Bigger is faster in the scalable adaptive immune response
Abstract
Zoonotic pathogens represent a growing global risk, yet the speed of adaptive immune activation across mammalian species remains poorly understood. Despite orders-of-magnitude differences in size and metabolic rate, we show that the time to initiate adaptive immunity is remarkably consistent across species. To understand this invariance, we analyse empirical data showing how the numbers and sizes of lymph nodes scale with body mass, finding that larger animals have both more and larger lymph nodes. Using scaling theory and our mathematical model, we show that larger lymph nodes enable faster search times, conferring an advantage to larger animals that otherwise face slower biological times. This enables mammals to maintain, or even accelerate, the time to initiate the adaptive immune response as body size increases. We validate our analysis in simulations and compare it to empirical data.
Description of the data and file structure
Main folder: IFCT.zip
This repository contains simulated T cell–dendritic cell (DC) initial first-contact time (IFCT) and mean first-contact time (MFCT) data under two different lymph node (LN) volume–mass scaling hypotheses and two different T cell migration modes. All simulations represent a population of naïve T cells searching for a cognate DC inside a 3-D lymph node.
Data are organized by:
LN scaling:
1. V_M0.5 — LN volume ∝ M0.5
2. V_M0.67 — LN volume ∝ M0.67
Migration mode:
1. BM — Brownian Motion (random walk)
2. CRW — Correlated Random Walk
DC scaling:
1. DCConstant — number of DCs does not scale with M
2. DCHalf — number of DCs scales as M^0.5
Each simulation produces distributions of first-contact times for multiple LN volumes (5 volumes per condition, corresponding to 5 LN sizes), and for 100 stochastic simulations per volume, the V_M^0.67 folder, which only contains 20 IFCT data for BM (DCConstant, DCHalf).
Directory Structure:
├── V_M^0.5/
│ ├── BM_V_M^0.5/
│ │ ├── BMDCConstant_RawData/
│ │ │ ├── BM_DCConstant11.csv
│ │ │ ├── BM_DCConstant12.csv
.
.
│ │ │ └── BM_DCConstant5100.csv
│ │ ├── BMDCHalf_RawData/
│ │ │ ├── BM_DCHalf11.csv
│ │ │ ├── BM_DCHalf12.csv
.
.
│ │ │ └── … BM_DCHalf5100.csv
│ │ ├── BM_IFCT_DCConstant.csv
│ │ ├── BM_IFCT_DCHalf.csv
│ │ ├── BM_MFCT_DCConstant.csv
│ │ └── BM_MFCT_DCHalf.csv
│ │
│ ├── CRW_V_M^0.5/
│ │ ├── CRWDCConstant_RawData/
│ │ │ ├── CRW_DCConstant11.csv
│ │ │ ├── CRW_DCConstant12.csv
.
.
│ │ │ └── CRW_DCConstant5100.csv
│ │ ├── CRWDCHalf_RawData/
│ │ │ ├── CRW_DCHalf11.csv
│ │ │ ├── CRW_DCHalf12.csv
.
.
│ │ │ └── CRW_DCHalf1100.csv
│ │ ├── CRW_IFCT_DCConstant.csv
│ │ ├── CRW_IFCT_DCHalf.csv
│ │ ├── CRW_MFCT_DCConstant.csv
│ │ └── CRW_MFCT_DCHalf.csv
│
└── V_M^0.67/
│ ├── BM_IFCT_DCConstant.csv
│ ├── BM_IFCT_DCHalf.csv
Code/Software: After extracting the zip file user can use any text editor to see the data file. The data is originally generated from the JAVA code.
Access information
Other publicly accessible locations of the data:
- NA
Data was derived from the following sources:
- https://github.com/BCLab-UNM/BiggerIsBetter (may not yet be published)
To validate our mathematical model, we implement an agent-based model (ABM), termed the Initial First Contact Time (IFCT) model, using the MASON libraries [1] in Java. The model simulates two types of agents - T cells (searchers) and Dendritic Cells (DCs) (targets). Both are uniformly distributed within a cubic representation of a Lymph Node (LN). LN space is modeled as a continuous Cartesian grid in three dimensions with fixed reflective boundaries.
The IFCT model is run as a discrete-time simulation, with each time step representing one second. At the beginning of each simulation run, a predefined number of T cells and DCs are initialized (see \Cref{tab:inputDataTable}). The positions of DC are static throughout the simulation. T cells, on the other hand, move in each time step with either Brownian motion or a persistent random walk, which was modeled from empirical data in Fricke et al.[2]. We model T cell motion without considering collisions so that T cells pass through each other.
We run the IFCT model for the two bounding cases, one in which NDC is proportional to M0, i.e., a constant, and another where NDC is proportional to M0.5. Each case is simulated for five different animal mass (M) values. For each M, we run 100 experimental replicas for each combination of factors, where the initial distribution of the T cells and DC is stochastic. We assume that there is a contact between a T cell and DC when their centers are within 10 microns. The simulation result from the IFCT model confirms that the distribution of contact times is exponential, an assumption that underpins the theoretical derivation.
| Mass (M) | 10 g | 10^2 ^g | 10^3 ^g | 10^4 ^g | 10^5 ^g |
|---|---|---|---|---|---|
| VLN ∝ M0.5ln(cM) (mm3) | 7.3 | 46 | 220 | 920 | 3600 |
| NTC ∝ M0.5 | 20 | 63 | 200 | 630 | 2000 |
| NDC ∝ M0.5 | 80 | 250 | 800 | 2500 | 8000 |
| NDC ∝ M0 | 200 | 200 | 200 | 200 | 200 |
[1] S. Luke, G. C. Balan, L. Panait, C. Cioffi-Revilla, S. Paus, MASON: A Java multi-agent simulation library, in Proceedings of Agent 2003 Conference on Challenges in Social Simulation, vol. 9 (2003).
[2] G. M. Fricke, K. A. Letendre, M. E. Moses, J. L. Cannon, Persistence and adaptation in immunity: T cells balance the extent and thoroughness of search. PLoS Computational Biology 12 (3), e1004818 (2016).
