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Home >> Faculties & Departments >> Microbiology >> CPOBLab
  • Bacterial Stress Response Group ››

    Semester I: MI211
    Semester II: MI212


    On behalf of the Department of Microbiology I would like to welcome you all to second year! We have designed a Microbiology course which we hope you will find stimulating and rewarding. The aim of the course is to provide you with a solid grounding in the fundamentals of Microbiology. Much of the information will be presented to you at the weekly lectures (3 per week) and these will be delivered by several different members of staff from the Department of Microbiology, including myself. In addition to the lectures the basic skills of a microbiologist will be taught at weekly practical sessions. The aim here is to give you as much “hands-on” experience as possible. We hope that you all enjoy the course and through it gain an understanding of the many ways that microbiology impacts our daily lives.

    This handout contains all the general information that you will need to know about how the Microbiology course is organised. It includes information on: (i) where and when the lectures take place; (ii) where and when the practicals take place; (iii) how the lecture and practical courses are assessed; (iv) lecture content; (v) the recommended course textbook; and (vi) where to find additional information. Please read it carefully and retain it throughout the year for reference.

    If you have difficulties with any aspect of the course please feel free to contact me. You can find me on the ground floor of the Department of Microbiology, either in my office (Room 105B) or in my lab (Room 113).

    Course Director,
    Dr Conor P O’Byrne.






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    The venues and times for 2nd Year Microbiology are as follows:

    • Monday, 9.00 am, Lecture Hall AM200, Patrick F Fottrell Theatre, Arts Millennium Building.
    • Wednesday, 11.00 am, Lecture Hall AM250, Colm O h’Eocha Theatre, Arts Millennium Building.
    • Thursday, 10.00 am, Lecture Hall AC003, D’Arcy Thompson Theatre, Concourse. 

    Students are requested, and expected, to attend all lectures. 

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    All Laboratory Practicals in both semesters take place in the 2nd Year laboratory, located on the first floor of the Department of Microbiology, NUI Galway. 

    For Laboratory Practicals, the 2nd Year Microbiology class is divided into three groups. Placement in a particular group is determined by the Department and is based on the students timetable with respect to their other 2nd Year subjects. The times for the 2nd Year Microbiology Laboratory Practicals are: 

    • Group A: Monday from 2.00 pm – 5.00 pm
    • Group B: Tuesday from 10.00 am – 1.00 pm
    • Group C: Wednesday from 1.00 pm – 4.00 pm

    Attendance at Laboratory Practicals is compulsory. All students will need a hard-cover laboratory note-book (the “Day Book”) and a white laboratory coat. Laboratory manuals are necessary and can be obtained from the Department of Microbiology.


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    2nd Year Microbiology students are recommended to obtain the following text-book for the 2nd Year Microbiology Lecture course:

    Brock “Biology of Microorganisms”, 11th Edition 
    by Madigan, Martinko & Parker. 

    This book is published by Prentice Hall International Inc. (ISBN 0-13-196893-9), and can be obtained from the University Bookshop, NUI Galway at a cost of €66.45. (Note: The 9th or 10th editions will also be ok for this course.)

    Students are encouraged to purchase their own copy of this textbook as an aid to revision, however there are 30 copies in the library (5 of which are on desk reserve).

    Click image below for link to textbook web site

    Brock, 11th Edition

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    As with many other 2nd Year Science subjects, the overall marks are composed of:

    • Semester I Written Exam Paper = 35% 
    • Semester II Written Exam Paper = 35% 
    • All Laboratory Practical Sessions = 30% 

    Progression to Honours Micrbiology: Students wishing to progress to honours Microbiology in 4th year must achieve at least 50% overall in 2nd year Microbiology.

    Students failing to reach this standard will be excluded from accessing 4th year Microbiology, unless they achieve 55% or greater in 3rd year Microbiology. However, such entry in not guaranteed and will be at the discretion of the Science Faculty Executive Committee in consultation with the Department of Microbiology.

    Please note that these academic standards are currently under review within the Science Faculty.

