Module Information For Visiting and Erasmus Students
2013/14
Department*
Microbiology
JS Modules 2013/14
Module Code*
MI3M01
Module Name*
Microbial Physiology and Biochemistry
ECTS Weighting*
Semester/term
taught*
Contact Hours*
Module Content/
Description*
10
First
56
Lectures
Microbial Physiology (A.Fleming): This course deals with bacterial motility, yeast
flocculation, chemotaxis, cell proliferation, nutrition, nutrient uptake, catabolite
repression, Embden-Meyerhof pathway, Entner Douderoff pathway, pentose
phosphate pathway, TCA cycle, the Glyoxylate by-pass, electron transport chains,
the chemiosmotic hypothesis, oxidative phosphorylation, anaerobic respiration,
diversity in energy metabolism, fermentation, biosynthesis, adaptation to nutrient
depletion and cell death.
Bacterial Surfaces (J. Geoghegan): This course will deal with aspects of bacterial
cell structure and function. Particular emphasis is placed on structures which
decorate bacterial surfaces. The structure and biosynthesis of these components
and their contributions to virulence are examined.
Protein Structure & Function (A. Khan): The lectures involve a description of
protein structure and folding, beginning with amino acid chemistry. The hierarchy
of protein folds, and the forces that shape a compact and globular 3-dimensional
structure are discussed. Specific examples are shown, such as DNA-binding
proteins, globins,and immunoglobulins to highlight the link between fold and
function. Prion proteins are discussed in the context of protein folding.
Protein Analysis (K. Mok): The lecture series will detail the different methods
used for the analysis of proteins including descriptions of techniques such as mass
spectroscopy and NMR spectroscopy. Lecture 1; The physical and analytical
chemistry of biological systems – Biophysics for the ‘rest of us’; Spectroscopy in
general. Lecture 2; UV/Vis spectrophotometry; “left or right-handed” molecules;
the world of fluorescence. Lecture 3; Partially-folded proteins; neurodegenerative
diseases; measuring protein stabilities. Lecture 4; Fluorescence polarization;
lasers; Why biochemists like to “FRET” about protein interactions. Lecture 5; Mass
spectrometry and proteomics; the structural genomics initiative.
Practicals
This course deals with preparation of inner and outer membranes of Escherichia
coli, preparation of cytoplasmic membranes of Micrococcus luteus, dry weight
determinations for cell yields of M. luteus, numeracy exercises, analytical
techniques for bacterial membranes including Lowry protein assay, solubilization
of membranes, SDS-PAGE, Western blotting and spectrophotometric assays of
membrane preparations for enzymes. The course is designed to maximize handson experience and to teach data handling and interpretation.
Assessment
Details*
MI3M01 lectures are examined during the annual examination period in Trinity
Term.
The practical is assessed at the end of the laboratory course.
Module Code*
Module Name*
MI3M02
Microbial Pathogenicity and Immunology
ECTS 10
Weighting*
Semester/term Second
taught*
Contact Hours*
56
Lectures
Module
Content/ Bacterial Pathogenicity (T. Foster):
Description*
The course covers the molecular basis of bacterial pathogenesis, including
adhesion to host cells and tissue, invasion of mammalian cells, survival within
professional phagocytes, evasion of innate immune responses and damage to host
tissue. The major bacterial protein toxins will be covered (cholera enterotoxin,
neurotoxins, pertussis, diphtheria and shiga toxins, pore-forming cytolysins, and
superantigens). Several important bacterial pathogens will be discussed including
Escherichia coli, Pseudomonas aeruginosa, Staphylococcus aureus, and Neisseria
meningitidis. Vaccines – toxoids, subunit vaccines, capsular polysaccharides, liveattenuated mutants and bacterins will also be described.
Virology I (K. Roberts):
This course discusses the diversity amongst viruses and how viruses are grouped
and classified. It describes a variety of virus replication strategies, and ways in
which viruses interact with host cells during entry and egress. Specific viruses are
showcased to highlight important aspects of virology, such as virus-host
interactions, disease, transmission and control methods. Viruses of topical
interested include: Picornaviruses; Influenza virus; Poxviruses; Papillomaviruses;
HIV; Hepatitis viruses. Ways of applying virology within industry and as future
therapeutic treatments will also be discussed.
Introduction to Immunology (C. Gardiner):
The study of the organs, cells, molecules and genes that work together in the body
to detect and respond to danger, damage, infection and malignancy. This course
introduces the cells and molecules involved and some of the mechanisms used to
exert their effects.
