DEPARTMENT OF BIOLOGY STUDENT CHOICE OF MODULES … · Page 1 of 60 DEPARTMENT OF BIOLOGY STUDENT CHOICE OF MODULES STAGE 2: 2014-2015 AND PROVISIONAL STAGE 3: 2015 - 2016 Biology

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DEPARTMENT OF BIOLOGY

STUDENT CHOICE OF MODULES

STAGE 2: 2014-2015

AND

PROVISIONAL STAGE 3: 2015 - 2016

Biology

Biotechnology and microbiology

Ecology

Genetics

Molecular cell biology

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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 2014 - 2015 12

AUTUMN TERM – 10 CREDIT MODULES 13

SPRING – SUMMER TERM – 10 CREDIT MODULES 17

AUTUMN – SPRING – SUMMER 2014 - 2015 – 20 and 30 credit modules 20

SPRING – SUMMER TERM – SKILLS PRACTICAL COURSES 22

SKILLS PRACTICALS – GROUP A 22

SKILLS PRACTICALS – GROUP B 25

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

AUTUMN TERM 31

SPRING TERM 41

MODULE CHOICE FORMS ERROR! BOOKMARK NOT DEFINED.

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RULES FOR CHOOSING YOUR PROGRAMME MODULES

Please note that the deadline for receipt of your module choices is Monday 3 March.

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.

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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

From gene to function – 20 credits – select this or Organisms in their environment or both

Organisms in their environment – 20 credits

select this or From gene to function or both

Note that if you select Organisms in their

environment but not From gene to function

we recommend you also select the Millport

field course

Immunology – 10 credits Behavioural ecology – 10 credits

Mechanisms of genetic change – 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

Population biology – 10 credits Neuroscience – 10 credits

Species-Environment interactions – 10 credits Post-genomic biotechnology – 10 credits

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Biotechnology and microbiology – compulsory modules highlighted



From gene to function – 20 credits - compulsory



Mechanisms of genetic change – 10 credits -

recommended

Cell biology – 10 credits - recommended



Molecular biotechnology – 10 credits -

compulsory

Evolutionary and population genetics – 10

credits


Species-Environment interactions – 10 credits Post-genomic biotechnology – 10 credits -

compulsory

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Ecology – compulsory modules highlighted



From gene to function – 20 credits

Organisms in their environment – 20 credits -

compulsory

Immunology – 10 credits Behavioural ecology – 10 credits -

recommended

Mechanisms of genetic change – 10 credits Cell biology – 10 credits


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

recommended


credits - recommended

Population biology – 10 credits - recommended Neuroscience – 10 credits

Species-Environment interactions – 10 credits -

recommended

Post-genomic biotechnology – 10 credits

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Genetics – compulsory modules highlighted







compulsory

Cell biology – 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

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Molecular cell biology – compulsory modules highlighted





Immunology – 10 credits - recommended Behavioural ecology – 10 credits


recommended

Cell biology – 10 credits - compulsory

Metabolism in health and disease – 10 credits -

compulsory

Developmental biology – 10 credits -

recommended



credits

Population biology – 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.

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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:

C) http://www.york.ac.uk/biology/intranet/currentundergraduatestudents/stage1biology/modules2013biologycohort

/

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 appropriate choices.

(b) Check when the elective module will be assessed and confirm that a final moderated mark will be available by the end of week 8 of the summer term. If a mark is not available by the 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 is available. On production of

the timetable if you find the elective module you have chosen clashes with your biology modules you will need to re-select another module.

(d) Remember that you will be assessed against students who are studying for a degree programme

in that area and are likely to have more knowledge of the subject matter than you. It is sometimes the case that marks for elective modules are lower than those normally achieved by students on their standard degree programme modules.

http://www.york.ac.uk/biology/intranet/currentundergraduatestudents/stage1biology/modules2013biologycohort/

http://www.york.ac.uk/biology/intranet/currentundergraduatestudents/stage1biology/modules2013biologycohort/

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

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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.

