Pathogens

A pathogen is something of biological origin that causes disease in a host and may include: Non-living agents - such as viruses and prions Living microorganisms - such as bacteria, fungi and eukaryotic parasites (typically protozoa, platyhelminthes and arthropods)

Viruses

Viruses are metabolically inert and incapable of reproducing independently of a host cell (hence are not living) Structurally, viruses consist of an inner core of nucleic acid surrounded by a protein coat (capsid) Simpler viruses may lack a capsid (viriods), while more complex viruses may contain an external lipid envelope Viruses can either be DNA-based (adenoviruses) or RNA-based (retroviruses)  Retroviruses require a special enzyme (reverse transcriptase) to convert its RNA into DNA form Viruses may either commandeer the host machinery to replicate independently of the host genome (lytic cycle) or integrate into

the host genome and be reproduced while dormant in cell progeny (lysogenic cycle) In both cases, the virus will eventually replicate itself thousands of times, before lysing the cell and releasing its infectious copies

(virions) Examples of adenoviruses include the rhinovirus (common cold) and herpes simplex virus (herpes and cold sores) An examples of a retrovirus is the human immunodeficiency virus - or HIV (responsible for AIDS) Viruses which infect bacteria are known as bacteriophages

Stages of Viral Replication

Prions A prion (proteinaceous infectious particle) is a protein that has refolded abnormally into a structure that is capable of causing

disease It is also able to convert normally folded protein molecules into the abnormal form (mechanism of conversion not well understood) Infectious prion proteins have a higher content of beta-pleated sheets, which increases structural stability making them more

resistant to denaturation This makes treatment of prion proteins extremely difficult (there are currently no known cures) Prion proteins aggregate together to form amyloid fibrils capable of causing disease Diseases caused by prion proteins are called spongiform encephalopathies, because they cause holes to form within the brain Examples of prion diseases include: Mad cow disease (affects cows) Scrapie (affects sheep) Creutzfeld-Jacob disorder (CJD) and kuru (affects humans)

Folding and Replication of Prion Protein

Bacteria Bacteria are unicellular prokaryotes and may be classified according to a number of different features, including: Shape (spherical = coccus ; rod = bacillus ; spiral = spirella / vibrio / spirochete) Associative patterns (pairs = diplo ; chains = strepto ; bunches = staphylo) Cell wall composition (Gram positive versus Gram negative) Gaseous requirements (aerobe, facultative anaerobe, obligate anaerobe)  Most bacteria are relatively harmless to humans and may even form a beneficial mutualistic relationship (e.g. normal flora in the

digestive tract) Harmful bacteria may cause disease by competing with beneficial bacteria and local cells for space and resources (e.g. nutrients) Bacteria may also cause disease by releasing poisonous substances called toxins Exotoxins are secreted into the surrounding environment by bacteria Endotoxins are internal components of a bacteria that become toxic when the bacteria cell is destroyed

As toxins retain their destructive capabilities after the death of the bacterium, they are often the cause of food poisoning (when food is heated sufficiently to destroy the bacteria but not the toxin)

Exotoxins versus Endotoxins

Fungi Fungi are important decomposers in biological systems They can be categorised according to whether they are unicellular (yeasts) or multicellular (moulds) - the majority of fungi are

moulds Fungi usually attack the body surfaces, including skin and mucous membranes The moulds consist of branching filaments called hyphae, which may form a mass of invading threads called mycelium Examples of fungal infections include: Yeast - Thrush (irritation of the mouth and vagina caused by the genus Candida) Moulds - Athlete's foot (irritation of the feet and finger webbing caused by the genus Tinea)

Hyphal Filaments of a Fungus

Parasites A parasite is an organism that grows, feeds and is sheltered on or in a different organism, while contributing nothing to the survival

of the host A parasite benefits at the expense of the host organism Parasites can be defined as either ectoparasites (living on the surface of the host) or endoparasites (living within the host)

