1. ©M J Larkin Biological Sciences. The Queen’s University of Belfast. Level 1 Microorganisms MCB1006 Coordinator : M J Larkin co-coordinator : L A Kulakov

2. ©M J Larkin Biological Sciences. The Queen’s University of Belfast. Professor Mike Larkin - Communications Room 108 MBC xt 2288 (Belfast 90972288 ) Email m.larkin@qub.ac.uk Pigeon hole in Biological Sciences Office ALWAYS LEAVE MESSAGE and HOW TO CONTACT YOU! WWW pages –http://www.qub.ac.uk//mlpage/page1/index.html –http://www.qub.ac.uk//mlpage/courses/level1/page.html Room 108 MBC xt 2288 (Belfast 90972288 ) Email m.larkin@qub.ac.uk Pigeon hole in Biological Sciences Office ALWAYS LEAVE MESSAGE and HOW TO CONTACT YOU! WWW pages –http://www.qub.ac.uk//mlpage/page1/index.html –http://www.qub.ac.uk//mlpage/courses/level1/page.html

3. ©M J Larkin Biological Sciences. The Queen’s University of Belfast. Course Theme. “to provide a thorough grounding in the range of diversity of microorganisms, their structure, nutrition, growth, physiology and genetics. Also to provide 'hands-on' practical experience in the isolation and cultivation of microorganisms”. Working as individuals in practical work and skills From group assignment work you will gain experience in working with a group, independent research and literature report writing.

4. ©M J Larkin Biological Sciences. The Queen’s University of Belfast. 10  m

5. ©M J Larkin Biological Sciences. The Queen’s University of Belfast. 5  m

6. ©M J Larkin Biological Sciences. The Queen’s University of Belfast. CONTENT A practical and theoretical introduction to the biology of bacteria, viruses, fungi and protozoa. Microbial cell morphology; structure and function of cell components. growth, reproduction and enumeration of microorganisms. Aspects of microbial genetics. The effects of physical and chemical environments on microbial growth. The diversity of microorganisms and aspects of their pathogenicity in plants and animals. The role of microorganisms in the environment, their uses and aspects of microbial biotechnology.

7. ©M J Larkin Biological Sciences. The Queen’s University of Belfast. STAFF Prof Mike Larkin (Module Co-ordinator) - Rm 108, MBC Dr Leonid Kulakov (co-coordinator) – Rm OG413B, MBC Dr John McGrath – Rm LG84 MBC; Prof Sheila Patrick – Microbiology, RVH; Dr Alistair McCracken – Applied Plant Science, Newforge Lane Tel: 90 255244; Dr Elizabeth Hoey - Rm 186/182, MBC; Dr John Hallsworth - Rm LG86 MBC xt 2314 There is a web site for the course with some support material and useful links at the following address: http://www.qub.ac.uk/mlpage/courses/level1/page.html

8. ©M J Larkin Biological Sciences. The Queen’s University of Belfast. Texts Prescott L M et al. Microbiology 7/e (McGraw-Hill Higher Education) £45.59 ISBN: 0071267271 Online learning at http://highered.mcgraw- hill.com/sites/0072320419/ freely availablehttp://highered.mcgraw- hill.com/sites/0072320419/ There are others listed equally as good. Brock T D & Madigan M T. Biology of Microorganisms 12th Edition £39.98 (Pearson Education) ISBN: 0321536150 Animated tutorials (10 th Edition) at: http://wps.prenhall.com/esm_madigan_brockbio_10/5 /1459/373652.cw/index.html http://wps.prenhall.com/esm_madigan_brockbio_10/5 /1459/373652.cw/index.html Pages and Chapters will be noted for some  DIRECTED READING.

9. ©M J Larkin Biological Sciences. The Queen’s University of Belfast. ASSESSMENT Written exam - 70%. Different format this year MCQs will also be used Practical exercises - 10%. Practical test - 5% 5 elements to the test and students must be satisfactory in ALL 5 elements. Mid-semester class-test - 5% MCQs in Week 5 Group assignment work - 10%.

10. ©M J Larkin Biological Sciences. The Queen’s University of Belfast. Practical and Assignment arrangements Session A: Those on Biological Science, Biochemistry, Environmental Biology, Microbiology, Genetics, Marine Biology, Molecular Biology and Zoology degree pathways Session B: Those on Biomedical Sciences, Food Quality, Safety and Nutrition, Physiology and Anatomy degree pathways Assignment Scheduled Practical ClassesStudy Project Session AWeeks 1,3,5,8,10Weeks 1,3,5,9,11 Session BWeeks 2,4,7*,9,11Weeks 2,4,7,8,11 *For some students the practical will have to be scheduled be in week 6

11. ©M J Larkin Biological Sciences. The Queen’s University of Belfast. Group Assignment Work in groups of 4 – same as the practical sessions The topic must relate to: “A significant advance in Microbiology that relates to your degree pathway subject”. We offer advice on this in the tutorials and it is an open learning exercise that relies on your initiative. Assessment will be on a short and simple report that: Assessed in practical in weeks 10 and 11.