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    The examination format for the Semester I Written Exam Paper is: 
    Questions 1 & 2: Cytology, Dr. Cyril Carroll 
    Questions 3 & 4: Genetics, Dr. Aoife Boyd 
    Questions 5 & 6: Physiology, Dr. Conor O’Byrne 
    Questions 7 & 8: Metabolism, Dr. Thomas Barry 
    Students must answer five of these eight questions within three hours. 
    The examination format for the Semester II Written Exam Paper is: 
    Question 1: Classification and Evolution, Dr Aoife Boyd
    Question 2: Classification and Evolution, Dr Ger Fleming
    Question 3&4: Microbial Ecology & Waste Treatment Systems, Dr Vincent O’Flaherty 
    Question 5: Virology, Prof. James Houghton
    Question 6&7: Microbes and Disease, Dr. Conor O’Byrne

    Students must answer five of these seven questions within three hours. 
    The Examination Result Grades applicable are: 
    % Range: 100-70%   69-60%   59-55%   54-50% 
    Grade:            A                B             C+             C- 
    % Range: 49-40%     39-35%   34-30%    29-0% 
    Grade:           D                E+           E-              F 

    - The pass standard is 40% or greater
    - First class honour is 70% or greater
    - Second class honour, grade I is 60-69%
    - Second class honour, grade II is 50-59%

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    One third of the marks allocated to the practicals are awarded for attendance (i.e. you can obtain 10% of the total marks for the year by attending all your practicals). If you have a legitimate excuse (e.g. medical reason) you will not lose marks, provided that you supply a medical certificate. Please give medical certs to the Microbiology secretary – Ms Caroline O’Connell, room 202 (do not give medical certs to the practical demonstrators). The remaining two thirds of the marks are allocated for practical write-ups in your Day Book (i.e. 20% of total years marks). These are to be written up on the day of the practical, and signed by a demonstrator. Please note, write-ups that are not signed and stamped by a demonstrator will not be marked. Day Books must be submitted for correction at the end of each semester. Failure to hand your Day Book in on time will lead to a loss of all marks for that semester (i.e. 10% of total years marks). Please note, it is the responsibility of the student to ensure that their Day Book is handed in to the Department and that their submission is registered in our records.

    IMPORTANT: Please note that if you fail to attend a practical session your Day Book write-up will not be marked for that practical. You will therefore lose both the attendance marks and write-up marks allocated to that practical. (Again, this excludes students who have a legitimate medical reason for their absence.) 

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    Notices relevant to 2nd year Microbiology will be posted on the 2nd year notice board, which is located on the first floor of the Microbiology Department, next to the Tyndall lecture theatre. 
    Information relevant to the course will also appear on the Q drive from time to time, at the following location; Q:\Microbiology\Conor OByrne\2nd year\ . 

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    SEMESTER I : MI211



    Lecture 1 - Introduction.
    LECTURER: Dr. Conor O’Byrne
    LECTURE DATE: Thursday September 6th
    This lecture will provide an overview of the first semester course. Information will be given on the schedule and requirements for the 2nd Year Microbiology laboratory practical course. It will also contain important information on how the course is assessed.


    Lectures 2 & 3. - Cell types and techniques to study cell cytology.
    LECTURER: Dr. Cyril Carroll
    LECTURE DATES: September 10th  & 12th   
    Procaryotic and Eucaryotic cells. Bacterial cell size, shape and arrangement. Cytological methods include microscope types, bacterial staining techniques, and cell disruption techniques.

    Lecture 4. - Bacterial cell envelope components.
    LECTURER: Dr. Cyril Carroll
    LECTURE DATE: September 13th   
    The cell envelope, Gram positive & Gram negative. The cell wall structure. Peptidoglycan.

    Lecture 5. - The bacterial cell membrane.
    LECTURER: Dr. Cyril Carroll
    LECTURE DATE: September 17th   
    Bacterial cell membrane structure and function. Phospholipids and proteins. Biosynthesis. Diffusion and transport. ATP synthesis. Electron transport chain. The outer membrane, structure and function. Lipopolysaccharides. Zones of adhesion. Periplasmic space. The cell capsule.

    Lecture 6. - Procaryotic & Eucaryotic intercellular components.
    LECTURER: Dr. Cyril Carroll
    LECTURE DATE: September 19th
    Differences between Procaryotic & Eucaryotic intercellular components. Plasma membranes.DNA structure, replication and segregation. Ribosome structure and function. Endoplasmic reticulum. Plasmids. Mesosomes. Gas vacuoles. Inclusion bodies.