Ectoparasites Ectoparasites are commonly arthropods (insects, spiders, etc.) and may cause disease in humans either directly or indirectly Arthropods such as lice, ticks and mites feed on the blood and may directly cause disease by injecting substances that act as

toxins Insects such as fleas and mosquitoes may not have an inherently harmful bite but may indirectly cause disease by acting as a

vector A vector is an organism that transmits a pathogen from a source to a host There are two types of vectors: Biological vectors accommodate the disease-causing microorganism while it undergoes part of its life cycle (e.g. the malarial

mosquito) Mechanical vectors are not involved in the growth and development of the microorganism and simply carry it from a source to a

host

Endoparasites Endoparasites live within the host and include microparasites (e.g. small, single-celled protozoa) or macroparasites (e.g.

multicellular helminths) Examples of protozoa which cause disease include Plasmodia (responsible for malaria) and Trypanosoma (African sleeping

sickness) Examples of helminth which cause disease include roundworm, tapeworm and flatworm (note: 'ringworm' is a fungal infection)

Transmission of Malaria   (Life Cycle of   Plasmodium )

First Line of DefenceThe first line of defence against infection are the surface barriers that prevent the entry of pathogenic substancesIn plants these barriers are of particular importance, as plants lack the cellular defences that animals possess

Surface Barriers in AnimalsThe main surface barriers in animals are the skin and mucous membranes

Skin Protects external structures (outer body areas) A dry, thick and tough region made of predominantly dead surface cells Contains biochemical defence agents (sebaceous glands secrete chemicals which inhibit the growth of some bacteria) The skin also releases acidic secretions to lower pH and prevent bacteria from growing

Mucous membranes Protect internal structures (externally accessable cavities and tubes, such as trachea, vagina and urethra) A thin region containing living surface cells that release fluids to wash away pathogens (mucus, tears, saliva, etc.) Contains biochemical defence agents (secretions contain lysozyme, which can destroy cell walls and cause cell lysis) Mucous membranes may be ciliated to aid in the removal of pathogens (along with physical actions such as coughing or sneezing)

Summary of Surface Barriers in Humans

Surface Barriers in PlantsPlants have no distinct immune system of the kind found in humans and most animalsInstead they have a number of structural and biochemical characteristics that provide protection against pathogens

Mechanical Barriers The waxy cuticle and outer epidermal cells provide a physical barrier for plants in the same way that skin does Many plants employ certain structures, including thorns, spines and prickles, to deter animals (and hence avoid potential vector-

based pathogens) When pathogens gain access to a plant via stomata (a common point of entry), layers of thickened cells (called cork) may form and

create protuberances (called galls) which limit the spread of the pathogen within the plant Some plants may even have mechanisms that result in the rapid death of tissue (apoptosis) that are under attack, thereby depriving

invading organisms of organic matter

Chemical Barriers Some plants resist disease by producing chemicals that have antimicrobial properties Saponins are a group of inactive compounds stored in vacuoles that may damage the cell membrane of pathogens when released Defensins are proteins which block the growth of pathogens and are typically released from germinating seeds Plants may additionally secrete a range of other anti-bacterial or anti-fungal agents, including resins and tannins

Some trees will produce oils that repel certain insect pests (and associated vector-borne diseases) Other plants may secrete gum around infected areas, essentially sealing the area off

Second Line of DefenceThe second line of defence against pathogenic invasion is the innate immune response, which has two key qualities:

It is non-specific (cannot differentiate between specific microorganisms) It is non-adaptive (produces the same response every time - in other words, it does not possess memory)

Blood and Lymph SystemsTwo inter-related fluid systems support the body's immune response - the blood system and the lymphatic systemThese two systems provide a transportation network for the cellular defenses that comprise the second and third lines of defence against infection

Blood System

The blood system produces the body's leukocytes (white blood cells) and transports these immune cells to the sites of infection All blood cells (erythrocytes, leukocytes and platelets) are produced by multipotent stem cells in the bone marrow (via

haematopoiesis) These cells circulate in the blood and are moved between arteries, capillaries and veins by the pumping of the heart

