Mathematics in Modern Immunology

Overview

Journal Interface Focus

Specialty Biology

Date 2016 Apr 7

PMID 27051512

Citations 11

Authors

Mario Castro

Grant Lythe

Carmen Molina-Paris

Ruy M Ribeiro

Affiliations

Soon will be listed here.

Abstract

Mathematical and statistical methods enable multidisciplinary approaches that catalyse discovery. Together with experimental methods, they identify key hypotheses, define measurable observables and reconcile disparate results. We collect a representative sample of studies in T-cell biology that illustrate the benefits of modelling-experimental collaborations and that have proven valuable or even groundbreaking. We conclude that it is possible to find excellent examples of synergy between mathematical modelling and experiment in immunology, which have brought significant insight that would not be available without these collaborations, but that much remains to be discovered.

Citing Articles

Integrative lymph node-mimicking models created with biomaterials and computational tools to study the immune system.

Shou Y, Johnson S, Quek Y, Li X, Tay A Mater Today Bio. 2022; 14:100269.

PMID: 35514433 PMC: 9062348. DOI: 10.1016/j.mtbio.2022.100269.

The Critical Importance of Spatial and Temporal Scales in Designing and Interpreting Immune Cell Migration Assays.

Frattolin J, Watson D, Bonneuil W, Russell M, Fasanella Masci F, Bandara M Cells. 2021; 10(12).

PMID: 34943947 PMC: 8700135. DOI: 10.3390/cells10123439.

Quantifying T Cell Cross-Reactivity: Influenza and Coronaviruses.

Gaevert J, Luque Duque D, Lythe G, Molina-Paris C, Thomas P Viruses. 2021; 13(9).

PMID: 34578367 PMC: 8472275. DOI: 10.3390/v13091786.

Affinity Selection in Germinal Centers: Cautionary Tales and New Opportunities.

Faro J, Castro M Cells. 2021; 10(5).

PMID: 33924933 PMC: 8145379. DOI: 10.3390/cells10051040.

Testing structural identifiability by a simple scaling method.

Castro M, De Boer R PLoS Comput Biol. 2020; 16(11):e1008248.

PMID: 33141821 PMC: 7665633. DOI: 10.1371/journal.pcbi.1008248.

References

Douek D, McFarland R, KEISER P, Gage E, Massey J, Haynes B . Changes in thymic function with age and during the treatment of HIV infection. Nature. 1999; 396(6712):690-5. DOI: 10.1038/25374. View

Stritesky G, Xing Y, Erickson J, Kalekar L, Wang X, Mueller D . Murine thymic selection quantified using a unique method to capture deleted T cells. Proc Natl Acad Sci U S A. 2013; 110(12):4679-84. PMC: 3606987. DOI: 10.1073/pnas.1217532110. View

Guy-Grand D, Azogui O, Celli S, Darche S, Nussenzweig M, Kourilsky P . Extrathymic T cell lymphopoiesis: ontogeny and contribution to gut intraepithelial lymphocytes in athymic and euthymic mice. J Exp Med. 2003; 197(3):333-41. PMC: 2193840. DOI: 10.1084/jem.20021639. View

Sakaue-Sawano A, Kurokawa H, Morimura T, Hanyu A, Hama H, Osawa H . Visualizing spatiotemporal dynamics of multicellular cell-cycle progression. Cell. 2008; 132(3):487-98. DOI: 10.1016/j.cell.2007.12.033. View

Ribeiro R, De Boer R . The contribution of the thymus to the recovery of peripheral naive T-cell numbers during antiretroviral treatment for HIV infection. J Acquir Immune Defic Syndr. 2008; 49(1):1-8. PMC: 2923093. DOI: 10.1097/QAI.0b013e318184fb28. View

Ariotti S, Beltman J, Chodaczek G, Hoekstra M, van Beek A, Gomez-Eerland R . Tissue-resident memory CD8+ T cells continuously patrol skin epithelia to quickly recognize local antigen. Proc Natl Acad Sci U S A. 2012; 109(48):19739-44. PMC: 3511734. DOI: 10.1073/pnas.1208927109. View

