5101 · IMM-L1 Basic Concepts of Immunology — 免疫學基本概念

ABCT 5101 Immunology Part Lectures · Lecture 1 · 21 Oct 2026. The lecturer's own annotated notes carry the section letters A–G; they are kept below so you can find any point on paper. Everything in the body is what was written on the board — the numbers, the lists and the wording are the lecturer's, not reconstructed.

Master Logic 主線邏輯 — the immune system as a three-layer national defence

• Outside world (pathogens, toxins, pollutants) vs inside world (cancer cells, transplanted tissue) — the system must answer both, and only the inside half is unique to this course's framing.
• First line = epithelium and skin, present from birth, non-specific.
• Second line = innate immunity — fast, non-specific, no memory, but it destroys the pathogen before it has been identified, and in parallel it stimulates adaptive immunity.
• Third line = adaptive immunity — antigen-specific, slow (days–weeks), and the only line with immunological memory.
• Both are needed — the lecturer's note: "We need to have both of them in our body to eliminate the pathogens or NON-SELF cells."

A · Three definitions 三個核心定義

B · Three lines of defence 三道防線

C · Key features and key players of the immune system

Three features define it: recognition (self vs non-self) → specificity of the response → immunological memory.

Key players = the major immune organs / tissues / cells. The lecturer's definition of the term itself: refer to those tissues / organs in which maturation, differentiation and proliferation of the immune cells take place.

E · Major organs and systems 淋巴器官

E1 · Primary lymphoid organs 初級淋巴器官

Two organs. Both are where immune cells are made; the bone marrow supplies the stem cells, the thymus finishes the T cells.

[1] Thymus — located near the neck region.
Functions: [1] production of lymphocytes; [2] major site of maturation of T-cells.

[2] Bone marrow — located in the long bones [e.g. femur, sternum and spine]; the lecturer counts 6 major sites for the production of immune cells.
Function: consists of various hematopoietic stem cells [HSC] which give rise to different types of blood cells and immune cells by hematopoiesis.

E2 · Secondary lymphoid organs 次級淋巴器官

[1] Tonsils 扁桃腺 — located near the oropharynx and nasopharynx.
Functions: [1] tonsils reach their largest size near puberty; [2] production of lymphocytes; [3] prevent entry of pathogens through the nasal and oral route; [4] production of immunoglobulins [antibody]; [5] fight off infection.

[2] Adenoid 腺樣體 — located behind the nasal cavity.
Functions: [1] production of antibody; [2] provide local immune protection; [3] undergo atrophy by puberty.

[3] Spleen 脾臟 — located under the ribcage and above the stomach in the left upper quadrant of the abdomen; one of the largest organs in the lymphatic system.
Functions: [1] production of WBC and antibodies (helps to fight infection); [2] filter blood to get rid of old and damaged blood cells; [3] production of red blood cells [RBC]; [4] blood storage organ.

[4] Lymph node 淋巴結 — located throughout the entire body, but mainly found in the neck, armpits, chest, abdomen and thigh regions.
Function: acts as a filter for foreign antigen [substances] — virus, bacteria, cancer cells, damaged cells etc.
Cell types: WBC (lymphocytes); B-cells; T-cells; macrophages; NK [Natural Killer] cells; Dendritic cells [DC] etc.

[5] Mucosal lymphoid system 黏膜淋巴系統 [MALT] — mucosal-associated lymphoid tissues, scattered along the mucosal lining in your body [submucosal membrane].
Examples: [1] gastrointestinal tract [G.I. tract] · [2] respiratory tract [R.T.] · [3] urogenital tract · [4] nasopharynx · [5] breast · [6] salivary gland system · [7] eye.
Functions: [1] fight off the foreign substances passing through the mucosal epithelium; [2] provide an important part in "local" immunity.

G · Two basic immune systems 兩大免疫系統

Key communication 細胞訊息傳遞

[1] Cytokines 細胞激素 — the "chemical messenger" in our immune system.
Small peptide cell-signalling molecules that aid "cell–cell communication" in our immune system and keep our immune system "functioning"; they stimulate the movement of immune cells toward the infection sites.
Involvement of immune cells — four pairings as written: [A] cell activation → immune response · [B] cell differentiation → immune cell development · [C] cell proliferation → immune response · [D] cell maturation → immune cell development.

[2] Antigen presenting cells [APC] 抗原呈遞細胞
Antigen: foreign substances [NON-SELF] stimulating the immune system.
APC: initiate adaptive immune response by presenting antigen captured from the environment / pathogens to adaptive immune cells [e.g. B-cells / T-cells].
APC examples: Macrophages (Mφ), Dendritic cells (DC).

Innate immunity 先天免疫 — the 1st line: external barriers 外部屏障

[1] Exogenous infection 外源性感染 — pathogen originating from a source outside the body (e.g. pathogens, toxins, allergens etc.).
Entry sites: skin, mucosal surface, ingestion, injection etc.

[2] Endogenous infection 內源性感染 — microbes already existing inside / on our body.
Examples: [1] opportunistic pathogens — normal flora in our body, which become pathogenic when your immune system is weakened; [2] antibiotic; [3] chemotherapy.   [2] Latent pathogen — dormant status.

