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T Cell Biology

A Modern Textbook — Chapters 1–15

1

What Is a T Cell?

TCR/CD3 complex, antigen specificity, clonal selection, helper/killer/regulatory programs, and canonical T cell states.

2

A Brief History of T Cells

From anatomical curiosity to cellular immunity — the experiments and conceptual breakthroughs that built modern T cell biology.

3

The T Cell Life Cycle as a Story Arc

Birth in the thymus, selection, naive surveillance, activation, effector function, memory formation, and dysfunction.

4

Where T Cells Live and Move

The spatial logic of immunity — lymphoid organs, recirculation, tissue residency, and how anatomy shapes T cell encounters.

5

T Cell Nomenclature and Phenotyping: How Not to Get Lost

Markers, surface phenotyping, lineage vs. state vs. function labels, and navigating the naming conventions of T cell biology.

6

The TCR Repertoire: Diversity as a Survival Strategy

V(D)J recombination, repertoire generation, clonal diversity, and how the immune system builds a receptor library to cover the antigen universe.

7

T Cells as Information-Processing Systems

Signal integration, decision logic, thresholds, feedback circuits, and how T cells compute responses from noisy inputs.

8

Experimental Models for T Cell Biology

In vivo and in vitro systems, transgenic models, adoptive transfer, organoids, and the tools that drive T cell discovery.

9

Clinical Panorama of T Cell–Dominated Biology

Autoimmunity, transplant rejection, immunodeficiency, cancer immunology, and how T cells drive clinical phenotypes across disease.

10

Safety, Ethics, and Dual–Use Boundaries in Engineered T Cell Therapies

Ethical frameworks, biosafety considerations, dual-use risks, regulatory landscapes, and responsible innovation in T cell engineering.

11

From Stem Cell to Thymus–Seeding Progenitor

Hematopoietic origins, bone marrow progenitors, thymus colonization, and the developmental journey that gives rise to T cell precursors.

12

The Thymic Microenvironment as a Teaching Machine

Thymic architecture, cortical and medullary compartments, stromal cells, and how the thymus instructs T cell development and selection.

13

T Lineage Commitment: Notch and the Gatekeeping Circuit

Notch signaling, lineage specification, transcriptional gatekeeping, and the molecular circuits that commit progenitors to the T cell fate.

14

TCR Gene Rearrangement: How T Cells Generate Specificity

V(D)J recombination mechanics, RAG enzymes, junctional diversity, allelic exclusion, and the molecular basis of TCR uniqueness.

15

β–Selection and the Pre–TCR Checkpoint

The pre-TCR complex, β-selection signaling, proliferative burst, rescue from apoptosis, and the critical developmental checkpoint for thymocytes.

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