Dataset Information

Dynamic scaling in the growth of a non-branching plant, Cardiocrinum cordatum.

ABSTRACT: We investigated whole-plant leaf area in relation to ontogenetic variation in leaf-size for a forest perennial herb, Cardiocrinum cordatum. The 200-fold ontogenetic variability in C. cordatum leaf area followed a power-law dependence on total leaf number, a measure of developmental stage. When we normalized for plant size, the function describing the size of single leaves along the stem was similar among different-sized plants, implying that the different-sized canopies observed at different times in the growth trajectory were fundamentally similar to each other. We conclude that the growth trajectory of a population of C. cordatum plant leaves obeyed a dynamic scaling law, the first reported for a growth trajectory at the whole-plant level.

SUBMITTER: Koyama K

PROVIDER: S-EPMC3446904 | biostudies-literature | 2012

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Dynamic scaling in the growth of a non-branching plant, Cardiocrinum cordatum.

Koyama Kohei K Hidaka Yoshiki Y Ushio Masayuki M

PloS one 20120919 9

We investigated whole-plant leaf area in relation to ontogenetic variation in leaf-size for a forest perennial herb, Cardiocrinum cordatum. The 200-fold ontogenetic variability in C. cordatum leaf area followed a power-law dependence on total leaf number, a measure of developmental stage. When we normalized for plant size, the function describing the size of single leaves along the stem was similar among different-sized plants, implying that the different-sized canopies observed at different tim ...[more]

PMID: 23028928

Similar Datasets

Project description:This study considers the problem of describing and predicting cleft formation during the early stages of branching morphogenesis in mouse submandibular salivary glands (SMG) under the influence of varied concentrations of epidermal growth factors (EGF). Given a time-lapse video of a growing SMG, first we build a descriptive model that captures the underlying biological process and quantifies the ground truth. Tissue-scale (global) and morphological features related to regions of interest (local features) are used to characterize the biological ground truth. Second, we devise a predictive growth model that simulates EGF-modulated branching morphogenesis using a dynamic graph algorithm, which is driven by biological parameters such as EGF concentration, mitosis rate, and cleft progression rate. Given the initial configuration of the SMG, the evolution of the dynamic graph predicts the cleft formation, while maintaining the local structural characteristics of the SMG. We determined that higher EGF concentrations cause the formation of higher number of buds and comparatively shallow cleft depths. Third, we compared the prediction accuracy of our model to the Glazier-Graner-Hogeweg (GGH) model, an on-lattice Monte-Carlo simulation model, under a specific energy function parameter set that allows new rounds of de novo cleft formation. The results demonstrate that the dynamic graph model yields comparable simulations of gland growth to that of the GGH model with a significantly lower computational complexity. Fourth, we enhanced this model to predict the SMG morphology for an EGF concentration without the assistance of a ground truth time-lapse biological video data; this is a substantial benefit of our model over other similar models that are guided and terminated by information regarding the final SMG morphology. Hence, our model is suitable for testing the impact of different biological parameters involved with the process of branching morphogenesis in silico, while reducing the requirement of in vivo experiments.

Project description:BackgroundThe superficial resemblance of phylogenetic trees to other branching structures allows searching for macroevolutionary patterns. However, such trees are just statistical inferences of particular historical events. Recent meta-analyses report finding regularities in the branching pattern of phylogenetic trees. But is this supported by evidence, or are such regularities just methodological artifacts? If so, is there any signal in a phylogeny?MethodologyIn order to evaluate the impact of polytomies and imbalance on tree shape, the distribution of all binary and polytomic trees of up to 7 taxa was assessed in tree-shape space. The relationship between the proportion of outgroups and the amount of imbalance introduced with them was assessed applying four different tree-building methods to 100 combinations from a set of 10 ingroup and 9 outgroup species, and performing covariance analyses. The relevance of this analysis was explored taking 61 published phylogenies, based on nucleic acid sequences and involving various taxa, taxonomic levels, and tree-building methods.Principal findingsAll methods of phylogenetic inference are quite sensitive to the artifacts introduced by outgroups. However, published phylogenies appear to be subject to a rather effective, albeit rather intuitive control against such artifacts. The data and methods used to build phylogenetic trees are varied, so any meta-analysis is subject to pitfalls due to their uneven intrinsic merits, which translate into artifacts in tree shape. The binary branching pattern is an imposition of methods, and seldom reflects true relationships in intraspecific analyses, yielding artifactual polytomies in short trees. Above the species level, the departure of real trees from simplistic random models is caused at least by two natural factors--uneven speciation and extinction rates; and artifacts such as choice of taxa included in the analysis, and imbalance introduced by outgroups and basal paraphyletic taxa. This artifactual imbalance accounts for tree shape convergence of large trees.SignificanceThere is no evidence for any universal scaling in the tree of life. Instead, there is a need for improved methods of tree analysis that can be used to discriminate the noise due to outgroups from the phylogenetic signal within the taxon of interest, and to evaluate realistic models of evolution, correcting the retrospective perspective and explicitly recognizing extinction as a driving force. Artifacts are pervasive, and can only be overcome through understanding the structure and biological meaning of phylogenetic trees. Catalan Abstract in Translation S1.

Dataset Information

Dynamic scaling in the growth of a non-branching plant, Cardiocrinum cordatum.

Publications

Dynamic scaling in the growth of a non-branching plant, Cardiocrinum cordatum.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets