MICR3032/3932
Molecular Microbiology (Concepts)
Course Information
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.
Unit of Study Overview
This Unit of Study introduces students to key areas of research in molecular microbiology. Building on knowledge gained in MICR2012 and MICR2022, as well as MBLG1001, it brings in the study of microbial evolution, pathogenesis, physiology, ecology, biotechnology and genetics, with each key theme explored with a series of 6 lectures led by an expert in the field. Lectures will be complemented with practical tutorial sessions that explore recent research in these areas.
MICR3032 will be assessed by one 1-hour exam (mid semester), one 2-hour exam (end of semester), one written assignment (report/essay), one presentation, one computer-based assessment exercise and attendance and participation in tutorial sessions
In MICR3932, the tutorial sessions will be used for small-group lessons on scientific writing that will teach students how to write and evaluate scientific papers. MICR3932 will be assessed by one 1-hour exam (mid semester), one 2-hour exam (end of semester), three written assignments based on the tutorial sessions on scientific writing and attendance and participation in tutorial sessions
Career Opportunities
MICR3X32 provides an excellent basis for careers in microbiology and biotechnology. Graduates will be employable in diagnostic and research laboratories in hospitals, universities, and government organizations such as CSIRO and Sydney Water, biotechnology companies and industries involved in the production of food, crops and pharmaceuticals, and in related areas such as education, sales, technical support and scientific journalism.
Course Coordinator Contact Details
A/Prof Dee Carter
Room: 501
Telephone: 9351 5383
E-mail: dee.carter@sydney.edu.au
Prerequisites
For BSc, prerequisites for MICR3X32 include 6 credit points of MBLG units and 6
credit points of junior microbiology (MICR2X22 or 2922 or 2X02 )
For BMedSci, prerequisites are 18 credit points of BMED units including
(BMED2401 and BMED2404) or (BMED2801 and BMED2802 and BMED2807).
For BScAg, prerequisites are PLNT2X01 and MICR2X24.
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.
Entry into MICR3932 requires at least one Distinction in a previous MICR unit (MICR2X21, 2X22, 2X24 or 3X11) or BMED unit (BMED2401 or BMED2404)
Timetable
MICR 3032:
Lectures: Mon 10-11 am, Tues 11 am-12 pm, Fri 10-11 am
Tutorials: Tues 1 - 3 pm
MICR3912:
Lectures: Mon 10-11 am, Tues 11 am-12 pm, Fri 10-11 am
Tutorials: Tues 3 - 5 pm
Textbooks
There is no formal text for the course. Prescott’s Microbiology or Brock’s Biology of Microorganisms are good general references. Links to articles from the scientific literature are provided.
Lecture Outlines
|
Week |
Lecture or tute/ prac # |
Lecture title |
Staff |
|---|---|---|---|
|
1
|
L1 |
Welcome/overview of Unit |
DC |
|
|
Theme 1: Molecular Principles of Fungal Pathogenesis |
DC |
|
|
L2 |
Introduction to the key fungal pathogens and the diseases that they cause |
DC |
|
|
L3 |
Evolution of fungal pathogenesis - phylogenetic and molecular perspectives |
DC |
|
|
|
No prac/tute in first week |
|
|
|
2 |
L4 |
Major fungal virulence factors |
DC |
|
L5 |
Antifungal agents and drug resistance |
DC |
|
|
L6 |
Host-pathogen interactions |
DC |
|
|
P1 |
Tutorial on aspects of medically important fungi; divide class into groups and assign topics |
DC |
|
|
3 |
L7 |
Genetic and proteomic analyses of fungal virulence |
DC |
|
|
Theme 2: Molecular Biology of Bacterial Pathogenesis |
PR |
|
|
L8 |
The many pathogenic forms of E. coli and the clone concept |
PR |
|
|
L9 |
Toxins and their role in pathogenesis |
PR |
|
|
P2 |
Small group discussions on aspects of medically important fungi |
DC |
|
|
4 |
L10 |
The role of specific adhesion in pathogenesis |
PR |
|
L11 |
How and why bacteria get into host cells |
