Microbial Molecular Biology and Genetics

Module leader : Dr S. Ahmed.

This is a general page for the parts of the 20CP module `Microbial Molecular Biology and Genetics' which are taught by Dr Steve Forsythe.

Academic year starting 2002 saw a significant change to this module, whereby previous lectures on microbial response to stress (heat shock, etc), these were partially replaced with a series of lectures and seminars on 'Biomics'. This term refers to the combined studies of 'Bioinformatics', 'Proteomics' and 'Genomics'.

These topics are of considerable relevance to all aspects of microbiology. If you don't know what 'BLAST' is then you will by the end of the lectures. The final 'practicals' will be teaching you how to search internet-based databases for genes, proteins, etc. in microbial genomes - no pipettes, test tubes, aseptic techniques required!

The text to accompany the lectures can be accessed HERE (WORD version). This is a Word version which is handy as the URL's are active but it does take a minute or two to download. This is a very detailed document and more goes into the background of bioinformatics than I will cover in the lectures. Some sections are easy to read, others are not! I would suggest that initially you keep to the bits you can follow and depending on how interested you are on the topic, then read the harder sections.
To help you realise the ease with which you can analyse sequnces, whether DNA or proteins, I have put together three exercises (sorry can't count!). You need to do these in order to follow the instructions for your formal report.

    Exercises
  1. Week 1: Searching PubMed for a sequence
  2. Week 2: BLAST searching
  3. Week 3: Locating a gene on a genome
  4. Week 4: Constructing a phylogenetic tree
  5. Week 5: Aligning bacterial genomes

You can print the documents off, or preferably leave it on screen as the hypertext links are active and this may help you navigate through the steps. It will take a little while to get used to having three windows open at the same time, but once you've mastered it you will be able to search microbial genomes extremely quickly. However if you just want to print the document then go here.

 

Here is your assessed practical: 'Practical' (Word version URLs active). The deadline is two weeks after the allocated 3h practical session with me.

 

I have also written some Powerpoint versions of my lectures which you can work through

    Lecture material
  1. Biomics 1
  2. Biomics 2
  3. Biomics 3
  4. Biomics 4
  5. Biomics 5
  6. Biomics 6

Recommended reading

Nicklin et al. 'Instant notes in Microbiology' is a Recommended textbook, which although insufficient to write assignments from, it will certainly help you understand many of the lectures. A larger, useful textbook is by Perry, Stanley and Lory 'Microbial Life' (which is use for many of my overheads and pictures) and Madigan, Martinko & Parker 'Brock Biology of Microorganisms'. However for 'Bioinformatics' you'll also need to look use the Internet sites given on the 'general 'Microbial Molecular Biology & Genetics' page.

Useful journals are:

These journals are useful for showing you how professional microbiologists write up their work for peer review and how tables, graphs and references are presented. If you have problems understanding what a `Summary’ or `Abstract’ section should contain then have a look at these journals. A good idea is to photocopy an article and use it as a detailed example. If you go to the 'general 'Microbial Molecular Biology & Genetics' page then you will be able to access a large number of journal titles.

The hypertext links given on the Index page are designed to show you the variety of information available on the Web and includes the Mars bug and an encyclopaedia of E. coli! There are a disproportionate number of `bioluminescence’ web sites given, but this reflects the number of interesting sites available.

Hope you find the topics interesting (homepage : www.theagarplate.com).