Lymphatic System The lymph system is a secondary transport system that serves to protect and maintain the internal fluid environment by producing

and filtering lymph Lymph is a clear fluid that contains white blood cells and arises from the drainage of fluid from the bloodstream and surrounding

tissue The fluid is filtered at points called lymph nodes - where pathogens are removed - before returning to venous circulation In addition to its key immune function, the lymphatic system also absorbs fats from the small intestine and absorbs excess tissue

fluid Major lymphatic organs include the spleen, thymus, tonsils and adenoids

Cellular DefensesThe cellular defenses of the innat immune system describe the types of cells employed along with the processes initiated by these cellsThese defenses include inflammation (by mast cells), phagocytosis, fever and clotting (by platelets)

Inflammation The inflammatory response is the way in which the body reacts when pathogens damage cells When tissue damage occurs, mast cells release a chemical called histamine, which causes local vasodilation and increased

capillary permeability It also releases chemotactic factors which recruit wandering macrophages (phagocytes) to the site of damage to fight the infection While inflammation is necessary to allow immune cells to access infected tissue, side effects include redness, swelling, heat and

pain Inflammation can be either short-term (acute) or long-term (chronic)

Histamine Release by Mast Cells Leading to Inflammation

Phagocytosis

Phagocytic leucocytes (macrophages) circulate in the blood but may move into body tissue (extravasation) in response to infection They concentrate at sites of infection due to the release of chemicals (such as histamine) from damaged body cells Pathogens are engulfed when cellular extensions (pseudopodia) surround the pathogen and then fuse, sequestering it in an

internal vesicle The vesicle may then fuse with the lysosome to digest the pathogen Some of the pathogens antigenic fragments may be presented on the surface of the macrophage, in order to help stimulate

antibody production This mechanism of endocytosis is called phagocytosis ('cell-eating')

Overview of Phagocytosis by a Leucocyte

Fever

A fever is an abnormally high body temperature associated with infection and is triggered by the release of prostaglandins Fever may help to combat infection by reducing the growth rate of pathogens (via the inactivation of enzymes and toxins required

by the invader) It may also increase metabolic activity of body cells and activate heat shock proteins in order to strengthen the overall immune

response Up to a certain point fever may be beneficial, but beyond a tolerable limit it can cause damage to a body's own enzymes

Blood Clotting

Clotting (haemostasis) is a mechanism that prevents the loss of blood from broken vessels Damaged cells and platelets release chemical signals called clotting factors which trigger a coagulation cascade: Clotting factors convert the inactive zymogen prothrombin into the activated enzyme thrombin Thrombin catalyses the conversion of the soluble plasma protein fibrinogen into an insoluble form (fibrin) Fibrin forms an insoluble mesh of fibres that trap blood cells at the site of damage Clotting factors also cause platelets to become sticky, which then adhere to the damaged region to form a solid plug called a clot The clot prevents further blood loss and blocks entry to foreign pathogens

Molecular Defenses

Molecular defenses involves a number of proteins that either attack invading microbes directly or hinder their ability to reproduceThese defenses include complement proteins, cytokines and interferons

Complement Proteins Complement proteins are produced by macrophages, monocytes and other body cells (particularly liver cells) These proteins are normally inactive in the blood, but in response to immune activation initiate a cascade of reactions that help

protect the body Activation of the complement system may provide protection in the following ways: Assist in the destruction of pathogenic organisms by destroying cell membranes Recruiting phagocytes to the site of infection (chemotaxis) Aid in identification of pathogens (opsonization) Intensifying the inflammatory response

Cytokines Cytokines are proteins produced in response to antigens and function as chemical messengers in the immune response They may facilitate immunity in three main ways: They may regulate the innate immune response (via chemotaxis and activation of the inflammatory response) They may regulate the adaptive immune response (via activation of lymphocytes) They may activate haematopoiesis (production and differentiation of new white blood cells)

