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The endoplasmic reticulum or ER makes up for more than half of the membranes in a cell and accounts for 10% of total cell volume. It is also the primary protein and lipid synthesis factory for most cell organelles, such as the Golgi apparatus, lysosomes, secretory vesicles, and the plasma membrane. Despite being the most extensive and functionally complex subcellular organelle, ER was the last to be discovered. After years of deliberation, Keith Porter and George Palade in the year 1954,...
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We developed nERdy and nERdy+ to reconstruct endoplasmic reticulum (ER) networks, improving accuracy over existing methods. These tools reveal how ER shaping proteins like Atlastin regulate ER structure and dynamics.

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Area of Science:

  • Cell Biology
  • Biophysics
  • Computational Biology

Background:

  • The endoplasmic reticulum (ER) has a complex morphology crucial for cellular function.
  • Understanding ER network dynamics and the role of ER shaping proteins requires advanced reconstruction methods.
  • Current methods for ER network reconstruction are limited by parameter sensitivity or extensive data requirements.

Purpose of the Study:

  • To develop novel computational tools for accurate reconstruction and analysis of the dynamic ER network.
  • To investigate the role of ER shaping proteins in tubular matrix formation and junction dynamics.

Main Methods:

  • Introduction of nERdy, an image processing approach for ER network extraction.
  • Development of nERdy+, a D4-equivariant neural network for enhanced ER network representation.
  • Analysis of live-cell confocal and STED microscopy time-series data.

Main Results:

  • nERdy and nERdy+ accurately extract and represent ER networks and junction dynamics, outperforming existing methods.
  • The methods distinguish tubular matrices from peripheral ER networks and analyze tripartite junction movement.
  • Atlastin and Reticulon 4 were identified to promote dynamic tubular matrix formation and enhance junction dynamics.

Conclusions:

  • nERdy and nERdy+ provide powerful tools for studying ER structure and dynamics.
  • Novel roles for Atlastin and Reticulon 4 in regulating ER morphology and dynamics were uncovered.
  • This work advances our understanding of ER shaping proteins and their contribution to cellular function.