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DEPARTMENT OF BIOLOGY

STUDENT CHOICE OF MODULES

STAGE 2

PROVISIONAL

Biology

Biotechnology and microbiology

Ecology, conservation and e

Genetics

Molecular cell biology



TAGE 2: 2013-2014

AND

PROVISIONAL STAGE 3: 2014 -

Biotechnology and microbiology

Ecology, conservation and environment

iology



- 2015


TABLE OF CONTENTS

RULES FOR CHOOSING YOUR PROGRAMME MODULES 3

COMPULSORY MODULES – STAGE 2 4

CHOICES AND COMPULSORY MODULES - STAGE 3 9

PREREQUISITES 9

ELECTIVE MODULES 9

FURTHER ADVICE ON MAKING YOUR MODULE CHOICES 10

CHANGING MODULES AFTER SELECTION 10

YOUR PROGRAMME PLANNER 11

STAGE 2 MODULE DESCRIPTIONS 2013-2014 12

AUTUMN TERM – 10 CREDIT MODULES 12

SPRING – SUMMER TERM – 10 CREDIT MODULES 16

AUTUMN – SPRING – SUMMER 2013-2014 – 20 and 30 credit modules 20

SPRING – SUMMER TERM – SKILLS PRACTICAL COURSES 22

SKILLS PRACTICALS – GROUP A 23

SKILLS PRACTICALS – GROUP B 25

STAGE 3 MODULE DESCRIPTIONS 2014-2015 (PROVISIONAL LIST) 30

AUTUMN TERM 31

SPRING TERM 38

MODULE CHOICE FORMS 48


RULES FOR CHOOSING YOUR PROGRAMME MODULES

Please note that the deadline for receipt of your module choices is Monday 4 March 2013.

This booklet explains how you will exercise your choices among the modules that are available during

your second and final year. It is through these choices that you can shape your degree programme to

suit your own particular interests and skills.

In the spring term of your first year you choose your Stage 2 modules.

In the spring term of your second year you choose your Stage 3 modules.

The breadth and nature of the choice open to you will depend on your degree programme, but all

students should plan their module selection so that the choices made in the second year provide an

appropriate springboard for those you wish to study in the final year. It is important, that your second

year choice of modules should form part of a larger plan for your whole degree programme.

You can make your choice from:

(a) Biology programme modules: Modules prepared for your programme, which form part of your

Programme Plan. You will find details of all biology modules in this booklet.

(b) Elective modules: Modules from other departments within the University that will generate an

assessment mark. Please read the section on elective modules carefully if you are considering

taking an elective module. Note that you may take a maximum of 20 credits of electives across

stages 2 and 3.

The Rules governing your stage 2 choices are:

Your credit total for stage 2 must come to 120 credits

The 120 credits must include the 30 credit skills module, plus 40 credits from the autumn term

and 50 credits from the spring term.

You must select at least one 20 credit module (this equates to 10 credits in autumn and spring

terms).

Your choices must include the Compulsory modules required for your programme of study.

You are allowed a maximum of 20 credits of electives across stages 2 and 3.

The Rules governing your stage 3 choices are:

Your credit total for stage 3 must come to 120 credits.

Your choices must include the Compulsory modules required for your programme of study.

Module credits must be equally distributed across the autumn and spring terms.

You are allowed a maximum of 20 credits of electives across stages 2 and 3.


COMPULSORY MODULES – STAGE 2

Your choices of modules in your second year should be shaped by the modules you would like to take in

your final year so we advise you to identify the stage 3 modules that interest you and check for

prerequisite stage 2 modules. Once you have done this, look through the stage 2 options.

We have provided tables of compulsory and recommended modules for all degree programmes to help

you select a cohesive group of modules. Biology students may wish to follow the suggestions for the

specialist degrees depending on their interests. We do advise you to discuss your choices with your

supervisor.

Biology – compulsory modules highlighted

Autumn Term Spring / Summer Term

Scientific skills and tutorials – 30 credits - compulsory

Animal and plant ecology – 20 credits – select this or From gene to function

From gene to function – 20 credits – select this or Animal and plant ecology

Genetics III – 10 credits Behavioural ecology – 10 credits

Immunology – 10 credits Cell biology – 10 credits

Metabolism in health and disease – 10 credits Developmental biology – 10 credits

Millport field course – 10 credits Environmental ecology – 10 credits

Molecular biotechnology – 10 credits Evolutionary and population genetics – 10

credits

Species-Environment interactions – 10 credits Neuroscience – 10 credits

Post-genomic biotechnology – 10 credits


Biotechnology and microbiology – compulsory modules highlighted



Animal and plant ecology – 20 credits

From gene to function – 20 credits - compulsory

Genetics III – 10 credits - recommended Behavioural ecology – 10 credits

Immunology – 10 credits Cell biology – 10 credits - recommended



Molecular biotechnology – 10 credits -

compulsory

Evolutionary and population genetics – 10

credits


Post-genomic biotechnology – 10 credits -

compulsory


Ecology – compulsory modules highlighted



Animal and plant ecology – 20 credits - compulsory

From gene to function – 20 credits

Genetics III – 10 credits Behavioural ecology – 10 credits -

recommended



Millport field course – 10 credits - recommended Environmental ecology – 10 credits -

recommended


credits - recommended

Species-Environment interactions – 10 credits -

recommended

Neuroscience – 10 credits

Post-genomic biotechnology – 10 credits


Genetics – compulsory modules highlighted





Genetics III – 10 credits - compulsory Behavioural ecology – 10 credits


Metabolism in health and disease – 10 credits Developmental biology – 10 credits -

recommended


Molecular biotechnology – 10 credits -

recommended

Evolutionary and population genetics – 10

credits - compulsory



recommended


Molecular cell biology – compulsory modules highlighted





Genetics III – 10 credits - recommended Behavioural ecology – 10 credits

Immunology – 10 credits - recommended Cell biology – 10 credits - compulsory

Metabolism in health and disease – 10 credits -

compulsory

Developmental biology – 10 credits -

recommended



credits

Species-Environment interactions – 10 credits Neuroscience – 10 credits - recommended


recommended

You should register your choice of modules for your second year by completing the appropriate form

for your degree programme at the end of this booklet.


CHOICES AND COMPULSORY MODULES - STAGE 3

You are advised to enter your choice of final year modules on your planner.

PREREQUISITES

Most modules list prerequisites, these are the modules or other qualifications that you must have

completed before attempting the module (in exceptional cases you can take a module without having its

prerequisites, provided that you can convince the module organiser that you have or can obtain the

necessary background). It is particularly important, therefore, that you first plan your choice of modules

for the final year, and then ensure that your choice of second year modules provides the necessary

prerequisites.

Information on prerequisites is:

a) In this booklet, in the form of a short summary of each Biology module, with details of

prerequisites, aims and learning outcomes.

b) On our WEB pages where full synopses of all modules included in this booklet (which will cover

information on individual lecture topics, practical classes, assessments and recommended

reading) available at:

http://www.york.ac.uk/biology/intranet/currentundergraduatestudents/stage1biology/modules2012biol

ogycohort/

ELECTIVE MODULES

Information on the elective modules offered by other Departments is available on the WEB at:

http://www.york.ac.uk/admin/sro/electives.htm. You may take a maximum of 20 credits of elective modules

across stages 2 and 3.

If you wish to take an elective module you must complete An Application To Register for An Elective

Module Form (available from the Biology Undergraduate Office). The form has to be signed by both the

Biology Department and the Department offering the module, so allow yourself time to do your research and

obtain the signatures.

What to consider when taking an elective module:

(a) Discuss the module with the organiser and your supervisor to ensure you are making appropriatechoices.

(b) Check when the elective module will be assessed and confirm that a final moderated mark will betransferred to Biology by the end of week 8 of the summer term. If a mark is not transferred bythe end of week 8 you may receive a zero mark for the elective module.

(c) You will have to make your module selections before the timetable for 2013/14 is available. Onproduction of the timetable if you find the elective module you have chosen clashes with yourbiology modules you will need to re-select another module.

(d) Remember that you will be assessed against students who are studying for a degree programmein that area and are likely to have more knowledge of the subject matter than you. It is

http://www.york.ac.uk/biology/intranet/currentundergraduatestudents/stage1biology/modules2012biologycohort/

http://www.york.ac.uk/biology/intranet/currentundergraduatestudents/stage1biology/modules2012biologycohort/

http://www.york.ac.uk/admin/sro/electives.htm


sometimes the case that marks for elective modules are lower than those normally achieved bystudents on their standard degree programme modules.

FURTHER ADVICE ON MAKING YOUR MODULE CHOICES

Make a provisional plan of all your selected modules in stage 2 and 3 on the Programme Planner sheet

provided. Be sure to fill in any compulsory modules required by your programme. Use this plan to fill in

your choices on the form provided at the end of the booklet (please ensure that you complete the correct

form for your degree category).

Take special note of the prerequisites of the modules that you choose.

We advise you to discuss your choices with your supervisor, particularly if you have selected a diverse

range of modules – Biology students for example have a completely free choice of modules apart from

the compulsory skills modules in stages II and III and the project in stage III.

Please note that sometimes (though rarely) modules are oversubscribed and it may be necessary to ask

students to re-select alternative choices. If this is the case you will be contacted by email during the

summer term. Modules may also be under-subscribed, a module will not run if fewer than 15 students

express an interest in taking it.

CHANGING MODULES AFTER SELECTION

You are allowed to change modules after your initial selection (with the exception of your stage II

practical skills which cannot be changed once allocated). However, you may find that once the

teaching and examination timetables have been finalised, numbers attending modules will be capped to fit

the teaching and examination room size allocated. If the lecture theatres/examination rooms for any one

module are at capacity you will not be able to change into that module.

All module changes MUST go through the Biology Undergraduate Office by completion of a Module Change

Form. Failure to inform the office of your module changes will result in you not receiving emails/notifications

of timetabling changes and you will not be registered for the examination.

In future terms, reconsider your overall plan, checking the details of the modules you have chosen. Please

check with the Biology Undergraduate Office before attending any timetabled classes relating to modules for

which you are not registered. The timetabled rooms may not be large enough to accommodate extra

students.