De Boer R, Mohri H, Ho D, Perelson A . Turnover rates of B cells, T cells, and NK cells in simian immunodeficiency virus-infected and uninfected rhesus macaques. J Immunol. 2003; 170(5):2479-87. DOI: 10.4049/jimmunol.170.5.2479. View

Subramanian V, Duffy K, Turner M, Hodgkin P . Determining the expected variability of immune responses using the cyton model. J Math Biol. 2007; 56(6):861-92. DOI: 10.1007/s00285-007-0142-2. View

Smith A, Adler F, Ribeiro R, Gutenkunst R, McAuley J, McCullers J . Kinetics of coinfection with influenza A virus and Streptococcus pneumoniae. PLoS Pathog. 2013; 9(3):e1003238. PMC: 3605146. DOI: 10.1371/journal.ppat.1003238. View

10.

Westera L, Drylewicz J, den Braber I, Mugwagwa T, van der Maas I, Kwast L . Closing the gap between T-cell life span estimates from stable isotope-labeling studies in mice and humans. Blood. 2013; 122(13):2205-12. DOI: 10.1182/blood-2013-03-488411. View

11.

Gerlach C, Rohr J, Perie L, van Rooij N, van Heijst J, Velds A . Heterogeneous differentiation patterns of individual CD8+ T cells. Science. 2013; 340(6132):635-9. DOI: 10.1126/science.1235487. View

12.

Dobzhansky T . BIOLOGY, MOLECULAR AND ORGANISMIC. Am Zool. 1964; 4:443-52. DOI: 10.1093/icb/4.4.443. View

13.

Marchingo J, Kan A, Sutherland R, Duffy K, Wellard C, Belz G . T cell signaling. Antigen affinity, costimulation, and cytokine inputs sum linearly to amplify T cell expansion. Science. 2014; 346(6213):1123-7. DOI: 10.1126/science.1260044. View

14.

Salameire D, Le Bris Y, Fabre B, Fauconnier J, Solly F, Pernollet M . Efficient characterization of the TCR repertoire in lymph nodes by flow cytometry. Cytometry A. 2009; 75(9):743-51. DOI: 10.1002/cyto.a.20767. View

15.

Graw F, Regoes R . Influence of the fibroblastic reticular network on cell-cell interactions in lymphoid organs. PLoS Comput Biol. 2012; 8(3):e1002436. PMC: 3310707. DOI: 10.1371/journal.pcbi.1002436. View

16.

Turner M, Hawkins E, Hodgkin P . Quantitative regulation of B cell division destiny by signal strength. J Immunol. 2008; 181(1):374-82. DOI: 10.4049/jimmunol.181.1.374. View

17.

Mohri H, Perelson A, Tung K, Ribeiro R, Ramratnam B, Markowitz M . Increased turnover of T lymphocytes in HIV-1 infection and its reduction by antiretroviral therapy. J Exp Med. 2001; 194(9):1277-87. PMC: 2195973. DOI: 10.1084/jem.194.9.1277. View

18.

Mempel T, Henrickson S, von Andrian U . T-cell priming by dendritic cells in lymph nodes occurs in three distinct phases. Nature. 2004; 427(6970):154-9. DOI: 10.1038/nature02238. View

19.

Verschuren M, Breit T, Noordzij J, van Wering E, van Dongen J . Preferential rearrangements of the T cell receptor-delta-deleting elements in human T cells. J Immunol. 1997; 158(3):1208-16. View

20.

Johnson P, Yates A, Goronzy J, Antia R . Peripheral selection rather than thymic involution explains sudden contraction in naive CD4 T-cell diversity with age. Proc Natl Acad Sci U S A. 2012; 109(52):21432-7. PMC: 3535632. DOI: 10.1073/pnas.1209283110. View