    Lecture 7. - Bacterial endospores.
    LECTURER: Dr. Cyril Carroll
    LECTURE DATE: September 20th   
    Endospore structure, function and formation.

    Lecture 8. - Bacterial cell motility.
    LECTURER: Dr. Cyril Carroll
    LECTURE DATE: September 24th   
    Methods of study. Flagellar structure, Gram positive & Gram negative. Chemotaxis. Pili.

    Lecture 9. - The cell cyle.
    LECTURER: Dr. Cyril Carroll
    LECTURE DATE: September 26th
    The Procaryotic cell cycle. The Eucaryotic cell cyle, G1, S, G2 & M phases.


    Lectures 10 & 11 - DNA as Information Molecule
    LECTURER: Dr. Aoife Boyd
    LECTURE DATES: September 27th & October 1st   
    Information flow in the cell. Information storage in DNA. DNA and genome structure. DNA replication during cell division.

    Lectures 12 & 13 - Protein Synthesis
    LECTURER: Dr. Aoife Boyd
    LECTURE DATES: October 3rd & 4th   
    Genes and gene expression. Transcription of genetic information from DNA to RNA. Translation of RNA into protein. The genetic code. The tRNA-amino acid complex as interpreter.

    Lecture 14 - Genetic Variation and Spontaneous Mutation
    LECTURER: Dr. Aoife Boyd
    LECTURE DATES: October 8th
    Inheritable changes in DNA. Importance of genetic variation. Spontaneous mutation. Consequences of mutations.

    Lectures 15 &16 - DNA Transfer
    LECTURER: Dr. Aoife Boyd
    LECTURE DATES: October 10th & 11th    
    Genome rearrangements. Genetic recombination. Mobile genetic elements. Horizontal DNA transfer by transformation, transduction and conjugation.

    Lectures 17 - Genetic Engineering
    LECTURER: Dr. Aoife Boyd
    LECTURE DATES: October 15th  
    Natural and engineered gene exchange. Genetically modified microorganisms. Transgenic organisms.


    Lecture 18 - Nutritional Requirements
    LECTURER: Dr. Conor O’Byrne
    LECTURE DATE: October 17th
    Microbial nutritional types. Elemental requirements of micro-organisms including carbon, hydrogen, phosphorous and sulphur. Requirement in metallic elements and their role in metabolism. Accessory growth requirements.

    Lecture 19 - Isolation of Microorganisms
    LECTURER: Dr. Conor O’Byrne
    LECTURE DATE: October 18th   
    Survival and growth of micro-organisms in oligotrophic environments. Laboratory culture in liquid and solid media. Isolation of bacteria and the techniques employed. Selective methods, including selective enrichment and selective repression. Differential media.

    Lectures 20, 21 & 22 - Physical Conditions Affecting Growth
    LECTURER: Dr. Conor O’Byrne
    LECTURE DATES: October 22nd, 24th & 25th
    The effects of temperature, gaseous atmosphere, pH, osmotic concentration, water activity, electromagnetic radiation and hydrostatic pressure on microbial growth will be discussed. Classification of micro-organisms based on these parameters will be elucidated, as will their influence on the metabolism and the occurrence of various species in different environments.

    Lecture 23 - Microbial Growth
    LECTURER: Dr. Conor O’Byrne
    LECTURE DATE: October 31st
    Microbial replication including binary fission of bacteria, budding of yeasts and filament formation in fungi. Bacterial growth in batch culture and the mathematics of exponential growth. Continuous culture by chemostat and turbidostat.

    Lectures 24 & 25 - Quantitative Measurement of Microbial Growth
    LECTURER: Dr. Conor O’Byrne
    LECTURE DATES: November 1st & 5th   
    Measurement of the microbial population by (i) quantification of cell numbers, (ii) quantification of cell mass, and (iii) microbial activity will be discussed. The techniques involved such as plate counting, membrane filtration, end-point dilution, microscopic counts, electronic cell counter, dry weight and turbidimetric measurements, radiometric methods, electrical impedance, ATP levels and dye reduction tests will be reviewed.