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YOUR PROGRAMME PLANNER

Terms Mod No Module Title Credits Prerequisites

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STAGE 2 MODULE DESCRIPTIONS 2014 - 2015

AUTUMN AND SPRING TERM 20 CREDIT MODULE

BIO00007I: FROM GENE TO FUNCTION

ORGANISER: Dr James Moir

RECOMMENDATIONS/PREREQUISITES: Genetics 1 BIO00007C

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

SPRING/SUMMER TERM 20 CREDIT MODULE

BIO00036I: ORGANISMS IN THEIR ENVIRONMENT

ORGANISER: Dr Olivier Missa

RECOMMENDATIONS/PREREQUISITES: BIO00037I Population Biology is recommended but not a prerequisite

SUMMARY:

This module focusses on the practical aspects of studying organisms in their environment, at two levels of

organisation, populations (single species) and communities (multiple interacting species).

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The module has two parts: a set of lectures and practicals run in the autumn and spring terms, followed by a field

course. The students have the choice of either joining a field course abroad for two weeks at the beginning of the

Easter break (likely to be run in Tanzania, open to students able to cover the cost of their flight), or joining a field

course in the North York Moors for one week (after the exams, in week 8 of the summer term, fully covered by the

department).

In the lectures and practicals, the theory and practical considerations of obtaining informative samples in the field

will be extensively covered, both for plants and animals. Then a number of numerical analyses will be presented to

extract fundamental information on populations (their size and spatial structure) and communities (their diversity,

structure and heterogeneity). A strong emphasis will be placed on interpreting critically the data and information

gained by these techniques and understanding their limitations.

In the field course, the students will have the opportunity to discover more directly how plants and animals live in

their environment, and to develop and execute an ecological investigation in groups of 3-4 students for 5 days.

After introduction to a range of habitats, the students under the supervision of a member of staff will overall be

responsible for (1) defining the aim of their study, (2) coming up with a sensible scientific design in one of the

available sites, (3) carrying out the survey or experiment, (4) processing the samples and analysing the results, and

(5) communicating their findings by means of a group presentation.

LEARNING OUTCOMES:

On completion of the module, the students will be able to:

identify some groups of plants and animals in the field, and be aware of identification keys

sample a plant population to identify its spatial structure

sample an animal population to estimate its population size

sample communities, using ordination methods to unravel the underlying structure of these communities

interpret with caution a number of properties (diversity, similarity, species richness, species accumulation curve, abundance rank-plot) being used to compare communities

use principles of experimental design to plan their research activities in the field

apply the right technique (both in terms of sampling and analysis) to a variety of questions

At the end of the field course, the students will also:

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

Be introduced to a range of habitats in the vicinity of the base.

Learn about the specific conservation concerns in these areas.

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.

AUTUMN TERM – 10 CREDIT MODULES

BIO00021I: MILLPORT FIELD COURSE

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 10/11 of the summer term (26th June – 4

th July 2014) at FSC Millport, 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:

At the end of the module, the students should

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

know of and have used several ecological sampling techniques

be able to plan and carry out field investigations

be able to interpret and statistically analyse data

be able to give a scientific presentation

write a scientific report and relate own findings to the literature

BIO00002I: IMMUNOLOGY

ORGANISER: TBC

RECOMMENDATIONS/PREREQUISITES: BIO00010C Microbiology / BIO00011C Cell and developmental

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 the induction of an immune response.

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

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

BIO00008I: MOLECULAR BIOTECHNOLOGY

ORGANISER: Dr Gavin Thomas

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

BIO00007I 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 modern biotechnology industry

A detailed understanding of the technology and problems relating to recombinant production of important protein 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 synthetic biology.

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BIO00022I: 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.

BIO00033I: MECHANISMS OF GENETIC CHANGE

ORGANISER: Dr Michael Schultze

RECOMMENDATIONS/PREREQUISITES: 1st year Biology/Biochemistry 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 guarantees 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.

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 will be discussed.

Emphasis will be given in discussing the relationship and regulation of recombination, 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 mutation, transposition and recombination can be exploited

to identify gene functions, and how the genome can be manipulated.

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Workshops and practical sessions 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 genome change.

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 and site-specific recombination.

Compare and contrast the properties of mobile genetic elements and their role in genome stability (transposons, insertion elements, retroviruses).

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.

