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School of Biology


Biology Module & Handbook Catalogue

see also: degree programme designer

This page lists biology undergraduate degree modules.
To view further details, please click on module titles.
To reorder this list, please click column headings (order by module code to view in year sequence)

Course Planning
code
title
(click title for further details of each module)
organiser
poster
handbook
(uni password)

BL4286
Advanced topics in Ecology and Evolution
Dr David Shuker
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pdf available
 

Advanced topics in Ecology and Evolution
code: BL4286
credits: 15
year: Senior Honours
semester: 2
description:

In this module, we will consider, from both molecular and whole organism approaches, a number of outstanding questions currently facing ecologists and evolutionary biologists today. These questions include why we get old and why we have sex, through to why the world is (mostly) green and how will life on earth come to an end. These questions will be relevant to both our understanding of the evolution and maintenance of the biosphere as we see it today, and also in terms of understanding humanity’s place in that biosphere. We will take Sherratt & Wilkinsons’s (2009) recent book Big Questions in Ecology and Evolution as our starting point, with student-led seminars bringing us classic and contemporary primary literature to address the topics in more detail. The result will be an exciting opportunity to get to grips with a number of big problems in ecology and evolution, from the perspective of the very latest research in those areas.

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BL3319
Animal Behaviour: a quantitative approach
Prof Kevin Laland
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Animal Behaviour: a quantitative approach
code: BL3319
credits: 20
year: Junior Honours
semester: 2
description: This module is designed to provide a broad and multifaceted perspective on animal behaviour, emphasising contemporary theoretical, mathematical and statistical approaches to the discipline. Nobel-Prize-winning ethologist, Niko Tinbergen, pointed out that to understand behaviour fully researchers had to answer four types of questions, about its causation, function, development and evolution. All four areas are covered in the course, which includes lectures on the genetic, neural, physiological and experiential (i.e. learning) influences on behaviour; behavioural development; foraging; sexual behaviour, sexual selection and mate choice; communication, cooperation and culture. The course contains extensive material of a formal theoretical nature, and emphasizes quantitative skills throughout. Students will be introduced to new mathematical and statistical approaches within the field.
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BL4281
Animal communication and cognition
Dr Vincent Janik
pdf available
pdf available
 

Animal communication and cognition
code: BL4281
credits: 15
year: Senior Honours
semester: 1
description: Learning to produce sounds is a particularly interesting subject as far as humans are concerned because it is such a notable feature of our own species. Why do we show it, and how did it evolve? As there is little evidence of it in any other primates we need to look further afield for clues. It is found in several other mammalian orders and in three orders of birds, and the evidence for it and nature of it will be examined in these examples. We will discuss why selection may have favoured it in each case. We will also consider vocal learning in a broader sense, including its use in animals that do not themselves produce sounds.
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BL3316
Animal Plant Interactions
Prof Pat Willmer
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pdf available
 

Animal Plant Interactions

code: BL3316
credits: 20
year: Junior Honours
semester: 2
description: This module concerns the coevolution of plants and animals, including the ecological, behavioural and physiological aspects of their interactions. Pollination biology and the constraints on participating plants and animals are dealt with in depth, including applied aspects of crop pollination, and this is followed by a review of seed dispersal. Then patterns of herbivory by insects, vertebrates and other animals are considered, illustrating the interactions of plant physical and chemical defences and herbivores reciprocal adaptations from feeding specializations and host plant selection through to detoxification systems and life history adaptations. Interactions with third parties are also explained, especially plant-fungus-insect systems. There is an introduction to other tritrophic interactions (whereby plants can recruit herbivores enemies as part of their defences, or recruit ants as biotic plant guards), to insects as plant pests, and to integrated and sustainable approaches to control measures and plant protection.
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BL4211
Antimicrobials – mode of action and resistance
Dr Peter Coote
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Antimicrobials – mode of action and resistance

code: BL4211
credits: 15
year: Senior Honours
semester: 1
description: This module will commence by establishing the fundamental basis of antimicrobial efficacy in terms of selective toxicity, with a brief history of antimicrobials and factors that make the ideal antimicrobial. This will be followed by: i) study of the known inhibitory action of antibacterial and antifungal drugs at the molecular level, and ii) study of the molecular basis of microbial resistance to these drugs. Lastly, potential new sources of antimicrobials will be considered, particularly antimicrobial peptides and ‘natural’ antimicrobials.
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BL3308
Aquatic Ecology
Dr Iain Matthews
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Aquatic Ecology

code: BL3308
credits: 20
year: Junior Honours
semester: 1
description: This module introduces the ecology of aquatic systems beginning with a description of the problems of life in a fluid medium. The module then considers the contrasting conditions that are inherent in freshwater, estuarine and marine systems. The influence of global climate variation and the close coupling between land and sea will be emphasised. Case studies will then be used to introduce the ecology of a variety of aquatic systems including tropical, temperate and polar systems.
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BL4215
Bacterial virulence factors
Dr Uli Schwarz-Linek
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Bacterial virulence factors
code: BL4215
credits: 15
year: Senior Honours
semester: 1
description:

In order to establish an infection in a host, pathogenic bacteria rely on mechanisms to adhere to host tissue, gain entry into cells, escape the hosts immune response and spread and survive within or on the host. These processes are mediated by bacterial virulence factors, i.e. proteins and other bacterial products that utilise and subvert diverse host cellular processes for the benefit of the pathogen. In this module students will explore how structural biology has led to significant breakthroughs in understanding the molecular bases of some important bacterial infections.

