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Semester 4: Microbiology and Immunology
Diversity and classification of microbes: History and evolution, microbial taxonomy, microbial phylogeny, classification of bacteria, microbial diversity, morphology and cell structure of viruses, bacteria, algae, fungi, protozoa
Diversity and Classification of Microbes
History and Evolution of Microbes
Microbes have existed for billions of years, with evidence tracing back to early Earth. Their evolution is marked by significant events such as the Great Oxygenation Event, which altered atmospheric composition and allowed for diversification. Understanding the evolutionary history of microbes provides insight into their adaptive mechanisms and survival strategies.
Microbial Taxonomy
Microbial taxonomy involves organizing microbes into groups based on shared characteristics. Traditionally, this has included morphological, physiological, and biochemical traits. Modern approaches utilize genetic information, allowing for more precise classification. The hierarchical system includes domains, kingdoms, phyla, classes, orders, families, genera, and species.
Microbial Phylogeny
Phylogenetics studies the evolutionary relationships among microbial species. Advances in molecular techniques, such as DNA sequencing, have transformed phylogenetic analysis. Phylogenetic trees illustrate evolutionary connections and help identify new species and understand microbial diversity.
Classification of Bacteria
Bacteria are classified based on various criteria, including shape (cocci, bacilli, spirilla), Gram staining (Gram-positive, Gram-negative), and metabolic capabilities (aerobic, anaerobic). This classification aids in understanding their ecological roles and interactions with humans.
Microbial Diversity
Microbial diversity refers to the variety of microbial life present in different environments. It includes the vast range of species and their genetic variability. Studying microbial diversity helps in ecology, biogeochemistry, and applications in biotechnology, medicine, and industry.
Morphology and Cell Structure of Microbes
Microbial morphology encompasses the physical form of microorganisms. Key structures include cell walls, membranes, and organelles. Bacteria typically possess a peptidoglycan cell wall, while fungi have chitin. Viruses, lacking cellular structures, are composed of genetic material encased in protein coats. Algae, fungi, and protozoa have diverse structures, aiding their respective functions in ecosystems.
Microbial growth: Growth curve, generation time, culture methods, microbial metabolism, bacterial reproduction including transformation, transduction, conjugation, endospores and sporulation
Microbial growth
The growth curve represents the growth of a microbial population over time, typically plotted as population size against time.
Lag phase: The initial phase where cells adjust to the environment, and no cell division occurs.
Log phase: Rapid cell division and population growth take place, resulting in exponential growth.
Stationary phase: Growth rate slows due to nutrient depletion or waste accumulation, leading to a plateau in population size.
Death phase: The decline in population size occurs as the number of dying cells exceeds the number of new cells being formed.
Generation time is the time taken for a microbial population to double in number.
It is crucial for understanding population dynamics and predicting microbial growth under various conditions.
Nutrient availability
Temperature
pH
Oxygen levels
Culture methods are techniques used to grow microorganisms under controlled laboratory conditions.
Aseptic techniques: Procedures to prevent contamination.
Liquid cultures: Growth in broth media.
Solid cultures: Growth on agar plates.
Selective media: Media that favor specific microbes.
Microbial metabolism encompasses the chemical processes that occur within microorganisms.
Catabolism: The breakdown of organic compounds to release energy.
Anabolism: The synthesis of complex molecules from simpler ones, requiring energy.
Phototrophy: Using light as an energy source.
Chemotrophy: Using chemicals as an energy source.
Bacterial reproduction primarily occurs through a process called binary fission.
The cell grows, replicates its DNA, and divides into two identical daughter cells.
The uptake of free DNA from the environment by a bacterial cell.
Allows for genetic variation and adaptation.
The transfer of genetic material between bacteria via bacteriophages.
Introduces new genetic variations.
The direct transfer of DNA between two bacterial cells through a physical connection called a pilus.
Often involves plasmids that encode beneficial traits.
Endospores are dormant, resistant structures formed by some bacteria to survive extreme conditions.
A complex developmental process initiated under unfavorable conditions that leads to the formation of endospores.
Endospores allow bacteria to endure harsh environments, ensuring survival and persistence.
Pathogen contamination and infectious diseases: Water microbiology, bacterial pollutants, sewage composition, food microbiology, major foodborne infections and intoxications, bacterial and viral diseases of humans
Pathogen contamination and infectious diseases
Water Microbiology
Water microbiology focuses on the microorganisms present in water bodies. Pathogens such as bacteria, viruses, and protozoa can contaminate water sources, leading to serious health risks. Common indicators of water quality include fecal coliform bacteria, which help assess the presence of harmful pathogens.
Bacterial Pollutants
Bacterial pollutants include pathogenic bacteria such as E. coli, Salmonella, and Vibrio cholerae. These bacteria can cause gastrointestinal diseases and can be found in contaminated water and food. Monitoring and controlling bacterial pollutants is crucial for public health.
