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Deriving shape space parameters from immunological data

D J Smith1, S Forrest, R R Hightower

  • 1Department of Computer Science, University of New Mexico, Albuquerque, NM, 87131, USA.

Journal of Theoretical Biology
|February 28, 1998
PubMed
Summary
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This study introduces a method to determine shape space parameters for immunological memory. The findings suggest specific dimensions and radii for Hamming and Euclidean shape spaces that align with experimental cross-reactive memory data.

Area of Science:

  • Immunology
  • Computational Biology
  • Theoretical Biology

Background:

  • Cross-reactive memory responses are crucial for secondary infections by related pathogens.
  • The quantity and distribution of memory B cells determine the extent of cross-reactivity.
  • B cell affinity for antigens defines a 'ball of stimulation' in shape space.

Purpose of the Study:

  • To develop a method for deriving shape space parameters consistent with immunological data.
  • To model cross-reactive memory responses using shape space analysis.
  • To identify optimal shape space parameters that match experimental observations.

Main Methods:

  • Derivation of formulas for the volume of intersection of 'balls of stimulation' in various shape spaces.
  • Analysis of how shape space dimensionality and alphabet size influence B cell distribution.

Related Experiment Videos

  • Application of the method to find parameters for Hamming and Euclidean shape spaces.

    • Main Results:

    • Shape space parameters significantly impact the number of cross-reactive B cells.
    • For Hamming shape spaces, 20-25 dimensions, a 3-4 letter alphabet, and radii of 5-6 match data.
    • For Euclidean shape spaces, 5-8 dimensions and radii of ~20% of the total space radius align with experiments.

    Conclusions:

    • The proposed method effectively derives shape space parameters from immunological data.
    • Specific parameter choices for Hamming and Euclidean shape spaces are identified, providing a framework for understanding cross-reactivity.
    • This work offers a quantitative approach to studying immune memory and B cell responses.