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BL2104
Biochemistry & Molecular Biology
Dr John Ingledew
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Biochemistry & Molecular Biology

code: BL2104
credits: 30
year: Second Year
semester: 2
description: This module builds on BL1201 Molecular Biology. The module will further develop the
understanding and application of techniques, skills and concepts, which are integral to the revolution that has occurred in the biological sciences in recent years. The module is essential underpinning for all branches of modern biology and biochemistry. The lectures include coursework on biological molecular architecture, cellular architecture, enzymes & metabolism, genomics and conclude with an introduction to the molecular basis of
infection and immunity. The laboratory element will develop practical skills and the use of bioinformatics resources.
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BL4219
Biocontrol: microbes as agents of biological control of pests
Dr Jim Kinghorn
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Biocontrol: microbes as agents of biological control of pests
code: BL4219
credits: 15
year: Senior Honours
semester: 1
description: Not available in 2011/12. Biocontrol is attracting interest as a possible replacement for chemical control of pests; a natural enemy such as a predator or parasite of the organism to be controlled is searched for from the wild and then developed as a control system. Microbes have wide and varied interactions with most organisms including pests, and
provide a pool of candidates for biocontrol measures. The microbial biocontrol agent is grown in large amounts in an industrial laboratory and tested rigorously against the target pest, as well as on a range of other organisms to determine host range and to estimate the potential impact on the environment.  This module will explore the possible use of microbes in the biological control of pests to replace harmful chemicals - the success stories, the failures, the shortcomings. In addition the future of biocontrol will be discussed.
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BL4293
Bioethics
Dr Morven Shearer
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Bioethics

code: BL4293
credits: 15
year: Senior Honours
semester: 1
description: Not available in 2011/12. The field of bioethics is rapidly expanding, as scientific discoveries push back boundaries and raise new questions and concerns, not just for the scientists involved, but for society as a whole. This module will begin by introducing the various schools of ethical thought used in considering bioethical dilemmas and will then move on to look at a number of traditional and emerging areas in bioethics, including topics such as research ethics, science in society, start of life/end of life issues, environmental ethics, genethics and neuroethics. Emphasis will be placed on the reading of key primary papers and case studies prior to each class, and informed discussion and debate within the teaching session will be encouraged.
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BL4273
Bioinformatics for Biologists
Dr Daniel Barker
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Bioinformatics for Biologists
code: BL4273
credits: 15
year: Senior Honours
semester: 1
description:  This module is about using computers to search and study protein and DNA sequences, and related data such as mRNA expression levels. Vast quantities of such data are publicly available, and, if viewed in the right way, can provide strong evidence concerning function, structure, and evolution of DNA, RNA, proteins and genes. Because of this, computational analysis has become a crucial component of modern biology, including biochemistry, molecular biology, ecology, evolutionary biology and biomedical research. With hundreds of genome sequences and vast quantities of expression data available, the approach has greater potential than ever before. This module will give an overview of the data, software and methods of analysis, and in-depth practical training in applying bioinformatics techniques to questions of biology and biomedical research. Case studies where researchers use genomes to ask questions about divergence, adaptation and speciation will be discussed. The emphasis of the module is not mathematical, but rather concerns data, the general features of methods, use of software, applications relevant to biology, and results. The module will involve use of computers and simple computer programming, for which training will be provided as part of the module.
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BL4282
Biology and Behaviour of Social Insects
Prof Pat Willmer
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Biology and Behaviour of Social Insects
code: BL4282
credits: 15
year: Senior Honours
semester: 2
description: This module will examine and compare the biology of the four main groups of social insects: termites, ants, wasps and bees. Sociality in other groups (aphids, beetles) will also be considered briefly. Topics will include the evolution of sociality, social organisation and social control systems, reproductive strategies, and diverse communication modes including pheromonal systems, acoustic systems, and ‘bee dances’. Aspects of foraging behaviour and learning abilities will also be considered, particularly for ants (leaf cutter ants, army ants, slave-making ants) and for bees both eusocial and semi-social. There will be strong evolutionary, ecological and behavioural themes, and relevance also to conservation issues.
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BL1101
Biology I
Dr V Anne Smith
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Biology I
code: BL1101
credits: 20
year: First Year
semester: 1
description: This module is an introduction to molecular and cellular biology. It covers cell diversity and the origins of life, cellular structures and fundamental processes. The central dogma of molecular biology is investigated through the examination of the structure and function of DNA, RNA and proteins, and how this knowledge led to modern developments in biotechnology. The final section of the module gives an introduction into molecular and population genetics with an emphasis on the process of evolution. Throughout the module the lecture material is complemented by extensive practical classes where biological laboratory techniques are taught an practiced through, for example, microscopy, DNA isolation, dissection and thin layer chromatography.
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BL1102
Biology II
Dr Iain Matthews
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Biology II
code: BL1102
credits: 20
year: First Year
semester: 2
description: This module provides an introduction to the diversity of life on Earth and will address key elements of organismal and ecological aspects of life. The module is divided into several sections beginning with the classification of life and an introduction to the kingdoms Monera, Fungi and Protista. Photosynthesis, respiration and the evolution and diversity of plants will be studied. Students will then look at the diversity of animals in the sea and the movement of some groups onto land. The module will also provide an introduction to animal behaviour and developmental biology, before finishing off by introducing ecology and the various factors promoting and threatening biodiversity. Throughout the module the lecture material is complemented by extensive practical classes introducing a variety of fieldwork and laboratory techniques.
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BL3318
Biology of Marine Organisms
Dr Valerie Smith
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Biology of Marine Organisms