BIO00034I: 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 membranes and signal transduction underpin the molecular basis of

signalling encountered throughout the module. The remaining lectures then focus on lipid and glucose metabolism,

covering cell and tissue biochemistry and physiology before focussing on ‘metabolic syndrome’, comprising the

major risk factors for cardiovascular disease, including obesity and diabetes. Finally, the energetic status of the cell

is linked to longevity and the quest to extend lifespan by caloric restriction and its related signalling pathways. The

lecture material is supported by two practicals, firstly mitochondrial function and dysfunction is studied in purified

mammalian mitochondria and then we will dissect a mammalian cell signalling pathway involving lipids and protein

phosphorylation.

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.

Solve metabolism-themed problems.

BIO00037I: POPULATION BIOLOGY

ORGANISER: Prof Calvin Dytham

RECOMMENDATIONS/PREREQUISITES: Recommended Stage 1 BIO00001C Ecology

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.

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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, predicting disease outbreaks and the strategy for conserving endangered species

SPRING – SUMMER TERM – 10 CREDIT MODULES

BIO00004I: DEVELOPMENTAL BIOLOGY

ORGANISER: Dr Harv Isaacs


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;

Understand the role of homeotic genes in plant and animals;

Appreciate the important cell movements during animal morphogenesis;

Understanding the signalling processes involved in the establishment of the vertebrate nervous system and the tetrapod the limb

Appreciate development in the context of evolution;

Gained practical experience in analysing the regulation of development in flies and fish;

BIO00005I: ENVIRONMENTAL ECOLOGY

ORGANISER: Kelly Redeker

RECOMMENDATIONS/PREREQUISITES: Module BIO00001C Ecology, but A-level Biology or equivalent 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

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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

BIO00009I: 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

Solve problems related to experimental neuroscience.

BIO00017I: 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 and determined by allele frequencies (i.e. Hardy-Weinberg principle);

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To appreciate that continuous variation has the same genetic origin as discontinuous variation and to be aware 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 gene flow between populations and to understand under what circumstances each of these is likely to be important;

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.

BIO00018I: POST-GENOMIC BIOTECHNOLOGY

ORGANISER: Dr James Chong

RECOMMENDATIONS/PREREQUISITES: BIO00004C Molecular biology and biochemistry and BIO00007C

Genetics I

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

BIO00020I: BEHAVIOURAL ECOLOGY

ORGANISER: Dr Daniel Franks

RECOMMENDATIONS/PREREQUISITES:

A-level Biology or equivalent 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

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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.

BIO00035I: 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.

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AUTUMN / SPRING/– SUMMER TERM – 30 CREDIT SKIILLS MODULE

BIO00032I: SCIENTIFIC SKILLS 2

ORGANISER: Dr Angela Hodge RECOMMENDATIONS/PREREQUISITES: None SUMMARY

Autumn Term:

As a group, students will plan and carry out a series of experiments, complete a risk assessment form, record and

analyse their data, draw conclusions and keep a diary on the VLE. Each group will prepare a poster which will

explain what the investigation has discovered and receive a viva based on their findings . Each student in the group

will write a summary of their findings. This part is done by individually rather than as a group.

Students will attend a series of 6 small group tutorials, and complete and get feedback on work including at least

two pieces of written work.

Spring / Summer terms:

Select two skills from the list below, one from each of the lists:

Group A:

Cell imaging

Electrophysiology

GIS Spacial Analysis

Modelling biological and biochemical dynamics

Polymerase chain reaction & DNA sequencing

Protein interactions

Taxonomy and collections

Group B:

Bioenterprise

Communicating Science to the public

Evolutionary trees

Genomics

Molecular imaging

Systems biology

Students will also attend a series of 8 small group tutorials, and complete 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 test appropriate hypotheses.

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

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SPRING – SUMMER TERM – SKILLS PRACTICAL COURSES

The spring term skills practicals are divided into two groups, you will take one skills practical from each group. List your preferences for the practicals in each group on your choice form at the end of the booklet and the Department will allocate you to one of your choices. Where possible we take account of student preference but numbers are limited on these courses.

SKILLS PRACTICALS – GROUP A

BIO00032I: SKILLS - CELL IMAGING

ORGANISER: Dr Gonzalo Blanco

RECOMMENDATIONS/PREREQUISITES: It is recommended that module BIO00035I, Cell biology, is taken

alongside this module.

SUMMARY:

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

culture, transfection, staining and fluorescent microscopy. 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.

