakly undulating margins, pavement cells in ferns had strongly undulating margins, and pavement cells in the eudicots showed no particular degree of undulation. Indeed, we found that cells with strongly undulating margins, like those of arabidopsis and maize, were in the minority in seed plants. At the organ level, we found a trend towards cells with more undulating margins on the abaxial leaf surface vs. the adaxial surface. We also detected a correlation between cell and leaf aspect ratio: highly elongated leaves tended to have highly elongated cells (low aspect ratio), but not in the eudicots. This indicates that while plant anatomy and plant morphology can be connected, superficially similar leaves can develop through very different underlying growth dynamics (cell expansion and division patterns). This work reveals the striking diversity of pavement cell shapes across vascular plants, and lays the quantitative groundwork for testing hypotheses about pavement cell form and function.

scholarly journals Pavement cells and the topology puzzle

2017 ◽  
Author(s):  
Ross Carter ◽  
Yara E. Sánchez-Corrales ◽  
Verônica A. Grieneisen ◽  
Athanasius F. M. Marée
Keyword(s):  
Surface Tension ◽  
Cell Shape ◽  
Direct Consequence ◽  
Cellular Division ◽  
Pavement Cell ◽  
Pavement Cells ◽  
Division Plane ◽  
Cell Shapes ◽  
Parsimonious Model

AbstractD’Arcy Thompson emphasised the importance of surface tension as a potential driving force in establishing cell shape and topology within tissues. Leaf epidermal pavement cells grow into jigsaw-piece shapes, highly deviating from such classical forms. We investigate the topology of developing Arabidopsis leaves composed solely of pavement cells. Image analysis of around 50,000 cells reveals a clear and unique topological signature, deviating from previously studied epidermal tissues. This topological distribution is however established early during leaf development, already before the typical pavement cell shapes emerge, with topological homestasis maintained throughout growth and unaltered between division and maturation zones. Simulating graph models, we identify a heuristic cellular division rule that reproduces the observed topology. Our parsimonious model predicts how and when cells effectively place their division plane with respect to their neighbours. We verify the predicted dynamics through in vivo tracking of 800 mitotic events, and conclude that the distinct topology is not a direct consequence of the jigsaw-like shape of the cells, but rather owes itself to a strongly life-history-driven process, with limited impact from cell surface mechanics.Summary statementDevelopment of the Arabidopsis leaf epidermis topology is driven by deceptively simple rules of cell division, independent of surface tension, cell size and, often complex, cell shape.

Foot asymmetry in healthy adults: Elliptic fourier analysis of standardized footprints

1998 ◽  
Vol 16 (6) ◽  
pp. 758-765 ◽  
Author(s):  
Chiarella Sforza ◽  
Giovanni Michielon ◽  
Nicola Fragnito ◽  
Virgilio F. Ferrario
Keyword(s):  
Fourier Analysis ◽  
Healthy Adults ◽  
Elliptic Fourier Analysis ◽  
Foot Asymmetry

Description and Quantification of Sexual Dimorphism of Pubic Body Shape in Hispanic Populations Using Elliptic Fourier Analysis

2021 ◽  
Author(s):  
Erica Cantor ◽  
Krista Latham ◽  
Stephen Nawrocki
Keyword(s):  
Fourier Analysis ◽  
North American ◽  
Principal Component ◽  
Pubic Bone ◽  
Biological Traits ◽  
Sex Estimation ◽  
Age At Death ◽  
Elliptic Fourier Analysis ◽  
Hispanic Populations ◽  
Effective Principal

Sex estimation is important in the creation of a biological profile for unidentified human remains, as positive identification cannot occur until the decedent’s biological traits have been determined and the range of possible matches has been narrowed. The pubic bone is cited as one of the best indicators of sex due to the constraints of childbirth. Current methods that use the pubic bone for sex estimation, however, rely on poorly defined and subjective observations that are susceptible to inter-and intraobserver error. Additionally, many of the methods currently in use are based on North American populations and thus may not necessarily model the variation seen in other populations around the globe. The aim of this study is to gain a better understanding of variation in pubic bone shape in Hispanic populations by separating the influences of sex, ancestry, and age at death. A total of 164 pubic bones from North American Hispanic and Chilean individuals were compared to 287 pubic bones from individuals of Euro-American ancestry from North American collections, using Elliptic Fourier analysis (EFA) of photographs, principal component analysis, and ANCOVA. EFA generated five effective principal components that collectively describe approximately 95% of the variation in the shape of the pubic body. Sex, age at death, and ancestry were all found to significantly influence shape but explained only 25% of the overall variation. The remaining 75% is likely influenced by variables that cannot be controlled for in anthropological analysis, underscoring how little variance in skeletal morphology is actually explainable.