YOUR PROGRAMME PLANNER

Terms Mod No Module Title Credits Prerequisites


STAGE 2 MODULE DESCRIPTIONS 2013-2014

AUTUMN TERM – 10 CREDIT MODULES

MODULE: GENETICS III

ORGANISER: Dr Michael Schultze

RECOMMENDATIONS/PREREQUISITES: 1st

year Biology Programme

SUMMARY:

This module will introduce the fundamental mechanisms of recombination, genome stability and maintenance.

Living organisms face the apparent conflict of having to keep their genome stable to survive, and of the need for

genetic change to allow for adaptation and evolution. Accurate genome replication in conjunction with repair

mechanisms guarantee genome stability, whereas recombination, chromosome rearrangements, and mutations

occur either at low frequency or in a tightly controlled manner.

The module will start with details on recombination and discuss classic experimental approaches that led to an

understanding of the mechanisms. In a workshop, mechanisms of mutation and DNA repair that were introduced in

the first year will be expanded upon through problem-based questions. This will be combined with lectures that

integrate mutational mechanisms and the specific types of DNA repair required to minimize the occurrence of

mutations. Also, the coordination of DNA replication and repair will be discussed, e.g. what happens when the

replication fork is stalled at sites of DNA damage.

A lot of genetic variability is caused by mobile genetic elements, including viruses, and here we will introduce the

actual mechanisms by which different types of transposable elements excise from and integrate into the genome.

In relation to this, the way viruses such as HIV integrate into their host genome will be discussed. Mechanisms of

site-specific recombination, such as seen in bacteriophage integration and excision, integration of F plasmids,

phase variation in Salmonella will be discussed.

Emphasis will be given in discussing the relationship and regulation of recombination, transpositions, DNA repair

and replication; that DNA repair tools can be used by specific cell types to enhance rather than suppress genetic

variation, e.g. in the generation of antibody diversity through somatic recombination and hypermutation.

Finally, the module will discuss how our knowledge on mutations and recombination can be exploited to identify

gene functions, and how precise in vivo genome-editing is possible through the design of site-specific

endonucleases.

Practical sessions/workshops will cover the main themes of this module: Recombination, site-specific

recombination, mutation and DNA repair.

LEARNING OUTCOMES:

Gain an understanding of fundamental genetic processes that govern genome stability and genomechange.

What the X and XX in recombination actually mean. Understand the basic molecular mechanisms of recombination and genome rearrangements. Understand the molecular mechanisms of transposition. Compare and contrast the multitude of mobile genetic elements (transposons, retroviruses). Understand site-specific recombination. Learn how DNA damage leads to mutations. Appreciate the importance of DNA repair mechanisms in genome maintenance and genome change. Understand how DNA replication and DNA repair act in concert. Appreciate how mutation and recombination can be exploited in genetic research. How the knowledge of recombination and repair have provided the tools for specific genome editing. Appreciate experimental approaches leading to key discoveries.


MODULE: IMMUNOLOGY

ORGANISER: Dr Adrian Mountford

RECOMMENDATIONS/PREREQUISITES: BIO00002C Cell and organismal biology

SUMMARY:

This module will introduce the immune system and the different types of immune responses induced by infectious

pathogens. The first part of the module will focus on the various types of cells of the immune system and describe

how some cells have the capacity to recognise foreign and self antigens through T cell receptors and antibodies. It

will deal with how these antigens are processed by antigen-presenting cells, and how the different components of

the immune system communicate with each other to fight infection and disease through different effector functions.

The second part of the module will provide an introduction to how viral and microbial pathogens infect the human or

animal host, and how they cause disease. The emphasis will be on our understanding of the host/pathogen

interface, and specifically how microbes survive despite the host’s immune response.

LEARNING OUTCOMES:

An understanding of the cellular components of the immune response, and how cells interact leading to theinduction of an immune response.

The mechanisms by which foreign antigen is recognised and processed leading to the generation ofantigen-specific immunity.

Knowledge of how microbes gain entry to, or interact with, host tissues/cells, and an understanding of howpathogens attempt to evade host defence mechanisms.

MODULE: METABOLISM IN HEALTH AND DISEASE

ORGANISER: Dr Gareth Evans

RECOMMENDATIONS/PREREQUISITES: First year Biology/Biochemistry or equivalent.

SUMMARY:

This module develops the cell signalling and metabolism material delivered in the Stage 1 Molecular Biology and

Biochemistry and Cell and Developmental Biology modules, and then discusses these processes in the context of

human disease. The first lectures on the principles of signal transduction and lipid metabolism underpin the

signalling encountered throughout the module. A description of mitochondrial function and dysfunction leads to a

description of one of the major consequences of compromised cell respiration, neurodegeneration. Several

lectures are then devoted to ‘metabolic syndrome’, comprising the major risk factors for cardiovascular disease,

including obesity and diabetes. Finally, ageing is also covered, focussing on genetic studies that have revealed a

role for the energetic status of the cell. The lecture material is reinforced by two practicals, firstly the biochemical

dissection of a mammalian cell signalling pathway involving lipids and protein phosphorylation. Secondly

mitochondrial function and dysfunction is studied in purified mammalian mitochondria.

LEARNING OUTCOMES:

Students studying this module will be able to:

Understand the fundamental principles of cell signalling and metabolism.

Discuss how fundamental metabolic pathways are compromised in human disease and ageing.

Evaluate whether particular signalling pathways are appropriate therapeutic targets for human disease.

Acquire, analyse and interpret experimental data to formulate hypotheses about cell signalling and metabolic

pathways.


MODULE: MILLPORT FIELD COURSE

MODULE NUMBER: BIO00021I

ORGANISER: Dr Julia Ferrari

RECOMMENDATIONS/PREREQUISITES: None

SUMMARY:

The main part of the module is a 9 day field course which takes place at the end of the 1st

undergraduate year in

week 11 of the summer term (29th

June – 7th

July 2013) at the University Marine Biology Station, Millport, Isle of

Cumbrae, Scotland. This module introduces several sampling techniques used in field ecology and introduces

students to a range of marine and terrestrial organisms. In the second half of the field course, students will work on

their own projects. On the return in the autumn, there will be support for writing up the project in the form of a

scientific report, which will be 100% of the assessment for the module.

LEARNING OUTCOMES:

To be able to identify some groups of inter-tidal organisms in the field, and to be aware of identificationkeys

To know of and have used several ecological sampling techniques To be able to plan and carry out field investigations To be able to interpret and statistically analyse data To be able to present To write a scientific report and relate own findings to the literature

MODULE: MOLECULAR BIOTECHNOLOGY


ORGANISER: Dr Gavin Thomas

RECOMMENDATIONS/PREREQUISITES: None, but recommend that students who take this course also taking

Gene to Function at Stage 2 level, but it is not essential.

SUMMARY:

Molecular biotechnology aims to provide students with a broad introduction to how recombinant DNA technology

is being used to make useful biological products, both small molecules and recombinant proteins, in microbial,

plant and animal systems. The module will provide a solid understanding of the biology and techniques used in

each of these biological systems drawing on a wide range of examples from the modern biotechnology industry.

LEARNING OUTCOMES:

A good overview of the types of products that are being made using biological systems in the modernbiotechnology industry

A detailed understanding of the technology and problems relating to recombinant production of importantprotein therapeutics.

An appreciation of how transgenic plants and animals can be produced and their key biological applications,with a practical to create a transgenic plant.

A brief overview of applications of microbes and plants in bioremediation and the use of microbes in syntheticbiology.


MODULE: SPECIES-ENVIRONMENT INTERACTIONS

ORGANISER: Dr Angela Hodge


SUMMARY:

This module will explore the relationships between microorganisms, higher organisms and their environments. In

particular it will focus on the physiological properties of organisms (nutritional abilities, responsiveness to stress)

and how these affect the interaction between the organism and its environment. A major part of the focus will be on

the relationship between microorganisms and higher organisms. In particular, (i) the interactions between plants

and their inherent microbiota that have a major impact on plant function, and (ii) the interactions between bacteria

and the human (mammalian) gut. To appreciate these two examples of inter-Kingdom interactions we need to

understand something more about the physiological properties of plants, and the nature of microbial diversity. This

will also be covered in depth.

LEARNING OUTCOMES:

To realise how the physiological properties of microbes and plants underpin their function in response to

different environmental conditions.

To appreciate the complex nature of the interaction between plants and microbes in the soil, and how this

impacts on plant function.

To be familiar with the diversity of microbial behaviour with respect to nutrient utilization and capacity to

inhabit extreme environments.

To understand the methods used for studying microbial communities, highlighting in particular the most

recent findings from molecular approaches that have revolutionised our view of the complexity and

structure of microbial ecology.

Appreciate that the bodies of humans and other animals are have rich microbial flora, and that these

microbes play multiple important roles in normal health as well as pathophysiological conditions.


SPRING – SUMMER TERM – 10 CREDIT MODULES

MODULE: BEHAVIOURAL ECOLOGY

RECOMMENDATIONS/PREREQUISITES:

A-level Biology plus prior directed reading is acceptable, while Module BIO00001C (Ecology) would be an

advantage. Some level of experience with Excel and/or SPSS, would help for one of the practical sessions.

SUMMARY:

This course covers the most fundamental concepts in behavioural ecology such as sociality, collective behaviour,

and predator avoidance. There will be an emphasis on the evolutionary mechanisms that underpin behavioural

ecology, and consideration of key types of behaviour (e.g. communication, fighting, courtship). Plentiful examples,

largely based on mammals, birds and insects, will be discussed throughout. The module will describe a varied mix

of traditional and modern approaches to study Behavioural ecology, with reference to both classic studies and the

most recent advances in the field.

LEARNING OUTCOMES:

On completion of this module you will have a detailed appreciation of key animal behaviours such as

communication, fighting and courtship. You will develop an understanding of how natural selection moulds the

behavioural strategies of animals. You will learn the importance of individuals making the correct behavioural

decisions either to benefit themselves, close relatives, of those in their social group, in terms of maximising

reproductive success. You will learn the strategies that animals adopt to work collectively towards a goal, forage

efficiently, avoid being eaten by predators, and to deceive others. You will be introduced to the complexity of

parental care and social systems and the various models to explain what is observed. You will learn to critically

examine models and theory behind behavioural ecology, and to appreciate the value of different empirical methods

for distinguishing between competing alternatives. This material will be taught through lectures and reinforced by a

set of hands-on practicals involving a laboratory study of behaviour in wood ants and a study of altruism in humans

(your fellow classmates!) using questionnaires and simple statistical analysis.