code: BL3318
credits: 20
year: Junior Honours
semester: 2
description: This module will include lectures on the range of microbial and metazoan organisms and ecological systems in the marine environment. The coverage will range from bacteria, to algae, invertebrates and vertebrates (fish, birds, reptiles and mammals). The biology of marine organisms is considered in the context of both adaptations at the level of the individual and its expression in terms of large-scale latitudinal and depth-related variations in productivity and food web structure. Examples from the poles to the tropics and from shallow water to the deep ocean will be included. Practicals will be field- and laboratory-based and will provide an experimental introduction to both ecological and physiological problems in marine biology.
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BL4284
Breeding Systems and Sexual Conflict
Dr Jeff Graves
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Breeding Systems and Sexual Conflict
code: BL4284
credits: 15
year: Senior Honours
semester: 2
description: Studies of mating systems in animals are primarily concerned with how animal societies are structured in relation to sexual behaviour. In plants, where many organisms do not have separate males and females, the term refers to the degree to which individuals are self-compatible or the amount of out-crossing that occurs. The effects of breeding system on sexual selection and sexual conflict, together with the costs of inbreeding and the
evolution of mating systems, are central concerns of this module.
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BL2101
Cell Structure and Function
Ms Lorna Sibbett
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Cell Structure and Function

code: BL2101
credits: 30
year: Second Year
semester: 1
description: This is an introductory module covering general aspects of animal cell structure and associated physiology. The module stars with a general overview of the regulation of the cell cycle, the roles of protein complexes essential to cell shape and adhesion and the homeostatic role of ion pumps, transporters and channels in the maintenance of solute compositions in both the intra- and extra-cellular fluid compartments. The module continues with detailed structure-function relationships within cells from three major tissues i) nerve cells and the mechanisms of generation and propagation of the action potential, ii) skeletal, cardiac and smooth muscle cells and mechanisms controlling contraction and finally iii) blood cells and O2 transport, immune response, coagulation and cell signaling pathways.
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BL4223
Chromosome replication and genome stability
Dr Stuart MacNeill
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Chromosome replication and genome stability
code: BL4223
credits: 15
year: Senior Honours
semester: 1
description: Highly-efficiently chromosomal DNA replication is essential for all forms of cellular life on Earth and requires the complex interplay of a large range of protein factors in a temporally- and spatiallycoordinated manner. In humans, defects in the replication process may lead to genetic disease or cancer. This module will summarise current knowledge of the enzymes and mechanisms of chromosomal DNA replication in bacterial, archaeal and eukaryotic cells with particular emphasis on exploring the diverse range of experimental systems and techniques used in the laboratory to probe the structure, function and regulation of the replication apparatus. Similarities and differences between cellular and viral DNA replication strategies will be explored and diverse aspects of the evolution of the replication machinery highlighted
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ID4001
Communication and teaching in science
Dr Rona Ramsay
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Communication and teaching in science

code: ID4001
credits: 15
year: Senior Honours
semester: 1
description: This module is based on the Undergraduate Ambassador Scheme launched in 2002. It provides final year students within the Faculty of Science with the opportunity to gain first hand experience of science education through a mentoring scheme with science teachers in local schools. Students will act initially as observers in the classroom and later as classroom assistants. With permission of the teacher-in-charge, students may also be given the opportunity to lead at least one lesson, or activity within a lesson, during their placement. This module will enable students to gain substantial experience of working in a challenging and unpredictable working environment, and of communicating scientific ideas at various different levels; and to gain a broad understanding of many of the key aspects of teaching science in schools. While of particular value to students aiming for a career in education, these core skills are equally important for any career that requires good communication. Entry to this module is by
selection following application and interview during the preceding semester.

Note: Students will not be allowed to sign up for this module until their application for a place has been accepted and they have been offered a place by the module organiser.

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BL2106
Comparative Physiology
Dr Gerald Prescott
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Comparative Physiology

code: BL2106
credits: 30
year: Second Year
semester: 2
description: This module covers the principles of physiological adaptation in a range of animals, including examples from all major taxa and from all habitats. Initial comparisons relating to scaling and design of animals will be followed by more specific units on: (A) Comparative principles of ionic and osmotic exchanges; water balance in aquatic and land animals, adaptations at skin, kidney, and respiratory surfaces. (B) Respiratory systems in water and on land, and associated circulatory mechanisms. (C) Principles of temperature balance; ectotherms and endotherms. (D) Feeding and digestive systems; food collection, ingestion, and absorption at different trophic levels; and waste disposal. (E) Sensory systems in different environments (especially visual, olfactory, auditory, and special senses). (F) Control systems using hormones and pheromones and (G) the immune system in a range of animals.
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BL4285
Complex Systems in Animal Behaviour
Dr V Anne Smith
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Complex Systems in Animal Behaviour
code: BL4285
credits: 15
year: Senior Honours
semester: 2
description: Behaving animals form complex systems, and can create complicated and beautiful phenomena, such as flocks of birds, termite nests, and patterns of army ant swarms. This course will look at research that examines animal behaviour from a complex systems perspective, where analyses range from captive housing of entire bird flocks, computer simulation, and use of robots to interact with the animals. Introductory lectures will be followed by seminar-style discussion of the primary literature, computer practicals, and hands-on practicals where students will identify complex systems in animal behaviour around St Andrews.
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BL4268
Conservation and Management of Biodiversity
Dr Iain Matthews
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Conservation and Management of Biodiversity

