Human physiology

Three main circuits: (i) Pulmonary (pressurised), (ii) Cardiovascular (pressurised) and (iii) Lymphatic
(non-pressurised).

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 Body’s defense system

1st line of defense: Physical barrier

Skin (~ 2 m2) & Mucosal lining (digestive, respiratory & reproductive tracts) (~ 400 m2 = 2 tennis fields!)

- Intact skin stops ~ 100% of pathogens, although minor abrasions can allow many to gain access
- Sweat has a lowered pH (3-5) which inhibits the growth of many bacteria
- Mucous secretions contain lysozyme, an enzyme that specifically cuts covalent bonds in the cell
walls of gram+ bacteria
- The human stomach has an extremely low pH which sterilizes all incoming food

Human skin: Epidermis & dermis stop nearly all pathogen entry

Some famous pathogens - hepatitis A virus, rotaviruses, and Shigella bacteria can survive the pH and
gain access to the human body. Stomach acid and H. pylori which can cause stomach ulcers. Urease is
found in the bacterial cytosol, but may also localize on the surface (although this may be an artefact)
and elicits a strong serum immunoglobulin response. Urease aids in colonization of the host by
neutralizing gastric acid and providing ammonia for bacterial protein synthesis. Host defences are
avoided by urease by continuing to neutralize acid locally and by shedding urease, which may be
bound by immunoglobulin, from the surface of the bacterium. Host tissues can be damaged directly
by the urease-mediated generation of ammonia and indirectly by urease-induced stimulation of the
inflammatory response, including recruitment of leukocytes and triggering of the oxidative burst in
neutrophils.

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Fun fact: Scientists Barry J. Marshall and J. Robin Warren from Perth Australia won the 2005 Nobel
Prize for their discovery of H. pylori bacterium and its role in stomach ulcers and gastritis. Unable to
make his case in studies with lab mice (because H. pylori affects only primates) and prohibited from
experimenting on people, Marshall grew desperate. Finally he ran an experiment on the only human
patient he could ethically recruit: himself. He took some H. pylori from the gut of an ailing patient,
stirred it into a broth, and drank it. As the days passed, he developed gastritis, the precursor to an
ulcer: He started vomiting, his breath began to stink, and he felt sick and exhausted. Back in the lab,
he biopsied his own gut, culturing H. pylori and proving unequivocally that bacteria were
the underlying cause of ulcers. (From a 2010 article from Discover magazine)

2nd line of defense: Innate immunity

Natural defense system in all humans that has evolved over a long, long time as part of the
evolutionary process. The red swollen area around a prick demonstrates the innate immunity in action
against the bacteria that was present on the splinter before it entered your body as soon as the 1st
line of defense is compromised. A brief description of the main sentinels of innate immunity is given
below (for more information, see the end of this document).

Complement system (comprises of ~ 20 different proteins): An elegant network of proteins working

in tandem to fight infection. These proteins can be activated by 3 different pathways:
(a) Through active self-degradation of molecules (Alternative pathway) – non-specific (targets the
common hydroxyl and amino groups on the bacteria)
(b) Through antibodies (Classical pathway) - specific
(c) Through mannose-binding lectin (MBL) – specific

This system is just for our knowledge and will not be discussed in detail.

Macrophages or professional phagocytes:

1. Common across all human beings. They contain surface receptors against common microbial
invaders (e.g. fats and carbohydrates not found in humans and molecular structures that are
not easily mutated). Not very effective, however, against viruses.
2. Produced in bone marrow and leave as monocytes that remain in blood for ~ 3 days. During
this time, they travel via blood vessels and capillaries and enter tissues through cracks
between the endothelial cells that line the capillaries. In tissues, the macrophages hang
around waiting for action!
3. Macrophage sensing of bacteria is not a random collision process. The macrophages actually
approach the bacteria as shown below.