MODULE: CELL BIOLOGY

ORGANISER: Dr Paul Genever

RECOMMENDATIONS/PREREQUISITES: BIO00011C Cell & Developmental Biology

SUMMARY:

This module will deal with the fundamental aspects of cell biology and consider the ways in which cell functions

participate in the determination and differentiation of specialised tissues. Topics covered in the module will include

cell cycle control, the cytoskeleton, cell motility, cell adhesion, signalling pathways, apoptosis, secretory

mechanisms and endocytosis. Later we will consider how knowledge of these phenomena contributes to our

understanding of cell differentiation, tissue remodelling and the development of complex multicellular organisms.

LEARNING OUTCOMES:

By the end of the module students should be able to:

Explain the mechanisms involved in the control of the cell cycle. Describe different types of cell adhesion molecules and their role cell function. Describe the nature of cell-cell and cell-matrix interactions and their role in differentiation, proliferation and

migration. Explain the structure and function of the cytoskeleton. Describe secretory and endocytic pathways within in a cell. Provide an overview of apoptosis and its role in health and disease.


Introduce different cell signalling mechanisms, receptor types and downstream signalling pathways. Explain the composition and function of the extracellular matrix. Provide details on remodelling mechanisms in bone and during wound healing. Describe the properties and regulation of embryonic and adult stem cells. Provide examples of how stem cells may be used in therapy.

MODULE: DEVELOPMENTAL BIOLOGY

ORGANISER: Dr Richard Waites


SUMMARY:

An intermediate level Biology module focussing on the molecular and genetic approaches used to study

developmental biology. This module examines development in a wide variety of model organisms. We start by

explaining the important approaches used to understand development. Key concepts and mechanisms of

development are then illustrated with important examples. We end the module by examining development in the

context of evolution and bringing together many of the themes running through this module.

LEARNING OUTCOMES:

Be knowledgeable about the major approaches used to understand development; Appreciate the wide variety of model organisms used to illustrate development; Be familiar with axis formation in plants and animals; Understand the segmented body plan in Drosophila and be aware of how boundaries and compartments

are established; Have a greater understanding the role of homeotic genes in plant and animals; Appreciate the important cell movements during animal morphogenesis; Understand how epistasis is used to determine the order of the genes in a complex developmental

pathway; Appreciate development in the context of evolution; Gained practical experience in the regulation of development in flies; Gained practical experience in plant developmental genetics;


MODULE: ENVIRONMENTAL ECOLOGY

ORGANISER: Professor Phil Ineson

RECOMMENDATIONS/PREREQUISITES: Module BIO00001C Ecology, but A-level Biology plus prior directed

reading is acceptable.

SUMMARY:

A detailed study of key contemporary environmental issues, largely focussing on global environmental change

(GEC). The module will introduce the general subject of GEC, including both natural historical changes in the

environment and changes resulting from human activity. Consideration will be given to the development of the

ecosystem approach, with reference to classical and contemporary major ecosystem studies (e.g. Hubbard Brook)

and leading to the concepts of provision of ecosystem services. The consequences of GEC for individual

ecosystems and the biosphere will be highlighted with particular emphasis placed on the impacts of GEC (e.g.

rising temperatures and atmospheric concentrations of CO2 etc) on ecosystems, considering the roles of plants and

soils in feedbacks to GEC. There will also be a consideration of the underlying causes. A wide array of other

environmental issues are also considered, including impacts of excess nitrogen and acid deposition in Europe and

developing countries, persistent organic pollutants (POPS) and anthropogenic changes in the global carbon,

sulphur and nitrogen cycles.

LEARNING OUTCOMES:

At the end of the course, students should be able to :

Recognise the degree to which GEC may occur independently of human influence. Relate current GEC issues to the behaviour of specific ecosystems Understand the role humanity now plays in changing the global environment. Be familiar with the role soils and plants play in ecosystems and in climate change Understand the impact of human-mediated GEC on the physiology and ecology of plants. Evaluate the effectiveness and appropriateness of strategies to cope with environmental impacts. Understand and be able to apply the concept of ecosystems as providers of a wide range of ecosystem

services

MODULE: EVOLUTIONARY AND POPULATION GENETICS

ORGANISER: Dr Julia Ferrari


SUMMARY:

The module will introduce the processes that affect changes of allele frequencies and therefore evolution in natural

populations (ranging from microbes to humans). Most of these concepts will be explored using a range of

examples as well as simple mathematical models.

LEARNING OUTCOMES:

To understand that under simplifying conditions genotype frequencies in populations are stable anddetermined by allele frequencies (i.e. Hardy-Weinberg principle);

To appreciate that continuous variation has the same genetic origin as discontinuous variation and to beaware of the techniques for studying continuous variation and its evolutionary significance;

To know that the main processes affecting allele frequencies are mutation, genetic drift, selection and geneflow between populations and to understand under what circumstances each of these is likely to beimportant;

To understand how genetic variation can be maintained; To appreciate how simple, if not totally realistic, algebraic models can provide insights into equilibrium

conditions and the tempo and mode of evolution; To know the characteristics of small populations and understand the population genetic processes that are

important in such populations;


To appreciate the effects of geographic isolation on populations; To be aware that different molecular markers are employed to address a range of issues in population

genetics and related fields; During practical workshops, to gain skills in simple numerical calculations based on theoretical results and

to gather data for exploring the concepts of genetic drift and heritability.

MODULE: NEUROSCIENCE


RECOMMENDATIONS/PREREQUISITES: 1st

year Biology/Biochemistry at York or equivalent

SUMMARY:

This module builds on the basics of neuronal morphology, signal propagation, migration and axon guidance taught

in Stage 1 Cell and Organismal Biology. We will begin with the cell biology of neurons and synapses and then

consider how neuronal cells are organised to form a nervous system, focussing on how neuronal circuits link

behaviour with the environment. Finally the basic mechanisms of sensory input and processing will be described.

The lectures will be supported by a computing workshop on aspects of synaptic transmission, and an assessed

practical on sensory behaviour, using Drosophila as a model system. The topics covered in this module will

provide a foundation for the Stage 3 neuroscience modules ‘Learning and Memory’ and ‘Brain in Health and

Disease’.

LEARNING OUTCOMES:

Students who complete this module will have the ability to:

Describe the structure and function of the nervous system at the level of synaptic transmission, gross

anatomy and circuitry and sensory input and processing.

Describe scientific techniques and design experimental strategies for neuroscience research.

Synthesise ideas from across the module into coherent arguments.

Acquire, analyse, interpret and write up experimental data.

MODULE: POST-GENOMIC BIOTECHNOLOGY

ORGANISER: Dr James Chong

RECOMMENDATIONS/PREREQUISITES: BIO00004C, BIO00007C Genetics I, BIO00009C Genetics II and

BIO00008I

SUMMARY:

This module will consider the technologies employed in post-genomic biological science which are transforming the

field. The principles underlying DNA-based technologies used in research will be explored along with cutting edge

approaches taken in the latest-generation high throughput DNA sequencing instruments. Methods for the

collection and analysis of metabolites, transcripts and proteins, particularly via massively parallel approaches will

be explained. How these technologies are realised, automated, visualized and interpreted will be discussed.

Important applications in fields from plant biology to medicine will be highlighted.

LEARNING OUTCOMES:

have a good awareness of a number of cutting-edge, high-throughput “omics” biotechnologies understand the biological as well as physical principles that underlie these technologies be able to identify an appropriate biotechnology for collection of a particular sort of data have an appreciation of the potential limitations of the data collected by these methods be able to describe the impact of these methods in specific fields


AUTUMN – SPRING – SUMMER 2013-2014 – 20 AND 30 CREDIT MODULES

MODULE: ANIMAL AND PLANT ECOLOGY


ORGANISER: Prof Chris Thomas


SUMMARY:

This module outlines the fundamentals of the ecology of animals and plants. It emphasizes population biology

(population growth and limits), how species interact with other species (dynamics, co-existence, extinction) and

how species interact with the environment. Topics of practical interest, such as harvesting fisheries, disease

epidemics and issues in conservation biology, are covered in light of the background material. The module

provides a methodological foundation in practical sampling techniques used in field ecology and in the analysis of

population and community data.

LEARNING OUTCOMES:

On completion of this module students should have developed an understanding of:

the determinants of population dynamics how interactions with other species affect the growth, dynamics and survival of populations how variation in the physical environment affects individual performance and populations and distributions

of species how to apply understanding of population and community ecology to socially relevant issues such as the

harvesting of a natural population, the consequences of species’ invasions, and the strategy for conservingendangered species

how to identify some groups of plants and insects in the field, and be aware of identification keys how to sample animal and plant populations to estimate their population size and spatial structure how to sample and interpret ecological community patterns (diversity, similarity, species richness, species

accumulation, curve, abundance rank-plot) being used to compare communities.

MODULE: FROM GENE TO FUNCTION


ORGANISER: Dr James Moir

RECOMMENDATIONS/PREREQUISITES: Genetics 1 BIO00007C Genetics II BIO00009C

SUMMARY:

This module will examine the molecular processes involved in enabling expression of genetic information in both

prokaryotic and eukaryotic cell types. The module will examine the mechanisms by which genetic information is

transformed into functional information, and how the processes involved are regulated. This includes the

mechanism and regulation of transcription and translation, and subsequent events such as post-translational

modification and trafficking that enable the regulation of the activity of the fully functional gene product at the level

of cellular function. The module will also examine the technologies available for the global analysis of gene

expression at the level of messenger RNA (transcriptomics) and protein (proteomics).

LEARNING OUTCOMES:

How core methods are used for analysing gene expression and function

The make-up of microbial genomes, how these are derived from genetic material that has been both

vertically and horizontally transmitted


The features of bacteriophages (bacterial viruses) that infect prokaryotic cells and can become incorporate

into genomes

The basic mechanisms of regulation of microbial gene expression at the transcriptional and post-

transcriptional level

How environmental signals are sensed, and the mechanisms used to respond to these signals

The molecular basis of cell growth and division in Prokaryotes

An understanding of how eukaryotic gene expression is regulated at many different levels

The importance of chromatin structure and chromatin modifications in control of transcription

How transcription initiation is controlled by cis- and trans-acting factors

The role that RNA processing plays in modulating gene expression

The role of non-coding RNAs in controlling gene expression

The generation of protein diversity through alternative splicing and RNA editing

How mRNAs are exported from the nucleus and localized in the cytoplasm

How proteins are generated by translation and subsequently modified for biological activity, either within

the cell or as a secreted product

The importance of mRNA and protein stability in gene expression and how these macromolecules are

degraded


MODULE: SCIENTIFIC SKILLS 2




SUMMARY

This module is divided into three distinct sections:

Autumn term experimental design – 10 creditsTutorials in the autumn, spring and summer – 10 creditsSpring/Summer skills courses – 5 credits each or 10 credits if you take Environmental field skills.

