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Related Concept Videos

Protein Modifications in the RER01:26

Protein Modifications in the RER

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Modification of secretory and transmembrane proteins entering the rough ER begins in the ER lumen. These modifications aid in protein folding and stabilize the acquired tertiary structure. Protein modifications in the rough ER co-occur at different stages of protein folding.
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Like aldehydes, ketones are named using IUPAC rules; in this case, by replacing “e” in the name of the longest hydrocarbon chain with “one.” In acyclic ketones, the ketonic carbon is given the lowest locant value. For instance, as shown below, a simple five-carbon ketone is named pentan-2-one, instead of pentan-4-one. IUPAC rules also allow the placing of the locant value before the parent name to give an alternate name, 2-pentanone.
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ER is the primary site for the maturation and folding of soluble and transmembrane secretory proteins. The calnexin cycle is a specific chaperone system that folds and assesses the confirmation of N-glycosylated proteins before they can exit the ER lumen. The primary players of this quality check pipeline are the lectins, ER-resident chaperones, and a glucosyl transferase enzyme. In case the calnexin system in the lumen fails to salvage a misfolded protein, it is transported to the cytoplasm...
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Bioremediation is the use of prokaryotes, fungi, or plants to remove pollutants from the environment. This process has been used to remove harmful toxins in groundwater as a byproduct of agricultural run-off and also to clean up oil spills.
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The BioRECIPE Knowledge Representation Format.

Emilee Holtzapple, Gaoxiang Zhou, Haomiao Luo

  • 1Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States.

ACS Synthetic Biology
|July 25, 2024
PubMed
Summary
This summary is machine-generated.

BioRECIPE is a new knowledge format for biological systems. It standardizes executable models for signaling pathways, enabling easier human-machine interaction and compatibility with various tools in systems and synthetic biology.

Keywords:
FAIR principlesautomationmodelingnetworksrepresentation formatsignaling pathways

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Area of Science:

  • Systems Biology
  • Synthetic Biology
  • Computational Biology

Background:

  • Standardization is crucial for developing and sharing executable biological models.
  • Current formats may hinder human-machine interaction and interoperability.
  • Facilitating model creation, verification, and curation is essential for biological research.

Purpose of the Study:

  • Introduce the BioRECIPE (Biological system Representation for Evaluation, Curation, Interoperability, Preserving, and Execution) knowledge representation format.
  • Standardize the creation and management of executable models for intra- and intercellular signaling.
  • Enhance human-machine interaction in biological modeling.

Main Methods:

  • Developed a novel knowledge representation format named BioRECIPE.
  • Ensured BioRECIPE is human-readable and machine-readable.
  • Designed BioRECIPE for compatibility with existing natural language processing, modeling, and database tools.

Main Results:

  • BioRECIPE standardizes the representation of biological systems for modeling.
  • The format facilitates easy previewing and modification of model components by users.
  • BioRECIPE models are processable by a suite of model development and analysis tools.
  • Achieved compatibility with diverse representation formats and community resources.

Conclusions:

  • BioRECIPE offers a standardized approach to biological knowledge representation.
  • The format enhances the creation, curation, and execution of executable biological models.
  • BioRECIPE promotes interoperability and facilitates advancements in systems and synthetic biology.