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%