Course outlines for senior Microbiology and Virology units of study within the Bachelor of Medical Science Last updated 18 November 2006

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1 Course outlines for senior Microbiology and Virology units of study within the Bachelor of Medical Science Last updated 18 November 2006 These course outlines are a guide only. They are provided for the information of prospective students. Although every effort is made to ensure the most up to date information is provided, timetables often change each semester due to the availability of rooms and resources. Content (including lecture/practical topics, assessment and textbooks) is also regularly reviewed to ensure relevance and effective learning.

2 Microbiology in Year 3 BMedSc This Unit of Study is well suited to students who are interested in diseases caused by microorganisms and the mechanisms used by pathogens to invade, establish infection and cause the symptoms associated with the disease. MICR3011 Microbes in Infection is designed to provide a deeper understanding of: 1. Microorganisms and their role in human disease. 2. The management of disease for good public health. 3. The importance and management of new and emerging diseases. To achieve this, the unit is divided into three themes: 1. Infections of body systems: bacterial and fungal infections that are problematic at particular sites, host defences, virulence mechanisms; 2. Public health microbiology: transmission, epidemiology, international public health, parasitic infections and causes of outbreaks; 3. Emerging and re-emerging diseases: the impact of societal change with respect to triggering new diseases and causing the re-emergence of past problems. The practical component is designed to enhance students practical skills and to complement the lecture series. Clinical tutorial sessions underpin and investigate the application of the material covered in the practical classes. MICR3011: Entry requires 42 credit points Intermediate BMED units including BMED(2807 and 2808) MICR3911: Entry requires 42 credit points Intermediate BMED units including Distinction in BMED(2807 or 2808) What to take with MICR3011/3911 In Semester 1, this Unit of Study pairs well with any of the BMedSc electives, but particularly with VIRO3001 Virology, BCHM3071/3971 Molecular Biology & Biochemistry - Genes and BCHM30881/3981 Molecular Biology and Biochemistry - Proteins, as well as PCOL3011/3911 Toxicology and PCOL3012/3912 Drug Design and Development. This Unit of Study complements in particular, the following Semester 2 electives: MICR3012/3912 Molecular Biology of Pathogens, MICR3022/3922 Microbial Biotechnology, IMMU3102 Molecular & Cellular Immunology and IMMU3202 Immunology in Human Disease, INFD3012 Infectious Diseases, CPAT3201 Pathogenesis of Human Disease 1 and CPAT3202 Pathogenesis of Disease 2 and BCHM3072/3972 Human Molecular Cell Biology and BCHM3082/3982 Medical & Metabolic Biochemistry. MICR3011: 2 lectures/week & 3 hours practical /week MICR3911: 2 lectures/week & 3 hours practical /week; plus 6x1hour advanced sessions Lectures: 10am Tues & Wed; 1pm Tues MICR3911 for 6 weeks Practicals: 2-5pm Tues or Wed (or possible alternative session 2-5pm Mon) Lecture Topics Infections of body systems: skin; respiratory tract; CNS; GIT Public health microbiology: transmission; epidemiology; diagnostics; water- & food-borne outbreaks Emerging & re-emerging diseases: causes; opportunism; old bacterial diseases posing new problems MICR3911 only: opportunistic Cryptococcus neoformans infections; student presentations in public health microbiology Practical sessions involve hands-on experiments and case studies with direct application in diagnostic and research microbiology. Case studies: Examination of patient case histories and testing of clinical material to isolate and identify the causative organism of skin, burn, wound, respiratory and gastrointestinal tract infections; group discussions; problem solving exercises Fungal & parasitic infections Hospital visit to Westmead ICPMR s Medical Microbiology 5 th ed., 2005, Murray, P.R. et al. Background reference material: Microbiology 6 th ed., 2005, Prescott, L.M., Harley, J.P. & Klein, D.A. Semester 1 Elective Microbes in Infection MICR3011/3911 (6CP) Helen Agus: Unit Co-ordinator: tel ; h.agus@mmb.usyd.edu.au

