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DEFINITIONS OF TERMS

Commensal flora (microbes) — the microbes that normally inhabit

our bodies and coexist with us without causing disease.

Sterile — free of any biological agents including microscopic

ones such as bacteria, fungi and viruses.

For a complete list of define terms, see the Glossary.

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Our natural defenses protect us from pathogens

We have now discussed several examples of how microbes can come into contact with humans to cause disease, but contact as we learned in Lesson 1.1, is not enough. The microbe must also evade our body’s natural defenses, and possibly outcompete the residential commensal flora that coexists within us.

First, let’s define the sterile inside and the non-sterile outside of the body. Although, this might seem like common sense, you may be surprised. Many of the locations people think of as being inside the body are actually considered to be on the outside. For example, the outside of the body includes not only the surface of the skin but any location where the skin (or mucous membranes) contacts the outside environment. Some outside locations such as the mouth, digestive tract, and the lower genital tract are heavily populated with microbes, and are therefore non-sterile. While, other outside locations are less hospitable, and have fewer, if any, microbes. Examples are the conjunctiva of the eyes, the lower respiratory tract, and the upper genital tract. These external sites of the body are probably mostly sterile so they can perform their functions.

In contrast to the outside of the body, it is critical to keep the inside of the body sterile to protect the health and functioning of organs. The inside of the body is anything beneath the epithelium (skin and mucous

LESSON 1.5 WORKBOOKSo, why aren't we always sick? Our body's defences

We are covered in bacteria and exposed to viruses all the time but we rarely get sick – why not? This lesson will focus on immune barriers that separate and protect us from pathogenic microbes in the environment. It is important for us to pay attention to how the immune barriers function because if they become damaged or pathogens adapt to get around them they lose their protective function.

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1. The following are considered to be “outside” the body EXCEPT

.a areas of the body in contact with the environment

.b non-sterile environments with microbes

.c areas with separation from the environment

.d areas with commensal flora __________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________

membranes) including organs such as the brain, the circulatory system, and the peritoneal cavity.

As we will see in this lesson, microbes are kept at bay in sterile areas by a series of protective barriers, which can be physical, chemical, or cellular. Surprisingly, our residential commensal microbes themselves also constitute another line of defense against infection.

The 1st line of defense: physical, chemical, and molecular barriers Epithelial cells separate the sterile inside of the body from the environment

Both the skin and mucous membranes are the major physical barrier between the outside and inside of our bodies, and they are made up of epithelial cells. The epithelium is constructed very much like a brick wall, where the bricks are laid in a row. The top apical side of the epithelium always faces the outside world — whether the outside happens to be the non-sterile surface of your skin or in the more sterile parts of the lungs.

The bottom, basal side of the epithelium faces the inside of the body and it is critical to keep this site sterile. To restrict microbes to the apical side of the epithelium, the cells are sealed together tightly just like the cementing between bricks in the brick wall, preventing microbes from squeezing between the cells. As we will see next, different locations require highly specialized types of epithelium. This is because some epithelium’s sole function is keeping microbes out, while others need to keep microbes out but also let nutrients into the body. In general, the skin is a tough barrier that few microbes can penetrate. This is why most infections through the skin happen when the skin is damaged. However, organs such as the lungs and intestines need to exchange nutrients with the outside world, so this epithelium needs to be permeable, leaving a challenge — how do we let nutrients in while keeping microbes out?

Figure 1: External areas of the body are outside of the epithelium, this includes the contents of our intestines.

Figure 2: Epithelium is like a brick wall of cells. The cells that face the outside are apical and the cell facing the inside are basal.

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DEFINITIONS OF TERMS

Keratin — a protein that is one of the key components of skin, nails,

and hair.

Cilia — hair-like organelles that are found on the surface of some

eukaryotic cells. In the trachea, they help brush up mucus and

dust particles away from the lungs.

For a complete list of defined terms, see the Glossary.

2. Some areas of the body like the gut, nose, and lungs have thin mucosal epithelium in order to perform other functions. To increase protection in these areas, the body has

.a mucus, a viscous fluid that sits on the outer layer of the epithelium.