Practicals
(i) Medical Microbiology (T. Foster): The course begins with the normal flora of
man and will involve isolation and identification of commensal bacteria from the
skin, the nose and the mouth using selective media, identification of bacteria
using classical biochemical tests and the API system, detailed characterization of
staphylococci, measurement of antibiotic susceptibility and resistance (disc tests,
minimum inhibitory concentrations) and characterization of pseudomonads and
streptococci. Attention will be paid to performing dilutions and to manipulating
molarities and concentrations. Students will become proficient in aseptic pure
culture technique.
(ii) Virology II (K. Roberts): This course is divided into 6 sessions. Two session are
wet-laboratory practicals. The first covers aseptic technique, cell culture, safe use
of Microbiological Safety Cabinets and some data handling. The second is an
investigation into influenza virus HA and NA activity. Two sessions are selfdirected tutorials in the computer lab. One computer session investigates virus
gene sequences and evolution. The other explores the ways in which viruses are
transmitted and how we try to control them. The final two sessions are
workshops. One workshop discusses HIV replication and treatment. The other is a
series of short presentations given by the class.
MI3M02 lectures examined during the annual examination period in Trinity Term.
Assessment
Details* (i)The practical is assessed at the end of the laboratory course. The assessment
takes the form of MCQ/Short Answer/Data handling or interpretation paper.
(ii) The practical course is assessed at the end of the practical sessions.
Assessment will take the form of a laboratory report of the wet-lab practical
classes.
Module Code*
Module Name*
MI3M04
Research Essay and Transferrable Skills
ECTS 5
Weighting*
Semester/term First
taught*
Contact Hours*
15
Lectures
Module
Content/ Research Essay (A. Fleming): A list of research essay titles is provided to the JS
Description* class who then devise a selection procedure such that individual members of the
academic staff are each allocated three or four students. The essay must be
based on a current literature search of published material including reviews,
journal articles, symposia, reports and textbooks. It must not be a summary of
standard textbook information. The emphasis is on the production of an up-todate mini-review of the current literature. A key/starter reference will be provided
by the academic supervisor concerned. Approximately six weeks are allowed to
write and submit the research essay which must be typed, must not exceed 4000
words and which should be written according to the style adopted by the journal
Molecular Microbiology. More specific instructions with regard to write-up are
issued to the class at the time (early November). The deadline for handing in
essays is usually towards the end of January.
Transferable Skills (Various Staff): Tutorials will be held in both Semesters and
will cover the following topics: (i) the Central Dogma of molecular biology, (ii)
performing a search of biomedical literature using PubMed, (iii) writing a research
essay (literature review), (iv) solving problems in cell surface analysis, (v)
understanding a research paper on antimicrobial agents and writing a summary,
(vi) preparing a Powerpoint slide show, (vii) solving problems in microbial and
molecular genetics, (viii) composing a bibliography using Endnote, and(ix) revision
in eukaryotic cell biology. The course is also designed to ensure that Sophister
students in Microbiology are fully aware of the computers, computing facilities
and IT resources available to them in College.
Cell Imaging description (D. Nolan):
This lecture course will introduce students
to imaging of cells in the broadest sense from high resolution electron microscopy
to imaging of cells and organelles with advanced light microscopy. It will cover
transmission and scanning electron microscopy, and light, fluorescence,
epifluorescence and confocal microscopy. The lectures will focus on illustrating
the techniques with worked examples and will highlight the applications and
limitations of the various approaches.
Assessment is based on student attendance and participation as well as marks
Assessment given to assignments.
Details*
The review essay is internally assessed as described above.
The cell imaging component will be assessed by short test at the end of the
course.
Module Code*
MI3M04
Module Name*
Bacterial Molecular Biology & Genetics
ECTS Weighting*
Semester/term
taught*
Contact Hours*
Module Content/
Description*
10
Second
54
Lectures
Microbial and Molecular Genetics (C.J. Dorman/K. Devine):
This
course
presents an evidence-based description of the basic cellular processes of
transcription, translation and DNA replication. The approach is to discuss in detail
the players involved and their roles in each of the processes. The major
mechanisms by which bacteria regulate expression of genetic material as well as
aspects of bacterial replication and recombination will be discussed. The course
covers the major events in transcription initiation, positive and negative control of
transcription, coordinated control of transcription, the operon, the regulon, the
stimulon, an introduction to global regulation, DNA structure and gene regulation,
environmental adaptation through variations in gene expression, stereotypic and
stochastic responses, and transposition – insertion sequences IS1 and IS3
Practicals
(i) Microbial and Molecular Genetics (C.J. Dorman):
This course covers the
theory and practice of bacterial molecular genetics, with an emphasis on gene
regulation and the bacterial response to environmental stress. Practical aspects
include the use of reporter gene fusions to detect environmentally-regulated
promoters, reporter gene assays, detection of regulatory genes by transposon
mutagenesis, marker rescue, characterization of regulatory mutants and
complementation tests. The course also covers the application of whole genome
analysis methods to the study of bacterial gene expression.
