Systems Issues in Solid Freeform Fabrication

This paper is concerned with the systems aspects of the Solid Freeform Fabrication (SFF) technology, i.e., the issues that deal with getting an external geometric CAD model to automatically control the physical layering fabrication process as directly as possible, regardless ofthe source of the model. The general systems issues are described, the state of systems research is given, and open research questions are posed.Mechanical Engineerin

Automatic CAD-model Repair: Shell-Closure

Shell-closure is critical to the repair of CAD-models described in the .STL file-format, the de facto solid freeform fabrication industry-standard. Polyhedral CAD-models that do not exhibit shell-closure, i.e. have cracks, holes, or gaps, do not constitute valid solids and frequently cause problems during fabrication. This paper describes a solution for achieving shell-closure of polyhedral CAD-models. The solution accommodates nonmanifold conditions, and guarantees orientable shells. There are several topologically ambiguous situations that might arise during the shell-closure process, and the solution applies intuitively pleasing heuristics in these cases.Mechanical Engineerin

Workshop on the Integration of Finite Element Modeling with Geometric Modeling

The workshop on the Integration of Finite Element Modeling with Geometric Modeling was held on 12 May 1987. It was held to discuss the geometric modeling requirements of the finite element modeling process and to better understand the technical aspects of the integration of these two areas. The 11 papers are presented except for one for which only the abstract is given

Overview of database projects

The use of entity and object oriented data modeling techniques for managing Computer Aided Design (CAD) is explored

Molecular visualization of cellular complexity.

Structural biology has paved the way for a ground-up description of biological systems, contributing atomic structures of proteins amenable to crystallography, uncovering high-resolution maps of ‘difficult’ proteins with the cryo-electron microscopy revolution, and filling knowledge gaps regarding dynamic and disordered proteins using nuclear magnetic resonance. From the very beginning, the cellular context of a protein of interest was considered; John Kendrew chose sperm whale myoglobin for crystallization because of myoglobin’s importance and abundance within the dark red tissues of diving animals and thereby solved the first three-dimensional protein structure1. Together, cell and structural biology work synergistically towards a common goal: to build a mechanistic description of biological systems

Generating Topological Information from a "Bucket of Facets"

The STL de facto data exchange standard for Solid Freefonn F*brication represents CAD models as a collection of unordered triangular planar facels. No topological connectivity information is provided; hence the term "bucket of facet." Such topological information can, however, be quite useful for performing model validity checking and speeding subsequent processing operations such as model slicing. lfhis paper discusses model topology and how to derive it given a collection of unordered tri,ngular facets which represent a valid model.Mechanical Engineerin

In situ architecture of the ER–mitochondria encounter structure

The endoplasmic reticulum and mitochondria are main hubs of eukaryotic membrane biogenesis that rely on lipid exchange via membrane contact sites1,2,3, but the underpinning mechanisms remain poorly understood. In yeast, tethering and lipid transfer between the two organelles is mediated by the endoplasmic reticulum–mitochondria encounter structure (ERMES), a four-subunit complex of unresolved stoichiometry and architecture4,5,6. Here we determined the molecular organization of ERMES within Saccharomyces cerevisiae cells using integrative structural biology by combining quantitative live imaging, cryo-correlative microscopy, subtomogram averaging and molecular modelling. We found that ERMES assembles into approximately 25 discrete bridge-like complexes distributed irregularly across a contact site. Each bridge consists of three synaptotagmin-like mitochondrial lipid binding protein domains oriented in a zig-zag arrangement. Our molecular model of ERMES reveals a pathway for lipids. These findings resolve the in situ supramolecular architecture of a major inter-organelle lipid transfer machinery and provide a basis for the mechanistic understanding of lipid fluxes in eukaryotic cells.<br/

Electron cryo-tomography reveals the subcellular architecture of growing axons in human brain organoids.