3 Microbiology in Year 3 BMedSc Semester 1 Elective Virology VIRO3001/3901 (6CP) This option for Year 3 BMedSc students is studied in Semester 1 and is one of two units in the field of virology that are collaborations between the Disciplines of Microbiology and Infectious Diseases. It builds on topics covered in the Year 2 core course BMED2802 Molecular Basis of Medical Sciences and in Year 3 is extended by taking VIRO3002 Medical and Applied Virology in Semester 2. VIRO3001: Qualification for this Unit of Study requires 42 credit points of Intermediate BMED units including BMED2802 Molecular Basis of Medical Sciences. VIRO3901: 42 credit points of Intermediate BMED units including Distinction in BMED2802 Molecular Basis of Medical Sciences. There is no quota for this option, but students considering this unit should have performed well in Year 2 in BMED2802 Molecular Basis of Medical Sciences, BMED2807 Microbes & Body Defences and BMED2808 Disease in Society. What to take with VIRO3001 Although MICR3011 Microbes in Infection is not a co-requisite for this Unit of Study, students are advised that important extension of microbial principles can be obtained by also taking MICR3011 in Semester 1. Also, students are very strongly advised to complete VIRO (3001 or 3901) before enrolling in VIRO3002 Medical and Applied Virology in Semester 2. This unit of study is designed to introduce students who have a basic understanding of molecular biology to the field of virology. Through an examination of virus structure, genomes, replication and gene expression, viral infection in plant and animal cells is covered, progressing to examine host-virus interactions, pathogenesis, cell injury and prevention and control of infection in both eukaryotic and prokaryotic cells. Bacteriophage structure and infection of prokaryotic cells is also covered. The structure and replication of sub-viral agents: viroids and prions, and their role in disease and significance in the context of transmission via blood products are discussed. Detection of viral illness by serology and molecular techniques such as ELISA, Western blotting, PCR and sequencing will also be covered. The hands-on practical component is designed to enhance students practical skills and to complement the lecture series by introducing students to cell culture, cytopathic effect, serology and molecular detection techniques. Tutorials and case studies will cover specific themes and problems and will involve student group research presentations and contributions from experts from clinical hospitals. VIRO3001: 2 lectures/week, 5 x 2hour tutorials and 6 x 4hour practical & associated activities VIRO3901: 2 lectures/ week, 5 x 2hour tutorials and 6 x 4hour practical & associated activities; 6x1hour advanced sessions Lectures: 10am Thurs & Fri; VIRO3901 only: 6x1hour advanced sessions Practicals: 1-5pm Thurs (or possible alternative session 1-5pm Fri) Topics covered in VIRO3001 and 3901 include: Virus structure & classification Viral molecular biology Viral infection VIRO3901 only: Current topics in virology Principles of Virology by Flint et al 2 nd ed., ASM, 2004 Reference Books: Basic Virology by Wagner, E.K. & Hewlett M.J.; 2 nd ed., Blackwell, 2004 Virus Taxonomy by Fauquet C.; Elsevier, 2005 Helen Agus: tel ; h.agus@mmb.usyd.edu.au The practical sessions involve hands-on experiments using diverse viral cultural and molecular techniques that have direct application in diagnostic and research virology: Cell culture, CPE, serology, ELISA, Western Blot, PCR

4 This Microbiology option for Year 3 BMedSc students is studied in Semester 2 to build on the discipline established in Year 2 in the core courses BMED2807 Microbes and Body Defences and BMED2808 Disease in Society and in Year 3 in the Semester 1 elective MICR3011 Microbes in Infection. Qualification for this Unit of Study requires 42 credit points of Intermediate BMED units including BMED (2802, 2807 and 2808). Although MICR3011 Microbes in Infection is not a qualifying Unit of Study, students are advised that important extension of microbial principles can be obtained by having taken MICR3011 in Semester 1. There is no quota for this option, but students considering this course should have performed well in BMED2802 Molecular Basis of Medical Sciences, BMED2807 Microbes and Body Defences and BMED2808 Disease in Society in Year 2 and/or in MICR3011 Microbes in Infection in Year 3 Semester 1. Entry into MICR3912 requires 42 credit points of Intermediate BMED units including at least one Distinction in BMED (2802 or 2807 or 2808) or MICR3011/3911. What to take with MICR3012 Although MICR3022 Microbial Biotechnology is not a co-requisite for this Unit of Study, students are advised that the content of both units are mutually supportive, extending the focus and experience of molecular microbiology. Students are therefore encouraged to also take MICR3022 in Semester 2. The Molecular Biology of Pathogens Unit of Study is designed to provide an understanding of disease processes and antimicrobial strategies at the molecular level. We will examine how some antimicrobial agents work, and some of the resistance mechanisms that microbes have evolved to counteract them. We will also look at how pathogens work to produce disease in the host by examining the nature and function of virulence factors such as adhesins, invasins and toxins, which allow the pathogen to attach to, invade, and damage human cells. The evolution of microbial virulence will also be discussed. Career opportunities MICR3012/3912 provides a good basis for careers in molecular, environmental or experimental microbiology. Graduates have found work in diagnostic and research laboratories based in hospitals, universities, government organizations such as the CSIRO and Sydney Water, and private industries including biotechnology companies and industries involved in the production of food, crops and pharmaceuticals. Employment can also be found in sectors related to these industries, such as sales, technical support, marketing, scientific journalism and communication, and education. MICR3012: 2 lectures/week; and a total of 40 hours practical and associated activities in weeks 2-10 MICR3912: As for MICR3012 plus 4x1 hour seminars and 2x1 hour student presentations Lectures: Practicals: Microbiology in Year 3 BMedSc 10am Thurs & Fri; 10am Mon weeks 2-9 for MICR3912 students only 1-5 pm Thurs OR 1-5 pm Fri in weeks 2-10 only Topics covered in MICR3012 and 3912 include: Antibiotics action and mechanisms of resistance Virulence mechanisms toxins, adhesins, invasins The origin of genetic diversity among diseasecausing organisms and viruses Evolutionary pressures acting on pathogenic determinants MICR3912 only: Case studies in molecular pathogenesis The practical sessions uses molecular techniques employed in diagnostic and research microbiology to investigate an outbreak scenario. There will be an opportunity for students enrolled in MICR3912 and MICR3922 to do a small research practical in place of the formal practical course. Salyers, A.A. & Whitt, D.D.: Bacterial Pathogenesis. A Molecular Approach. 2 nd Ed. ASM Press Semester 2 Elective Molecular Biology of Pathogens MICR3012/3912 (6CP) Dr. Dee Carter: Unit Co-ordinator, tel ; d.carter@mmb.usyd.edu.au

