Field Epidemiology Manual Wiki

Applied Immunology

Last modified at 11/30/2013 9:28 AM by Arnold Bosman

Objectives of this chapter:

  • Understand the difference between innate and addaptive immune system
  • Define basic components of adaptive immune system
  • Define important terms in immunology
  • Explain major applications of immunology

Immunology is a broad branch of biomedical science that covers the study of all aspects of the immune systems in all living organisms. It deals with the physiological functioning of the immune system in states of both health and disease.

This chapter focusses on how the immune system deals with infectious diseases. 

The immune system is the defense against all the pathogens that we may encounter during our life and it consists of 2 main systems: the innate immune system and the adaptive immune system.

The innate immune system

This is a general level of defense and is called 'innate' because we are born with it and it is genetically encoded; these traits that protect us from pathogens can also be passed to our offspring. The best general defense barrier we have is our skin; it is the physical barrier that protects our vital organs and is able to capture and kill organisms that try to penetrate it.

The best routes that pathogenic organisms can take to successfully penetrate our body is through our airways, via the food and drinks that we consume or by being injected through the skin directly into our blood (e.g. through an insect bite). However, also these 'ports of entry' have well developed innate defenses. Pathogens that enter our nose and throat are assaulted by chemicals and physical weapons. This includes the mucus (slime) that the epithelial cells in our airways produce, the tiny hairs (cilia) that use wiping movements to move the mucus (containing the captured pathogens) out of our body and last but not least pathogen-eating cells (phagocytes).

These physical defenses above aim to prevent that pathogenic organisms enter our bloodstream or penetrate our cells. However, even when that fails, the innate defenses still have some options left:

For example when a virus enters a cell, it is recognized by the cell as an invader within minutes and the cell initiates a cascade of chemical signals to mobilize its defenses. Some molecules that the cell produces turn the intensity of the defense up or down and some molecules give signals to neighboring cells to start similar defense responses. Again other molecules damage the virus itself. If that is not enough to kill the virus, then sometimes the cell self-destructs in order to prevent the virus from further spreading.

All these defenses are examples of innate defenses, which aim to contain any invading pathogen. These responses also trigger a more specific defense that are specifically adapted to attack the pathogenic organism: the adaptive immune system. Virtually every successful vertebrate virus has developed mechanisms to circumvent the deadly traps that our innate immune system has put in place in our defense. This is why the adaptive immune system is so important.

The adaptive immune system

This system develops as we are exposed to pathogens throughout our lives: it is an acquired immune system. This system has a characteristic that the innate immune system lacks: immunological memory. Cells from the adaptive immune system are able to remember which pathogen they encountered, and store that memory for future rapid defense responses throughout our lives. The innate and the adaptive immune systems work closely together, for example some of the innate system's cells are so called antigen presenting cells, have ast task to capture antigens from pathogens that have intruded in the human body and to present those antigens to the adaptive system, in order to start producing specific antibodies against the pathogen. 

The key players of the adaptive system are T-cells (named so because they originate in the Thymus) and B-cells (originating from the bone marrow). Each of these cells have proteins in their outer coat that can bind with foreign antigens. There is almost an infinite range of different foreign antigens that the proteins on our B and T cells can recognize. This is similar to finding the key that fits a specific lock. The Antigen Presenting Cells of the innate immune system present foreign antigens that they have detected to our B and T cells in order to stimulate them for a response. This process usually takes place in the lymph nodes in our body.

B-cells have as one of their tasks to produce antibodies, that can then circulate in our blood stream to neutralize circulating pathogens while they are still outside of our cells. T-cells can directly kill an infected cell in our body, which will then stop the further replication and spread of the infecting pathogen. How to T-cells know that one of our cells is infected? Remember we said above that an infected cell can send chemical signals to mobilize our defenses? Well, some of these chemical signals attract T-cells. The next step is that the T-cells recognize some foreign antigens (from the invading pathogen) on the surface of our infected cells. That is usually the trigger for the T-cell to start killing the infected cell. This is a very effective and efficient way of dealing with pathogenic organisms, because only infected cells and only the pathogens are attacked, and our healthy cells are left alone.

There are disorders of our immune system that leads to attacks of our healthy cells: these so called 'auto-immune disorders' will not be discussed here.

Once T-cells and B-cells have been triggered for the very first time to respond to a specific infecting pathogen (thanks to the complex interaction with the innate system), they will remember this throughout our lives. This immunological memory will allow the T-cells and B-cells to respond immediately each time when this same pathogen tries to infect us again. This is the key concept in [[wiki:/fem/w/wiki/vaccination.aspx|vaccination]], where we artificially introduce harmless foreign antigens from dangerous pathogens, in order to trigger a lifelong immunological memory, without actually having to go through the dangerous primary natural infection.

Summary of our defenses

So in short, we have several lines of defenses:

  • physical barriers such as our skin, the mucus and the sweeping cilia (hair cells) in our airways, the acid in our stomach
  • mechanism to detect invasion by foreign organisms
  • control and command centres (such as our lymph nodes) where targeted responses are coordinated, once detected
  • our actual defense weapons: B- and T-cells and the antibodies, all grown to neutralize and kill invaders

Pretty sophisticated eh? With such specialized defenses, we are bound to be safe!

Unfortunately, the pathogenic organisms that surround us day by day have developed various smart ways of evasive action, to circumvent our defenses. Curious how? Read further here.


  • Introductory Course EPIET/EUPHEM - Immunology lecture.
  • Epidemics - the Dynamics of Infectious Diseases by Dr. Marcel Salathé, Dr. Ottar N. Bjornstad, Dr. Rachel A. Smith, Dr. Mary L. Poss, Dr. David P. Hughes, Dr. Peter Hudson, Dr. Matthew Ferrari, Dr. Andrew Read.Coursera course by PennState university.