Autumn Term Experimental Design:As a group, students will plan and carry out a series of experiments, complete a risk assessment form, record andanalyse their data, draw conclusions and keep a diary on the VLE. Each group will prepare a poster which willexplain what the investigation has discovered and receive a viva based on their findings . Each student in the groupwill write a summary of their findings. This part is done by individually rather than as a group.

Autumn Term Tutorials:Students will attend a series of 6 small group tutorials (these are not linked to the experimental design componentof the programme) and complete and get feedback on work including at least two pieces of written work.

Spring / Summer Term Skills Courses:Students will select EITHER Environmental field skills (10 credits) OR two skills from the list below, one from eachof the lists:

Group A:Cell biology and cytometry

Electrophysiology

Polymerase chain reaction & DNA sequencing

Protein interactions

Group B:Bioenterprise

Communicating science & outreach

Evolutionary trees

Genomics

Molecular imaging

Systems biology

Spring / Summer Term Tutorials:Students will attend a series of 8 small group tutorials (6 in the spring and 2 early in the summer term), andcomplete and get feedback on work including at least one extended essay based on a research topic.

LEARNING OUTCOMES:

To learn how to plan and carry out research, and to collect useful data which can be analysed to testappropriate hypotheses.

To interpret the results and conclusions which are obtained, and to present project findings in anappropriate format.

To improve communication skills orally and in written work. To confidently discuss scientific issues in a group setting. To undertake effective literature research into a given scientific area, and write an extended and well

structured account of the area.

SPRING – SUMMER TERM – SKILLS PRACTICAL COURSES

The spring term skills practicals are divided into two groups, you will take one skills practical from eachgroup. List your preferences for the practicals in each group on your choice form at the end of thebooklet and the Department will allocate you to one of your choices. Where possible we take account ofstudent preference but numbers are limited on these courses. If you take Environmental Field Skills youdo not take the spring term skills practicals.


MODULE: ENVIRONMENTAL FIELD SKILLS

ORGANISER: Dr Olivier Missa

RECOMMENDATIONS/PREREQUISITES: First year biology modules

SUMMARY:

Environmental field skills enable students to develop and execute an ecological investigation. After introduction to a range of

habitats students design their own small group ecological study in one of the available sites. They then gather the

appropriate data, process the results and prepare a scientific presentation about their findings.

LEARNING OUTCOMES:

On completion of this module the students will:

Be aware of the constraints and opportunities provided by ecological fieldwork.

Be introduced to a range of British habitats in the vicinity of the base, in particular coastal, moorland,

woodland and meadowland habitats.

Learn about the specific conservation concerns in these areas, which have wide applicability in the United

Kingdom.

Conduct a short project in small groups (3-4 students) in the field to learn aspects of experimental design

and analysis in relation to field ecology.

Develop these skills further with a class practical on plant diversity in a calcareous meadow.

Learn other more specific skills in relation to data gathering for the particular project that they conduct,

which will involve species identification and field methodology.

SKILLS PRACTICALS – GROUP A

MODULE: CELL BIOLOGY AND CYTOMETRY

ORGANISER: Dr Gonzalo Blanco

RECOMMENDATIONS/PREREQUISITES: Module BIO00002I Immunology. It is recommended that module

BIO00011I, Cell biology, is taken alongside this module.

SUMMARY:

Two experimental systems of mammalian cell biology will be used to introduce technique such as in vitro cell

culture, transfection, fluorescent microscopy, cell proliferation assays, and flow cytometry. The students will gain

an appreciation of how different techniques can be used to study the biology of the cell, and how they can be used

in combination to answer specific questions relating to cell function.

LEARNING OUTCOMES:

Upon completing this module, students will have the ability to:

Understand basic in vitro cell culture and cytometry techniques used commonly in cell biological research.

Use transfection to study the biology of the mammalian cell, and examine the expression of molecules by

fluorescence microscopy.

A broad appreciation of the applications and limitations of flow cytometry techniques based upon laser

discrimination of labelled cell populations.

Design labelling procedures and the appropriate use of controls to confirm specificity of the labelling

procedure.

Understand how to measure cell proliferation, with specific reference to the division of lymphocytes in

response to antigenic stimulation.


Analyse data qualitatively and quantitatively, and how to use each appropriately to answer specific questions

related to cell biology.

Use literature available in the library and via the internet to further explore advances in techniques relevant

to the study of animal cell biology.

MODULE: POLYMERASE CHAIN REACTION AND DNA SEQUENCING


ORGANISER: Michael Schultze

RECOMMENDATIONS/PREREQUISITES: Very basic knowledge of how to use a computer. For example, you

need to know how to copy a file, what is a pull-down menu, etc.

SUMMARY:

The polymerase chain reaction (PCR) is perhaps the most important innovation in modern techniques in molecular biology

since the introduction of DNA sequencing and the use of plasmids and restriction enzymes. PCR is now widely used in a vast

variety of disciplines such as gene cloning, mRNA quantification, DNA subcloning and site directed mutagenesis, diagnostic

techniques in forensic and clinical studies, as well as in molecular evolution and population genetics. PCR can be used to

detect pathogens in food products, to identify transgenes in genetically manipulated organisms, to study populations of

insect communities, to conduct DNA finger printing or to diagnose genetic diseases at an early stage during pregnancy. The

list of applications has virtually no end. In addition, automated DNA sequencing is related to PCR in that it is based on a

thermal cycling procedure. This practical course is to introduce students to some of the applications of the PCR reaction. The

course involves introductory lectures and practicals.

LEARNING OUTCOMES:

To provide knowledge of some of the many PCR applications.

To demonstrate the power of PCR in diagnostic/forensic applications.

To learn how to use PCR for gene expression studies (such as RT-PCR, Q-PCR)

To inform about the parameters that are critical for successful PCR.

To confer the ability to design oligonucleotide primers.

To provide knowledge of how to program a thermal cycler.

To provide knowledge of automated DNA sequencing.

To introduce to the use of computer programmes for DNA sequence analysis.

MODULE: PROTEIN INTERACTIONS

ORGANISER: Dr Daniel Ungar

RECOMMENDATIONS/PREREQUISITES: Stage 1 Molecular Biology and Biochemistry

SUMMARY:

Protein interactions are centrally important for all cellular functions including signalling, movement, structure,

proliferation or defence. Protein interactions can generate complexes that exist either transiently or permanently

depending on the needs of the process involved. The nature of the complex is also determined by the strength of

the protein interactions, stronger interactions often, but not exclusively, being more permanent. In this module we

will introduce two very basic methods for the biochemical characterisation of protein interaction, the two-hybrid and

the pull-down techniques. In addition we will use western blotting, which is especially useful for the analysis of

weak interactions that are often important in transient signalling complexes. The two lectures leading up to the

practical will explain the theory behind the methods and highlight how they can be applied to different protein

interaction studies. The workshops will be used for planning the experiments, and for analysing and interpreting

the obtained data.


LEARNING OUTCOMES:

To deepen the experience in biochemical methodology acquired in To provide novel practical knowledge of some techniques used to study protein interactions To practice experimental design and data analysis

SKILLS PRACTICALS – GROUP B

MODULE: BIOENTERPRISE


ORGANISER: Dr Kelly Redeker


SUMMARY:

The module will introduce students to BioEnterprise – to appreciate what enterprise means and how to develop an

idea or discovery in biology – from areas of biochemistry, cell biology, genetics, ecology, microbiology and

animal/plant biology - into a commercial application. The module will begin by providing background information on

various topics, and guidance on how to develop a business plan. The major activity will then involve groups of up to

five students agreeing an idea and developing a business plan with the aim of securing funding to turn the idea into

a commercial venture.

LEARNING OUTCOMES:

By the end of these workshop sessions students should have the knowledge and skills to take an idea of their own

for a Biotech product or service and, as a group, develop this idea to produce a business plan to manufacture,

market and distribute this product. The module will develop an appreciation of the nature of enterprise and how to

turn ideas into business proposals and projects. The students will learn about intellectual property, company

‘values’, corporate ethics and governance, what a business plan is and how to assess markets. Specific skills

developed will include team-working, negotiating; planning, presentational skills (writing and oral) and the costing

of activities. Students will be given training in how to write an effective business plan and pitch (present) a coherent

proposal to a group of experts. Each group will be assigned a member of staff as mentor to guide the development

of their business plan.

MODULE: COMMUNICATING SCIENCE TO THE PUBLIC

ORGANISER: Dr Adrian Harrison

RECOMMENDATIONS/PREREQUISITES: First year Scientific Skills module

SUMMARY:

This module is designed to help students to develop an understanding of the need for scientists to effectively

communicate their research beyond a scientific audience. The course will consist of workshops that will explore the

issues surrounding science communication. To put into practice these skills, as groups, students will design an

outreach activity suitable for school pupils in the 11-14 year age group. These activities will then be run for school

groups as a circus of activities on a designated date in the last week of the spring term.

LEARNING OUTCOMES:


Specific learning objectives are:

To improve communication skills

Develop an understanding of the difficulties of communicating scientific concepts to a lay audience.

To be aware of the range of groups that need to be communicated with.

To understand why scientists need to communicate their research to a wider audience

To be aware of the different methods and opportunities available to scientist to communicate their science.

To be able to develop and deliver an outreach activity for school age children.

To be aware of the funding streams, organisations involved in and career opportunities for science

communicators.

MODULE: EVOLUTIONARY TREES

MODULE NUMBER: 0220508

ORGANISER: Dr Peter Mayhew

RECOMMENDATIONS/PREREQUISITES: First year biology modules

SUMMARY:

This module covers the techniques which biologists use to name and classify organisms, to estimate their

evolutionary relationships, and to infer evolutionary correlations among characters such as ecological traits. It

considers the problems of which philosophy and what data should underpin classification, what names organisms

should be given, how to find the most likely evolutionary tree linking them together, and how to use those trees to

make inferences about how evolution has occurred. The module consists of four lectures followed by practical

workshops designed to encourage deep experiential learning.