code: BL4268
credits: 15
year: Senior Honours
semester: 1
description: This module will focus on the scientific problems associated with the conservation and
sustainable use of animals and plants, and on the way in which scientific advice on these issues is provided. Initial lectures will cover sustainable development and the precautionary principle; the causes of extinction; the economics of conservation; management of exploitation; and estimating species richness. After this student-led seminars will cover a range of more specialist issues of current concern. Practical work on population viability analysis, classifying populations using the IUCN criteria, and species richness estimation may be included.
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BL4267
Conservation field research methods : Sampling of individuals and communities
Dr Will Cresswell
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Conservation field research methods : Sampling of individuals and communities

code: BL4267
credits: 15
year: Senior Honours
semester: 2
description: Not available in 2011-12. The conservation of animal and plant populations relies on unbiased information on individuals and communities. This information can only be collected by fieldwork that uses proper sampling methods. This course teaches basic field techniques that underpin unbiased sampling. Each week the theory behind a different technique is introduced, the technique is then taught and practiced in the field and then data collected by the technique is analysed and discussed in a workshop at the end of the week, so that a full understanding of a technique and its proper application is gained. The module ends with students carrying out a project applying the techniques they have learnt, which forms the basis of the assessment for the module. Techniques taught in this module are: sampling design, behavioural sampling, estimation of birth and survival rates and environmental sampling using indicators.
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BL4266
Conservation field research methods: Estimating population size
Dr Will Cresswell
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Conservation field research methods: Estimating population size

code: BL4266
credits: 15
year: Senior Honours
semester: 1
description: The conservation of animal and plant populations relies initially on information of population sizes and trends. This information can only be collected by fieldwork. This module teaches the basic field techniques that underpin the monitoring of populations. Each week the theory behind a different technique is introduced, then the technique is practiced in the field, and finally data collected by the technique are analysed and
discussed in a workshop at the end of the week, so that a full understanding of a technique and its proper application is gained. The module ends with students carrying out a project applying and integrating the techniques they have learnt.
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BL4221
Conus Venom Peptides, Receptor and Ion Channel Targets, and Drug Design
Dr Roger Griffiths
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Conus Venom Peptides, Receptor and Ion Channel Targets, and Drug Design

code: BL4221
credits: 15
year: Senior Honours
semester: 1
description: Neurotoxins have highly specific actions on molecular targets, and many have been adapted for use as therapeutic, diagnostic and insecticidal agents, and as tools that reveal physiological, cellular and molecular mechanisms underlying brain function.  Amongst the predatory cone snails (Conus) each is a specialist in neuropharmacology, using venom to capture prey, to escape from and defend against predators, and possibly to deter competitors. Most conotoxins are small, structurally-constrained, disulphide-rich peptides. The module explores their selective targeting of specific isoforms of receptor or ion channels within a variety of molecular targets, namely, voltage-gated and ligand-gated ion channel subtypes, G protein-linked receptors, and transporter proteins. This module therefor
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BL3315
Developmental Biology
Dr Martin Milner
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Developmental Biology
code: BL3315
credits: 20
year: Junior Honours
semester: 2
description: This module considers the enigma of development, how complexity arises from apparent
simplicity when an adult develops from an egg. It examines development from fertilisation to maturity in a range of organisms, but concentrates on higher vertebrates including man, and the fruitfly Drosophila. Early-acting mechanisms for generating differences between initially identical cell populations to produce patterning and structure in embryos will be considered. The development of the nervous system will be examined in depth.  Drosophila embryonic development and the hormonal control of metamorphosis in flies and amphibians will also be studied.
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GG3096
Earth System Science: Terrestrial Ecosystems and Environmental Change
Dr Yit Arn Teh
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Earth System Science: Terrestrial Ecosystems and Environmental Change
code: GG3096
credits: 15
year: Junior Honours
semester: 2
description:

Terrestrial ecosystems play a central role in modulating the flow of energy and materials in the Earth system, regulating trace gas exchange with the atmosphere, the transfer of carbon and nutrients with rivers and oceans, and the natural attenuation of pollutants. Understanding how terrestrial ecosystems function is crucial to addressing problems such as climate change, stratospheric ozone loss, and environmental pollution. This module will develop principles of ecosystems ecology and biogeochemistry, focusing on major elemental cycles, soil processes, and human activity. In addition to students in Geography and Geosciences, this module also welcomes students from Sustainable Development, Biology and Chemistry.

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BL2105
Ecology & Evolution
Prof Mike Ritchie
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Ecology & Evolution
code: BL2105
credits: 30
year: Second Year
semester: 2
description: Ecology and Evolution are central to our understanding of life on Earth and the relationships between all organisms and their biotic and abiotic environment. The principles of Ecology and Evolution have determined the variety and distribution of all organisms and will determine their future responses to global change. This module will introduce students to principles and patterns of Ecology, ranging from the global (for example, patterns of energy flow through ecosystems and the biogeography of organisms and communities) to the individual (competition between and within species) and the history and processes of Evolutionary Biology (Darwin, natural selection, population genetics, the evolution of sex and speciation).
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BL3309
Ecosystems and Conservation
Dr Will Cresswell
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Ecosystems and Conservation