Regulation of cell shape in Euglena gracilis. III. Involvement of stable microtubules

1985 ◽  
Vol 74 (1) ◽  
pp. 219-237
Author(s):  
C.L. Lachney ◽  
T.A. Lonergan
Keyword(s):  
Euglena Gracilis ◽  
Cell Shape ◽  
Microtubule Assembly ◽  
Live Cells ◽  
Microtubule Depolymerization ◽  
Cytoplasmic Microtubule ◽  
Intact Cells ◽  
Calmodulin Antagonist ◽  
Cell Shapes ◽  
In Cells

The role of cytoplasmic microtubules in a recently reported biological clock-controlled rhythm in cell shape of the alga Euglena gracilis (strain Z) was examined using indirect immunofluorescence microscopy. The resulting fluorescent patterns indicated that, unlike many other cell systems, Euglena cells apparently change from round to long to round cell shape without associated cytoplasmic microtubule assembly and disassembly. Instead, the different cell shapes were correlated with microtubule patterns, which suggested that movement of stable microtubules to accomplish cell shape changes. In live intact cells, these microtubules were demonstrated by immunofluorescence to be stable to lowered temperature and elevated intracellular Ca2+ levels, treatments that are commonly used to depolymerize microtubules. In cells extracted in detergent at low temperature or in the presence of elevated Ca2+ levels, the fluorescent image of the microtubules was disrupted. Transmission electron microscopy confirmed the loss of one subset of pellicle microtubules. The difference in microtubule stability to these agents between live intact cells and cells extracted in detergent suggested the presence of a microtubule-stabilizing factor in live cells, which is released from the cell by extraction with detergent, thereby permitting microtubule depolymerization by Ca2+ or lowered temperature. The calmodulin antagonist trifluoperazine prevented the Ca2+-induced disruption of the fluorescent microtubule pattern in cells extracted in detergent. These results implied the involvement of calmodulin in the sensitivity to Ca2+ of the microtubules of cells extracted in detergent.

Shape difference of mud clasts depending on depositional facies: application of newly modified elliptic Fourier analysis to hybrid event beds

2020 ◽  
Vol 90 (10) ◽  
pp. 1410-1435
Author(s):  
Sojiro Fukuda ◽  
Hajime Naruse
Keyword(s):  
Fourier Analysis ◽  
Shape Analysis ◽  
Transport Processes ◽  
Transport Systems ◽  
Shape Parameters ◽  
Elliptic Fourier Analysis ◽  
Depositional Facies ◽  
Size And Shape ◽  
Muddy Sediments ◽  
Hybrid Event

ABSTRACT Hybrid event beds are the deposits from sediment gravity flows that change their rheological behavior through their passage, entraining muddy sediments and damping turbulence. Muddy facies of hybrid event beds are often associated with abundant mud clasts which show a wide variety of size and shape. The variation of clast occurrence in hybrid event beds is expected to preserve the information of entrainment and transport processes of muddy sediments in submarine density currents. However, previous analyses of hybrid event beds have focused on describing the overall clast occurrence rather than the statistical size and shape analyses because traditional shape parameters are incapable of characterizing the complex shape of mud clasts. Here, a new quantitative grain-shape analysis of mud clasts is conducted and allows visualization of the spatial variation of clast size and shape, which suggests the wide variety of origin and transport systems of entrained mud clasts. This new method revises the traditional elliptic Fourier analysis, substituting Fourier power spectra (FPS) for traditional elliptic Fourier descriptors to overcome the mirror-wise shape problem. Further, principal-component analysis is shown to capture significant shape attributes more effectively than traditional shape parameters. The proposed method is applied to mud clasts in sediment-gravity-flow deposits in the lower Pleistocene Otadai Formation, central Japan. Results imply that there are distinctive shape and size differences of mud clasts that are strongly associated with depositional facies rather than the distance from the source. The clasts have a higher angularity than other facies in the debrite intervals in hybrid event beds. It is also shown that clasts in sandy, structureless facies have different characteristics in shapes based on elongation and convexity compared to laminated facies. Comparison between different shape-analysis methods demonstrates that none of the traditional methods are able to visualize these trends as effectively as the method presented herein. These results highlight the importance of the quantitative shape analysis of sediment grains and the effectiveness of FPS-based elliptic Fourier analysis.

Local differentiation of cell wall matrix polysaccharides in sinuous pavement cells: its possible involvement in the flexibility of cell shape

Plant Biology ◽  
2018 ◽  
Vol 20 (2) ◽  
pp. 223-237 ◽  
Author(s):  
P. Sotiriou ◽  
E. Giannoutsou ◽  
E. Panteris ◽  
B. Galatis ◽  
P. Apostolakos
Keyword(s):  
Cell Wall ◽  
Cell Shape ◽  
Pavement Cells ◽  
Local Differentiation ◽  
Cell Wall Matrix
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