(ii) Statistics Tutorials (M. Fares): The main objective of this course is to make
students see the need for understanding data analyses as a step preceding the
design of new experiments. These tutorials include: 1. Description of main
concepts in Statistics including Sampling, descriptive statistics and probability
distributions. 2. Probabilities and Probability Distributions. 3. Hypothesis testing.
4. Analysis of Variance. 5. Linearity testing of relationships between variables. 6.
Factor variance analysis and re-building of new hypothesis. The course is given in
4 sessions of two hours each and the understanding of the students is examined
through a final test, which includes 4 questions. Two of the questions are short
answers and the other two consist on developing a problem and unfolding the
possible conceptual and statistical solutions. The course is highly active and
requires the active participation of the students. This is assured by presenting
example problems and by asking students to form groups to address the problem.
Assessment
Details*
MI3M04 lectures are examined during the annual examination period in Trinity
Term.
The practical is assessed by written examination immediately after the end of the
course.
The statistics practical component is assessed by test at the end of the lecture
course.
Module Code*
MI3M05
Module Name*
Bacterial Molecular Biology & Genetics
ECTS Weighting*
Semester/term
taught*
Contact Hours*
Module Content/
Description*
10
Second
48
Lectures
Molecular Biology of Fungal & Protozoal Pathogens (A. Bell): This course covers
the following: survey of pathogenic species of fungi and protozoa; biology of
Candida, Trypanosoma, Leishmania and Plasmodium species; diseases caused by
them; molecular and cellular biology of major eukaryotic pathogens, especially
nuclear and extranuclear genomes, gene expression, variant antigen switching,
unusual metabolic pathways, chemotherapy and vaccines.
Eukaryotic Molecular & Cell Biology (U. Bond): This course will include aspects of
eukaryotic cell biology under the general headings of gene expression, protein
folding, trafficking and modification, and control of the cell division cycle.
Molecular Biotechnology (U. Bond):
This course is designed to introduce the
student to ways in which molecular biology techniques can be applied to current
problems in Industry, Agriculture and Medicine. Topics covered will include
recombinant DNA techniques, production of biological pesticides, bio-remediation
and genetic engineering in plants, large scale production of proteins in prokaryotic
and eukaryotic cells and human gene therapy.
Eukaryotic Gene Expression (M. Ramaswami): This course will cover all aspects
of eukaryotic gene expression from transcription to translation.
Cell Cycle (S. Martin): This course discusses issues relating to how cell division is
regulated by forces external to a cell (growth factors, contact with neighbouring
cells) as well as by internal forces (the tumor suppressor proteins Retinoblastoma
protein and p53) and how cancer develops as a result of mutation of many of the
genes that regulate cell division. Most of the major gene products involved in
regulating entry into the cell cycle, progression across the G1 restriction point and
through the S, G2 and M cell cycle phases are covered. The discovery of the
cyclins and cyclin-dependent kinases (CDKs) and their regulators, the CDK
inhibitors, will be discussed in some detail. The role of Rb as a brake on cell cycle
progression, p53, E2F, and their role in oncogenesis will also be examined.
Practicals
This laboratory course introduces students to a variety of techniques used in
microbial genetics, molecular biology and biotechnology. Topics will include the
life cycle of haploid and diploid cells of the common bakers’ yeast Saccharomyces
cerevisiae, mating between haploid cells and the ability of yeast strains to carry
out fermentation of sugars to alcohol. Students will also carry out a large scale
lager brew using industrial lager strains of yeast. In addition, students will develop
an understanding of commonly used techniques in microbial genetics such as
plasmid transformation, DNA amplification by polymerase chain reaction, plasmid
isolation and DNA separation by gel electrophoresis. Students will also gain
experience in recombinant protein purification and enzyme-linked
immunosorbent assay.
Assessment
Details*
MI3M05 lectures are examined during the annual examination period in Trinity
Term.
This practical is assessed at the end of the laboratory course. A written
assessment will be assigned and will include elements of problem solving.