LEARNING OUTCOMES:

A knowledge of contemporary taxonomic schemes and terminology.

An understanding of the reasons for shared phylogenetic similarity, and homologous versus analogous

traits.

The ability to analyze a morphological data set to estimate evolutionary relationships. An understanding

of parsimony and some simple tree-searching algorithms.

An understanding of how sequence data may contain phylogenetic information.

A knowledge of how to access sequence data on the web, and of some simple techniques for extracting

phylogenetic information from DNA sequences.

An understanding of the need to control for phylogenetic relationships in comparative analyses and how

this can be achieved.

MODULE: GENOMICS FOR CELL AND DEVELOPMENTAL BIOLOGY


ORGANISER: Ms Emma Rand

RECOMMENDATIONS/PREREQUISITES: none

SUMMARY:

Most biologists working on a wide range of problems in genetics, cell, molecular and developmental biology need

the basic skills to deal with accessing molecular databases for information about the genes, proteins, protein

families etc. This has been driven by the growth in our knowledge of sequences and gene expression. Accessing

and analysing these data is increasingly important for all laboratory-based molecular scientists. This module aims

to provide knowledge of how to access/question the commonly used DNA, protein and gene expression databases.


The module is aimed at teaching skills used by all molecular cell biologists. It is not about algorithms and ‘heavy’

computing, but introduces the data (and databases) available, the commonly used programs and the methods

needed to carry out research on them. This module would also open up areas of biological research that do not

involve laboratory work and increase the range of projects you might feel confident to tackle in the final year.

The module is a mix of led workshops and case studies, finishing with a small group project. The module starts

with 3 two-hour workshops covering the types of data, databases and programs used in their analysis. These are

followed by 2 two-hour workshops covering two case studies of problems in cell and developmental biology. In the

final workshop students will work in groups on a small project for the assessment. There will be a selection of

projects given during the module from which groups choose. At the end of term students will give a ten-minute

group presentation on the results of their analysis and write a short individual report.

LEARNING OUTCOMES:

By the end of this module students should

Appreciate the volume and some of the diversity of data available

Appreciate some of the limitations in data annotation

Be able to retrieve sequences from GenBank using keyword and similarity searches and understand

BLAST output.

Have a broad understanding of the information available in KEGG, ArrayExpress, Pfam and SCOP

Appreciate how protein functions are described using Gene Ontology terms

Understand the principles of multiple sequence alignment and be able to use Clustal to perform one

Be able to apply skills and knowledge taught in earlier workshops to work on problems in cell and

developmental biology

Develop group working skills

Gain confidence in presenting results to a group of peers

MODULE: MOLECULAR IMAGING


ORGANISER: Dr Frans Maathuis


SUMMARY:

Light in particular and electromagnetic waves (EMW) in general are essential means to relay information about the

physical world. It can help reveal structure from the macroscopic level to the atomic level and is therefore an

indispensable technique to understand biology. For example EMW-based imaging can reveal the location of

cancer tumours but also the movement of a single molecule during muscle contraction. The lectures and practicals

in this module will introduce students to the basic principles of light, EMW, bright field microscopy, confocal

microscopy and atomic force microscopy, to show how such techniques can be applied to study important

problems in modern biology. In addition to the lectures, students will participate in computer based workshops and

a confocal microscopy demonstration.

LEARNING OUTCOMES:

Understanding the basic principles of light and other EM radiation with respect to wave and particleproperties

Understanding the basic principles of various types of light, fluorescence, confocal and electron microscopy Understanding how the usage of various chromophores to label cells, cellular compartments and proteins

can be used to visualise these Understanding how imaging approaches can be applied to study molecular, cellular and tissue location

dynamics in space and time Understanding how imaging techniques can show dynamics and location of gene and protein expression


Ability to critically assess the suitability, advantages and disadvantages of specific imaging techniques tostudy defined biological questions


MODULE: SYSTEMS BIOLOGY

ORGANISER: Dr Leo Caves


SUMMARY:

Systems Biology is an approach to tackling the complexity of biological systems. This module introduces systems

approaches in terms of its concepts, methods and tools. The aim is to provide an appreciation of the structure,

organisation and properties of biosystems and some of the methods and practice of systems biology.

LEARNING OUTCOMES:

By the end of this skills module, students should:

Gain a general understanding of the structure and organisation of biosystems across many scales.

Be familiar with network representations of biological systems.

Be familiar with some of the main methods, tools and strategies of systems biology.

Gain an appreciation of applications and prospects of systems biology.


STAGE 3 MODULE DESCRIPTIONS 2014-2015 (PROVISIONAL LIST)

AUTUMN TERM 2014 / SPRING TERM 2015 COMPULSORY MODULES

MODULE: RESEARCH SKILLS

MODULE NUMBER: BIO00027H

ORGANISER: Dr Calvin Dytham

RECOMMENDATIONS/PREREQUISITES: Stage 1 / stage 2 Biology skills modules

SUMMARY: This module aims to provide students with skills to support their development as they

proceed to become biology graduates. Students will be exposed to research seminars given by internal

and external speakers as part of departmental research seminar series. Additionally, students will take

part in “Journal club” type activities in which they will read analyse and criticise recent research papers in

small groups with academics acting as conveners. Additional sessions will be included to provide generic

support for students skills in areas such as writing essays / reports / CVs and presentation skills.

LEARNING OUTCOMES:

Ability to select appropriate information and take contemporaneous notes during research seminars

Ability to analyse and criticise the scientific literature

Improved communication skills (through journal club)

Writing skills relevant to preparation of essays under time-limited conditions

Writing complex reports involving presentation and analysis of research findings from own researchproject or analysing those of others.

Confidence in preparation for life as a graduate, through careers advice / CV writing skills etc.

MODULE: RESEARCH PROJECT


ORGANISER: Biology Undergraduate Studies Board


SUMMARY: To provide the practical and/or intellectual skills needed for the research biologist in the

design and execution of a research project involving the collection and/or analysis of primary biological

data.

LEARNING OUTCOMES: Know how to design a research project

Be able to present and defend research findings orally.

Be able to write up a report based on the findings of a piece of independent and novel scientific research.


AUTUMN TERM

MODULE ASSESSMENT: Modules are assessed by a closed examination paper comprising a variety of

short answer, problem and method questions as well as an essay question. The assessments for autumn

term 10 credit modules are normally held in week 1 of the spring term.

CREDITS: All modules are worth 10 credits unless otherwise stated.

MODULE: CANCER AND THE CELL CYCLE


ORGANISER: Dr Dawn Coverley


2011 Cohort: BIO00011I Cell Biology and BIO00007I From gene to function modules

2012 Cohort: BIO00035I Cell Biology and BIO00007I From gene to function modules

SUMMARY:

This module will review current knowledge, underpinning principles and recurrent themes in the field of

molecular cancer cell biology. We will discuss in detail the regulatory pathways governing cell cycle

commitment and progression, and their disruption in cancer cells. DNA damage, surveillance checkpoints

and repair pathways will also be discussed in the context of hereditary cancer susceptibility syndromes,

leading on to the emerging molecular description of nuclear organization in cancer cells. The module will

also outline current knowledge of cancer stem cells, mechanisms of metastasis, and the value of

experimental model systems relevant to bladder cancer, ending with an overview of post-genome

approaches to cancer diagnosis and therapy that aims to explain what we can and can’t do with the

wealth of information that is now available.

LEARNING OUTCOMES:

Successful completion of this module will result in an understanding of:

The Hallmarks of cancer The pathways that govern cell cycle commitment and progression Their disruption in cancer cells and the concepts of oncogenes and tumour suppressors DNA damage, repair and surveillance pathways that protect the genome Nuclear organization and its disruption in cancer cells The principles underlying the spread of cancers Aberrant adult stem cell activity and its contribution to tumour formation Current approaches in cancer research Modern approaches to cancer diagnosis and therapy, and the promise of personalized medicine.


MODULE: CELL AND TISSUE ENGINEERING


ORGANISER: Paul Genever


2011 Cohort: BIO00011I Cell Biology

2012 Cohort: BIO00035I Cell Biology

SUMMARY:

The module will explore how recent advances in cell and molecular biology have enabled us to engineer

cells and tissues for specific purposes. For example, cells can be genetically, chemically and mechanically

modified or reprogrammed to address specific biological questions. Tissues can be engineered to mimic

living counterparts. It is anticipated that these approaches will lead to new cell-based therapies for age-

related and degenerative conditions such as Parkinson’s disease, cardiovascular disease, arthritis and

bone disorders. The lectures will cover the sourcing and selection of cells, embryonic stem cells, adult

stem cells and induced pluripotent (iPS) cells, the principles of tissue engineering, molecular manipulation

and gene therapy, biomaterials used to construct scaffolds, imaging, bioreactor design, scaling-up

processes and clinical applications using specific cell and tissue types.

LEARNING OUTCOMES:

By the end of this module, a student should be able to:

Provide an overview of cell and tissue engineering applications and their use in current and futuretherapies, giving specific examples in hard and soft tissue engineering.

Explain how to isolate and maintain different cell types and the use of different culture techniques. Describe how cells and cellular components may be modified by mechanical, chemical and

genetic engineering. Give examples of different scaffold materials, describe their properties and suitability for cell

support and explain how they are manufactured. Explain advanced bioengineering strategies, including the use of computer-aided design, custom-

built biomaterials, micro/nano-patterning and “smart scaffolds”. Discuss way in which cell performance may be monitored using imaging, bioreporters and

fluorescent indicators. Describe the challenges and opportunities for the commercialisation of cell and tissue

engineering, from bench to bedside.

MODULE: ENVIRONMENTAL MICROBIOLOGY


ORGANISER: Dr Thorunn Helgason


SUMMARY:

The course will draw on principles that students will have covered in a variety of Stage 2 courses such as

Genes to Function, Environmental Interactions, Human Genetics, Biotechnology, and consolidate those

into an understanding of the identity and function of microbes in environmental contexts. An introductory


lecture will cover definitions and revise the important analytical and quantitative techniques that will be

covered. The following sessions will use a “journal club” format, where 2-3 key papers will be studied in

depth each week on topics such as human gut microbiomes, fungal diversity in soils, and metagenomics.