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 4. They engulf bacteria through a process called phagocytosis. Once engulfed in the phagosome,
the bacteria are broken down with the help of lysosomes that contain powerful chemicals and
enzymes such as lysozymes inside vesicles.

Fun fact: Macrophages will eat anything! Scientists have fed them iron filings in order to separate
them from cell mixtures.

5. In addition to phagocytosis, macrophages send-off signals to increase blood flow towards the
site of action (the red pussy area) by contracting the cells lining the blood vessels.
6. Stimulate nerves in the tissues sending pain signals to the brain
7. Generate a “respiratory/oxidative burst” releasing oxygen radicals that damage surrounding
pathogens and cells.
8. Secrete inflammatory cytokines to recruit other immune components (monocytes,
complement proteins, NK killer cells etc. that are able to destroy bacteria, virus-infected cells
and tumor cells).

Overall summary on macrophages is that they exist in 3 states:

Resting Activated (aka Primed) Hyperactive

1. Primary job as garbage 1. Activated through cytokine 1. When direct signals
collectors in tissues signalling received from pathogens.
E.g. LPS, mannose etc.
2. Exist as sentinels at the 2. Upregulate class II MHC 2. Increase in lysozyme, ROS
body's openings. E.g. lungs, molecules + function as an antigen & TNF-alpha to kill infection
skin, intestines. Can stay alive presenting cell (APC) by displaying & activate other cells
for months invaders for helper T cells to see

There are no gears between these states. This is a continuum process that exists based on the type
and strength of activation signals received.

Neutrophils (also professional phagocytes):

1. Main foot soldiers of the innate immune response and certainly the most abundant (~ 70% of
all WBCs).
2. Less versatile than macrophages as their job is to only kill 'on call'.

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 3. Can phagocytize particles, release a respiratory burst and produce inflammatory cytokines,
however, unlike macrophages, they also contain internal caches of anti-microbial substances
called granules and destructive chemicals.
4. Not APC
5. Live for ~ 5 days after which most of them die by programmed cell death known as apoptosis
to save our body from toxic soup.

The on-call process is again highly sophisticated. Read page 18 – 19 in Ref. 1 for more information.

3rd line of defense: Adaptive immunity

Historical perspective: Hints about adaptive immunity were first discovered in 1790s when British
scientist Edward Jenner observed that milkmaids frequently contracted a disease called cowpox which
caused lesions on their hands that looked similar to the sores caused by the smallpox virus. Jenner
also noted that milkmaids who had had cowpox almost never got smallpox (which, it turns out, is
caused by a close relative of the cowpox virus). So, Jenner conducted a daring experiment. He
inoculated a young boy with the pus from the sores of the milkmaid followed by re-inoculation with
the pus from the sores of the person infected with smallpox. The boy did not acquire smallpox
suggesting that given enough time to prepare, body’s immune response can provide protection
against an invader it had never seen before. Also, since the boy was able to get measles, mumps etc.,
the defense appeared specific.

Adaptive immunity is personal, acquired based on number of invaders encountered in a lifetime,

genetics etc. Its main features include specificity, diversity (through modular genetic design),
immunological memory, clonal expansion, specialization and non-reactivity to self. A brief description
of the main sentinels of innate immunity is given below (for more information, see the end of this
document).

B-cells:
Low number of B-cells of all kinds exist in the immune system that are ready to deal with any invader
but required a sophisticated activation process in order to deal with as many as 100 million types of
invaders. This process of activation is called clonal selection. This is one of the most elegant processes
in immunology.

B cell receptors (BCRs) or ‘test batch’ antibodies

The 100 million different BCRs (ready to specifically flight a 100 million different invaders) are made
using a modular mix & match approach. Even though the human gene set is limited (~ 25000), certain
gene segments/DNA modules in the heavy chain segment of the BCRs, are randomly placed during the
B-cell maturation process in order to make many different types of BCRs. This is quite unique since it
means each B-cell has a different DNA structure. Dr. Susumu Tonegawa got the Nobel Prize for the
discovery of this modular design of DNA in B cells in 1977.