AIMS:

This module aims to give students a theoretical and practical understanding of some of the techniques commonly

used in cell biology. The students will receive introductory explanations of the theory behind the use of different

techniques, and will then gain direct practical experience of these approaches. Skills acquired in this module will

aid students wishing to undertake final year research projects particularly related to animal cell biology.

LEARNING OUTCOMES:

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

Understand basic in vitro cell culture.

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

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

Observe changes in cellular phenotypes using fluorescence microscopy.

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, the vle and via the Internet to further explore advances in techniques relevant to the study of animal cell biology.

BIO00032I: SKILLS - ELECTROPHYSIOLOGY ORGANISER: Dr C.J. H. Elliott RECOMMENDATIONS/PREREQUISITES: None

SUMMARY:

Students will undertake 5 practicals to explore the neural activity of simple nervous systems.

LEARNING OUTCOMES:

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

Understand basic electrophysiology techniques used in neuroscience research.

Discriminate real data from artefacts, and deal with problems in assembling equipment

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Use simple invertebrates to record basic principles of neurophysiology

Recognise the roles of adaptation in sensory, CNS and motor systems

Analyse the interaction of sensory and motor systems in the neural control of behaviour

Know the basic pharmacological methods

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

BIO00032I: SKILLS – GIS SPATIAL ANALYSIS

ORGANISER: Colin Beale

RECOMMENDATIONS/PREREQUISITES: Stage 1 BIO00006C Scientific Skills

SUMMARY:

From macroecology and phylogenetics to GPS tracking of individual animals and disease cluster analysis, biology

is increasingly a spatial science. This module will introduce students to the skills required to undertake spatial

analyses, introducing GIS software, GPS technology online spatial data repositories and the statistical analysis of

spatial data. The course will consist of one general introductory lecture, followed by a series of workshops in the

field and computer laboratory enabling students to gain hands on experience before undertaking an individual

project.

LEARNING OUTCOMES:

Specific learning objectives are:

To gain a knowledge of the questions amenable to spatial analysis.

To gain familiarity with GIS software for digitising and visualising spatial data.

To gain experience of working with GPS.

To know how to access and process online spatial data.

To gain a foundation in the statistical analysis of point and raster data.

BIO00032I: SKILLS – MODELLING BIOLOGICAL DYNAMICS

ORGANISER: Dr Jon Pitchford

RECOMMENDATIONS/PREREQUISITES: Stage 1 BIO00006C Scientific Skills

SUMMARY:

This module will train students in some key techniques in mathematical modelling and programming. In addition,

students will gain experience of group working, and of undertaking and presenting interdisciplinary work. There will

be training in: project management; developing, criticising and implementing computational and mathematical

models; and oral and written presentation.

LEARNING OUTCOMES:


To understand and to have experience of key elements of algorithmic programming, using Matlab.

To understand and to have experience of the key biological, mathematical and computational elements

involved in modelling biological and biochemical systems.

To be able to understand the key elements of differential equation models for biological dynamics: linear

interactions (leading to exponential dynamics); nonlinear interactions; inter- and intra- processes.

To have experience of interdisciplinary group work, including delegation of tasks and time management,

and presentation of results.

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BIO00032I: SKILLS - 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.

BIO00032I: SKILLS - PROTEIN INTERACTIONS

ORGANISER: Dr Daniel Ungar

RECOMMENDATIONS/PREREQUISITES: Stage 1 BIO00004C 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

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Be able to comprehend and critique neurophysiology literature available in the library and via the internet to further explore advances in techniques relevant to the study of brain and behaviour.

BIO00032I: SKILLS – TAXONOMY AND COLLECTIONS ORGANISER: Dr Thorunn Helgason RECOMMENDATIONS/PREREQUISITES: Stage 1 BIO00006C Scientific Skills

SUMMARY:

Much of our understanding of the relationships among animal and plant species is founded upon collections of

specimens maintained by museums and botanic gardens. The Linnean system of taxonomy was developed using

such collections and to this day, it is still possible to refer to the specimens he inspected in order to give a species

a name. The aim of this course is to look at how organisms are given their names and how keys are written and

used in order to put those names to unknown specimens, using samples that we collect from around campus. We

will also look at the role that museum collections play in our understanding of the distribution of animal and plant

species. The Yorkshire Museums Trust holds a nationally significant collection of natural history specimens. In

collaboration with the science curators, students will have an opportunity to learn more about the challenges of

cataloguing, preserving and managing such a collection and to learn about the wealth of information that is held

within such a collection. This will include a “behind the scenes” trip to the collection store. Students will therefore

gain insight into two key skill areas for biologists interested in field work and or the “heritage” sector – using keys to

identify plants and animals, and how collections are managed to retain and maintain that information.

