Dataset Information

Estimation of three-dimensional chromatin morphology for nuclear classification and characterisation.

ABSTRACT: Classification and characterisation of cellular morphological states are vital for understanding cell differentiation, development, proliferation and diverse pathological conditions. As the onset of morphological changes transpires following genetic alterations in the chromatin configuration inside the nucleus, the nuclear texture as one of the low-level properties if detected and quantified accurately has the potential to provide insights on nuclear organisation and enable early diagnosis and prognosis. This study presents a three dimensional (3D) nuclear texture description method for cell nucleus classification and variation measurement in chromatin patterns on the transition to another phenotypic state. The proposed approach includes third plane information using hyperplanes into the design of the Sorted Random Projections (SRP) texture feature and is evaluated on publicly available 3D image datasets of human fibroblast and human prostate cancer cell lines obtained from the Statistics Online Computational Resource. Results show that 3D SRP and 3D Local Binary Pattern provide better classification results than other feature descriptors. In addition, the proposed metrics based on 3D SRP validate the change in intensity and aggregation of heterochromatin on transition to another state and characterise the intermediate and ultimate phenotypic states.

SUBMITTER: Rana P

PROVIDER: S-EPMC7873284 | biostudies-literature | 2021 Feb

REPOSITORIES: biostudies-literature

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Estimation of three-dimensional chromatin morphology for nuclear classification and characterisation.

Rana Priyanka P Sowmya Arcot A Meijering Erik E Song Yang Y

Scientific reports 20210209 1

Classification and characterisation of cellular morphological states are vital for understanding cell differentiation, development, proliferation and diverse pathological conditions. As the onset of morphological changes transpires following genetic alterations in the chromatin configuration inside the nucleus, the nuclear texture as one of the low-level properties if detected and quantified accurately has the potential to provide insights on nuclear organisation and enable early diagnosis and p ...[more]

PMID: 33564040

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Project description:BackgroundThe infraorder Mygalomorphae (i.e., trapdoor spiders, tarantulas, funnel web spiders, etc.) is one of three main lineages of spiders. Comprising 15 families, 325 genera, and over 2,600 species, the group is a diverse assemblage that has retained a number of features considered primitive for spiders. Despite an evolutionary history dating back to the lower Triassic, the group has received comparatively little attention with respect to its phylogeny and higher classification. The few phylogenies published all share the common thread that a stable classification scheme for the group remains unresolved.Methods and findingsWe report here a reevaluation of mygalomorph phylogeny using the rRNA genes 18S and 28S, the nuclear protein-coding gene EF-1γ, and a morphological character matrix. Taxon sampling includes members of all 15 families representing 58 genera. The following results are supported in our phylogenetic analyses of the data: (1) the Atypoidea (i.e., antrodiaetids, atypids, and mecicobothriids) is a monophyletic group sister to all other mygalomorphs; and (2) the families Mecicobothriidae, Hexathelidae, Cyrtaucheniidae, Nemesiidae, Ctenizidae, and Dipluridae are not monophyletic. The Microstigmatidae is likely to be subsumed into Nemesiidae. Nearly half of all mygalomorph families require reevaluation of generic composition and placement. The polyphyletic family Cyrtaucheniidae is most problematic, representing no fewer than four unrelated lineages.ConclusionsBased on these analyses we propose the following nomenclatural changes: (1) the establishment of the family Euctenizidae (NEW RANK); (2) establishment of the subfamily Apomastinae within the Euctenizidae; and (3) the transfer of the cyrtaucheniid genus Kiama to Nemesiidae. Additional changes include relimitation of Domiothelina and Theraphosoidea, and the establishment of the Euctenizoidina clade (Idiopidae + Euctenizidae). In addition to these changes, we propose a "road map" for future sampling across the infraorder with the aim of solving many remaining questions that hinder mygalomorph systematics.

Dataset Information

Estimation of three-dimensional chromatin morphology for nuclear classification and characterisation.

Publications

Estimation of three-dimensional chromatin morphology for nuclear classification and characterisation.

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