Sewage Composition
Sewage contains a mixture of organic matter, nutrients, pathogens, and chemicals. Understanding sewage composition is important for effective treatment and management. Pathogens in sewage, such as enteric bacteria, can pose significant health risks if untreated.
Food Microbiology
Food microbiology studies microorganisms in food, focusing on both beneficial and harmful effects. Foodborne pathogens can cause infections and intoxications. Essential practices include proper cooking, storage, and handling to prevent food contamination.
Major Foodborne Infections and Intoxications
Foodborne infections arise from consuming contaminated food, whereas foodborne intoxications occur due to toxins produced by bacteria. Common examples include Salmonellosis (infection) and Staphylococcal food poisoning (intoxication). Awareness of these risks is crucial for food safety.
Bacterial and Viral Diseases of Humans
Various bacterial and viral diseases are linked to the consumption of contaminated food and water. Bacterial diseases include tuberculosis and cholera, while viral diseases encompass hepatitis A and norovirus infections. Preventative measures like vaccination and sanitation are essential to control these diseases.
Sterilization, cultivation and staining: Methods of sterilization, cultivation and maintenance of microorganisms, isolation methods, principles and types of staining
Sterilization, cultivation and staining
Methods of Sterilization
Sterilization involves killing or removing all forms of microbial life. Common methods include autoclaving, dry heat sterilization, and chemical sterilants. Autoclaving uses steam under pressure, while dry heat sterilization uses hot air. Chemicals like ethylene oxide are also effective.
Cultivation and Maintenance of Microorganisms
Cultivation of microorganisms requires specific growth conditions including temperature, pH, and nutrient availability. Maintenance can be achieved through subculturing, cryopreservation, or lyophilization. Different media types, like solid and liquid media, are used based on the microorganism's requirements.
Isolation Methods
Isolation of pure cultures can be achieved using techniques such as streak plating, spread plating, and serial dilution. These methods help separate individual colonies from a mixed population, allowing for the study of specific microorganisms.
Principles of Staining
Staining enhances visibility of microorganisms under a microscope. Stains interact with cellular components, imparting color. The choice of stain depends on the organism and the information needed.
Types of Staining
Common staining techniques include simple staining, differential staining such as Gram staining, and special staining methods like acid-fast and negative staining. Each technique provides unique insights into the morphology and structure of the microorganism.
Introduction to immune system: Components of mammalian immune system, innate and adaptive immunity, humoral and cell mediated immune response, clonal selection theory, primary and secondary immune responses
Introduction to Immune System
Components of Mammalian Immune System
The mammalian immune system comprises various components that play critical roles in defending against pathogens. Key components include white blood cells, antibodies, the complement system, lymphatic organs (such as lymph nodes and the spleen), and various signaling molecules known as cytokines. Each component has specific functions that contribute to the overall immune response.
Innate and Adaptive Immunity
Innate immunity is the first line of defense and is non-specific, providing immediate response to pathogens. It includes barriers like skin, mucous membranes, and immune cells such as macrophages and neutrophils. Adaptive immunity, on the other hand, is specific and involves a tailored response to particular pathogens through T and B lymphocytes and the production of antibodies.
Humoral and Cell-Mediated Immune Response
Humoral immunity focuses on the production of antibodies by B cells that target extracellular pathogens and toxins. Cell-mediated immunity involves T cells that recognize and destroy infected cells or help activate other immune cells. Both responses are essential for effectively combating infections.
Clonal Selection Theory
The clonal selection theory explains how specific B and T cells are activated and proliferate upon encountering their specific antigen. This process leads to the production of a large number of clones that are specific to the pathogen, facilitating a more effective immune response.
Primary and Secondary Immune Responses
The primary immune response occurs upon first exposure to an antigen and takes time to develop as the body produces antibodies. The secondary immune response is faster and stronger, occurring when the same antigen is encountered again due to memory B and T cells that were generated during the primary response. This difference is why vaccinations are effective.
Antigen and Antibody structure and diversity: Antigens, epitopes, adjuvants, immunoglobulin structure, B- and T-cell receptors, maturation, antibody diversity, somatic gene rearrangements
Antigen and Antibody Structure and Diversity
Antigens
Antigens are substances that provoke an immune response. They can be proteins, polysaccharides, or nucleic acids. Antigens can be classified as self or non-self, with non-self antigens being foreign substances that the immune system targets.
Epitopes
Epitopes are specific parts of an antigen recognized by antibodies or immune cells. A single antigen may have multiple epitopes that can elicit different immune responses. B cells recognize epitopes on intact antigens, while T cells recognize linear epitopes presented by major histocompatibility complex (MHC) molecules.
Adjuvants
Adjuvants are substances that enhance the immune response to an antigen. They are often used in vaccines to improve their effectiveness. Adjuvants can stimulate the innate immune system and prolong the presence of antigens in the body.
Immunoglobulin Structure
Immunoglobulins, or antibodies, are glycoproteins produced by B cells. They consist of two heavy and two light chains linked by disulfide bonds. Each immunoglobulin has variable regions that determine antigen specificity and constant regions that mediate effector functions.
