Self-organization of developing embryo using scale-invariant approach

Tiraihi, Ali; Tiraihi, Mujtaba; Tiraihi, Taki

doi:10.1186/1742-4682-8-17

Cited by 13 publications

(14 citation statements)

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“…The fractal concept has improved our understanding of many physiological phenomena, for instance, metabolic rate, intracellular bio-energetic dynamics, drug clearance, population genetics, tissue organization and tumor growth. Fractality describes very well the complexity of macroscopic and microscopic anatomic structures and reveals the design principles of organisms [2–67] .…”

Section: Fractality: a General Concept In Biology And Medicinementioning

confidence: 99%

Fractal dimension of chromatin: potential molecular diagnostic applications for cancer prognosis

Metze

2013

Expert Review of Molecular Diagnostics

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Fractal characteristics of chromatin, revealed by light or electron microscopy, have been reported during the last 20 years. Fractal features can easily be estimated in digitalized microscopic images and are helpful for diagnosis and prognosis of neoplasias. During carcinogenesis and tumor progression, an increase of the fractal dimension (FD) of stained nuclei has been shown in intraepithelial lesions of the uterine cervix and the anus, oral squamous cell carcinomas or adenocarcinomas of the pancreas. Furthermore, an increased FD of chromatin is an unfavorable prognostic factor in squamous cell carcinomas of the oral cavity and the larynx, melanomas and multiple myelomas. High goodness-of-fit of the regression line of the FD is a favorable prognostic factor in acute leukemias and multiple myelomas. The nucleus has fractal and power-law organization in several different levels, which might in part be interrelated. Some possible relations between modifications of the chromatin organization during carcinogenesis and tumor progression and an increase of the FD of stained chromatin are suggested. Furthermore, increased complexity of the chromatin structure, loss of heterochromatin and a less-perfect self-organization of the nucleus in aggressive neoplasias are discussed.

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Section: Fractality: a General Concept In Biology And Medicinementioning

confidence: 99%

Fractal dimension of chromatin: potential molecular diagnostic applications for cancer prognosis

Metze

2013

Expert Review of Molecular Diagnostics

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“…In nematodes, differentiation trees allow us to relate the binary, mostly asymmetric cell divisions to the broader context of embryonic tissue differentiation. Alternative methods include meta-Boolean models [14], complex networks [10], algorithmic complexity [15], and scale-invariant power laws [16]. One method that relies upon simply reorganizing the lineage tree by the occurrence of differentiation waves is called differentiation tree analysis [11].…”

Section: Analysis Of Developmentmentioning

confidence: 99%

Data-theoretical Synthesis of the Early Developmental Process

Alicea

Gordon

Portegys

2018

Preprint

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Biological development is often described as a dynamic, emergent process. Yet beyond the observation of gene expression in individual cells, it is hard to conceptualize large-scale patterns that confirm this description. We provide an example of combining theoretical insights with a data science approach. The availability of quantitative data allows us to examine aggregate trends across development, from the spatial organization of embryo cells to the temporal trends as they differentiate. The first half of this paper lays out alternatives to the gene-centric view of development: namely, the view that developmental genes and their expression determine the complexity of the developmental phenotype. Caenorhabditis elegans biology provides us with a highly-deterministic developmental cell lineage and clear linkage between zygote and cells of the adult phenotype. These properties allow us to examine time-dependent properties of the embryonic phenotype. We utilize the unique life-history properties of C. elegans to demonstrate how these emergent properties can be linked together by relational processes and data analysis. The second half of this paper focuses on the process of developmental cell terminal differentiation, and how terminally-differentiated cells contribute to structure and function of the adult phenotype. An analysis is conducted for cells that were present during discrete time intervals covering 200 to 400 minutes of embryogenesis, providing us with basic statistics on the tempo of the process in addition to the appearance of specific cell types and their order relative to developmental time. As with ideas presented in the first section, these data may also provide clues as to the timing for the initial onset of stereotyped and autonomic behaviors of the developing animal. Taken together, these overlapping approaches can provide critical links across life-history, anatomy and function.

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“…interactions, plots as a descending straight line). Several authors have therefore suggested that self-organization in development might be identified by seeking power-law topologies (Kurakin, 2005;Tiraihi et al 2011). Some features of systems known, through experiment, to self-organize do show power-law behaviour: imaging the anatomy of a branching epithelial or vascular tree using voxels of a range of dimensions, assessing the fraction of voxels containing at least some of the tree in each case, and log-plotting the occupancy vs. voxel size yields a power-law line, at least until the voxels become smaller than the smallest tubules (see Fig.…”

Section: Identifying Adaptive Self-organizationmentioning

confidence: 99%

Adaptive self‐organization in the embryo: its importance to adult anatomy and to tissue engineering

Davies

2017

Journal of Anatomy

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The anatomy of healthy humans shows much minor variation, and twin‐studies reveal at least some of this variation cannot be explained genetically. A plausible explanation is that fine‐scale anatomy is not specified directly in a genetic programme, but emerges from self‐organizing behaviours of cells that, for example, place a new capillary where it happens to be needed to prevent local hypoxia. Self‐organizing behaviour can be identified by manipulating growing tissues (e.g. putting them under a spatial constraint) and observing an adaptive change that conserves the character of the normal tissue while altering its precise anatomy. Self‐organization can be practically useful in tissue engineering but it is limited; generally, it is good for producing realistic small‐scale anatomy but large‐scale features will be missing. This is because self‐organizing organoids miss critical symmetry‐breaking influences present in the embryo: simulating these artificially, for example, with local signal sources, makes anatomy realistic even at large scales. A growing understanding of the mechanisms of self‐organization is now allowing synthetic biologists to take their first tentative steps towards constructing artificial multicellular systems that spontaneously organize themselves into patterns, which may soon be extended into three‐dimensional shapes.

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Self-organization of developing embryo using scale-invariant approach

Cited by 13 publications

References 100 publications

Fractal dimension of chromatin: potential molecular diagnostic applications for cancer prognosis

Fractal dimension of chromatin: potential molecular diagnostic applications for cancer prognosis

Data-theoretical Synthesis of the Early Developmental Process

Adaptive self‐organization in the embryo: its importance to adult anatomy and to tissue engineering

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