    Lecture 26 - Introduction to Metabolism.
    LECTURER: Dr. Thomas Barry
    LECTURE DATE: November 7th   
    Introduction to biological energy systems, with emphasis on integrated systems of metabolism in living organisms. Central metabolic systems. Introduction to concepts such as nutrients, catabolism and anabolism. The placement of microorganims into metabolic classes such as phototrophs, chemotrophs and chemoorganotrophs.

    Lecture 27, 28 & 29 - The Fundamentals of Metabolism.
    LECTURER: Dr. Thomas Barry
    LECTURE DATES: November 8th, 12th & 14th  
    The three fundamentals of metabolism. (1) The laws of thermodynamics, free energy reactions. (2) Enzyme catalysis. (3) Oxidation-Reduction reactions. Release and harvesting of energy in metabolic systems. The currency of living cells. High energy compounds.

    Lecture 30, 31 & 32 - Microbial Metabolic Systems.
    LECTURER: Dr. Thomas Barry
    LECTURE DATES: November 15th, 19th, 21st & 22nd
    Nutrient uptake, activation and streamlining in bacteria. Catabolic systems of bacteria. Fermentation systems, aerobic and anaerobic respiration systems. Substrate level phosphorylation. Energy conservation and the electron transport chain. Oxidative phosphorylation. Energy costs and energy balance sheets of metabolic systems. Oxygenic photosynthesis. The Light reactions, Photosystems I and II. High energy compound synthesis. Noncyclic photophosphorylation. Anoxygenic photosynthesis. The dark reactions, autotrophic CO2 fixation. The Calvin cycle.

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    Lecture 1: Microbial Classification Systems
    LECTURER: Dr. Aoife Boyd
    LECTURE DATE: January 14th   
    Importance of microbial classification systems. Domains of life: Bacteria, Archaea and Eukarya. Hierarchial organisation. Phenotypic Classification: Traditional and standard methods for classification and identification of microbes based on appearance, behaviour and cellular composition.

    Lecture 2 & 3: Genotypic and Phylogenetic Classification
    LECTURER: Dr. Aoife Boyd
    LECTURE DATE: January 16th & 17th   
    Newer approaches to classification and identification of microbes based on genetic characteristics. Understanding and establishing evolutionary relationships between microbes. Small SubUnit RNA as target molecule for phylogenetics and for identification.

    Lecture 4-7: Microbial Taxonomy and Nomenclature.
    LECTURER: Dr Ger Fleming
    LECTURE DATE: January 21st, 23rd, 24th, & 28th   
    The previous lecture series (Dr. Boyd) has given you an insight into how microorganisms are classified into their various groupings using classical and molecular techniques.  Conventionally, bacteria are grouped (systematics) using criteria contained in Bergey’s Manual of Systematic Bacteriology.  These tomes (consisting of five volumes) provide the professional microbiologist with the foundations/details of microbial taxonomy. They are far too complex and are perceived as stoical when used as a teaching tool. This series of lectures is designed to give you an insight into the vast diversity of bacteria that are contained in this unique ecosystem called earth. The approach we are going to take is quiet different.  Whilst recognisance will be paid to the taxonomic principles contained within Bergey’s manual, we will investigate the characteristics of bacteria under the following headings: (1) Bacteria with industrial applications, (2) Bacteria that are relevant from an environmental perspective, (3) Medically important bacteria and, (4) the Cyanobacteria. The lecture series will mainly be based on chapter twelve of Brock and details will be provided throughout the course of the lecture series on how possible questions should be attempted in the summer examination.


    Lectures 8 to 14 - Animal Viruses
    LECTURER: Prof. James A. Houghton
    LECTURE DATES: January 30th, 31st, February 4th, 6th, 7th, 11th, & 13th.
    The composition, morphology and classification of animal viruses. The life cycle of typical animal viruses. Viral disease of Man and animals (including influenza, measles, chickenpox, smallpox, German measles, hepatitis, herpes, rabies, myxomatosis, etc.). Chronic viral infections. "Slow" viruses and prions. Viruses and cancer.


    Lectures 15 and 16:
    LECTURER: Dr. Vincent O’Flaherty
    LECTURE DATES: February 14th & 18th   
    The microbial planet. Ecosystems and habitats. What roles do microbes play in the environment? Introduction to microbial ecology.

