MICR3042/3942

Molecular Microbiology Research Skills

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

The lectures, pracs and tutorials in MICR3X42 aim to teach research principles and methods in molecular microbiology anddevelop practical skills that are essential for laboratory work. Such principles and skills are important for biomedical and biotechnology jobs in diverse sectors such as medicine, agriculture, and environmental science The unit will also teach general skills in planning experiments, use of lab notebooks, analysis and presentation of scientific data, and using the primary scientific literature.

We will focus on three key areas of modern microbiology: Environmental Microbiology and the techniques required for the study of complex microbial communities; Microbial Biotechnology, which explores how microbes can be used as cellular factories to produce useful products; and Medical Microbiology, where we will introduce some important modern DNA techniques aimed at analysing the molecular basis of microbial pathogenesis.

Course Coordinator Contact Details

A/Prof Dee Carter

Room: 501

Telephone: 9351 5383

E-mail: dee.carter@sydney.edu.au

Prerequisites

For all students, MICR3X32 Molecular Microbiology Concepts is a co-requisite for MICR3X42, and must also be taken if students wish to enrol in MICR3X42.

For BSc., prerequisites for MICR3X42 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 MICR3942 requires at least one Distinction in a previous MICR unit (MICR2X21, 2X22, 2X24 or 3X11) or BMED unit (BMED2401 or BMED2404)

Timetable

MICR3042: 1 x 1 hr lecture per week (total 13 hr); 1 x 4 hr prac per week (total 48 hr)
MICR3942: 1 x 1 hr lecture per week (total 13 hr);
Research project replaces prac (total 48 hr)

Lectures: Thurs 10-11 am - TBA

Practicals: Thurs or Fri 1-5 pm - Lab 542 School of Molecular Bioscience Building (G08) (formally known as Biochem/Microbiol 542 lab)



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

A detailed lecture outline is given in the Table below. Pracs are on three topics:
1. Microbial biotechnology Using microbial enzymes and genetic elements to clone and express foreign genes, how to make and characterise recombinant microbes.

2. Molecular analysis of microbial populations Community analysis methods and molecular ecological tools eg. next-generation sequencing, microarrays, DGGE, SIP

3. Molecular biology of eukaryotic microbes: comparison of genotyping methods used for pathogenic fungi, incl. PFGE, VTNR, MLST.

Practical Course

MICR3042Practicals in MICR3042 will be hands-on lab classes that will give experience in microbiological and molecular methods. The prac classes for MICR3042 are shown in the Table below. Pracs are on three topics:

1. Microbial biotechnology Using the E.coli BL21-pET system to make a commercial recombinant enzyme product: the Pfu DNA polymerase used for PCR.

2. Molecular analysis of microbial populations Using qPCR, DGGE, FISH and tag-sequencing to test the effect of diet on mouse gut microbial community.

3. Molecular biology of eukaryotic microbes: genotyping using PFGE, VTNR, and MLST to investigate an outbreak of Cryptococcus infection in koalas.

MICR3942 In MICR3942, research projects replace the practical component of this unit of study. This research project takes place in an academic lab in the Discipline of Microbiology in the School of Molecular Bioscience. Students are expected to contribute approximately 45 hours to their research project between weeks 2-12 of semester 2. Assessment for research projects comprises of three components: Poster Presentation (60%), Lab book (25%) Supervisor mark (15%).

Detailed Timetable

MICR3042 and MICR3942 attend the same lectures, but do separate pracs. The prac titles shown below are for MICR3042 only. The MICR3942 prac topics and timetabling are variable, depending on the research supervisor and project.

Week

 #

Lecture / Prac title

Staff

1

L1

Welcome/overview of Unit

NC

 

No prac in first week

 

 

 

 

 

Theme 1: Microbial biotechnology

 

2

L2

Cloning and overexpressing genes in E.coli. Includes: theory and applications of pET expression system for overexpression of His-tag proteins.

NC

P1

Microbial biotechnology 1: Growth of recombinant bacteria, induction of protein expression. Check on structure of pUS30 by digest and junction PCR

NC

3

L3

Microbes as protein factories. Includes: explanation of different cell lysis and protein purification methods

NC

P2

Microbial biotechnology 2: Purification of recombinant protein by heat treatment, affinity chromatography, and dialysis. Purification of junction PCRs.

NC

4

L4

Polymerases and PCR. Includes: types of thermostable and other polymerases, and troubleshooting of PCR.

NC

P3

Microbial biotechnology 3: Testing effectiveness of polymerase preps as catalyst for 16S rDNA PCR, Quantify junction PCRs via Nanodrop, set up sequencing.

NC

5

L5

DNA sequencing in microbiology. Includes: theory and applications of traditional and next-gen sequencing and strategies for sequence analysis

NC

P4

Microbial biotechnology 4: Make SDS PAGE gels, run polymerase protein preparations. Analysis of junction sequence data. General discussion.

NC

 

 

 

Theme 2: Genetic variation in eukaryotic microbes

 

6

L6

Analysing genoplasticity in eukaryotic microbes.

DC

P5

Eukaryotic microbes 1: Chromosomal level genotype analysis using pulsed-field gel electrophoresis (PFGE).

DC

7

L7

Chromosomal level analysis of microbes – techniques and applications.

DC

P6

Eukaryotic microbes 2: Genotype analysis using variable numbers of tandem repeats (VNTR) and multilocus sequence typing (MLST) techniques.

DC

 

8

L8

Genotyping microbial strains via sequence level analysis – techniques and applications.

DC

P7

Eukaryotic microbes 3: Interpretation of data and comparison of featured techniques.

DC

 

 

 

 

Theme 3: Molecular analysis of microbial populations

 

9

L9

Introduction to molecular ecology and sample design 

AH

P8

Impact of diet on gut microbiota:  DNA extraction and PCR recovery of 16S sequences

AH

10

L10

Community profiling: classification and analysis of nucleic acids

AH

P9

Impact of diet on gut microbiota:  DGGE fingerprinting and sequence-based community profiling

AH

11

L11

Phylogenetic group-specific probes and their applications.

AH

P10

Impact of diet on gut microbiota:  Phylogenetic group-specific probes for FISH and qPCR

AH

12

L12

Linking uncultured organisms to in situ activity

AH

P11

Impact of diet on gut microbiota:  Class data compilation and analysis.

AH

Staff list

NC: Nick Coleman
DC: Dee Carter
AH: Andy Holmes

Assessment

Practical 60%; Theory 40%. 1 x 1 hour theory exam. 1 x 1 hour problem-based theory-of-prac exam. Prac course also includes in-lab practical assessment of experimental results, a quiz, and 2 short prac reports. )