PR |
|
|
L12 |
Antigen variation and antigen diversity as evolutionary strategies |
PR |
|
|
P3 |
Small group discussions on aspects of medically important fungi |
DC |
|
|
5 |
L13 |
Genomics and analysis of pathogenesis |
PR |
|
|
Theme 3: Bacterial adaptation to new environments, including hosts |
TF |
|
|
L14 |
Bacterial adaptation to environmental differences - sensing and responding to change |
TF |
|
|
L15 |
Transcriptional responses to environmental stresses - sigma factor regulated |
TF |
|
|
P4 |
Assessment exercise on aspects of medically important fungi |
DC |
|
|
6 |
L16 |
Transcriptional responses to environmental signals - 2-component and other transcription factors |
TF |
|
L17 |
Metabolic adaptation in populations in response to change - aerobic/anaerobic transitions |
TF |
|
|
L18 |
Mutational adaptation in populations - amplification, stress-induced mutation rate, mutators, accepting foreign DNA |
TF |
|
|
P5 |
Tutorial on experimental analysis of host-bacterial interaction |
AH |
|
|
7 |
L19 |
Diversity and robustness in adapting to change |
TF |
|
L20 |
Tutorial on lectures by DC, PR and TF |
DC,PR,TF |
|
|
|
Theme 4: Bacterial systems biology |
SC |
|
|
L21 |
Structure / characterization of bacterial membrane proteins |
SC |
|
|
P6 |
Tutorial on experimental analysis of host bacterial interaction. |
AH |
|
|
8 |
L22 |
Resistance against stress (oxidative stress, heat stress, etc. |
SC |
|
L23 |
Glycosylation of bacterial proteins |
SC |
|
|
L24 |
Systems biology of bacterial regulation - stimulons and regulons |
SC |
|
|
P7 |
Assessment exercise on experimental and directed evolution |
AH |
|
|
9 |
L25 |
Secreted proteins and secretion systems (toxins and proteases) |
SC |
|
L26 |
Immunogenic proteins and vaccine design / development |
SC |
|
|
|
Theme 5: In situ Microbiology |
AH |
|
|
L27 |
Investigating in situ microbial populations and their activities |
AH |
|
|
P8 |
MID SEMESTER EXAM: 60 min, on lects 1-13 by DC an PR |
DC |
|
|
10 |
L28 |
The human microbiota: our microbiome |
AH |
|
L29 |
Properties of the Microbiome: effects on metabolism and intestinal tissue |
AH |
|
|
L30 |
Properties of the Microbiome: immune system effects |
AH |
|
|
P9 |
Bioinformatics exercise 1: introduction Using ORF Finder, Using BLAST |
NC |
|
|
11 |
L31 |
Microbiome Dysbiosis: Diseases involving the microbiome |
AH |
|
L32 |
Managing the microbiome for health |
AH |
|
|
|
Theme 6: Microbial Enzymes and Biotechnology |
NC |
|
|
L33 |
Microbial enzymes DNA manipulation |
NC |
|
|
P10 |
Bioinformatics exercise 2: More on BLAST using KEGG, using UMBBD |
NC |
|
|
12
|
L34 |
Mobile genetic elements as tools for biotechnology |
NC |
|
L35 |
Advanced tools for cloning and knockouts in bacteria |
NC |
|
|
L36 |
Microbial enzymes in Agricultural Biotechnology |
NC |
|
|
P11 |
Bioinformatics exercise 3: Making alignments and phylogenetic trees |
NC |
|
|
13
|
L37 |
Microbial enzymes in Biotechnology: Hydrolases |
NC |
|
L38 |
Microbial enzymes in Agricultural Biotechnology |
NC |
|
|
L39 |
Tutorial on lectures by SC, AH and NC |
PR, AH, NC |
|
|
P12 |
Bioinformatics exercise 4: Making primers and cloning your genes. |
AH/NC |
Lecture Outlines Advanced
|
Week |
Lecture or tute/ prac # |
Lecture title |
Staff |
|---|---|---|---|
|
1
|
L1 |
Welcome/overview of Unit |
DC |
|
|
Theme 1: Molecular Principles of Fungal Pathogenesis |
DC |
|
|
L2 |
Introduction to the key fungal pathogens and the diseases that they cause |
DC |
|
|
L3 |
Evolution of fungal pathogenesis - phylogenetic and molecular perspectives |
DC |
|
|
|
No prac/tute in first week |
|
|
|
2 |
L4 |
Major fungal virulence factors |
DC |
|
L5 |
Antifungal agents and drug resistance |
DC |
|
|
L6 |
Host-pathogen interactions |
DC |
|
|
P1 |
Research Presentation Skills: 1 - Introduction and selection of general topics |
DC |
|
|
3 |
L7 |