code: BL3309
credits: 20
year: Junior Honours
semester: 2
description: This module will examine how ecosystems function and how they provide services for humans: information which is essential for ecologists, conservationists and land managers. The module will consider examples of natural systems being altered by man to demonstrate how ecosystems function and the consequences of anthropogenic change. Disturbance and regulation in ecosystems, atmospheric and hydrological regulation, (including the green house effect and acidification), soil ecology, conservation and management of natural resources, agricultural and grazed ecosystems (including GMOs), urban ecosystems and aspects of sustainable development will also be discussed.
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BL3306
Environmental Physiology
Dr Gerald Prescott
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Environmental Physiology

code: BL3306
credits: 20
year: Junior Honours
semester: 1
description: This module deals with how physiological processes allow organisms to cope with variations in particular aspects of their external environments. A central feature of the course will be an exploration of the responses of organisms (animals in particular, with some comparative studies of plants) to variation in temperature, water availability and osmotic stress, nutrient levels, light, and pressure, both at the molecular and whole organism level, and covering a range of animals from marine, freshwater, terrestrial and parasitic habitats. There will also be analyses of seasonally induced physiological responses, including reproduction, food intake and fattening, torpor and hibernation, including analysis of the mechanisms involved in monitoring and responding to changing conditions.
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BL3307
Evolution
Prof Thomas Meagher
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Evolution

code: BL3307
credits: 20
year: Junior Honours
semester: 1
description: Topics in this module will include: molecular variation and evolution, including phylogeny reconstruction; the evolution and maintenance of sex; the genetics of continuous traits, and the relative importance of continuous and discontinuous variation in evolution; evolution of population genetic structure; the genetics of speciation, covering the evolution of pre- and post- zygotic isolation, reproductive displacement and reinforcement, and parapatric, sympatric and island speciation. Practicals will involve computer simulations to investigate a range of evolutionary phenomena, plus use of molecular markers to examine population structure and speciation.
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BL4280
Evolution and Human Behaviour
Prof Kevin Laland
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Evolution and Human Behaviour
code: BL4280
credits: 15
year: Senior Honours
semester: 1
description: Evolutionary biologists, anthropologists and psychologists have taken evolutionary principles and used them to explain a range of human characteristics, such as homicide, religion and sex differences in behaviour. Other researchers are sceptical of these interpretations, and critical of the methods. Moreover, researchers disagree as to the best ways to use evolution to explore humanity, and a number of schools of thought have emerged.  This module will introduce and critically evaluate the main evolutionary approaches currently being used, including socio-biology, evolutionary psychology, behavioural ecology and gene-culture co-evolution.
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BL4275
Evolution in action
Prof Thomas Meagher
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Evolution in action
code: BL4275
credits: 15
year: Senior Honours
semester: 1
description: This module will focus on recent developments in evolutionary biology, placing particular emphasis on research related to application or public policy. Examples of topics to be covered include: emergent diseases, biodiversity policy, conservation management, biological impacts of climate change, and public understanding of science.
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BL4274
Evolutionary Developmental Biology
Dr Dave Ferrier
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Evolutionary Developmental Biology
code: BL4274
credits: 15
year: Senior Honours
semester: 2
description:

Evolution of new morphologies involves changes to the development of organisms. The field of evolutionary developmental biology is thus becoming established as a major and essential component of any comprehensive understanding of evolutionary biology. This module aims to cover some of the main, current themes in evolutionary developmental biology. Since animal life evolved in the sea, much of what we can learn about the major events in animal evolution can be obtained from studying marine invertebrates. Consequently the examples covered in this module will tend to be drawn from these organisms.

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BL4201
Experimental Research Project
Prof Pat Willmer
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Experimental Research Project

code: BL4201
credits: 60
year: Senior Honours
semester: 3
description: This project will involve extensive laboratory or field research to investigate a defined problem within biology, appropriate to the degree programme being studied by each student. The project will involve diligence, initiative and independence in pursuing the literature, good experimental design, good experimental and/or analytical technique either in the field or the laboratory, and excellent record keeping. The project will culminate in the production of a high-quality report that demonstrates a deep understanding of the chosen area of research. Students will be allocated to a member of staff within the School of Biology who will guide and advise them in research activities throughout the academic year.
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BL3000
Field Course
Dr Claire Golléty
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Field Course

code: BL3000
credits: 5
year: Junior Honours
semester: 1
description: This module involves field-based exercises in a range of aquatic and/or terrestrial habitats. Students will examine and measure biodiversity, ecophysiological adaptation, and community structure, with both plant and animal material. Class exercises are used to develop good sampling techniques and to generate and analyse large data sets. Students also work in small project groups to develop individual skills in experimental design, practical manipulations, time-management and personal initiative, and in verbal/written presentation of project results.
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BL4254
Fisheries Research
Dr Charles Paxton
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Fisheries Research
code: BL4254
credits: 15
year: Senior Honours
semester: 2
description: This module will provide an introduction to the utilization of fish stocks in a sustainable way.  It will focus on how the status of these stocks can be assessed, the problems associated with determining catch limits, and how advice from fisheries scientists is communicated to managers. There will be a mixture of dedicated lectures (including talks from outside experts), student-led seminars, tutorials and practical computer sessions.
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BL4258
Foraging in Marine Mammals
Prof Michael Fedak
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Foraging in Marine Mammals