.b cilia, hair-like organelles whose movement can transport substances.

.c both a and b

.d neither a and b ____________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________

The skin is a thick and durable type of epithelium

The skin is a specialized epithelium that is a highly effective physical barrier. It has three layers: the epidermis, dermis, and hypodermis. The epidermis is enriched with a protein, keratin, that is impermeable to most microbes and very resistant to mechanical stress. As epidermal cells get older, they get more keratinized, and are continually pushed outward by newer cells born at the junction of the epidermis and the dermis. The oldest, most keratinized cells in the topmost layers are continually shed, while newer skin forms below. As a result, highly protective epidermal barrier, the dermis and the hypodermis beneath, can normally be kept sterile.

Mucosal epithelium is thinner and more delicate

Mucosal epithelium has to be permeable to allow nutrients and small molecules to pass through it in order to get to the underlying tissues. Therefore it requires additional protection compared to the epithelium of

the skin. It has physical barriers such as hair, which traps large particulate matter, and it has chemical and molecular barriers which will be discussed below. Some of these factors are always present, while others only appear if a microbial breach appears.

Chemical barriers on mucosal epithelium restrict colonization

Some mucosal epithelia are covered with a layer of mucus. Mucus, as you may know, is a viscous gel. It entraps particles and prevents them from reaching the apical membrane of the epithelium. Once entrapped,

particles like viruses and bacteria can be swept away along with the mucus, by the cilia on the epithelial cells. The mucus and particles are then moved out of the body or are swallowed.

Figure 3: The three layers of the skin. The epidermis is a barrier that keeps the under-lying layers sterile.

Figure 4: Image of the airway epithelium showing ciliated cells.

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DEFINITIONS OF TERMS

Antibodies — proteins produced by B cells of the immune system that bind to and eliminate foreign

bodies such as microbes.

For a complete list of defined terms, see the Glossary.

3. The skin is a highly effective physical barrier because

.a it has three layers — the epidermis, dermis, and the hypodermis.

.b the keratin on the epidermis are impermeable by most microbes.

.c the epithelia is equipped with chemical and molecular barriers such as mucus.

.d it has defensins that prevents the passage of unwanted microbes.

.e all of the above________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________

In the lungs, the cilia prevent microbes from reaching the deepest airways in the lower lungs. Mucus secretion can increase during times of infection and is important for preventing infection. We might also cough to further keep particles out of your lungs. What if these reflexes are damaged? One type of damage to these reflexes is cigarette smoke. The heat and chemicals in cigarette smoke actually paralyzes the cilia, thereby preventing them from sweeping debris and microbes out of the lung. Since the cilia can’t function, particles that are taken in with air are more likely to enter the lungs. This is why smokers are very susceptible to respiratory infections like bronchitis.

Another chemical barrier is the extremely low pH (ranging from 1.5–3.5) of our stomach acid. It is sufficient to kill most of the bacteria that enter the stomach. In fact, for decades people believed that the

stomach is a sterile organ since they could not imagine how a living organism can thrive in such low pH. But now we know that there are a few species that have found a way to colonize the stomach. Some of them are benign while others can cause disease such as stomach ulcers.

Molecular barriers on mucosal epithelium restrict colonization by microbial invaders

The skin and mucus membranes also host several specific molecules that work to prevent microbial invasion. Many of them are always present, while others are only made when high numbers of bacteria are encountered. For instance, the enzyme lysozyme is present in large amounts in tears, sweat, saliva, and in the blood. Lysozyme acts mainly to digest the cell wall of Gram-positive bacteria. Remember, Gram-negative cell walls are shielded by an outer membrane, so lysozyme only works on Gram-negative bacteria when their outer membrane is damaged.

Mucus also contains antibodies (we will learn more about antibodies in Unit 5), and antimicrobial peptides such as defensins. Defensins are small positively charged peptides, that can poke holes in negatively charged membranes of bacteria or fungi causing them to leak and die. As

Figure 5: Electron micrograph of the epithelium in the airway show-ing the cilia that sweep debris out of the lung. Chemicals in smoke paralyse them. The scale bar (white line at the bottom left) is 1 micron.