Module Code*
Module Name*
MI3M06
Practical Applied and Environmental Microbiology
ECTS 5
Weighting*
Semester/term
Second
taught*
Contact Hours* 60
Lectures
Module This course allows students to put into practice microbiological methods in
Content/ analysis and study of environmental conditions and samples. It will also cover
Description* analytical microbiology in the food, agricultural and pharmaceutical industries
through a number of mini projects. Control of microbial growth and its assessment
will also be covered. Students work individually in this course allowing each to
develop hands-on aseptic skills, planning and data handling capabilities
Practicals
This laboratory course introduces students to a variety of techniques used in
microbial genetics, molecular biology and biotechnology. Topics will include the
life cycle of haploid and diploid cells of the common bakers’ yeast Saccharomyces
cerevisiae, mating between haploid cells and the ability of yeast strains to carry
out fermentation of sugars to alcohol. Students will also carry out a large scale
lager brew using industrial lager strains of yeast. In addition, students will develop
an understanding of commonly used techniques in microbial genetics such as
plasmid transformation, DNA amplification by polymerase chain reaction, plasmid
isolation and DNA separation by gel electrophoresis. Students will also gain
experience in recombinant protein purification and enzyme-linked
immunosorbent assay.
MI3M06 lectures are assessed at annual exams and end of year.
Assessment
Details* The practical is assessed by MCQ at the last session of the course.
Module Code*
Module Name*
MI3M07
Genomics & Current Topics in Microbiology
ECTS
10
Weighting*
Semester/term
Second
taught*
Contact Hours*
29
Genomics and Systems Biology (F. Wellmer): The course offers an introduction
Module into global and system-wide analysis methods used in biology. Topics discussed in
Content/ the class include: What does -omics mean? What is Systems Biology? What is a
Description* biological system? Reductionist vs. system approaches in biology; how a genome
is sequenced: BAC-to-BAC Sequencing and Shotgun Sequencing Example: The
Human Genome Project. Gene Finding: Expressed Sequence Tags and
Computational Gene Prediction; Comparative Genomics; Personalized Medicine;
Ultra-High Throughput Sequencing; Functional Genomics: Microarray technology;
Example: breast cancer profiling; Example: gene expression profiling during
Drosophila development; Gene finding by microarrays. Gene Regulatory
Networks: Characteristics of a network and network Motifs; Identification of cis-
regulatory elements by comparative genomics; Proteomics: 2D-gel
electrophoresis, protein identification by mass-spec analysis; Protein-protein
interaction networks (yeast 2-hybrid screening, tandem affinity purification).
Bioinformatics (K. Wolfe): This lecture course introduces bioinformatics
databases and software, and their uses in genomics. Topics include: Evolution and
development of sequence databases. Genome browsers. Example - the human
alpha-globin gene. Structure of a DNA sequence database entry. Gene duplication
and protein families.
The NCBI database system. Literature databases: PubMed, Science Citation Index,
Google Scholar. Sequence variation and haplotypes: SNP databases. Haplotypes
and the HapMap project. Mutations and genetic disease: the OMIM database.
Personal genomics: example – 23andMe. Genetic determinism and your genome.
Sharing of haplotypes among relatives. Simple web tools for working with
sequences. Example – the SMS sequence manipulation suite. Sequencing and
sequence assemblers (example - CAP3). Other databanks in molecular biology:
protein, protein structures, gene expression databases, metabolic pathway
databases. Comparative genomics: Genome organization in prokaryotes vs
eukaryotes. What can happen to a gene during evolution? Conservation of
noncoding sequences (example – mammalian genomes in the UCSD browser).
Model organism genomics and databases (example – the Saccharomyces genome
database). Gene ontology: making sense of lists of genes. Sequence comparisons:
Evolution and genomic change. Homologues and gene/protein families. Pattern
matching. Dot matrix plots. Sequence alignment – pairwise. Global and local
alignments. Scoring schemes and optimal alignments. Multiple sequence
alignment (CLUSTAL, Muscle). BLAST for similarity searching of databases.
Interpreting BLAST results: HSPs and E-values. The importance of annotation (or
lack of annotation). Sequence filtering. Phylogenetics: Interpreting phylogenetic
trees. Constructing phylogenetic trees: clustering methods, cladistic methods,
Bayesian (ML) methods. Artifacts due to rapid sequence evolution.
Current Topics in Microbiology (Micro Staff): This course will feature tutorials
with various members of staff in which current topics in microbiology will be
discussed. The course may require the student to attend selected Microbiology
seminars given by visiting academics, which will then be discussed. Alternatively,
tutorials may be based on recent scientific discoveries or topics of interest
highlighted in the press. The course is designed to be flexible in order to
accommodate current microbiological topics of interest and will allow the student
to actively lead or participate or discussions.
OR
Broad Curriculum Cross Faculty course (5 ECTS Credits)
Assessment
Details* MI3M07 lectures are examined during the annual examination period in Trinity
Term. A research essay will also be assessed.