code: BL4258
credits: 15
year: Senior Honours
semester: 1
description: Not available in 2011/12. This module will provide primarily seminar and practical-based analysis of the life-history requirements of foraging in marine mammals, geographical and physiological constraints on finding food, food and feeding with a focus on types of prey and adaptations by the prey, adaptations for marine mammals feeding in the marine environment, optimal foraging theory, and optimal diving theory. Initial lectures will focus on theoretical issues and description of methods to study foraging. Students will then conduct case-studies of marine-mammal foraging, which will be presented in a seminar format as a group. Some practical work will also be included.
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BL3302
Gene Regulation
Dr Daniel Barker
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Gene Regulation
code: BL3302
credits: 20
year: Junior Honours
semester: 1
description: This module builds on material covered in BL1201 Molecular Biology and BL2104 Biochemistry & Molecular Biology. It first considers the structure of genes and the composition of genomes and then examines genetic activity in eukaryotes in relation to nuclear organization, chromatin structure and epigenetic mechanisms. Regulation of expression at the levels of gene transcription, RNA processing, RNA stability and translation, are next covered in detail, drawing particular attention to the nature of protein-nucleic acid interactions. Specific control mechanisms in different prokaryotic and eukaryotic systems, induced by environmental, cell cycle, metabolic and developmental signals, are highlighted.
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BL4220
Geomicrobiology - from gold mines to global warming: how microbes influence our planet
Dr Shiela Unkles
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Geomicrobiology - from gold mines to global warming: how microbes influence our planet
code: BL4220
credits: 15
year: Senior Honours
semester: 1
description: Not Available in 2011/12. Geomicrobiology explores the interactions between microbes and materials within inorganic environments and investigates the effects of microbial activity on these substances. Throughout the Earth's history, microbes have successfully colonised numerous and different inorganic environments, and in the process have
changed the chemical nature of geological materials therein. The current interest in geomicrobiology has been reawakened by climate change and environmental issues.
The module will commence by investigating very early Earth and its initial colonisers 3.7 BYA - the sulphatereducing and methane-producing anaerobic bacteria - and later development of the aerobic environment. Then issues concerning today's Earth and the consequences of geomicrobial cycling are investigated, as well tomorrow's Earth and the influence of microbial activity on global climate change. What are the future implications of geomicrobiological activity? Finally, hypotheses regarding the geomicrobiology of a variety of newly explored space environments are considered.  Class Hour: To be arranged.
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BL4292
History of Genetics and Evolution
Dr Martin Milner
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History of Genetics and Evolution

code: BL4292
credits: 15
year: Senior Honours
semester: 2
description: Over the past century and a half, biology has been dominated by the emergence and rise to prominence of two related fields – genetics and evolution. This module provides the opportunity to examine the life and work of key figures in these fields, and also to compare the way science worked in the nineteenth century with the way it operates today. The course will start with two lectures on the History of Biology, and students will then read material on the life and times of four key individuals – Darwin, Mendel, Watson and Crick, followed by tutorial discussion. In each case, both original documents (eg. Mendel’s papers), and biographies (such as the excellent biography of Frances Crick published in 2006) will be discussed in tutorials. Other key figures in the field will be studied, and aberrations such as Francis Galton and eugenics, and T.D. Lysenko and Soviet genetics will be discussed.
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BL4212
How enzymes work
Dr Rona Ramsay
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How enzymes work
code: BL4212
credits: 15
year: Senior Honours
semester: 1
description:

All cells depend on enzymes to catalyse the reactions that produce the energy required for life and that make and repair DNA, proteins and lipids. Understanding enzymes and their regulation underpins research on, for example, drug development. This module will study how the structures and molecular functions of selected examples enable the biological roles. Topics will include flavoproteins, DNA repair enzymes, nitric oxides synthases and other enzymes depending on the research interests of the academic staff. It will develop deductive skills, literature research, and communication of specific knowledge from reviews and primary research articles, and will encourage integration of previous basic knowledge of bioenergetics, protein structure and function, gene expression and metabolic regulation into the exploration of the cellular roles of enzymes.

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BL4248
Human physiology of diving
Dr Clare Peddie
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pdf available
 

Human physiology of diving
code: BL4248
credits: 15
year: Senior Honours
semester: 1
description: This module will provide an understanding of diving physics and how pressure changes affect the physiology of the human diver. It will use both tutorials and self-study sessions to cover theoretical topics such as oxygen toxicity, nitrogen narcosis and the symptoms and treatment of decompression illness. Thermal considerations of diving, long term effects and the physiology of technical mixed gas and rebreather diving will also be investigated. Students will also explore applied topics such as the management of diving casualties and the treatment of diving-associated illnesses. The final emphasis will be on how our understanding of diving physiology directs current practice in the UK on safe diving practices.
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BL4269
Iceandic Ecology : Conservation and sustainable development
Prof David Paterson
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Iceandic Ecology : Conservation and sustainable development

code: BL4269
credits: 15
year: Senior Honours
semester: 1
description: NOT AVAILABLE 2011/12.Students will visit three sites in Iceland and be introduced to aspects of terrestrial, freshwater and marine issues that are relevant to the status of Icelandic ecology and conservation. After introduction to the issues during the visit to Iceland and with the help of regular structured tutorials, students will select and specialise in a particular area of research.  On return to St Andrews students will research their topic by the selective collation of general information over a broad background. Material relevant to their area of study, including detailed research of historical and present day
status of selected area, analysis of current status and critique of future management issues will be presented to the group. This will result in an interactive seminar and a written report. Students will be supported by an individual tutor and regular class seminars.
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BL3311
Infection & Disease
Dr Peter Coote
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Infection & Disease