5 This Microbiology option for Year 3 BMedSc students is studied in Semester 2 to build on the discipline established in Year 2 in the core courses BMED2802 Molecular Basis of Medical Sciences and BMED2807 Microbes and Body Defences and in Year 3 in the Semester 1 elective MICR3011 Microbes in Infection. Entry to this Unit of Study requires 42 credit points of Intermediate BMED units including BMED (2802 and 2807). Although MICR3011 Microbes in Infection is not a qualifying Unit of Study, students are advised that important extension of microbial principles can be obtained by having taken MICR3011 in Semester 1. There is no quota for this option, but students considering this course should have performed well in BMED2802 Molecular Basis of Medical Sciences and BMED2807 Microbes and Body Defences in Year 2 and/or in MICR3011 Microbes in Infection in Year 3 Semester 1. Entry into MICR3922 requires 42 credit points of Intermediate BMED units including Distinction in BMED (2802 or 2807) or MICR3011/3911. What to take with MICR3022 Although MICR3012 Molecular Biology of Pathogens is not a co-requisite for this Unit of Study, students are advised that the content of both units are mutually supportive, extending the focus and experience of molecular microbiology. Students are therefore encouraged to also take MICR3012 in Semester 2. This unit of study will cover both traditional microbial biotechnologies and the impact of new technologies on healthcare and the emergence of new industries. Existing biotechnology is largely based on a remarkably small proportion of microbial diversity managed in pure cultures. The past ten years have seen dramatic advances in the capacity to explore microbial diversity and actively manage microbial communities. This course will focus on how these new techniques are creating new opportunities in biotechnology. General applications to be covered include human health (managing diseases that do not have a single causative agent), environmental health (waste treatment and alternative energy production), and production of bioactive compounds (enzymes, antibiotics). Specific techniques covered will include gene discovery via environmental metagenomics; genetic engineering; high throughput screening for isolation and recovery of producers of novel bioactive compounds (e.g. antibiotics). Career opportunities MICR3022/3922 provides a good basis for careers in molecular microbiology. Graduates have found work in diagnostic and research laboratories based in hospitals, universities, government organizations such as the CSIRO and Sydney Water, and private industries including biotechnology companies and industries involved in the production of food, crops and pharmaceuticals. Employment can also be found in sectors related to these industries, such as sales, technical support, marketing, scientific journalism and communication, and education. MICR3022: MICR3922: Lectures: Practicals: 2 lectures week & 30 hours practical & associated activities distributed over 8 weeks 2 lectures/week, 2 advanced lectures & 30 hours laboratory work on individual project 11am Tues & Thurs; 10am alternate Mondays MICR3922 only 1-5pm Wed (alternative session 1-5pm Tues) Introduction to microbial biotechnology Production of small molecules (antibiotics, biofuels) Genetic engineering and protein production Communities as sources of new products Community management in health (gut, oral) MICR3922 only: Current research topics The practical sessions involve hands-on experiments using diverse molecular techniques that have direct application in microbial biotechnology. There will be an opportunity for students enrolled in MICR3912 and MICR3922 to do a small research practical in place of the formal practical course. Additional reading and references are drawn from a variety of sources and provided throughout the semester. Microbiology in Year 3 BMedSc Semester 2 Elective Microbial Biotechnology MICR3022/3922 (6CP) Dr. Andy Holmes: Unit Co-ordinator, tel ; a.holmes@mmb.usyd.edu.au