12. ©M J Larkin Biological Sciences. The Queen’s University of Belfast. COMPULSORY ELEMENTS Practical and tutorial attendance 80%; (with valid excuse for non attendance needed) Continuous assessment mark (practicals, tests and project) 35%; Written exam 35%. These represent the minimum requirements for modular credit. PRACTICAL SESSIONS: The class will be divided into two groups to be taught on EITHER Tuesdays OR Thursdays 3-6 pm in Lab. 117, 1st floor MBC. A list is be posted outside the Laboratory A clean white laboratory coat and a permanent, waterproof fine marker-pen will be required for ALL practical sessions. Practical manuals are available from The School Office

13. ©M J Larkin Biological Sciences. The Queen’s University of Belfast. Lecture outline History/Introduction Microbiological Techniques/ Diversity Diversity/ Structure and function Prokaryotic structure and function –Nuclear structure, cell walls etc…. Prokaryotic structure and function Bacterial growth. Bacterial Genetic systems (LK)

14. ©M J Larkin Biological Sciences. The Queen’s University of Belfast. Microbiology History A. Definition: “Microbiology is the study of organisms too small to be seen with the unaided human eye”. Diameter less than 0.1mm Some Metazoa, Protozoa and Algae. Usually Fungi, Bacteria (Archaebacteria and Eubacteria) and Viruses.

15. ©M J Larkin Biological Sciences. The Queen’s University of Belfast.

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17. Microbiology History cont…….. B. Discovery of Microorganisms (?) Antonie Van Leeuwenhoek Royal Soc London Fellow 1680-1723. Simple Microscope. 1767 Linneaus - SIX species in class “Chaos” 1838 600 TYPES known

18. ©M J Larkin Biological Sciences. The Queen’s University of Belfast. Microbiology History cont…….. C. Spontaneous generation. ABIOGENESIS. 1665 Redi. Flies from meat. 1729 Spallazani. Boiled meat infusions Late 1700’s Oxygen needed for life 1822-1895 Pasteur 1837 Schwann. Cell theory. 1877 Tyndall. Spores survive boiling.

19. ©M J Larkin Biological Sciences. The Queen’s University of Belfast. Microbiology History cont…….. D. Microbial transformations of matter 1837 Yeast-Sugar-Alcohol 1839 Leibig and Wohler 1857 Pasteur. Anaerobiosis “life without air”

20. ©M J Larkin Biological Sciences. The Queen’s University of Belfast. Microbiology History cont…….. E. Microorganisms in disease 1813 Fungi and wheat. 1845 Fungi. Potato blight. 1840 Fungi. Skin diseases. 1864 Lister and surgical asepsis (1847 Semmelweis childbed fever and asepsis!) 1876 Koch. Anthrax “Kochs Postulates” MICROBIOLOGY HAS ARRIVED. Koch. German School. Pasteur. French School. Vaccines.

21. ©M J Larkin Biological Sciences. The Queen’s University of Belfast. Microbiology History cont…….. F. The 20th century. 1900 yellow fever transmitted 1903 Antibodies 1910 First chemical antibiotics (Erlich) 1915 bacterial viruses discovered. 1928 Genetic transformation. 1929 Penicillin discovered 1941 Fungal genetics. Gene theory. 1943 Bacterial genetics. 1944 Streptomycin discovered. 1944 DNA holds the genetic code. 1953 Structure of DNA

22. ©M J Larkin Biological Sciences. The Queen’s University of Belfast. Microbiology History cont…….. G. Molecular Biology. 1961 Operon Model. E. coli. 1960’s Bacteriophage development as a molecular model. Lambda phage central to these studies 1968 Insertion sequences / transposable DNA. 1970 restriction endonucleases. Arber and Smith. 1974 onwards. Gene cloning and genetic engineering 1980’s rapid DNA sequencing and gene construction 1990’s BIOTECHNOLOGY HAS ARRIVED.  DIRECTED READING: Prescott. Chapter 1.

23. ©M J Larkin Biological Sciences. The Queen’s University of Belfast. Microbiology History cont…….. G. The genome era - crowded with discoveries. 1970’s early sequencing efforts – Sanger et al 1972 First gene sequenced Walter Frier - Ghent: bacteriophage MS2 1975-1977 Extended sequencing : Maxam Gilbert and Sanger methodologies : http://www.sanger.ac.uk/http://www.sanger.ac.uk/ 1975 The first complete DNA genome: bacteriophage φX174 1983 Mullis PCR with Tag polymerase (based on method of Kleppe 1971) 1986-1987 Automated sequencers 1995 Fluorescent dye base sequencing 1995 Sequence of smallest bacterium, Mycoplasma genitalium 1996 Archaea and yeast sequences 1997 E. coli K12 sequence – major landmark – Blattner vs Kohara race 2006 Final Human genome sequence completed 2006 High throughput pyrosequencing Metagenomics arrives!

24. ©M J Larkin Biological Sciences. The Queen’s University of Belfast. Microbiology History cont…….. Microbial genome sequencing links Sanger Institute UK http://www.sanger.ac.uk/Projects/ Lists bacterial pathogens sequenced and ongoing Joint Genome Institute USA http://www.jgi.doe.gov/ Many environmental microorganisms and metagenomic projects