LEARNING OUTCOMES:

At the end of this module students will:

Know the history and protocols governing taxonomic systems for plants and animals

Know the different types of keys and have experience using them to identify a wide variety of organisms, including plants, animals and cryptogams

Gain insight into the value of museum collections, their curation and the challenges faced by the smaller UK collections.

Be able to prepare specimens for incorporation into collections.

SKILLS PRACTICALS – GROUP B

BIO00032I: SKILLS - 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

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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.

BIO00032I: SKILLS - COMMUNICATING SCIENCE TO THE PUBLIC

ORGANISER: Dr Adrian Harrison

RECOMMENDATIONS/PREREQUISITES: First year BIO00006C 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:


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.

BIO00032I: SKILLS - EVOLUTIONARY TREES

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.

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

this can be achieved.

BIO00032I: SKILLS - GENOMICS

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

BIO00032I: SKILLS - 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 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 and EMW, various imaging techniues such as bright field

microscopy, confocal microscopy, electron microscopy and atomic force microscopy, and the lectures contain many

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examples 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 attend a confocal demonstration in the

Technology Facility.

LEARNING OUTCOMES:

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

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 to study defined biological questions

BIO00032I: SKILLS - 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. An

introduction will be given to the complexity of biological systems across a range of scales from sub-cellular

networks to ecosystems. Systems thinking is introduced with its emphasis on relationships of system components.

The characteristics of the organisation of biological systems are introduced in terms of networks, their

representation and their properties. The methods, tools and strategies of (postgenomic) systems biology are

outlined. The implications of systems research to medicine are provided to illustrate the potential of these

approaches.

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 approaches to medicine.

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STAGE 3 MODULE DESCRIPTIONS 2015-2016 (PROVISIONAL LIST)

AUTUMN TERM 2015 / SPRING TERM 2016 COMPULSORY MODULES

BIO00027H: RESEARCH SKILLS

ORGANISER: Dr Calvin Dytham

RECOMMENDATIONS/PREREQUISITES: Stage 1 BIO00006C Scientific and transferable

skills: stage 2 BIO00032I Scientific skills and tutorials.

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 research project or analysing those of others.

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

BIO00028H 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.

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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.

BIO00008H: CANCER AND THE CELL CYCLE

ORGANISER: Dr Dawn Coverley

RECOMMENDATIONS/PREREQUISITES: BIO00011I/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.

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BIO00009H: CELL AND TISSUE ENGINEERING

ORGANISER: Paul Genever

RECOMMENDATIONS/PREREQUISITES: BIO00011I/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 future therapies, 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.

BIO00014H: EVOLUTIONARY ECOLOGY

ORGANISER: Dr Peter Mayhew

RECOMMENDATIONS/PREREQUISITES BIO00001C Ecology, BIO00007C and BIO00009C Genetics I

and II

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.

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LEARNING OUTCOMES:

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

A critical awareness of current theory and evidence.

BIO00015H: GLOBAL CHANGE ECOLOGY

ORGANISER: TBC

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’ ecological issues, ranging from types of field experimentation through to the use of stable isotopes in environmental research.

BIO00017H: 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 students will have the

opportunity to practice problem/method style questions.

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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.

BIO00019H: 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.

BIO00023H: 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.

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The module will cover key 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 medicinal compounds and fibres will be discussed.

Strategies and tools for fast-track breeding using molecular markers and association studies will be

introduced. 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

To become familiar with genomics platforms to support breeding programs

How to make use of natural and induced genetic variation in crops.

How molecular breeding helps in improving medicinal plants.

BIO00025H: PROTEIN-PROTEIN RECOGNITION

ORGANISER: Prof Anthony J Wilkinson

RECOMMENDATIONS/PREREQUISITES: BIO00004C Molecular biology & biochemistry, BIO00008C

Biochemical skills and CHE00011I Proteins in 3D

SUMMARY:

Protein-protein recognition lies at the heart of most cellular processes, and is the current focus of

worldwide efforts aimed at uncovering all the interprotein interactions of organisms on a genomic scale.