Interferons Interferons are a specific type of cytokine that provide protection against viruses and tumor cells Infected cells release interferons which alert surrounding cells to reduce their susceptibility to infection (e.g. by activating antiviral

agents) Interferons will also recruit natural killer cells (NK cells) which target and destroy infected cells

Third Line of Defence

The third line of defence against pathogenic invasion is the adaptive immune response, which has two key qualities: It is specific (it can differentiate between specific microorganisms and respond accordingly) It is adaptive (it can produce a heightened response upon re-exposure - in other words, it has memory)

Antigen Presentation An antigen is a substance that the body recognises as foreign and can evoke an immune response

The immune system can differentiate between foreign ('non-self') and native ('self') cells due to the presence of identification markers (MHC molecules)

All body cells (excluding red blood cells) possess MHC class I markers on their cell surface, identifying them as part of the organism

Certain immune cells (e.g. macrophages) possess MHC class II markers, which present foreign substances to the adaptive immune system

The body is initially capable of recognising invaders as they do not possess the molecular markers that designated them as 'self' (MHC class I)

When non-specific macrophages engulf a pathogen and destroy it (via the lysosome), they present antigenic fragments on their surface, complexed with MHC class II molecules ('non-self')

This allows cells of the adaptive immune system (i.e. lymphocytes) to generate a specific response against that particular antigenic determinant

Infected body cells (e.g. viruses and tumors) may present antigenic fragments on MHC class I molecules, denoting that the cell is now compromised and needs to be destroyed

Comparison of Class I and Class II Major Histocompatability Complex (MHC) Molecules

Antibody Production The adaptive immune response functions by producing proteins called antibodies (or immunoglobulins) which are each specific to a

particular antigen Antibodies are made up of 4 polypeptide chains (2 light and 2 heavy chains) joined together by disulphide bonds to form a Y-

shaped molecule The ends of the arms are where the antigens bind and these areas are called the variable regions, as these will differ between

antibodies Each type of antibody will recognise a unique antigenic fragment, making this interaction specific (like enzyme-substrate

interactions) 

Structure of a Generalised Antibody

Humoral Immunity Humoral immunity describes the production of antibodies by B lymphocytes (B cells) B cells are antibody-producing cells that develop in the bone marrow to produce a highly specific antibody that recognises one type

of antigen Each B lymphocyte has a specific antibody on its surface that is capable of recognising a specific antigen When antigens are presented to B cells (and TH cells) by macrophages, only the B cell with the appropriate antibody will become

activated and clone The majority of B cell clones will differentiate into antibody-producing plasma cells, a minority will become memory B cells (BM cells) Plasma cells produce massive quantities of specific antibody for a limited time (~2,000 molecules per second for ~4 - 5 days) Because pathogens may contain several antigenic determinants, several B cell clones may become activated (polyclonal

activation)

Clonal Selection

Cell-Mediated Immunity Cell-mediated immunity describes the activation of humoral immunity by T helper cells and the targeted destruction of infected cells

by cytotoxic T cells It is important to recognise that humoral immunity will not occur without activation by cell-mediated immunity

Helper T Lymphocytes (TH cells) When a pathogen invades the body, it is engulfed by wandering macrophages which present the antigenic fragments on its surface This macrophage becomes an antigen-presenting cell, and presents the antigen to helper T cells (TH cells) The TH cells bind to the antigen and become activated, and in turn activate the B cell with the specific antibody for the antigen This B cell clones and differentiates into plasma cells and memory cells

Antibody Production via the Activation of Helper T cells

Cytotoxic T Lymphocytes (TC cells)

Cytotoxic T cells recognise antigenic fragments on infected cells (bound to MHC-I markers) and kill these cells before the virus has time to replicate