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PROCESS OF CLONAL SELECTION

Each cycle of proliferation takes ~

12 h and the entire process lasts
for a week in order to clone
approx. 20,000 identical B cells.
This is enough to mount defense.
~ 2000 antibodies/s/B cell.

Ultimately, death A small portion of B cells remain as

of B cells. memory B cells to deal better with
future invasions. Exist in higher
concentrations around lymph nodes.

Fact: The evolution has led to a clonally diverse anticipatory repertoire in which each lymphocyte
bears a unique antigen for recognizing and repelling pathogen invaders. In spite of this, vaccination is
required by individuals for many reasons. (i) Viruses and bacteria can mutate rather quickly (within 1
generation). (ii) The memory B cells generated through the process of vaccination can be quickly
activated in spite of their information being present in the immune system. This is more crucial for
infants who do not have a fully developed immune system. (iii) During pregnancy, antibodies are
transferred from mother to child. Further immune factors are received through breast milk,
particularly in the early months of life. This maternal protection is a crucial support for the infant
immune system during its development – but it does not cover everything. Mothers can pass on
antibodies against diseases she herself has had in the past or those against which she has been
vaccinated. Because antibodies are quickly degraded, the child is left without protection from 6-12
months after birth and also shortly after their mother discontinues breastfeeding. (iv) Antibodies
against certain infectious – like whooping cough, for example – are non-transferrable so the baby
cannot depend on maternal antibodies for protection in all cases.

Antibodies:
1. Integral part of the adaptive immune response. Although there are five classes of antibodies
- IgG, IgM, IgE, IgA and IgD, IgGs are the most abundant in blood (~75%).
2. Proteins are ideal molecules for making antibodies since their complex folding structures yield
many shapes with specific binding affinity against antigens.
3. Antibodies (Abs) do not themselves kill. They tag or ‘opsonize’ (a German word meaning ‘to
prepare for eating’) an invader for destruction.

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 4. Bind to the invader with their Fab regions, leaving their Fc tails available to bind to Fc receptors
on the surface of cells such as macrophages. Using this strategy, antibodies can form a bridge
between the invader and the phagocyte (e.g., a macrophage), bringing the invader in close,
and preparing it for phagocytosis. Although the macrophages themselves have proteins for
direct binding to invaders, antibody bridging widens their fishing net and also increases their
appetite for phagocytosis.

Region that binds to Fc receptors

on cells like macrophages. Also
determines its class (IgA vs IgE
etc.) and function.

5. In case of viral attacks, a virus enters our cells by highjacking certain naturally present
receptors (such as Fc receptor etc.) and then uses our cell’s machinery to make many copies
of itself. These viruses sometimes bust open the cell and spread by infecting to neighboring
cells. Antibodies can bind to these viruses while they are outside of a cell, neutralizing them
against cell docking, entry, or even replication once it has entered the cell.
6. Only able to deal with viruses when they are outside. For internalized cells, T-cells are
required.

Fun fact: To protect us from all possible invaders, immunologists predict we would need around 100
million different antibodies. But human cells only have ~ 25,000 genes in all. How is this possible? This
problem was solved by Dr. Susumu Tonegawa who got the Nobel Prize for his discovery in 1977. He
showed that in every B cell, on the chromosomes that encode the antibody heavy chain, there are
multiple copies of four types of DNA modules (gene segments) called V, D, J, and C. Each copy of a
given module is slightly different from the other copies of that module. For example, in humans there
are about 40 different V segments, about 25 different D segments, six different J segments, and so on.
To assemble a mature heavy chain gene, each B cell chooses (more or less at random) one of each
kind of segment and pastes them together like this:

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T-cells:
Optically indistinguishable from B cells under the microscope and function much in the same way. Key
differences/similarities with B cells.