Figure 6: Lysozyme: A natural antimicrobial in tears, sweat, saliva, and in the blood.

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DEFINITIONS OF TERMS

Complement system — pro-teins produced by the body that

are toxic to microbes.

Phagocyte — special cells that swallow up and destroy dying

host cells and microbes.

For a complete list of defined terms, see the Glossary.

4. The stomach’s primary protection from microbes is

.a keratin found in epithelial cells

.b the strong acid it secretes to break down bacteria

.c its ability to produce antibodies

.d secretion of mucus________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________

you might expect, our own membranes are resistant to the actions of defensins!

What happens if the external barriers are breached, and microbes gain access to normally sterile sites of the body?

If microbes do manage to cross the skin and mucous membranes they will encounter even more powerful molecular and cellular immune defenses. In this lesson we will meet these cells and in Unit 5 we will see how they work to fight infection.

Molecular and cellular defences in the blood

Molecular defences like the complement system in the blood restrict microbial survival

The blood has molecular defences that are always present and ready to respond to an infection. One of these defences is the complement system. Complement, like defensins, acts like a toxin that kills any cell lacking an antidote protein. Fortunately, all of our self-cells display this antidote protein, but microbes

aren’t so lucky. So, when microbes are exposed to the complement they are usually killed. The complement system is made up of more than 35 proteins that work together to lyse microbes. Like lysozyme, complement punches holes in bacteria or enveloped viruses by inserting donut-shaped protein complexes into their membranes and forming pores. These pores destabilize the membranes of the microbes, causing them to burst or lyse. Complement proteins can also mark microbes, like painting a target on them, so they can be detected by and phagocytosed by immune cells.

Innate immune cells are the first cells to respond to an infection

Innate immune cells have a defined set of receptors on their surfaces that can detect microbes but they cannot learn to respond to specific microbes. This means that if we are exposed to the same pathogen ten times, on the tenth exposure innate cells act the same as they did on the first.

Phagocytes are a type of innate cells

All epithelial surfaces are possible crossover sites for microbe entry into the sterile parts of the body. The

Figure 7: Electron microscope high magnification image of comple-ment-made pores (black holes) in bacterial membrane (gray layer).

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DEFINITIONS OF TERMS

Phagocytosis — the process of swallowing up and destroying

dying host cells and microbes.

Bone marrow — the soft tissues inside the bones, where our

blood cells are made.

Thymus — soft organ behind the breast bone where T cells

mature (develop) to respond to pathogens.

For a complete list of defined terms, see the Glossary.

5. When a pathogen is able to enter into the body’s sterile parts, it has to face obstacles such as

.a types of phagocytes that respond through chemicals or phagocytosis

.b types of phagocytes that phagocytose invading microbes

.c T and B cells that use receptors specific to a particular microbe to protect against future infection

.d all of the above ____________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________

large intestine in particular has a huge microbial population sitting just one epithelial layer away from the host’s sterile interior. So, immune cells called phagocytes, constantly patrol the basal surface of the epithelium to remove the rare microbe that manages to pass through the intact epithelium. If a microbe does break in, phagocytes respond quickly by chemical attack, phagocytosis, and by sounding the alarm to alert other cells of the immune system. As we will see in Unit 5, this contributes to inflammation.

In addition to killing invaders, phagocytes use their eating skills to mop up the dead host cells and debris left from fighting infections and normal cell death.

Adaptive immune cells are comprised of B and T cells and they are the last line of defense

If innate cells, such as phagocytes, cannot clear an infection, they help to activate adaptive immune cells — B and T cells. Unlike innate cells, adaptive B and T cells learn how to respond to a select pathogen upon infection. They do this using special receptors that are very specific to a small part of the microbe. Then if we are exposed to the microbe again in the future, the B and T cells have a memory of the microbe. This memory is the basis for vaccination and natural immunity to infections.