LEARNING OUTCOMES:

An understanding of the techniques used to identify the presence, abundance and function ofmicrobes from environmental samples.

An understanding of the roles that microbial communities play in soil ecosystems and inanimal/human environments

An understanding of how data from such studies can be used in policy environments to promoteanimal, plant and/or human health.

MODULE: EVOLUTION AND BEHAVIOUR


ORGANISER: TBC

RECOMMENDATIONS/PREREQUISITES: BIO00020I Behavioural Ecology and BIO00017I Evolutionary

& Population Genetics might be advantageous, but neither is essential.

SUMMARY:

This module will cover a broad range of topics in evolutionary biology, with a focus on the evolution of

behaviour. We will look at how species-specific behaviours have evolved under natural and sexual

selection, how they interact and are traded off against each other, and how flexible they can be. There will

be a particular focus on methods used in the study of behaviour, and on recent and classic case studies

from the literature

LEARNING OUTCOMES:

Students will learn how natural selection and sexual operate and how they are studied, with particular

reference to the influence of these mechanisms on the evolution of animal behaviour. At the end of the

module, students will understand the central role of behavioural ecology in the study of evolution, and the

role of genes, development, and experience on the range of behaviours expressed. Students will also

learn in some depth how the evolutionary mechanisms underlying behaviours are unravelled using a

variety of experimental and analytical approaches to the study of behaviour.


MODULE: EVOLUTIONARY ECOLOGY


ORGANISER: Dr Peter Mayhew

RECOMMENDATIONS/PREREQUISITES: BIO00001C Ecology, BIO00007C and

BIO00009C Genetics modules

SUMMARY:

Evolutionary Ecology is the field covering the interaction between ecological and evolutionary processes.

Ecology can affect evolution by imposing selective and other forces on lineages, forcing them to change

over time. It can also create the conditions for new species to form or go extinct. Evolution can affect

ecology if the characteristics that evolve impact on the organisms interactions with other organisms and

the environment. By thinking across both disciplines, evolutionary ecologists are able to make powerful

predictions about the world to which scientists in only one discipline would be blind. The module will take

all these issues and discuss them in depth by reference to topical case studies.

LEARNING OUTCOMES:

An understanding of the relevance of observational, experimental and comparative evidence, andof population genetic, optimization and ESS and adaptive dynamics theory to answeringquestions in evolutionary ecology.

A critical awareness of current theory and evidence.

MODULE: GLOBAL CHANGE ECOLOGY


ORGANISER: Dr Phil Ineson

RECOMMENDATIONS/PREREQUISITES: Basic knowledge of chemistry

SUMMARY:

The course will consider the role of ecosystems in global change. This will include the importance of

man’s activities at the global scale, including the topics of anthropogenic influences on the major global

nutrient cycles, atmospheric chemistry, and climate.

LEARNING OUTCOMES:

To provide a knowledge of basic concepts in biogeochemistry To provide an understanding of the importance of micro-organisms in biogeochemical cycles To provide a detailed insight into the nature of three major global nutrient cycles To demonstrate the global significance of human activity to these cycles To provide the scientific evidence behind the ‘global warming’ debate, to include a full understanding

of the role played by the key trace gases To provide information on the suggested impacts of global change on the world’s ecosystems, with

particular reference to the UK To demonstrate the central role of global and ecosystem modelling in informing policy To provide a ‘case study’ on the impacts of elevated CO2 on ecosystems, demonstrating the role of

experimentation and modelling in making science-based predictions.


To provide an insight into some of the techniques and tools used to address ‘global’ ecologicalissues, ranging from types of field experimentation through to the use of stable isotopes inenvironmental research.

MODULE: LEARNING AND MEMORY



RECOMMENDATIONS/PREREQUISITES: BIO00009I Neuroscience

SUMMARY:

This module covers the anatomy and physiology of the synapse, exploring the ways in which it is modified

during learning and the storage of memory. Molecular, cellular and behavioural examples will be used to

explain how synaptic properties are linked to memory. In addition to the lectures, there will be two seminar

sessions where scientific papers relating to the lecture material are dissected and the opportunity to

practice comprehension and criticism style questions.

LEARNING OUTCOMES:

This module will enable students to:

Understand learning and memory at the neurological, cellular and molecular level. Compare and contrast the ways in which synaptic transmission can be altered in learning. Compare and contrast the techniques and animal models that have been used to investigate the

mechanisms of learning and memory. Relate the molecular function of neuronal proteins to their role in animal behaviour. Comprehend and criticise scientific studies of learning and memory.

MODULE: MOLECULAR MACHINES


ORGANISER: Christoph Baumann

RECOMMENDATIONS/PREREQUISITES: BIO00004C Molecular Biology and Biochemistry of the Cell,

or equivalent module

SUMMARY:

Cells contain molecular machines composed of complex protein and nucleic assemblies that are required

for biological function. Over the last few years there have been significant advances in our understanding

of both the structures of such machines and their underlying molecular mechanisms. This module will

address the structure and mode of action of cellular molecular machines involved in the biogenesis of

DNA, RNA and proteins. Organismal motion is a requirement of eukaryotes and prokaryotes alike,

involving the transduction of chemical or electrochemical energy by molecular motors into directed

movement. The module will include a detailed appraisal of actin and tubulin-based molecular motors,

involved in muscle contraction and cellular/organellar motion, respectively, as well rotatory motors

involved in ATP synthesis and bacterial flagellular motion.


LEARNING OUTCOMES:

This module will focus on a number of macromolecular machines that underpin various biological

functions. The aims of this module are to assist students in gaining a critical understanding of:

the structure and architecture of large macromolecular assemblies how chemical energy is transduced into motion by molecular machines the machines that synthesise biological macromolecules an understanding and appreciation of the methods and techniques used to investigate molecular

machines.

MODULE: MOLECULAR MICROBIOLOGY


ORGANISER: James Moir

RECOMMENDATIONS/PREREQUISITES: BIO0007I From Gene to Function

SUMMARY:

This course focuses on the molecular basis of bacterial behaviour. Using a variety of examples of

biological phenomena, the mechanisms by which these apparently simple organisms coordinate a wide

array of activities will be exposed and discussed. The emphasis will be on the ways in which control is

exerted to allow complex behavioural patterns to occur.

LEARNING OUTCOMES:

Taught sessions will focus on the molecular basis of cellular function in the prokaryotes. There will be

broad coverage of this discipline, and in each session a few specific examples will be explored in depth. It

is expected that by the end of the course students will have developed an understanding of:

key molecular mechanisms employed by bacteria to carry out processes how complex processes are controlled the ways in which specific molecular processes influence overall biological functions (such as

diseases) the methodological approaches used to gain knowledge about molecular mechanisms in microbes

Molecular mechanism, control of biological processes, and relevance of specific molecular events to

processes at a larger scale will run as themes throughout the course, and it will be expected that students

will be able to draw information from different lectures and their private reading in the answering of

questions that span parts of the course.


MODULE: PLANT BIOTECHNOLOGY


ORGANISER: Dr Michael Schultze


SUMMARY:

The tools of modern molecular biology have enabled plant breeders to introduce desired traits into crops

at an unprecedented rate and precision. Moreover, plants have a huge potential as environment friendly

“factories”. Research in Plant Biotechnology is one of strong points of the Biology Department, including

the Centre for Novel Agricultural Products (CNAP). This module will give you an opportunity to obtain an

overview on the latest developments in a rapidly expanding field.

The module will cover the latest developments in crop improvement, including areas such as disease

resistance, salt and cold tolerance, alteration of plant architecture to improve yields, etc. In addition, the

use of plants as factories for the production of health-promoting substances, medicinal compounds, fibres,

vaccines, and biodegradable plastics will be discussed. The module will also discuss the tools to alter

gene expression in plants in a highly controlled manner, as well as strategies to increase biosafety.

LEARNING OUTCOMES:

Become familiar with the latest developments in crop improvement To become informed about the strategies to modify gene expression in plants in a controlled and

safe manner Learn what strategies can be used to improve crop yield, disease resistance, and stress tolerance Learn how plants can be modified to produce large quantities of biologically active metabolites

and proteins To know what progress has been made in using plants as factories such as for the production of

biodegradable plastics. How molecular breeding helps in improving medicinal plants


SPRING TERM

TERM 8 MODULE ASSESSMENT: Modules are assessed by a closed examination paper comprising a

variety of short answer, problem and method questions as well as an essay question. The assessments

are timetabled in weeks 5-7 of the summer term.

CREDITS: All modules are worth 10 credits unless otherwise stated.

MODULE: ADVANCED TOPICS IN DEVELOPMENTAL BIOLOGY


ORGANISER: Dr Betsy Pownall

RECOMMENDATIONS/PREREQUISITES: Genetic and molecular approaches to studying

developmental biology will be covered in the stage 2 module BIO00004I Developmental Biology.

SUMMARY:

This module will use a new approach to final year teaching being taught as a series of seminars focussed on

understanding the primary scientific literature that underpins the current models of how development works.

The style of each lecture take the style of a journal club where 3 or 4 primary papers (no more) are presented

and the experimental evidence that supports current understanding of developmental mechanisms is gone

through in detail.

LEARNING OUTCOMES:

By the end of the module students will:

Be able to read and understand primary research papers.

Appreciate advantages in using a variety of model organisms in the study of development.

Understand a wide variety of molecular and genetic techniques used in the study ofdevelopment.

Have a detailed understanding of some of the current topics being studied by Developmental Biologists inanimals.

MODULE: ADVANCED TOPICS IN IMMUNOLOGY


ORGANISER: Adrian Mountford

RECOMMENDATIONS/PREREQUISITES: BIO00002I Immunology

SUMMARY: The spread of HIV and the rising incidence of tuberculosis in recent years have highlighted

the importance of immunology. Allergies have also increased, and autoimmune diseases are an ever-

present problem. The first six lectures will cover various aspects of leucocyte cell biology, including the

interface with innate immunity, antigen processing and presentation, the diversity of T helper lymphocyte


subsets, and the trafficking of immune cells around the body. The last three lectures deal with problems

in applied immunology, namely the mechanisms of inflammation, autoimmunity, and how to make better

vaccines.