Some TC cells can even destroy certain types of cancer cells Cytotoxic T cells destroy infected cells by releasing lymphotoxins, which cause cell lysis Once the infected cells have been destroyed, suppressor T cells inhibit the TC cells, to ensure that normal cells are not

subsequently attacked TC cells (adaptive immunity) differ from natural killer cells (innate immunity) in their ability to form memory cells for subsequent

reinfections

Immunological Memory

Because the adaptive immune response is dependent on clonal expansion to create sufficiently large amounts of antibodies, there is a delay between initial exposure and the production of antibodies

When B and T cells divide and differentiate in order to produce antibodies, a small proportion of clones will differentiate into memory cells

Memory cells remain in the body for years (or even a lifetime) If a second infection with the same antigen occurs, the memory cells react faster and more vigorously than the initial immune

response, such that the symptoms of the infection do not normally appear

Because the individual no longer presents with the symptoms of infection upon exposure, the individual is thus said to be immune

Disorders of the Immune System

The purpose of the immune response is maintain normal health, however abnormal functioning of the immune system may lead to a disease stateThe immune system may over-react (allergies), fail to distinguish between 'self' and 'non-self' (autoimmune) or cease working entirely (immunodeficiency)

Hypersensitivity Disorders Hypersensitivity refers to an excessive or abnormal sensitivity to a substance that may not be inherently harmful Such reactions require a pre-sensitized immune state of the host (i.e. prior exposure) Upon re-exposure, the immune system responds excessively in a manner detrimental to the host Allergic reactions are a common example of a (type I) hypersensitivity disorder

Allergic Reactions An allergy is a local inflammatory response to an environmental substance that is not capable of causing disease (an allergen) When a B cell first encounters the allergen (initial exposure) it differentiates into a plasma cell and makes large amounts of antigen-

specific IgE The IgE molecules attach to mast cells (effectively 'priming' them) Upon re-exposure, the IgE-primed mast cells release large amounts of histamine and other inflammatory chemicals, leading to

swelling and redness These reactions tend to be localised to the region of exposure - often the airways and throat A severe systemic allergic reaction is called anaphylaxis and can be fatal

Overview of an Allergic Reaction

Autoimmune Disorders An autoimmune disorder occurs when the immune system fails to recognise its own body cells as 'self' and begins to attack its own

cells and tissues Some pathogens try to evade the immune system be producing antigens which closely resemble those of its host (antigenic

mimicry) If the pathogen is detected and destroyed, B-cells will be activated that produce antibodies specific to molecules similar to those on

body tissues This may lead to the destruction of tissues that contain those molecular fragments Examples of autoimmune diseases include: Type I diabetes mellitus (insulin dependent) - the insulin-secreting beta cells in the pancreas are destroyed by the immune system Rheumatoid arthritis - chronic inflammation of the joints caused by a localised autoimmune response within the joint capsule Multiple sclerosis - the myelin sheath is degraded as a result of an autoimmune response

Antigenic Mimicry Leading to an Autoimmune Response  

Immunodeficiency DisordersImmunodeficiency is a state in which the immune system's ability to fight infectious diseases is compromised or absent entirelyThese disorders may be inherited (e.g. SCIDs), of pathogenic origin (e.g. AIDS) or caused by drug treatments (e.g. cytotoxic drugs)

Acquired Immune Deficiency Syndrome (AIDS) AIDS is caused by the human immunodeficiency virus (HIV) - a retrovirus that infects helper T lymphcytes (TH cells) Reverse transciptase allows viral DNA to be produced from its RNA code, which is integrated into the host cells genome After a number of years of inactivity (during which infected TH cells have continually reproduced), the virus becomes active and

begins to spread, destroying the TH cells in the process (via the lysogenic cycle) This results in lower immunity as antibody production is compromised - the individual is now susceptible to opportunistic infections

Timeline of HIV Infection

Acquired Immunity

Immunity can be described as either passive or active, depending on how it is acquired: Active immunity is due to the production of antibodies by the organism itself after the body's defence mechanisms are stimulated

by antigens Passive immunity results from the acquisition of antibodies from another organism in which active immunity has been stimulated