B and T cells are named according to the location they develop in the body: B cells develop in the bone marrow, and T cells develop in the thymus. Each B and T cell has one type of receptor that recognizes only one target. These are called the B cell receptor (BCR) and the T cell receptor (TCR), respectively. Another name for the BCRs that you may have heard is an antibody. We will discuss how B and T cells learn to recognize a specific infection in Unit 5, for now, we can think of them as the last line of defense.

Figure 8: A phagocyte (large yellow body) phagocytosing (ingesting) bacteria (orange rods).

Figure 9: B and T cells. Can you guess what the small red spherical cells on the left are?

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DEFINITIONS OF TERMS

Colonization — the process of bacteria adapting to permanently

inhabit our bodies.

Microbiota — all the microbes living normally on and inside our

bodies.

For a complete list of defined terms, see the Glossary.

6. The body benefits from the existing normal flora because of all of the following EXCEPT

.a the formation of biofilm

.b it helps in digestion

.c it competes with unwanted microbes

.d production of vitamins __________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________

The special host defense: our commensal flora (the microbiota)

Throughout our history, we have coexisted and coevolved with the microbial world. During that time our bodies have designated some spaces as safe to share with microbes. As a result a healthy human body normally contains thousands of species of bacteria and a smaller number of viruses, fungi, and protozoa, chiefly located in areas that we have learned are non-sterile. These are the moist areas of the skin including the groin, between the toes, the upper part of the respiratory tract, the mouth and intestines, and the lower parts of the urethra, and the vagina. In these sites, the number of microbes varies widely but the densest possible packing (about a million per milliliter) is found in

the pockets around the teeth and in normal feces, which is about one-third bacteria by weight.

The so-called commensal organisms or normal flora are extremely complex. For example, the intestinal flora of just one person has about 500 – 1,000 distinct species of bacteria. Most commensal flora coexist with humans without causing harm and many provide benefits such as aiding in digesting our food and the production of vitamins, e.g., vitamin K. We know call the collection of these helpful microbes, our microbiota!

To put this in perspective consider the following: our bodies are composed of ten times as many bacteria as human cells. In this respect we are an ecosystem. And this colonization takes place within days of birth, as bacteria are transferred from mother to child.

Any newly invading microbe with plans to colonize the human body must not only resist host mechanisms that could dislodge or kill them, they must also compete with the pre-existing flora. This is especially true in sites like the intestine, where commensal flora takes up all the free space. Not surprisingly, competition between microbes does not play a big role at sites that normally carry a sparse load of microbes. In fact, if a pathogenic microbe lodges here, alarm bells will sound and our body will immediately respond to eliminate it.

Figure 10: Areas colored orange have high levels of commensal organisms — our normal flora.

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Remember to identify your sources

Why do smokers have a high incidence of respiratory infections?

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TERMS

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TERM DEFINITION

Antibodies Proteins produced by the immune system that bind to and eliminate foreign bodies.

Bone marrow The soft tissues inside the bones, producing our blood cells.

Cilia Hair-like organelles that are found on the surface of some eukaryotic cells. In the trachea, they help brush up mucus and dust particles away from the lungs.

Colonization The process of bacteria adapting to permanently inhabit our bodies.

Commensal flora The microbes that normally inhabit our bodies and coexist with us without causing disease.

Commensal microbes (flora)

The microbes that normally reside within a host.

Commensalism Symbiotic relationship in which one organism derives a benefit, and the other is unharmed.

Complement system Proteins produced by the body that are toxic to microbes.

Defensins Small peptides, that can poke holes microbial cell membrane causing them to die.

Keratin Protein that is one of the key components of skin, nails, and hair.

Lysozyme An enzyme found on skin or in saliva that can degrade the cell walls of Gram-positive bacteria.

Peritoneal cavity Space between the organs in the abdominal cavity and the abdominal wall.

Phagocyte Scavenger cell that engulfs and samples foreign bodies.

Phagocytosis The process of engulfing of solid particles by a phagocyte.

Sterile Free of any biological agents including microscopic ones such as bacteria, fungi and viruses.

Thymus Soft organ behind the breast bone where T cells mature (develop) to respond to pathogens.