LEARNING OUTCOMES: At the end of this module you should have acquired an understanding of:

How a pathogen first stimulates the innate host defences and then, via antigen processing pathways,initiates an acquired immune response.

How T lymphocytes provide specific immune recognition, responding to stimulation by proliferating,differentiating, and orchestrating immune effector responses.

Via examples from chronic inflammatory and autoimmune conditions, that not all aspects of animmune response are beneficial, and can even be life threatening.

How the immune response can be manipulated to enhance protection against infectious agents.

MODULE: BIOCATALYSIS


ORGANISER: Prof Neil Bruce

RECOMMENDATIONS/PREREQUISITES: BIO00004C Molecular biology and biochemistry

SUMMARY:

This option looks at advanced aspects of biological catalysis, including sections on enzyme cofactors, and

how these are exploited in Nature for complex processes, the engineering of enzymes for industrial

biotechnology, and also an introduction to the fascinating catalytic properties of another

biomacromolecule, RNA.

The first section builds on your knowledge of organic co-factors (coenzymes) from Year 2. The history,

mechanisms of activity, developments and biotechnological applications of coenzyme dependent activities

will be described. The second section deals with the engineering of enzymatic activity for mechanistic

investigations and biotechnological applications. The final section deals with catalytic RNA (ribozymes)

and their in vitro evolution.

LEARNING OUTCOMES:

The learning objectives given below should be considered guides to core knowledge. As in all modules,

you are expected to read around the subject and understand how the various objectives are related. The

aims of the module given above provide the overarching framework for viewing the specific objectives

listed below:

An understanding of coenzyme dependent enzyme catalysis

An appreciation of the use of enzymes for biotechnological applications

An understanding of how site-directed mutagenesis experiments can be used to probe enzymecatalysis and improve/alter enzyme activity and specificity.

An understanding of how ‘random mutagenesis’ or ‘in vitro’ evolution experiments can be used toimprove or alter the catalytic properties of enzymes

An understanding of how RNA can act as a catalyst and how ‘in vitro’ evolution can be used togenerate novel RNA catalysts


MODULE: BIOFUELS & BIOTECHNOLOGY


ORGANISER: Dr Gavin Thomas

PREREQUISITES: BIO00008I Molecular Biotechnology

SUMMARY:

The course aims to take a modern view on the biotechnology that is driving forward progress in the

development of biofuels. These renewable energy sources have the potential to make a significant

contribution to global energy supplies and biotechnology can make major impacts on the economic

competitiveness of this industry. We first examine our current dependencies on petrochemicals and how

biomass is used to generate energy by combustion. Then we examine the major classes of current

biofuels being produced including second generation biofuels like biobutanol and biodiesel. The use of

non-food lignocellulose feedstock is a key component of making biofuels economically and we will take a

detail look at the plant cell wall, both how it is assembled and then degraded by a range of organisms.

Fermentation of the released sugars into the major biofuel products will then be considered, first in

naturally occurring organisms and then in genetically modified bacterial augmented for both lignocellulose

degradation and subsequent fermentation of these products into fuels, so called consolidated

bioprocessing. The module ends with a synoptic view on the future of biofuels within a larger global

economic framework.

LEARNING OUTCOMES:

By the end of this module, students will have:

An understanding the current dependencies of humanity of petrochemicals and other sources ofenergy and how biomass currently contributes to this.

An overview of the major types of biofuels that being used or developed for future use.

A detailed understanding of the structure of lignocellulose and its degradation by a range of organisms,including animals, fungi and bacteria.

An appreciation of the metabolic pathways required for the conversion of sugars to biofuel products.

A clear understanding of how synthetic biology can be applied to biofuel production

The ability to critically assessment both the scientific and socio-economic factors that will influence thelong-term viability of biofuels.


MODULE: BIOREMEDIATION


ORGANISER: Dr Adrian Harrison

RECOMMENDATIONS/PREREQUISITES: BIO00010C Microbiology

SUMMARY:

The course is intended to illustrate the role that biological systems play in the clean-up of compounds that

are either accidentally or deliberately released into the environment (microbial bioremediation and

phytoremediation).

LEARNING OUTCOMES:

To introduce the concept of pollution being many things to many different people, and that it can befound in any environment.

To illustrate the importance of biological systems in the treatment of pollution and pollution prevention. To develop the idea of industrial biology introduced in the second year of the course into the area of

pollution prevention and treatment To introduce the metabolic abilities of plants and micro-organisms that is exploited in the treatment of

wastes and contamination. Highlight the future prospects for biological systems to replace chemical processes, resulting in

decreased operation costs and reduced pollution Look at specific examples of biological treatment of pollution and polluting materials. In particular

phytoremediation, the treatment of wastes and the bioremediation of oil spills. To compare biological treatment of waste with physico-chemical treatment options.

MODULE: BRAIN IN HEALTH AND DISEASE


ORGANISER: Chris Elliott

RECOMMENDATIONS/PREREQUISITES: BIO00009I Neuroscience

SUMMARY:

This module covers the role of toxins, genes and other factors which lead to the major diseases of the

nervous system, outlines their symptoms, and (where appropriate) treatment, setting them in the context

of normal CNS function.

LEARNING OUTCOMES:

A competent student will show knowledge of the vertebrate brain, the impact of toxins on neural function

and the main diseases of the nervous system. She/He will be able to draw together information from

different lectures to provide a cohesive view of anatomical, cellular, molecular, physiological and

behavioural approaches.


MODULE: CONSERVATION ECOLOGY & BIODIVERSITY


ORGANISER: Prof Jane Hill

RECOMMENDATIONS/PREREQUISITES: An understanding of concepts and topics covered in Stage 2

modules BIO00023I (Animal and Plant Ecology) and BIO00005I (Environmental Ecology) is

recommended

SUMMARY:

Many species and their habitats are currently under threat as a consequence of human impacts on the

environment. This course will cover the causes of these major threats (including ecological impacts of

climate change, habitat fragmentation, introduction of alien species), and their impacts on biodiversity. It

will address issues such as: what is the scale of the problem, how many species are affected, what are

the causes for species’ declines, which species are most vulnerable? It will explore the ecological

processes that promote and maintain biodiversity and will consider the consequences of diversity loss. It

will demonstrate how an understanding of basic ecological principals of community and population

ecology is crucial in successful conservation. The course will make extensive use of case studies to

illustrate these principals, taken from temperate and tropical ecosystems.

LEARNING OUTCOMES:

On completion of this module you will appreciate the factors which affect the global distribution of

diversity. You will learn which factors cause the loss of biodiversity and the consequences of biodiversity

loss. You will learn which threats are currently having the most detrimental effects on species, and be

introduced to the problems conservationists face in terms of understanding the complexity of reasons for

species’ declines. You will learn to appreciate that an understanding of the principles of population and

community ecology is necessary for effective conservation. Through discussion and examination of case

studies you will be encouraged to question received wisdom in ecology and conservation, and to assess

critically the reasons for why some conservation programmes have failed but others have succeeded.

MODULE: ECOLOGICAL GENETICS


ORGANISER: Prof Michi Hofreiter


SUMMARY: This course will investigate the evolutionary effects of population size changes, migration

and hybridization and other ecological processes. To this end it will combine elements from population

genetics, molecular genetics, ecology and evolutionary biology covering most of the range of modern

molecular ecology research.

At the beginning of the course the types of markers and technologies available for studying molecular

ecology will be introduced and the basic principles of population genetics will be revisited. There will be a

range of biological topics that will be covered, starting with the effects of genetic drift, migration,

geographical barriers and environmental changes on the amount and structure of genetic diversity in

different species. This part will include examples of long-term population size changes investigated by the

use of ancient DNA as well as studies in conservation genetics. Following on from this, the different


mechanisms of speciation will be discussed with an emphasis on the role of genetics in the speciation

process as well as ecological circumstances under which species barriers can break down. Finally, the

genetics of adaptive processes, including evolutionary arms races will be discussed. In summary, this

module will give an overview how ecological and genetic factors play together in forming an evolutionary

response in species.

Lectures will treat the topics mentioned above with a strong emphasis on examples from the recent

literature, including journal-club like elements whereby students play an active role during the lecture.

An understanding of the material and concepts taught in Stage 2 Evolutionary and Population Genetics or

Human Genetics is recommended.

LEARNING OUTCOMES:

At the end of this module students should have an understanding of the different concepts within

molecular ecology. This will include a comprehensive knowledge about the available molecular markers,

the technologies used and the insights that can be gained by different markers. Students will have an

understanding how molecular techniques can be used to determine structure and change in genetic

diversity, how to date events in the genetic history of a species as well as how to estimate levels of

historical gene flow and determine paternity. They will learn how these techniques can be applied to get a

better understanding of diverse evolutionary processes that are important for understanding both the past

and the future of species in an ever-changing environment

MODULE: EPIGENETICS IN DEVELOPMENT & DISEASE


ORGANISER: Dr Louise Jones

RECOMMENDATIONS/PREREQUISITES: BIO00007I From gene to function

SUMMARY:

Epigenetic mechanisms enable the expression status of genes or even entire chromosomes to be

inherited. These mechanisms involve modifications to DNA and/or chromatin and play critical roles in

controlling the output of information from a genome. Epigenetics is therefore central to the biology of an

organism and is an area of high current interest. In this module we will begin by covering the molecular

mechanisms of epigenetics before looking at specific examples in development and disease. Epigenetic

mechanisms are conserved across kingdoms and therefore studies from both animal and plant science

will be used. The importance of epigenetics in development has long been realised and we will look at

how epigenetic mechanisms control key developmental events including dosage compensation and

imprinting. We will also consider epigenetic reprogramming events that occur naturally or artificially in

stem cell production and animal cloning. In recent years the role of epigenetic processes in diverse

diseases has been realised and we will discuss whether cancer and ageing can be considered to be

epigenetic diseases. Finally we will discuss whether changes in the environment can result in heritable

changes in gene expression and will examine the evidence and discuss the implications of this potentially

controversial area.