Funder: Natural Sciences and Engineering Research Council of Canada; FundRef: http://dx.doi.org/10.13039/501100000038During brain development, axons must extend over great distances in a relatively short amount of time. How the subcellular architecture of the growing axon sustains the requirements for such rapid build-up of cellular constituents has remained elusive. Human axons have been particularly poorly accessible to imaging at high resolution in a near-native context. Here, we present a method that combines cryo-correlative light microscopy and electron tomography with human cerebral organoid technology to visualize growing axon tracts. Our data reveal a wealth of structural details on the arrangement of macromolecules, cytoskeletal components, and organelles in elongating axon shafts. In particular, the intricate shape of the endoplasmic reticulum is consistent with its role in fulfilling the high demand for lipid biosynthesis to support growth. Furthermore, the scarcity of ribosomes within the growing shaft suggests limited translational competence during expansion of this compartment. These findings establish our approach as a powerful resource for investigating the ultrastructure of defined neuronal compartments

Dynamic conformational changes of a tardigrade group-3 late embryogenesis abundant protein modulate membrane biophysical properties

A number of intrinsically disordered proteins (IDPs) encoded in stress-tolerant organisms, such as tardigrade, can confer fitness advantage and abiotic stress tolerance when heterologously expressed. Tardigrade-specific disordered proteins including the cytosolic-abundant heat-soluble proteins are proposed to confer stress tolerance through vitrification or gelation, whereas evolutionarily conserved IDPs in tardigrades may contribute to stress tolerance through other biophysical mechanisms. In this study, we characterized the mechanism of action of an evolutionarily conserved, tardigrade IDP, HeLEA1, which belongs to the group-3 late embryogenesis abundant (LEA) protein family. HeLEA1 homologs are found across different kingdoms of life. HeLEA1 is intrinsically disordered in solution but shows a propensity for helical structure across its entire sequence. HeLEA1 interacts with negatively charged membranes via dynamic disorder-to-helical transition, mainly driven by electrostatic interactions. Membrane interaction of HeLEA1 is shown to ameliorate excess surface tension and lipid packing defects. HeLEA1 localizes to the mitochondrial matrix when expressed in yeast and interacts with model membranes mimicking inner mitochondrial membrane. Yeast expressing HeLEA1 shows enhanced tolerance to hyperosmotic stress under nonfermentative growth and increased mitochondrial membrane potential. Evolutionary analysis suggests that although HeLEA1 homologs have diverged their sequences to localize to different subcellular organelles, all homologs maintain a weak hydrophobic moment that is characteristic of weak and reversible membrane interaction. We suggest that such dynamic and weak protein-membrane interaction buffering alterations in lipid packing could be a conserved strategy for regulating membrane properties and represent a general biophysical solution for stress tolerance across the domains of life.</p

Dynamic conformational changes of a tardigrade group-3 late embryogenesis abundant protein modulate membrane biophysical properties

A number of intrinsically disordered proteins (IDPs) encoded in stress-tolerant organisms, such as tardigrade, can confer fitness advantage and abiotic stress tolerance when heterologously expressed. Tardigrade-specific disordered proteins including the cytosolic-abundant heat-soluble proteins are proposed to confer stress tolerance through vitrification or gelation, whereas evolutionarily conserved IDPs in tardigrades may contribute to stress tolerance through other biophysical mechanisms. In this study, we characterized the mechanism of action of an evolutionarily conserved, tardigrade IDP, HeLEA1, which belongs to the group-3 late embryogenesis abundant (LEA) protein family. HeLEA1 homologs are found across different kingdoms of life. HeLEA1 is intrinsically disordered in solution but shows a propensity for helical structure across its entire sequence. HeLEA1 interacts with negatively charged membranes via dynamic disorder-to-helical transition, mainly driven by electrostatic interactions. Membrane interaction of HeLEA1 is shown to ameliorate excess surface tension and lipid packing defects. HeLEA1 localizes to the mitochondrial matrix when expressed in yeast and interacts with model membranes mimicking inner mitochondrial membrane. Yeast expressing HeLEA1 shows enhanced tolerance to hyperosmotic stress under nonfermentative growth and increased mitochondrial membrane potential. Evolutionary analysis suggests that although HeLEA1 homologs have diverged their sequences to localize to different subcellular organelles, all homologs maintain a weak hydrophobic moment that is characteristic of weak and reversible membrane interaction. We suggest that such dynamic and weak protein-membrane interaction buffering alterations in lipid packing could be a conserved strategy for regulating membrane properties and represent a general biophysical solution for stress tolerance across the domains of life.</p