Both types of immunity can also be described as natural or artificial, depending on whether the acquisition of antibodies was natural or induced

Natural Active Immunity:  Producing antibodies in response to pathogenic infection (i.e. challenge and response) Artificial Active Immunity:  Producing antibodies in response to a controlled exposure to an attenuated pathogen (i.e. vaccination) Natural Passive Immunity:  Receiving antibodies from an external source naturally (e.g. to fetus via colostrum and to newborn via

breast milk) Artificial Passive Immunity:  Receiving antibodies from an external source via injection (e.g. blood transfusion of monoclonal

antibodies)

Vaccinations Vaccinations induce artificial active immunity by stimulating the production of memory cells  A vaccine contains weakened or attenuated forms of the pathogen and is (usually) injected into the bloodstream Because a modified form of the pathogen is injected, the individual should not develop disease symptoms The body responds to the vaccine by initiating a primary immune response, resulting in the production of memory cells When exposed to the actual pathogen, the memory cells trigger a secondary immune response that is much faster and stronger Vaccines confer long-term immunity, however because memory cells may not survive a life time, booster shots may be required

Benefits: Vaccination results in active immunity It can limit the spread of infectious diseases (pandemics / epidemics) Diseases may be eradicated entirely (e.g. smallpox) Vaccination programs may reduce the mortality rate of a disease as well as protect vulnerable groups (e.g. youth, elderly) Vaccinations will decrease the crippling effects of certain diseases (e.g. polio)  It will decrease health care costs associated with treating disease conditions

Risks: Vaccinated individuals may produce (mild) symptoms of the disease There may be human error in the preparation, storage or administration of the vaccine Individuals may react badly to vaccines (e.g. hypersensitive / allergic reactions) Immunity may not be life long - booster shots may be required There may be possible toxic effects of mercury-based preservatives used in vaccines

Monoclonal Antibodies Monoclonal antibodies (mAb) are antibodies derived from a single B cell clone and are an example of artificial passive immunity

An animal (typically a mouse) is injected with an antigen and produces specific plasma cells The plasma cells are removed and fused (hybridised) with tumor cells capable of endless divisions (immortal cell line) The resulting hybridoma is capable of synthesising large quantities of specific antigen, for use in diagnosis and treatment

Production of Monoclonal Antibodies

Treatment Use:

Monoclonal antibodies can be used for the emergency treatment of rabies Because the rabies virus is potentially fatal in non-vaccinated individuals, injecting purified quantities of antibody is an effective

emergency treatment for a very serious viral infection

Antimicrobial Agents In addition to providing immunity via the acquisition of antibodies, diseases may be treated with antimicrobial agents (i.e.

pharmaceutical drugs) that specifically target particular pathogens Antibiotics are substances or compounds that kill or inhibit the growth of bacteria by targeting the metabolic pathways of

prokaryotes Specific prokaryotic features that may be targeted by antibiotics include key enzymes, 70S ribosomes and the bacterial cell wall Because eukaryotic cells do not have these features, antibiotic can kill bacterial cells without harming humans Antibiotic agents can be categorised according to their specificity as either broad spectrum or narrow spectrum Broad spectrum antibiotics are effective against a wide variety of bacteria Narrow spectrum antibiotics are very specific against certain bacteria and of limited use in a wider context Antibiotics may also be described as bacteriostatic or bacteriocidal according to their effect Bacteriostatic drugs inhibit bacterial growth but do not kill the bacteria (good for allowing immunity to develop) Bacteriocidal drugs kill the bacteria (good for particularly dangerous strains of  bacteria)

Bacteriostatic versus Bacteriocidal Agents

Virus do not carry out metabolic reactions themselves but instead infect host cells and take over their cellular machinery Because viruses do not have metabolism, antibiotic agents are not effective against viruses

Viruses need to be treated with specific antiviral agents that target features specific to viruses (e.g. reverse transcriptase in retroviruses)

Similarly, fungal infections and helminth infections can be treated with agents that target fungal cell features and helminth features respectively