code: BL3311
credits: 20
year: Junior Honours
semester: 2
description: This module has lectures in three component areas: parasite infections, viral disease, and
pathogenicity of common bacterial infections, and will include consideration of host defences and effective treatment. In all three component areas the emphasis will be on understanding at the molecular level.
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BL4260
Introduction to Biological Oceanography
Dr Patrick Miller
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Introduction to Biological Oceanography
code: BL4260
credits: 15
year: Senior Honours
semester: 1
description: Not available in 2011-12. This module will provide primarily seminar-based instruction on the fundamentals of Biological Oceanography (BO). A few introductory lectures will focus on basic principles in BO and oceanography, including physical and geochemical principles as they apply to biological oceanography.Students will present seminars on particular focus areas within each lecture topic, based upon reading primary literature. BO is a broad field, so the modulewill provide an overview of the field with depth in a few chosen areas. At least one practical will be offered on the use of remote-sensing data for ocean observation, and we hope to develop a practical of zooplankton sampling. This module should coordinate especially well with marine acoustics and scientific diving.
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BL4200
Literature-based Research Project
Dr Roger Griffiths
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Literature-based Research Project

code: BL4200
credits: 45
year: Senior Honours
semester: 3
description: This project will involve an extensive literature review to investigate a defined hypothesis or problem within the field of biology, appropriate to the degree programme being studied by each student. The project will involve diligence, initiative and independence in pursuing the literature, and the production of a high-quality dissertation that demonstrates a deep understanding of the chosen area of research. Students will be allocated to a member of staff within the School of Biology who will guide and advise them in research activities throughout the academic year. The project will be written up in the form of a research dissertation, and presented in the form of an academic poster and an oral presentation.
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BL4256
Marine acoustics
Prof Andrew Brierley
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Marine acoustics
code: BL4256
credits: 15
year: Senior Honours
semester: 2
description: This module will provide seminar- and practical-based work on both active and passive uses of acoustics in the marine environment. It investigates sound propagation in the ocean, use of sound by man as a sampling tool (active acoustic sampling of the water column and seabed), and use of sound by marine mammals for communication and prey detection (as monitored by humans using passive listening techniques). It will also
examine sound-based conflicts between humans and marine organisms. Two practical sessions will be included, one looking at active use of sound by humans gathering data at sea, the other exploring sound transmission at sea.
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BL4255
Marine biotechnology
Dr Valerie Smith
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Marine biotechnology
code: BL4255
credits: 15
year: Senior Honours
semester: 2
description: This module will examine the diversity of useful natural products from the sea, consider the ways in which genomic and other approaches are being used to bioprospect for new substances (especially from micro-organisms), learn how genomic approaches are overcoming the problem of unculturability of many marine prokaryotes to find such compounds, and explore some of the more unusual applications of materials derived from
marine invertebrates. It will also consider how marine biotechnology is contributing to improved disease control in aquaculture, how it can help the 'greening' of more conventional 'dirty' industries and may enable us to meet our future energy needs via renewable biofuels. The societal, ethical and environmental issues associated with the
development of environmental biotechnology are also considered.
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BL4257
Marine invertebrate larval ecology
Prof Chris Todd
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Marine invertebrate larval ecology

code: BL4257
credits: 15
year: Senior Honours
semester: 2
description: Not available in 2011/12.  Most marine invertebrates include a planktonic larval stage within their life cycle. The adaptive and ecological significance of a larval stage to otherwise benthic (bottom-dwelling) species is open to numerous interpretations, but for species that are sessile as adults, dispersal and colonization potential appears to be of major significance. This module will focus both on larval growth and development during the planktonic stage and also settlement and metamorphosis to the benthic juvenile state. Successful establishment of the post-larval stage is crucial to the completion of the life cycle and understanding the control of larval settlement has major socioeconomic
implications for species viewed as being detrimental (e.g. fouling) or beneficial (e.g. mariculture) components of marine ecosystems.
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BL4259
Marine Mammals and Man
Prof Philip Hammond
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Marine Mammals and Man
code: BL4259
credits: 15
year: Senior Honours
semester: 2
description: Marine mammals interact with human activities in a variety of ways and are frequently the focus of more general concerns about the health and exploitation of marine ecosystems. This module explores the impact of these activities on individuals and populations of seals and cetaceans, and vice versa. Topics covered include marine mammal-fisheries interactions, exploitation of seals and whales, contaminants and disease, and habitat degradation. Most marine mammals species are long-lived and slow reproducing and the impacts of unmanaged human activities can be severe; a number of species or populations are threatened as a result. The module explores how best to provide robust scientific advice to inform conservation and management at local, national and international level.
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BL3303
Membranes & Cell Communication
Dr Rona Ramsay
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Membranes & Cell Communication