The module addresses the reductionist approaches that are classically taken to understand how and why

proteins form complexes with each other as well as describing some of the latest approaches being used

to define the interaction networks of cells. Protein-protein interactions are increasingly being seen as

potential drug targets; the module will highlight why finding such small molecule inhibitors is problematic

but also describe some recent successes. Emphasis is given to the understanding of protein-protein

recognition and protein interaction networks through structural, kinetic and thermodynamic dissection of a

number of model systems, including: the immune system; bacterial two-component regulators: peptide-

binding proteins; protein inhibitors of cytotoxic nucleases; signal transduction; microtubule regulation; and

transcriptional activation. The variety of biophysical and genetic methods used to analyse these and other

systems will also be addressed, and structural generalisations that have come from studies on model

systems will be emphasized.

LEARNING OUTCOMES:

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

modules, you are expected to read around the subject and understand how the various lectures are

related. The specific objectives of the module include:

The importance of combining structural, kinetic and thermodynamic approaches to obtain a

holistic view of protein-protein interactions;

An understanding of the basic structural features of protein-protein complexes, the role that

solvent plays in recognition and how conformational changes can influence binding. Appreciate

different types of symmetry observed in protein assemblies, from simple cyclic oligomers to more

complex icosahedral virus particles.

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An understanding of how biophysical approaches can be coupled with display technologies to

probe how complexes are formed;

Understanding the importance of structural plasticity and conformational changes in protein-

protein recognition; one-to-many and many-to-one interactions.

Appreciate how cells comprise networks of protein complexes and understand how to use

information available in databases.

Understanding the distinction between affinity and specificity in protein-protein interactions.

Understanding the importance of protein modular design in interaction networks and in particular

the role of intrinsically unstructured regions of proteins

Appreciate the difficulties and successes in the design of small molecule inhibitors of protein-

protein interactions as novel therapeutics

BIO00038H: ENVIRONMENTAL MICROBIOLOGY

ORGANISER: Dr Thorunn Helgason

RECOMMENDATIONS/PREREQUISITES: none but postgenomic biotechnology and environmental

interactions are both especially useful previous study.

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 of microbes from environmental samples.

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

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

BIO00039H: ADVANCED TOPICS IN ANIMAL BEHAVIOUR

ORGANISER: Prof Calvin Dytham

RECOMMENDATIONS/PREREQUISITES: BIO00020I Behavioural Ecology

SUMMARY:

Animal behaviour affects the key decisions in an animal’s life – when to mate, when to forage, whether to

raise young or abandon them, whether to fight or flee, whether to cheat or cooperate. With recent

advances in both animal tracking (through tags and GPS recorders) and population level genomic

information, many of the unknowns of behavioural studies are being revealed. New information on, for

example, the relatedness of individuals in groups, the rate of extra-pair paternities or high quality spatial

locations to show the extent of exploration behaviour is overturning many long-held beliefs about the

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evolution and maintenance of behaviours. During this module, a series of research topics, where new

types of information are becoming available, will be highlighted.

LEARNING OUTCOMES:

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

To appreciate the diversity of biological roles for behaviour To understand why animal behaviour is so important in evolution

To have considered how behaviour interacts with other aspects of life history

To appreciate how groups, especially social groups, influence the evolution and fitness of behaviours

To understand when and how behaviours might be transmitted genetically, culturally or epigenetically

To appreciate that phylogeny has a role in the understanding of animal behaviour

To appreciate the critical role of inclusive fitness in shaping the evolution of behaviour

BIO00040H: BACTERIAL PATHOGENESIS

ORGANISER: Marjan van der Woude

RECOMMENDATIONS/PREREQUISITES: Prerequisite: Stage 2 BIO00007I Gene to Function (BMS

stream in due course). Recommendation: BIO00011I/BIO00035I Cell Biology

SUMMARY:

In this module the student will gain an understanding of complex and variable strategies that allow a microbe,

specifically bacteria, to be a successful pathogen. This will include aspects of survival in the environment, vector

and transmission, entry and colonization, dissemination, and interactions with the host /avoiding host defences

from the bacterial strategic point of view. Drawing upon both groundbreaking historical discoveries and novel

findings, virulence strategies employed by different pathogens will be discussed. Experimental approaches, model

systems and their limitations will be critically discussed in context of recent papers. This is a fast moving field and

emphasis within the lectures will be adapted to ensure that material reflects not just basic principles but also

cutting edge science.

