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BIO-Complexity
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ISSN (Print) 2151-7444 - ISSN (Online) 2151-7444
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  • An Engineering Perspective on the Bacterial Flagellum: Part 3 –
           Observations

    • Authors: Waldean A Schulz
      Abstract: The flagellum is the organelle imparting motility to common bacteria. This paper, the third of three, takes a systems engineering and systems biology perspective on the bacterial flagellum. The first paper (Part 1 of the series) provided a constructive or top-down view from a systems engineering viewpoint. It detailed the typical environment, the purpose, the required existing and new resources, the necessary functional requirements, the various constraints, the control means, and the self-assembly for any kind of bacterial motility organelle. The specification of these requirements was intended to be independent of knowledge about the actual flagellum. A converse approach was detailed in the second paper (Part 2 of the series). It was an analytical or bottom-up view, which discussed the known 40+ protein components and the observed and inferred structure, control, and assembly of a typical bacterial flagellum. This cellular subsystem is well researched. Much of that research was reviewed in Part 2 from a systems biology viewpoint, including the chemotaxis feedback control system. Part 2 included a very detailed dependency graph of the orchestrated assembly not found elsewhere. This third paper (Part 3) concludes the three-part study with original observations. The observations include an ontology of the exceedingly specific protein binding relationships in the flagellum. The latter observation is new and significant and suggests research to further elaborate the details of the molecular configurations of the proteins. Part 3 also compares the independent constructive and analytical views, which correlate well. Finally, it is suggested that a motility organelle of this scope and scale seems profoundly unlikely to naturally evolve in the absence of foresight and mindful intent.
      PubDate: 2021-10-13
      Issue No: Vol. 2021 (2021)
       
  • An Engineering Perspective on the Bacterial Flagellum: Part 2 –
           Analytic View

    • Authors: Waldean A Schulz
      Abstract: This paper, the second of three, takes a systems biology view of the bacterial flagellum. The flagellum is the organelle imparting motility to common bacteria. The first paper was a constructive or top-down view from a systems engineering viewpoint: “An Engineering Perspective on the Bacterial Flagellum, Part 1 – Constructive View”. It detailed the typical environment, the purpose, the required existing and new resources, the necessary functional requirements, various constraints, the control means, and the self-assembly of any kind of bacterial motility organelle. The specification of these requirements was intended to be independent from knowledge about the actual flagellum. A converse approach is detailed in this Part 2. It is an analytical, reductionist, or bottom-up view, which discusses the known 40+ protein components and the observed and inferred structure, control, and assembly of a typical bacterial flagellum. This cellular subsystem is well-researched. Much of that research is reviewed herein. However, the assembly orchestration is illustrated in a form and detail not found elsewhere. Part 3 will compare the two views and will conclude with original observations. Those include an ontology of the exceedingly specific protein binding relationships in the flagellum. The latter observation is new and significant.
      PubDate: 2021-09-05
      Issue No: Vol. 2021 (2021)
       
  • An Engineering Perspective on the Bacterial Flagellum: Part 1 -
           Constructive View

    • Authors: Waldean A Schulz
      Abstract: This study examines the bacterial flagellum from an engineering viewpoint. This examination concentrates on the structure, proteins, control, and assembly of a typical flagellum, which is the organelle imparting motility to common bacteria. Two very different, independent approaches are applied and then compared in three separate papers: Parts 1, 2, and 3. The first approach is a constructive or top-down approach, covered in this Part 1. It considers the purpose of a bacterial motility system, its typical environment, new and existing required resources, and its physiology. It sets forth the logically necessary functional requirements, constraints, assembly, and relationships. The functionality includes a motility control subsystem and provision for self-assembly. The specification of these requirements is intended to be independent from knowledge of the flagellar structures. This is original material not covered in academic papers on the flagellum. Part 2 will cover the second approach, an analytical or bottom-up approach. It will document the known 40+ protein components and the structure, assembly, and control of a typical flagellum. The bacterial flagellum is a well-researched molecular subsystem. However, in Part 2 the assembly relationships will be illustrated graphically in a form and detail not found in previous literature. Part 3 will compare the two approaches and conclude with several original observations. Those include the coherent assembly orchestration and an ontology of the exceedingly specific protein-binding properties. The latter observation is significant, and it suggests future modeling to elucidate how the strong, coherent, multi-way protein binding is achieved at the molecular level.
      PubDate: 2021-07-02
      Issue No: Vol. 2021 (2021)
       
 
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