T cells B cells
Produced in bone marrow Produced in bone marrow
Mature in thymus Mature in bone marrow
Specialize only against protein antigens
Specialize against any organic molecule
T cell receptors (TCRs) stay put on the T cells
Secrete antibodies that leave the B cell
surface.
Need antigen presentation by the cells Recognize antigen by themselves.
internalizing the virus (aka antigen
presenting cells or APCs) in order to
recognize antigens.

APCs take peptide fragments of the virus

and transport it to their surface via class I
MHC molecules (that function as
billboards!). T cells sense these peptides and
destroy the APC.

Similarly, there are class II MHC molecules

but we won’t discuss them here….

Types of T cells:
(a) Killer T cells: Kill APCs in order to kill the virus
(b) Helper T cells: Release cytokines (IL-2, IFN- etc.) for mounting further defense.
(c) Regulatory T cells: Not fully understood. Perhaps keep immune response from over-reacting.
(d) Memory T cells: Those that remain after the infection has been conquered (for future defense)

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Lymphocytic system: The role of secondary lymphoid organs (SLOs) in immunity

Q. What is a lymphatic system?

It’s a drainage system for the body to remove excess fluid from the blood capillaries. It also acts as a
filter against debris and supports fight against infection using lymphocytes that reside in the lymph
nodes.

When a body gets invaded by a virus/bacterium, the infection stays local in spite of the fact
that we see blood. The local infection in a tissue is fought off my macrophages but more importantly,
the bacteria (alone or along with the macrophages) get pulled into the lymphatic system where they
are is carried to the nearest lymph nodes. Numerous B-cells and T-cells are waiting for these
pathogens in the lymph nodes where they get "taken care of". Just imagine, if there was no lymphatic
system, the infection would travel from the tissue to the entire body through blood circulation which
can cause a complex cascade of immune response and fatal medical issues. At times, it does happen
but very rarely.

1. Lymphatic circuit is like an essential drainage system accessory for the venous system. Thinner
than capillaries (although 3 cell layer thick).
2. Contains primary lympahtic organs such as thymus gland & red bone marrow, and secondary
lympahtic organs such as lymph ducts, lypmh vessels, lymph nodes etc. that are connected to
the tissues and veins/blood capillaries all throughout the body.
3. Lymph flow is guided in upward motion, taking lymph from the lower organs and pushing it
up via a series of 1 way valves and muscle-contraction guided motion.
4. Carries antigens, APCs, T and B cells to nearest lymph nodes and maximizes interaction
between the various cargos and hence, activation (kind of like dating bars).
5. Also a hangout for “memory B and T cells”.

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Q. How does the lymphatic system move fluid?

The lymphatic system does not have a heart of its own to pump fluid. But its designed in such a way
that the heart pump is enough to push liquid along with some help from other elements like:

(i) Smooth muscle lining that exist on the walls of the lymphatic vessels. Their contractile motion helps
in fluid movement.

(ii) Skeletal muscle squeezing that we do voluntarily throughout the day also helps in this regard

(iii) There exist many valves along the lymph capillary that only allow unidirectional flow of liquid from
all directions to the neck where the lymph vessel finally meets the venous blood stream located near
the collar bones.

(iv) The location of the lymph vessel is smartly designed in such a way that it re-enters near the neck
at the end of the venous blood stream. Here, the pressure is very low (5 mm Hg vs 120 mm Hg at the
artery pumping end of the heart). This further aids in lymph movement.

