from-voxels-to-knowledge-practical-guide-to-segmentation-complex

From Voxels to Knowledge: A Practical Guide to the Segmentation of Complex Electron Microscopy 3D-Data

Modern 3D electron microscopy approaches have recently allowed unprecedented insight into the 3D ultrastructural organization of cells and tissues, ...

Lawrence Berkeley National Laboratory

Throughout their life, plants typically remain in one location utilizing sunlight for the synthesis of carbohydrates, which serve as their sole source of energy as well as building blocks of a protective extracellular matrix, called the cell wall. During the course of evolution, plants have repeatedly adapted to their respective niche, which is reflected in the changes of their body plan and the specific design of cell walls. Cell walls not only changed throughout evolution but also are constantly remodelled and reconstructed during the development of an individual plant, and in response to environmental stress or pathogen attacks. Carbohydrate-rich cell walls display complex designs, which together with the presence of phenolic polymers constitutes a barrier for microbes, fungi, and animals. Throughout evolution microbes have co-evolved strategies for efficient breakdown of cell walls. Our current understanding of cell walls and their evolutionary changes are limited as our knowledge is mainly derived from biochemical and genetic studies, complemented by a few targeted yet very informative imaging studies. Comprehensive plant cell wall models will aid in the re-design of plant cell walls for the purpose of commercially viable lignocellulosic biofuel production as well as for the timber, textile, and paper industries. Such knowledge will also be of great interest in the context of agriculture and to plant biologists in general. It is expected that detailed plant cell wall models will require integrated correlative multimodal, multiscale imaging and modelling approaches, which are currently underway.

Plant cell walls throughout evolution: towards a molecular understanding of their design principles.

Cellular degeneration is essential for many developmental and stress acclimation processes. Undifferentiated parenchymatous cells in the central vascular cylinder of pea primary roots degenerate under hypoxic conditions created by flooding at temperatures >15°C, forming a long vascular cavity that seems to provide a conduit for longitudinal oxygen transport in the roots. We show that specific changes in the cell wall ultrastructure accompanied previously detected cytoplasmic and organellar degradation in the cavity-forming roots. The degenerating cells had thinner primary cell walls, less electron-dense middle lamellae, and less abundant cell wall homogalacturonans in altered patterns, compared to healthy cells of roots grown under cold, nonflooded conditions. Cellular breakdown and changes in wall ultrastructure, however, remained confined to cells within a 50-μm radius around the root center, even after full development of the cavity. Cells farther away maintained cellular integrity and had signs of wall synthesis, perhaps from tight regulation of wall metabolism over short distances. These observations suggest that the cell degeneration might involve programmed cell death. We also show that warm, nonflooded or cold, flooded conditions that typically do not induce vascular cavity formation can also induce variations in cell wall ultrastructure.

Changes in cell wall ultrastructure induced by sudden flooding at 25{degrees}C in Pisum sativum (Fabaceae) primary roots.

Flooding at warm temperatures induces hypoxic stress in Pisum sativum seedling roots. In response, some undifferentiated cells in the primary root vascular cylinder start degenerating and form a longitudinal vascular cavity. Changes in cellular morphology and cell wall ultrastructure detected previously in the late stages of cavity formation suggest possible involvement of programmed cell death (PCD). In this study, cytological events occurring in the early stages of cavity formation were investigated. Systematic DNA fragmentation, a feature of many PCD pathways, was detected in the cavity-forming roots after 3 h of flooding in situ by terminal deoxynucleotidyl transferase-mediated dUTP nick end-labeling assay and in isolated total DNA by gel electrophoresis. High molecular weight DNA fragments of about 20-30 kb were detected by pulse-field gel electrophoresis, but no low-molecular weight internucleosomal DNA fragments were detected by conventional gel electrophoresis. Release of mitochondrial cytochrome c protein into the cytosol, an integral part of mitochondria-dependent PCD pathways, was detected in the cavity-forming roots within 2 h of flooding by fluorescence microscopy of immunolabeled cytochrome c in situ and in isolated mitochondrial and cytosolic protein fractions by western blotting. DNA fragmentation and cytochrome c release remained confined to the undifferentiated cells in center of the root vascular cylinders, even after 24 h of flooding, while outer vascular cylinder cells and cortical cells maintained cellular integrity and normal activity. These findings confirm that hypoxia-induced vascular cavity formation in P. sativum roots involves PCD, and provides a chronological model of cytological events involved in this rare and understudied PCD system.

Purbasha Sarkar

Joint Bioenergy Institute,
Physical Biosciences Division,
Joint Bioenergy Institute, Physical Biosciences Division

Lawrence Berkeley National Laboratory

From Voxels to Knowledge: A Practical Guide to the Segmentation of Complex Electron Microscopy 3D-Data

Purbasha Sarkar

Joint Bioenergy Institute,Physical Biosciences Division,Joint Bioenergy Institute, Physical Biosciences Division

Lawrence Berkeley National Laboratory

From Voxels to Knowledge: A Practical Guide to the Segmentation of Complex Electron Microscopy 3D-Data

Joint Bioenergy Institute,
Physical Biosciences Division,
Joint Bioenergy Institute, Physical Biosciences Division