Module Information For Visiting and Erasmus Students 2014/15

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Module Information For Visiting and Erasmus Students

2014/15

Department*

Microbiology

JS Modules 2013/14

Module Code* MI3M01

Module Name* Microbial Physiology and Biochemistry ECTS Weighting* 10 Semester/term taught* First Contact Hours* 56 Module Content/ Description* 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;

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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 hands-‐ on 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* MI3M02

Module Name* Microbial Pathogenicity and Immunology

ECTS Weighting* 10 Semester/term taught* Second Contact Hours* 56 Module Content/ Description* Lectures

Bacterial Pathogenicity (T. Foster):

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, live-‐

attenuated mutants and bacterins will also be described.

Virology I (K. Roberts):

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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 self-‐ directed 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.

Assessment

Details*

MI3M02 lectures examined during the annual examination period in Trinity Term. (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.

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Module Code* MI3M04

Module Name* Research Essay and Transferrable Skills

ECTS Weighting* 5 Semester/term taught* First Contact Hours* 15 Module Content/ Description* Lectures

Research Essay (A. Fleming): A list of research essay titles is provided to the JS 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-‐to-‐ date 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.

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Assessment

Details*

Assessment is based on student attendance and participation as well as marks given to assignments.

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* 10 Semester/term taught* Second Contact Hours* 54 Module Content/ Description* 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

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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.

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* 10 Semester/term taught* Second Contact Hours* 48 Module Content/ Description*

There will be some changes to this module and details have yet to be confirmed. Please contact the Department to discuss possible changes.

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.

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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.

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* MI3M06

Module Name* Practical Applied and Environmental Microbiology

ECTS

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Semester/term taught* Second Contact Hours* 60 Module Content/ Description* Lectures

This course allows students to put into practice microbiological methods in analysis and study of environmental conditions and samples. It will also cover 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.

Assessment

Details*

MI3M06 lectures are assessed at annual exams and end of year. The practical is assessed by MCQ at the last session of the course.

Module Code* MI3M07

Module Name* Genomics & Current Topics in Microbiology

ECTS Weighting* 10 Semester/term taught* Second Contact Hours* 29 Module Content/ Description*

There will be some changes to this module and details have yet to be confirmed. Please contact the Department to discuss possible changes.

Genomics and Systems Biology (F. Wellmer): The course offers an introduction into global and system-‐wide analysis methods used in biology. Topics discussed in the class include: What does -‐omics mean? What is Systems Biology? What is a 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

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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.

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Assessment

Details* MI3M07 lectures are examined during the annual examination period in Trinity

Term. A research essay will also be assessed.