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References:

1. Chap. 1 of How the Immune System Works by Lauren Sompayrac

2. General web resources like:
http://theibdimmunologist.com/learning/basic-immunology
http://biobook.kuensting.org/bb/systems/immunology.htm
https://www.youtube.com/watch?v=AIcAF34MPpU&t=62s
https://www.youtube.com/watch?v=zQGOcOUBi6s
https://kgmu.org/download/virtualclass/anatomy/lymphatic_system.ppt

Additional content:

Dendritic Cells (DCs): These are also phagocytic cells, but they have the special ability of initiating an
adaptive immune response. Unlike neutrophils and macrophages, DCs are not simple foot soldiers.
Instead, they function more as spies and provide intelligence about invaders to T cells through a
phenomenon called “antigen presentation” and through cytokine production.

Natural Killer (NK) Cells: The name implies their function. These cells, however, do not kill pathogens
directly. Instead, these cells have the ability to recognize when other cells that are harboring internal
pathogens using special receptors and then kill them. Situations where this might occur is during viral
and mycobacterial infections. These intracellular pathogens find ways to block lysosome fusion and
their own destruction.

Mast Cells: Responsible for classic signs of inflammation including redness, swelling and heat. Though
well known for their association with allergy, they also can detect PAMPs and DAMPs through
receptors and become immunologically active. Mast cells exert their functions mainly through
cytokine and granule release. Unlike neutrophils, which release antimicrobial substances, mast cells
release histamine and heparin. Histamine is well known for its vasodilator function and ability to allow
fluid to leak between cells, causing redness and swelling. It also causes inflammatory itching by
triggering neurons (unmyelinated C-fibers) responsible for the itch feeling. Heparin prevents blood
coagulation.

T cell-like Cells: Most T cells are part of the adaptive immune response as they have adaptive T cell
receptors (receptors that learn to recognize pathogens). NK T cells and γδ T cells, however, use
invariant T cell receptors (receptors that do not rearrange) or semi-invariant T cell receptors and
participate in the innate immune response. NK T cells are similar to the NK cells mentioned above. Not
so much in function, but more in how they look. These cells share many of the same surface protein
markers. NK T cells, however, do not kill compromised cells. Instead, they are quick cytokine
producers. In doing so, they quickly notify all surrounding cells that there is problem when they
recognize PAMPs presented to them via dendritic cells.

The γδ T cells are important for innate immune reactions and the adaptive immune response as they
have invariant and variant T cell receptors. Their precise function remains unclear, but they can
secrete cytokines and, like the NK T cells above, participate in alerting and strengthening local
immune responses29.

Non-cellular Systems of the Innate Immune Response: Besides cells, there are also defenses in your
body that are ready to react to pathogens as soon as they are encountered, much like booby traps.
These systems rely on small proteins that are found within the bodily fluids.

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Complement System: The liver synthesizes the proteins of the complement system and they work in
concert to aid in phagocytosis, bacteria lysing and immune cell attraction. One can visualize it as a self-
assembling machine that starts to assemble as soon as the first proteins are bound and in place. The
complement “machine” is known to be initiated by three different pathways: the classical pathway,
the alternative pathway and the lectin pathway. The classical pathway is triggered when antibodies
are bound to a pathogen. The alternative pathway is triggered when the victim is unable to block the
cascade (normal cells can, while pathogens cannot). The lectin pathway uses free lectin proteins
(lectins are proteins that bind sugars) to bind sugars associated with bacterial cell walls).

E.g. Complement proteins work by puncturing the pathogenic cell membranes.

Acute Phase Proteins: These proteins are also produced by the liver and especially during
inflammation when pro-inflammatory cytokines are produced. Many are designed to coat pathogens
and have chemotactic properties (have the ability to attract cells). Some inhibit microbial growth by
sequestering iron from the environment. The lectins from the lectin pathway of complement
activation are considered acute phase proteins.

Anti-microbial Peptides: Often called “defensins”, these peptides function as natural antibiotics and
our produced by cells that guard the external surfaces and internal surfaces such as the skin and the
gastrointestinal system. In the skin, the main sources are keratinocytes, mast cells, neutrophils,
sebocytes and eccine epithelial cells. In the intestines, one of the main producers are the Paneth cells
of intestinal crypts.

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