code: BL3303
credits: 20
year: Junior Honours
semester: 1
description: This module deals with the structural and functional organisation of biological membranes. The dynamic molecular components of biological membranes are studied by investigating the mechanisms involved in the control of membrane fluidity, the measurement of membrane fluidity and the biogenesis of new molecular components of the membrane. The central role that biological membranes play in the regulation of the movement of molecules between different extracellular, intracellular and transcellular compartments is also considered. The process of molecular transport is studied at both a theoretical and practical level. The interaction between the structural and functional organisation of the cell membrane is highlighted by studying the specialisation seen in the major transporting ephithelial tissues. Topics covered include: (i) structural and kinetic analysis of ligand-receptor interactions; (ii) GTP-binding proteins and the generation of intracellular second messengers: cyclic AMP, cyclic GMP, diacyl glycerol and inositol triphosphate; (iii) the activation of receptor and intracellular protein kinases: serine/threonine and tyrosine kinases; (iv) de-sensitisation of signal responses and receptor cross-talk; (v) direct and indirect activation of plasma membrane ion channels; (vi) nuclear receptors and the regulation of gene expression. The practical component includes experiments to illustrate methods used to elucidate signalling pathways as well as providing training in laboratory and transferable skills.
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BL4222
Metabolic and Clinical Biochemistry
Dr John Ingledew
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Metabolic and Clinical Biochemistry
code: BL4222
credits: 15
year: Senior Honours
semester: 1
description: This module extends the students' knowledge of human metabolism and applies it to pathologies. The syllabus includes: a study of the integration of whole body metabolic processes, discussion of the role of biochemistry in investigating and monitoring human disease, the methods of diagnosing and treating some common diseases. Topics will cover integration of whole body metabolism, starvation processes, diabetes, metabolic variability, inborn errors of metabolism, endocrinology, homeostasis, plasma protein metabolism, muscle and hepatic metabolism, drug disposition and metabolism, and defects in glucose and lipid metabolism.
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BL3310
Metabolism and Bioenergetics
Dr John Ingledew
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Metabolism and Bioenergetics

code: BL3310
credits: 20
year: Junior Honours
semester: 2
description: The module presents an integrated review of human metabolism and the methods of diagnosing and treating some common metabolic diseases. The syllabus includes: (i) a review of human metabolism and its control; (ii) overall body energy expenditure and nutritional requirements; (iii) processing of dietary constituents; (iv) metabolic changes associated with starvation, obesity and exercise, and their underlying hormonal controls and regulatory systems; (v) discussion of the role of biochemistry in investigating and monitoring human disease, which will include metabolic variability, inborn errors of metabolism, endocrinology, homeostasis, plasma protein metabolism, muscle and hepatic metabolism, drug disposition and metabolism, and defects in glucose and lipid metabolism. Practical classes will introduce students to the methods used in these fields of study.
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BL4272
Molecular Ecology
Dr Jeff Graves
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Molecular Ecology

code: BL4272
credits: 15
year: Senior Honours
semester: 1
description:  This module will consider modern molecular approaches used in conservation and population genetics, phylogeography, and ecological genetics; aspects of molecular adaptation; and the use of molecular data for phylogenetic and genealogical inference.
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BL4224
Molecular Mechanisms of Membrane Trafficking
Dr Gerald Prescott
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Molecular Mechanisms of Membrane Trafficking

code: BL4224
credits: 15
year: Senior Honours
semester: 2
description: Membrane trafficking mediates the transport of substances between different cellular organelles and the secretion of substances from cells.  As such, regulation of membrane trafficking is applicable to all cell types, but especially to specialised secretory cells such as neurons, which secrete neurotransmitters and pancreatic beta-cells which secrete insulin. This module will consider how molecules control the movement of substances through the secretory pathway, but will focus on how cells regulate the release of contents.  Within the module you will look at the proteins involved, the different experiments used to study the process and how model organisms are enhancing our understanding.
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    BL4213
    Molecular virology
    Prof Richard Randall
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    Molecular virology
    code: BL4213
    credits: 15
    year: Senior Honours
    semester: 1
    description: Viruses as a group include many important human and veterinary pathogens such as influenza virus, hepatitis C virus, foot and mouth disease virus as well as emerging viruses like Ebola virus, and remain a continuing threat to human and animal welfare. This module will consist of a mixture of lectures, tutorials and personal-based learning on aspects of RNA virus host interactions. The topics covered will include comparison of the molecular mechanisms employed by enveloped and non-enveloped viruses to enter and exit from cells, discussion of how small RNA viruses maximize their coding capacity, comparison of the replication of positive and negative strand RNA viruses, discussion of how selected viruses reprogram the host cell to ensure their own replication, description of how RNA viruses intercede with innate immune responses, and understanding of how selected viruses interact with their vectors. In addition, discussion of virus-related topics that have made headline news in recent years will be addressed, and an understanding of the more commonly used molecular techniques to study viruses will be expected.
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    BL4235
    Motorneurons: From Physiology to Pathology
    Dr Gareth Miles
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    Motorneurons: From Physiology to Pathology
    code: BL4235
    credits: 15
    year: Senior Honours
    semester: 1
    description:

    This module aims to provide in depth knowledge of key aspects of neuronal function and potential dysfunction by focussing on one of the most studied and best characterised classes of neurons in the central nervous system, motoneurons. The module will cover topics such as: the history of motoneurons in neuroscience research; the genetics controlling motoneuron development, the intrinsic electrical properties of motoneurons; synaptic inputs received by motoneurons; motoneuron recruitment; and motoneuron disease.

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      BL4290
      Networks in Biology
      Dr V Anne Smith
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      Networks in Biology
      code: BL4290
      credits: 15
      year: Senior Honours
      semester: 2
      description:

      What do spread of a disease, climate change, visual perception, and development of a sea urchin have in common? They are all involved with or impact biological networks. This module will investigate networks that exist in biological systems across various levels of biological organisation, covering molecular, neural, ecological, and social networks.

      The techniques and theory of network analyses will be covered, as well as specific features of networks. Introductory lectures will be followed by seminar-style discussion of the primary literature, and computer-based practicals investigating network behaviour. Students will also participate in and analyse results of a social network experiment.

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      BL4232
      Neural mechanisms of Predatory and Avoidance Behaviours
      Dr Bill Heitler
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