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Junior Sophister Modules are available to visitors if they are deemed suitably qualified.

Module Code & Name ECTs credits Duration and semester Prerequisite Assessment Contact Hours Contact Details

MIU33011 Microbial Physiology

05 ECTs Michaelmas Term n/a Examination – 100% TBA Prof. Alastair Fleming


This course considers various aspects of microbial physiology. The best understood bacterial and yeast systems are used as examples throughout. The lectures deal with specialized bacterial and fungal cell wall components, nutrient uptake mechanisms and regulation, microbial metabolism (glycolysis, aerobic and anaerobic respiration, fermentation), adaptation to nutrient depletion, and cell death.
The aim is to give an overview of how microbial cells take up and utilise nutrients, and how cells cope with nutrient exhaustion. Indeed, how microbes contend with low nutrient conditions is arguably the most relevant physiological condition, yet it is the least studied.
The lectures on bacterial cell structure aim to provide a comprehensive overview of the structure and function of bacterial envelope components, surface proteins and polysaccharides. The contribution of each component to bacterial survival, biofilm formation and pathogenesis is examined. Biosynthesis, post-translational modification and export of protein and polysaccharide structures are described. The potential to use bacterial surface structures as vaccine antigens and to exploit our knowledge of biosynthetic pathways to discover new antimicrobial drug targets are discussed. This module has no practicals. Practicals supporting this module will be the ones delivered in MIU33019 (Experimental Microbiology I).

On successful completion of this module, students should be able to:

• Compare and contrast mechanisms of nutrient sensing and uptake in bacteria and yeast.
• Describe the major metabolic pathways in bacteria and yeast.
• Describe how microbes adapt to low nutrient conditions
• Describe secretion pathways in bacteria.
• Assess the contribution of each of the major components of the bacterial cell to virulence and survival of the organism.
• Describe the steps involved in the biosynthesis of the major bacterial surface and envelope structures. Assess which steps represent good targets for antimicrobial therapy.
• Appraise experimental approaches to examining protein structure, folding and function and dissecting metabolic and biosynthetic pathways in bacteria and yeast.

Module Code & Name ECTs credits Duration and semester Prerequisite Assessment Contact Hours Contact Details

MIU33012 Microbial Pathogenicity

05 ECTs Hilary Term n/a Examination – 100% TBA Prof Sinead Corr


This module covers two topics: Bacterial Pathogenicity and Virology.
The bacterial pathogenicity course covers the molecular basis of bacterial pathogenesis including adhesion of bacteria to host cells and tissue, invasion of mammalian cells, survival within professional phagocytes, evasion of innate immune responses and damage to host tissue. The major bacterial protein toxins will be covered (cholera enterotoxin, neurotoxins, and shiga toxins, pore-forming cytolysins). Several important bacterial pathogens will be discussed including Escherichia coli, Listeria monocytogenes, Shigella flexneri and Streptococci pneumoniae.
The virology component of this course compares and contrasts the diversity of viral genomes and replication strategies, and discusses how virus replication and evasions of host immune responses contributes to disease. Several important viruses are used to illustrate the core concepts. Emerging viruses, virus evolution, virus transmission and methods for interrupting virus replication, including vaccines, antiviral drugs and non-pharmaceutical interventions, are also discussed.

Virology Lecture Topics:

An introduction to the diversity of viruses; their shapes, structures, genomes and patterns of disease are discussed.
• The replication of +ssRNA viruses are discussed, with a focus on poliovirus to illustrate core concepts
• Coronavirus replication and diseases are discussed.
• The replication of -ssRNA viruses are discussed, with a focus on influenza viruses.
• The replication of cytoplasmic dsDNA viruses are discussed with a focus on poxviruses.
• The replication of herpes and papilloma dsDNA viruses are compared.
• The replication and disease caused by Human Immunodeficiency Virus is discussed
• The different types of viruses that cause hepatitis are compared and contrasted.
• The problem of emerging viruses is discussed, including factors which contribute to zoonotic transmission, outbreaks of “novel” viruses and viral characteristics that contribute to “pandemic potential”
• Virus evolution and strategies for genetic diversity are discussed.
• Also discussed are the different pharmaceutical and non-pharmaceutical methods we use to reduce virus transmission and disease.

Bacterial Pathogenicity Lecture Topics:

• Overview of bacterial Pathogenicity, main concepts and definitions, routes of access to host tissues, overview of key modes of infection and mechanisms of damage.
• Neurotoxins: Clostridia; mechanism of action of botulinum toxin and tetanus toxin
• Bacterial Toxins: Cholera; pathogenesis of Vibrio cholera and the action of its toxin, cholera toxin
• E. coli: EHEC; Introduction to Escherichia coli, focus on Enterohemorrhagic E. coli
• E.coli & IBD: AIEC; overview of the gut microbiome in inflammatory bowel disease (IBD) and the recent evidence of a role for Adherent-Invasive E.coli in the pathogenesis of IBD
• Listeria monocytogenes; Overview of the pathogenesis of Listeria infection with a focus on its intracellular lifecycle
• Streptococci pneumonia; Introduction to Streptococci, with a focus on Pneumococcal disease
• Shigella; Introduction to Shigella spp., focus on the pathogenesis of Bacillar Dysentery/Shigellosis
• Clostridia difficile; Clostridium difficile colitis: pathogenesis and host defence
• Final Summary: Overview of main virulence mechanism employed and insight therapeutic strategies to target these components of bacterial pathogenesis.

On successful completion of this module, students should be able to:

• Students will be able to critically discuss the virulence mechanisms employed by bacterial pathogens to establish infection, damage host tissue and some of the therapeutic strategies to target these pathogenic mechanisms.
• Students will be able to discuss how the nature of a viral genome influences its replication cycle and pattern of disease.
• Students will be able to illustrate core concepts of virology, such as virus entry, genome replication, transmission, disease, immune evasion, etc using topical examples of viruses that cause disease in humans.
This module has no practicals. Practicals supporting this module will be the ones delivered in MIU33020 (Experimental Microbiology).