Biology subjects

Mody, T. A.

Publications and source records attributed to Mody, T. A..

4 recordsLinked to original sources

bioRxiv2024

The inner integument controls embryo sac development and seed shape in Arabidopsis thaliana

The angiosperm ovule is characterized by the close association of the two generations, with the haploid female gametophyte or embryo sac being encapsulated by the diploid sporophyte, which usually forms two integuments. How the gametophyte and sporophyte coordinate their development has long been of interest. However, the function of the inner integument in embryo sac development has remained elusive. Here, we addressed this question. We applied a genetic ablation strategy to achieve an early block in inner integument outgrowth. We generated plants expressing BARNASE under the control of an early acting endothelium-specific promoter. Corresponding lines carried ovules lacking most of the inner integument. The genetic and cell biological data revealed that in the near absence of an inner integument embryo sac development is blocked at the mono-nuclear embryo sac stage in most pre-fertilization ovules. Approximately 10 percent of the ovules developed a functional embryo sac and underwent fertilization. Subsequent embryo and endosperm development appeared unperturbed and viable seeds were produced albeit of altered shape. Our results show that the inner integument plays an important role in early embryo sac development as well as ovule and seed shape, but is dispensable for embryo and endosperm development. Key words: embryo sac, embryo, endothelium, female gametophyte, integument, seed development HighlightGenetic ablation of the inner integument demonstrates its role in embryo sac development and its irrelevance for embryogenesis.

plant biology↗

bioRxiv2024

A deep learning-based toolkit for 3D nuclei segmentation and quantitative analysis in cellular and tissue context

We present a new set of computational tools that enable accurate and widely applicable 3D segmentation of nuclei in various 3D digital organs. We developed a novel approach for ground truth generation and iterative training of 3D nuclear segmentation models, which we applied to popular CellPose, PlantSeg, and StarDist algorithms. We provide two high-quality models trained on plant nuclei that enable 3D segmentation of nuclei in datasets obtained from fixed or live samples, acquired from different plant and animal tissues, and stained with various nuclear stains or fluorescent protein-based nuclear reporters. We also share a diverse high-quality training dataset of about 10,000 nuclei. Furthermore, we advanced the MorphoGraphX analysis and visualization software by, among other things, providing a method for linking 3D segmented nuclei to their surrounding cells in 3D digital organs. We found that the nuclear-to-cell volume ratio varies between different ovule tissues and during the development of a tissue. Finally, we extended the PlantSeg 3D segmentation pipeline with a proofreading script that uses 3D segmented nuclei as seeds to correct cell segmentation errors in difficult-to-segment tissues. Summary StatementWe present computational tools that allow versatile and accurate 3D nuclear segmentation in plant organs, enable the analysis of cell-nucleus geometric relationships, and improve the accuracy of 3D cell segmentation.

plant biology↗

bioRxiv2023

Diverse 3D cellular patterns underlie the development of Cardamine hirsuta and Arabidopsis thaliana ovules

A fundamental question in biology is how organ morphogenesis comes about. The ovules of Arabidopsis thaliana have been established as a successful model to study numerous aspects of tissue morphogenesis; however, little is known regarding the relative contributions and dynamics of differential tissue and cellular growth and architecture in establishing ovule morphogenesis in different species. To address this issue, we generated a 3D digital atlas of Cardamine hirsuta ovule development with full cellular resolution. We combined quantitative comparative morphometrics and topological analysis to explore similarities and differences in the 3D cellular architectures underlying ovule development of the two species. We discovered that they show diversity in the way the three radial cell layers of the primordium contribute to its growth, in the formation of a new cell layer in the inner integument and, in certain cases, in the topological properties of the 3D cell architectures of homologous tissues despite their similar shape. Our work demonstrates the power of comparative 3D cellular morphometry and the importance of internal tissues and their cellular architecture in organ morphogenesis. Summary StatementQuantitative morphometric comparison of 3D digital ovules at full cellular resolution reveals diversity in internal 3D cellular architectures between similarly shaped ovules of Cardamine hirsuta and Arabidopsis thaliana.

plant biology↗

bioRxiv2021

The annotation and analysis of complex 3D plant organs using 3DCoordX

A fundamental question in biology concerns how molecular and cellular processes become integrated during morphogenesis. In plants, characterization of 3D digital representations of organs at single-cell resolution represents a promising approach to addressing this problem. A major challenge is to provide organ-centric spatial context to cells of an organ. We developed several general rules for the annotation of cell position and embodied them in 3DCoordX, a user-interactive computer toolbox implemented in the open-source software MorphoGraphX. It enables rapid spatial annotation of cells even in highly curved biological shapes. With the help of 3DCoordX we obtained new insight by analyzing cellular growth patterns in organs of several species. For example, the data indicated the presence of a basal cell proliferation zone in the ovule primordium of Arabidopsis thaliana. Proof-of-concept analyses suggested a preferential increase in cell length associated with neck elongation in the archegonium of Marchantia polymorpha and variations in cell volume linked to central morphogenetic features of a trap of the carnivorous plant Utricularia gibba. Our work demonstrates the broad applicability of the developed strategies as they provide organ-centric spatial context to cellular features in plant organs of diverse shape complexity.

plant biology↗