    Lecture 17:
    LECTURER: Dr. Vincent O’Flaherty
    LECTURE DATES: February 20th 
    Biogeochemistry and biogeochemical cycles – how do they drive the biosphere? The role of microorganisms in primary production and decomposition.

    Lectures 18 & 19 - Biogeochemical cycling of Carbon, Nitrogen & Phosphorus (1).
    LECTURER: Dr. Vincent O’Flaherty
    LECTURE DATE: February 21st & 25th    
    The biological Carbon cycle in terrestrial and aquatic ecosystems. The impact of humans on the carbon cycle – global warming.

    Lectures 20 & 21 - Biogeochemical cycling of Carbon, Nitrogen & Phosphorus (2).
    LECTURER: Dr. Vincent O’Flaherty
    LECTURE DATE: February 27th & 28th    
    The biological nitrogen and phosphorus cycles. Primary microorganisms involved. Environmental consequences of these cycles.

    Lectures 22 & 23 - Waste and wastewater treatment (1).
    LECTURER: Dr. Vincent O’Flaherty
    LECTURE DATE: March 3rd & 5th    
    Waste treatment - why? Objectives of waste treatment: 1. To destroy/improve organic compounds in waste materials. 2. To destroy pathogens. 3. Biotransformation to maintain environmental quality.

    Lecture 24 - Waste and wastewater treatment (2).
    LECTURER: Dr. Vincent O’Flaherty
    LECTURE DATE: March 6th
    Aerobic and anaerobic wastewater treatment systems and biology. The role of biofilms in these systems.


    Lecture 25 - 27:  – Pasteur and Koch; the founding fathers of Medical Microbiology.
    LECTURER: Dr. Conor O’Byrne
    LECTURE DATE: March 10th, 12th, & 13th
    A historical overview of the roles played Louis Pasteur and Robert Koch in establishing that microorganisms are responsible for decay and disease. Pasteur’s Swan-neck flask experiments and the debunking of the theory of “Spontaneous generation”. “Koch’s postulates” in the context of anthrax and tuberculosis.


    Lecture 28 – The commensal microflora of man.
    LECTURER: Dr. Conor O’Byrne
    LECTURE DATE: March 31st
    The normal (commensal) flora of humans. Factors affecting the profile of microorganisms found on host surfaces. Examination of the microflora found at different anatomical locations including, skin, upper and lower respiratory tract, eye (conjunctiva), gastrointestinal tract and the urogenital tract. Highlight members of the normal flora that are known pathogens.

    Lecture 29 – Host defence against invading microorganisms: The immune system.
    LECTURER: Dr. Conor O’Byrne
    LECTURE DATE: April 2nd
    The human immune system. Specific and non-specific defence mechanisms against microorganisms. Phagocytosis. Anitibodies and antigens. The structures and roles of the different classes of antibodies. The complement system. Primary versus secondary immune responses.

    Lecture 30 – Anthrax and Bio-terrorism
    LECTURER: Dr. Conor O’Byrne
    LECTURE DATE: April 3rd   
    A historical overview of bio-terrorism. Routes of infection by Bacillus anthracis and clinical manifestations of anthrax. Practical implications of using B. anthracis as an agent of biological warfare.

    Lectures 31 – GI infections: Escherichia coli.
    LECTURER: Dr. Conor O’Byrne
    LECTURE DATE: April 7th   
    Commensal versus pathogenic E. coli strains. How E. coli strains are characterised by serotype. Enteropathogenic E. coli (EPEC), Enterotoxigenic E. coli (ETEC) and Enterohemorrhagic E. coli (EHEC). Symptoms and prevention of infection.

    Lectures 32 - Helicobacter pylori and ulcers.
    LECTURER: Dr. Conor O’Byrne
    LECTURE DATE: April 9th   
    Recent discovery of the causative agent of stomach ulcers in humans: Helicobacter pylori and Koch’s postulates. Clinical symptoms of infection with H. pylori. Strategies used by H. pylori to survive in the human stomach. Detection and treatment of the disease.

    Lecture 33 – Summary and exam tips.
    LECTURER: Dr. Conor O’Byrne
    LECTURE DATE: April 10th  
    Summary and conclusion of the “Microbes and disease” lectures. Advice on how to approach the end of year written exam in Microbiology. Course feedback questionnaires.

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    Bacterial Stress Response Group