[6] Types of external barriers 外部屏障三大類

[5] Physical barriers · [1] Skin epidermis 皮膚表皮 — three main layers:

[5] Physical barriers · [2] Cilia 纖毛 — present in the respiratory tract mucosa. The chain as drawn: mucosa → produce mucus; the mucus traps unwanted materials; the outside cilia are "sweeping", so the trapped load is moved out. A mucus escalator, not a wall.

[1] Chemical barriers 化學屏障 — three groups, and this table is the one to memorise because the lecturer gave exact figures:

[3] Microbiological barriers 微生物屏障 · Normal flora 正常菌群 — normal flora (commensal flora) colonize on the external interfaces of our body.
Examples: G.I. tract · respiratory tract · skin · mouth · vagina · eye.
Functions: [1] normal flora form a protective layer to prevent pathogens from colonizing and invading our body; [2] producing anti-microbial substances.

Innate immunity — the 2nd line: cell (immune) and chemical

Phagocytosis 吞噬作用 — an important cellular processing and eliminating foreign particles (e.g. pathogens, foreign substances, damaged cells etc.).
It is the 2nd line of defence in innate immunity, against pathogens that have penetrated the 1st line of defence.

Adaptive immunity 適應性免疫

Cell-mediated immunity 細胞免疫 — the adaptive arm is executed by cells, not by soluble molecules. Details are covered in Lecture 2 (4 Nov).

How do immune cells recognise the pathogen 免疫細胞如何識別病原體

The central mechanism of the lecture. Innate cells read PAMPs on the pathogen and DAMPs released by your own damaged cells; adaptive cells read antigen. Both are detected by PRRs on the immune cell surface.

[1] DAMPs [Damage-associated molecular patterns]
• Endogenous signal — danger protein signal molecules released by dying cells, stressed, or damaged cells
• activation of innate immunity
• Example: [1] Heat shock protein [HSP] — released from stressed cells; it is a stress protein

[2] PAMPs [Pathogen-associated molecular patterns]
• only be found in the pathogen (e.g. bacteria, virus, fungi etc.)
• conserved molecular structure found on the surface or inside the pathogen

[3] PRRs [Pathogen-recognition Receptors]
• specialised receptors of the innate immune system
• immune cells have these types of receptor to detect the pathogen or "NON-SELF" or damaged cells etc.
• detect the PAMPs and/or DAMPs

The lecturer drew three types of PRRs as a three-branch tree and labelled only the first branch — Type I: extra-cellular PRRs — before the sheet turned to TLRs. The other two branches were not filled in on the day.

Toll-like receptors [TLRs] — the Type I example the lecturer developed:
[1] TLR originally was found fruitfly [Drosophila]
[2] recognize PAMPs and DAMPs
[3] mainly associated with defence against bacteria, virus, fungal infection etc.
[4] activate signalling pathways → leading to production of cytokines / chemokines
[5] 10 different types of known TLRs (human)

Page-by-page details from the handwritten Lecture 7 notes

After re-reading all 30 handwritten pages at full size, these are the details the note was missing or had only as a name. In a multiple-choice exam, these are exactly what separates the options.

1 · The lecturer's own numbering

2 · The three lines of defence, in his words (p4)

The immune system is not only about infection — his list of seven: inflammation, infectious diseases, tumour immunity, autoimmune diseases, allergy, vaccination, organ transplantation.

3 · Three features + 3R (p5, p12–13)

Features: distinguish self / non-self, specificity, immunological memory.
Behaviour: 3R — Recognition → Respond → Resolve/Recover. His cartoon says it plainly: “hello” to self, “who r u?” to non-self, and in the end only the non-self is eliminated.

4 · Organs: what each one does (p6–p11)

5 · Portals of entry (p19)

Nine portals on his diagram: skin (including broken skin), conjunctiva of the eye, nose, mouth, placenta, vagina, urethra, anus, insect bite. That is why mucosa is the main battlefield of the first line.

6 · Exogenous vs endogenous infection (p18)

7 · The numbers behind the barriers (p20–p22)

8 · The “cellular + chemical” list of line two (p23)

9 · Phagocytosis in three steps (p28–p29)

Professional vs non-professional phagocytes: professionals (Mφ, DC, neutrophil, monocyte) are recruited rapidly by chemotaxis; non-professionals (fibroblasts, endothelial cells, epithelial cells) are immotile, slower and limited in what they can engulf.

10 · Innate vs adaptive in nine lines (p14)

Kinetics (p17): innate peaks first → adaptive is induced → adaptive takes over → immunological memory. The response falls once the pathogen is cleared, but memory cells remain.

11 · Three definitions that get examined (p16, p30)

• Cytokine: small peptide signalling molecules for cell–cell communication, attracting immune cells to the infection site; involved in activation, differentiation, proliferation and maturation.
• Antigen-presenting cell (APC): captures antigen from the environment and presents it to adaptive immune cells (B/T); e.g. Mφ, DC.
• DAMP: endogenous danger signal released by dying, stressed or damaged cells, activating innate immunity; e.g. heat shock protein (HSP).