LEARNING OUTCOMES:

To understand what is epigenetics and why the definition is not always straightforward


To appreciate the diversity of biological roles for epigenetics To understand why DNA methylation and histone modifications influence gene expression and to

consider whether they are heritable To have considered the involvement of non-coding RNAs in epigenetic events To appreciate how epigenomes differ between species and kingdoms, and also at different points in

development To appreciate the critical role played by epigenetic mechanisms during development To understand how epigenetic mechanisms can influence disease, particularly cancer To understand that the environment can influence the epigenome and to have considered some of the

consequences of this To be familiar with current techniques in epigenetics and epigenomics.

MODULE: GLYCOBIOLOGY


ORGANISER: Dr Daniel Ungar


SUMMARY:

Protein and lipid linked oligosaccharides – aka glycans – are the forgotten siblings of biological polymers,

and are just emerging from the shadows of DNA, RNA and proteins. Their biosynthesis is a lot more

complex than that of the other polymers, and partly for that reason they have been very difficult to

analyse. Whereas during the advent of molecular biology glycans were only viewed as annoying tags on

proteins, recent advances in glycan analysis have shed light to a fascinating array of biological roles for

them both in prokaryotic and eukaryotic organisms. This includes physiological roles in signalling and

attachment for example, generating critical roles in development and infection. In bacteria the expression

of glycosylated surface molecules, such as lipopolysaccharide and capsule, are the main way in which

these organisms interact with their environment and are often essential for colonisation of humans. At the

same time in eukaryotic cells, pathological states such as cancer metastasis and inflammation have been

associated with changes in glycan structures, an area of intense study at the moment. This module will

start by explaining our current knowledge of the biosynthesis and structure of glycans, in both eukaryotes

and prokaryotes, and how glycan structures can be analysed with modern techniques. The second half of

the module will look at the biological function of these underestimated biological molecules, including their

role in various diseases.

LEARNING OUTCOMES:

Students will acquire knowledge of the classification and structure of protein lipid linked sugar chains, their

analysis and their biological function. They will be able to assess the new developments in the emerging

field of glycobiology both in conjunction with medical and biotechnological applications. The module will

also prepare students to analyse the primary literature, and evaluate papers published in the field of

glycobiology.


MODULE: MOLECULAR AND CELLULAR PARASITOLOGY


ORGANISER: Prof Deborah Smith

RECOMMENDATIONS/PREREQUISITES: BIO00002I Immunology and BIO00007I From gene to

function

SUMMARY:

The burden of disease caused by parasitic protozoa and helminths remains high in many parts of theworld, especially the tropics and sub-tropics, where prevailing climatic conditions favour transmission. Thecurrent options for effective therapies against these infections are poor, however. In the area of drugdevelopment, research on new chemotherapeutic agents of low toxicity and high efficacy has beenlimited, while drug resistance is on the increase in many regions. Similarly, while the development ofcheap and effective vaccines would revolutionise the possibilities for disease control, progress has beenslow with no useful products available to date. Unfortunately, parasites have large and complex genomes,allowing them to deploy sophisticated immune evasion strategies which are underpinned by unusualmolecular and biochemical pathways. However, recent genome sequencing projects are revealing manysurprises in how parasites organise and express their genes, supporting new strategies for vaccine anddrug development. Understanding how parasites infect man and considering how best to prevent thishappening provides the context for this module.

LEARNING OUTCOMES:

At the end of this module you should have acquired an understanding of:

The major protozoan (Plasmodium, Leishmania,Trypanosoma) and helminth (Schistosoma, filarialnematodes) parasites causing disease in humans, their complexity and the difficulty of finding drugtargets or protective antigens.

The way in which parasites cause disease in the human host, often by manipulating the host immunesystem to their advantage.

The strengths and weaknesses of current chemotherapeutic treatments.

The way in which parasites, particularly those that inhabit the bloodstream, can evade host immunedefences, so preventing vaccine development.

How researchers are attempting to circumvent these obstacles to make progress in the development ofnew therapies, including vaccines and drugs.

MODULE: NUTRIENT ACQUISITION AND CYCLING IN NATURAL AND

AGRICULTURAL SYSTEMS




SUMMARY:

The course will consider the way in which nutrients are made available in soil and acquired by plants,

specifically how plants capture nutrients from the heterogeneous soil environment, symbiotic associations

plants may form in order to enhance nutrient acquisition and the cycling of key nutrients within the

ecosystem. It will range from the micro-scale, considering the controls on the availability of nutrients in


soil determined by physico-chemical processes and microbial activity, to the macro-scale, covering the

cycling of nutrients, especially nitrogen and phosphorus, in natural ecosystems, and the lessons that can

be drawn from these to determine the sustainability of agro-ecosystems in different parts of the world.

LEARNING OUTCOMES:

Knowledge and understanding of:

key features of the soil environment as they affect nutrient supply to plants

the behaviour of roots in heterogeneous soils

the interactions between roots and microbes (the rhizosphere)

biological nitrogen fixation

the ecological function and significance of mycorrhizal symbioses in nutrient capture

the dynamics of nitrogen in soil-plant systems

the limiting factors to sustainable agriculture

MODULE: PROTEIN-NUCLEIC ACID INTERACTIONS


ORGANISER: Dr Christoph Baumann

RECOMMENDATIONS/PREREQUISITES: BIO00004C Molecular Biology and Biochemistry of the Cell,

or equivalent module

SUMMARY:

The recognition of nucleic acids by proteins is fundamentally important in regulating and determining

fidelity in the transmission and expression of genetic information. Biochemical, structural and genetic

approaches have combined to increase our understanding at the molecular level of the interactions

between these two species, and increasingly our understanding is being further enhanced by studies at

the single-molecule level.

This module surveys the main features of protein-nucleic acid interactions and the methods used to study

them. The topics discussed focus on well characterised systems, chiefly drawn from transcription and the

proteins that regulate gene expression.

The module is designed for biochemists, molecular cell biologists and geneticists who are interested in

learning more about molecular recognition and the mechanisms underlying genetic control processes.

LEARNING OUTCOMES:

At the end of this module, students should be able to:

explain the structural basis of sequence-specific DNA recognition by different protein superfamilies

describe and appraise the common techniques used to study DNA-protein interactions in vitro and invivo

describe the structural features of E. coli RNA polymerase

understand the role of sigma factors and DNA promoter strength in transcriptional initiation by E. coliRNA polymerase


describe systems involved in the positive and negative control of DNA transcription

discuss the use of chromatin immunoprecipitation and microarray technology to probe transcription andchromosome organisation in vivo

MODULE: SYSTEMS AND SYNTHETIC BIOLOGY


ORGANISER: Dr A Jamie Wood

RECOMMENDATIONS/PREREQUISITES: It will be advantageous but not essential for students to have

completed the following modules:

2011 Cohort: BIO00003I Experimental design and practical skills (Systems Biology)

2012 Cohort: BIO00032I Scientific skills and tutorials (Systems Biology)

SUMMARY:

The module will provide an introduction to the relatively new subjects of systems biology and synthetic

biology and how these more quantitative and mathematical approaches are being used to solve biological

problems. The module will begin with three overview lectures including the issues related to systems

thinking and interdisciplinary working, mathematical techniques and the possibilities of synthetic biology.

The remainder of the module will present examples of important research advances in this field, including

metabolic models, network inference, categorisation of modules and motifs and large scale kinetic

models. This integration of mathematical techniques with biology is of paramount importance as we look

for new ways to comprehend the huge volumes of data now available.

LEARNING OUTCOMES:

By the end of this module, a student should be able to:

Provide an overview of systems biology applications and their impact on biology.

Be aware of the principle mathematical techniques used in systems biology and how cycles ofmathematical and experimental study can lead to new biological insights.

Understand the process of whole organism metabolic model construction and analysis using fluxbalance analysis.

To understand the importance of motifs and modules in networks and describe a subset of importancemotifs

Realise the great potential of large-scale kinetic models, but understand the complexities of creatingand parameterising them.

Describe the potential of Systems and Synthetic Biology but be mindful of the problems.


MODULE CHOICE FORMS

SECOND YEAR MODULE CHOICES 2013-2014

Student: BIOLOGY

Module No Module name Term taught Credits

BIO00032I Experimental design and practical skills. Practical

skills (please indicate your preferred choices from

Group 1 and 2 below or select the field skills option).

Skills Group A:

Cell biology and cytometry 1 2 3 4

Electrophysiology 1 2 3 4

Polymerase chain reactions 1 2 3 4

Protein interactions 1 2 3 4

Skills Group B:

Bioenterprise 1 2 3 4

Communicating science 1 2 3 4

Evolutionary trees 1 2 3 4

Genomics 1 2 3 4

Molecular imaging 1 2 3 4

Systems biology 1 2 3 4

Or Environmental Field Skills or X (indicate)

Aut, Spr, Sum 30

Module credit total (must total 120 credits for the year)

DEADLINE FOR SUBMISSION TO UNDERGRADUATE OFFICE – MONDAY 4 MARCH



Student: Biotechnology and Microbiology

Mod No Module name Term taught Credits

BIO00032I Experimental design and practical skills. Please indicate

your preferences from both Group A and Group B or

select the field skills option.

Skills Group A:





Skills Group B:




Genomics 1 2 3 4




Aut, Spr, Sum 30

BIO00007I From gene to function Aut, Spr, Sum 20

BIO00008I Molecular biotechnology Aut 10

BIO00018I Post-genomic biotechnology Spr 10





Student: ECOLOGY

Mod No Module name Term taught Credits

BIO00032I Experimental design and practical skills. Please indicate

your preferences from both Group A and Group B or

select the field skills option.

Skills Group A:





Skills Group B:




Genomics 1 2 3 4




Aut, Spr, Sum 30

BIO00023I Animal and plant ecology Aut, Spr, Sum 20





Student: GENETICS


BIO00032I Experimental design and practical skills. Please

indicate your preferences from both Group A and

Group B or select the field skills option.

Skills Group A:





Skills Group B:




Genomics 1 2 3 4




Aut, Spr, Sum 30


BIO00033I Genetics III Aut 10

BIO00017I Evolutionary and population genetics Spr 10


DEADLINE FOR SUBMISSION TO UNDERGRADUATE OFFICE –MONDAY 4 MARCH



Student: Molecular cell biology


BIO00032I Experimental design and practical skills. Please

indicate your preferences from both Group A and

Group B or select the field skills option.

Skills Group A:





Skills Group B:




Genomics 1 2 3 4




Aut, Spr, Sum 30


BIO00034I Metabolism in health and disease Aut 10

BIO00035I Cell biology Spr 10



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