B-Cell Receptors
B-cell receptors (BCRs) are membrane-bound immunoglobulins that recognize specific antigens. Upon binding to an antigen, B cells undergo activation, proliferation, and differentiation into plasma cells that secrete antibodies.
T-Cell Receptors
T-cell receptors (TCRs) are specialized proteins on T cells that recognize specific antigens presented by MHC molecules. TCRs are essential for T cell activation and differentiation into effector and memory T cells.
Maturation of B and T Cells
B cells and T cells undergo maturation processes in the bone marrow and thymus, respectively. These processes involve selection mechanisms to ensure that self-reactive cells are eliminated and only those that can successfully recognize foreign antigens are allowed to mature.
Antibody Diversity
Antibody diversity arises from multiple mechanisms, including somatic hypermutation and class-switch recombination. Additionally, the rearrangement of gene segments coding for immunoglobulin heavy and light chains during B cell development contributes to the generation of a diverse antibody repertoire.
Somatic Gene Rearrangements
Somatic gene rearrangements are a genetic mechanism that generates diversity in antibody and T cell receptor repertoires. This process involves the recombination of specific gene segments (V, D, and J segments) in B and T cells, allowing for a vast array of receptors that can recognize different antigens.
MHC, antigen processing and presentation: Major histocompatibility complex class I & II, antigen processing, autoimmune diseases, immunodeficiency including AIDS and SCID
MHC, antigen processing and presentation
Major Histocompatibility Complex (MHC)
MHC molecules are crucial for the immune system. They present antigens to T cells, allowing for the recognition of pathogens. MHC class I presents to CD8+ (cytotoxic) T cells, while MHC class II presents to CD4+ (helper) T cells.
MHC Class I
MHC class I molecules are expressed on all nucleated cells. They present endogenous antigens (proteins produced within the cell) to cytotoxic T cells. This is critical for the detection and elimination of infected or cancerous cells.
MHC Class II
MHC class II molecules are mainly found on professional antigen-presenting cells (APCs) such as dendritic cells, macrophages, and B cells. They present exogenous antigens (derived from outside the cell) to helper T cells, which then assist in orchestrating the immune response.
Antigen Processing
Antigen processing refers to the breakdown of proteins into peptides that can be presented by MHC molecules. In class I, antigens are processed in the cytoplasm and transported to the endoplasmic reticulum. In class II, antigens are engulfed and processed in lysosomes.
Autoimmune Diseases
Autoimmune diseases occur when the immune system mistakenly attacks the body's own cells. This can involve erroneous recognition of self-antigens presented on MHC molecules. Examples include rheumatoid arthritis, lupus, and multiple sclerosis.
Immunodeficiency Diseases
Immunodeficiency involves a weakened immune response, making the body susceptible to infections. Two notable examples are: 1. AIDS: Caused by HIV, which targets CD4+ T cells, impairing MHC class II-mediated responses. 2. SCID: Severe combined immunodeficiency results from defects in both T and B cell functions, affecting antigen processing and presentation.
Immunological Techniques and Vaccines: Immunodiagnostics techniques including precipitation, agglutination, RIA, ELISA, immunofluorescence, passive & active immunization, types of vaccines (DNA, recombinant, inactivated), common indigenous vaccines
Immunological Techniques and Vaccines
Immunodiagnostic techniques are used to detect and measure the presence of antibodies or antigens in a sample.
Common techniques include precipitation, agglutination, enzyme-linked immunosorbent assay (ELISA), radioimmunoassay (RIA), and immunofluorescence.
Precipitation occurs when soluble antigens react with soluble antibodies to form visible complexes.
It is used in various assays like radial immunodiffusion.
Agglutination testing involves the clumping of particles, such as bacteria or red blood cells, in the presence of specific antibodies.
It is widely used in blood typing and diagnosing infections.
RIA is a sensitive method for detecting antigens or hormones using radioactively labeled antibodies.
It is often used in research and clinical laboratories.
ELISA is frequently used for quantifying proteins, antibodies, and hormones in samples.
It involves an enzyme-linked antibody and a substrate that produces a measurable signal.
Immunofluorescence uses fluorescently labeled antibodies to visualize the location of antigens in cells or tissue.
It is valuable for diagnosing autoimmune diseases and infections.
Passive immunization provides direct antibodies to an individual, offering immediate protection.
Active immunization involves stimulating the immune system to produce its own antibodies, typically through vaccination.
Vaccines can be categorized as DNA vaccines, recombinant vaccines, and inactivated vaccines.
DNA vaccines deliver genetic material to elicit an immune response.
Recombinant vaccines use genetically engineered organisms to express antigens.
Inactivated vaccines contain killed pathogens.
Indigenous vaccines vary by region and typically include those for common diseases like tuberculosis, hepatitis B, and measles.
Their development often considers local epidemiological needs.