Genetic and proteomic analyses of fungal virulence |
DC |
|
|
Theme 2: Molecular Biology of Bacterial Pathogenesis |
PR |
|
|
L8 |
The many pathogenic forms of E. coli and the clone concept |
PR |
|
|
L9 |
Toxins and their role in pathogenesis |
PR |
|
|
P2 |
Research Presentation Skills: 2. Discussion and selection of specific research area |
DC |
|
|
4 |
L10 |
The role of specific adhesion in pathogenesis |
PR |
|
L11 |
How and why bacteria get into host cells |
PR |
|
|
L12 |
Antigen variation and antigen diversity as evolutionary strategies |
PR |
|
|
P3 |
Research Presentation Skills: 3 - Discussion and independent study. |
DC |
|
|
5 |
L13 |
Genomics and analysis of pathogenesis |
PR |
|
|
Theme 3: Bacterial adaptation to new environments, including hosts |
TF |
|
|
L14 |
Bacterial adaptation to environmental differences - sensing and responding to change |
TF |
|
|
L15 |
Transcriptional responses to environmental stresses - sigma factor regulated |
TF |
|
|
P4 |
Research Presentation Skills 4 - Student Presentations |
DC |
|
|
6 |
L16 |
Transcriptional responses to environmental signals - 2-component and other transcription factors |
TF |
|
L17 |
Metabolic adaptation in populations in response to change - aerobic/anaerobic transitions |
TF |
|
|
L18 |
Mutational adaptation in populations - amplification, stress-induced mutation rate, mutators, accepting foreign DNA |
TF |
|
|
P5 |
Experimental analysis of host-bacterial interactions: 1. Overview of methods and data interpretation |
DC |
|
|
7 |
L19 |
Diversity and robustness in adapting to change |
TF |
|
L20 |
Tutorial on lectures by DC, PR and TF |
DC,PR,TF |
|
|
|
Theme 4: Bacterial systems biology |
SC |
|
|
L21 |
Structure / characterization of bacterial membrane proteins |
PR |
|
|
P6 |
Exeprimental analysis of host-bacterial interactions: 2. Analysis and interpretation of data sets |
AH |
|
|
8 |
L22 |
Resistance against stress (oxidative stress, heat stress, etc. |
PR |
|
L23 |
Glycosylation of bacterial proteins |
PR |
|
|
L24 |
Systems biology of bacterial regulation - stimulons and regulons |
PR |
|
|
P7 |
Experimental analysis of host-bacterial interactions: 3. Open book assessment of data interpretation skills |
AH |
|
|
9 |
L25 |
Secreted proteins and secretion systems (toxins and proteases) |
PR |
|
L26 |
Immunogenic proteins and vaccine design / development |
PR |
|
|
|
Theme 5: In situ Microbiology |
AH |
|
|
L27 |
Investigating in situ microbial populations and their activities |
AH |
|
|
P8 |
MID SEMESTER EXAM: 60 min on lects 1-13 by DC and PR |
DC |
|
|
10 |
L28 |
The human microbiota: our microbiome |
AH |
|
L29 |
Properties of the Microbiome: effects on metabolism and intestinal tissue |
AH |
|
|
L30 |
Properties of the Microbiome: immune system effects |
AH |
|
|
P9 |
Critical review of scientific literature: 1 - Introduction to mobile genetic elements and integrons |
NC |
|
|
11 |
L31 |
Microbiome Dysbiosis: Diseases involving the microbiome |
AH |
|
L32 |
Managing the microbiome for health |
AH |
|
|
|
Theme 6: Microbial Enzymes and Biotechnology |
NC |
|
|
L33 |
Microbial enzymes DNA manipulation |
NC |
|
|
P10 |
Critical review of scientific literature: 2 - Integrons and gene cassettes in the soil metagenome |
DC |
|
|
12
|
L34 |
Mobile genetic elements as tools for biotechnology |
NC |
|
L35 |
Advanced tools for cloning and knockouts in bacteria |
NC |
|
|
L36 |
Microbial enzymes in Agricultural Biotechnology |
NC |
|
|
P11 |
Critical review of scientific literature: 3. New tools for analysis of integrons in Pseudomonas |
NC |
|
|
13
|
L37 |
Microbial enzymes in Biotechnology: Hydrolases |
NC |
|
L38 |
Microbial enzymes in Agricultural Biotechnology |
NC |
|
|
L39 |
Tutorial on lectures by SC, AH and NC |
SC, AH, NC |
|
|
P12 |
PCritical review of scientific literature: 4 - New Assessment by 1 hr exam |
NC |
Assessment
Theory 60%; Practical 40%