LEARNING OUTCOMES:

Explain the different stages of infection in context of different pathogens

Describe virulence strategies used in the context of these stages of infection.

Identify the role “normal” physiology and regulation plays in the life of a pathogen

Compare virulence factors that allow bacterial pathogens to be “successful” and discuss how they contribute to that success

Identify experimental approaches to study pathogenesis

Critically discuss strengths and limitations of experimental approaches discussed in detail, and identify challenges for the future.

Outline approaches to and problems encountered in, our fight against infectious (bacterial) disease.

Illustrate key concepts with examples

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BIO00041H: PRINCIPLES OF MOLECULAR VIROLOGY

ORGANISER: Nathalie Signoret (lead) with Dimitris Lagos and Reidun Twarock

RECOMMENDATIONS/PREREQUISITES: BIO00002I Immunology

SUMMARY:

Viruses have been with us for millions of years evolving to survive and adapt to new host environments

while driving the evolution of host genes. Diseases that are causally linked to viral infections are major

contributors to morbidity and mortality in the animal and human populations globally. On the other hand,

several viral infections are asymptomatic or only cause minor diseases. This module will examine

overarching principles in molecular virology, addressing structural, molecular, and cellular biology aspects

underpinning the fascinating interaction between viruses and the host. Focusing primarily on animal

viruses, we will study key aspects of viral evolution, replication, and gene expression linked to infectivity

that will be reviewed based on ground breaking past discoveries and recent advances in research from

published literature.

LEARNING OUTCOMES:

Investigate viruses as distinct forms of living organisms: Highly structured particles with a protein

core, protecting a nucleic acid genome, which make them infectious.

Assess viral molecular mechanisms from the replication cycle that are essential for the structural

integrity, multiplication and propagation of viruses.

Explore the mechanisms employed by viruses to regulate expression of their own and host genes

in order to achieve infection, persistence, and spreading.

Develop a coherent argument depicting the potential application of viral strategies towards

disease control.

BIO00042H HUMAN GENETICS

ORGANISER: Gonzalo Blanco

RECOMMENDATIONS/PREREQUISITES: BIO00007C Genetics I, BIO00009C Genetics II, BIO00017I

Evolutionary and Population Genetics

NB: Students who took module BIO00015I Human Genetics in Spring 2012 or earlier may not take this

module.

SUMMARY: This course will first introduce a description of the human genome and its evolution, with an

emphasis on the features that can explain the prevalence of certain diseases in modern day humans. The

process of mutation identification in single gene disorders and examples of calculations of genetic risk in

human pedigrees will follow this. The final lecture will provide an introduction to the identification of risk

alleles in complex diseases. Some lectures will combine an in depth review of the topics outlined in the

synopsis with brief oral critiques by the students of selected papers.

LEARNING OUTCOMES: Students studying this module will be able to:

Describe the human genome and the processes that affect it.

Explain how comparative genomics has led to our current picture of the origin of modern humans.

Discuss examples of genes that have been under selection in human history.

Describe, with examples, the basis of single gene and complex disorders.

Explain how genes associated with Mendelian or multifactorial disorders can be identified.

Calculate the genotype probability in human pedigrees in simple and complex scenarios.

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BIO00043H: ANTIBIOTICS

ORGANISER: Maggie Smith

RECOMMENDATIONS: CHE00011I Proteins in 3D

PREREQUISITES: BIO00007I From Gene to function

SUMMARY:

Antibiotics are the platform on which modern medicine is built. The ‘golden age’ of antibiotic discovery in

the 1940-1960s led to new innovations in medicine by massively reducing the risk of infection. But the

numbers of useful antibiotics are declining as more organisms become resistant, and few new

therapeutics are discovered. Why are we in this situation and how do we get out of it?

Most antibiotics in use today are made by microorganisms. Antibiotics and other natural products are

secondary metabolites and, although thousands of natural products have been described, not all are

suitable as therapeutic agents. While we use antibiotics to kill pathogens, there is evidence building that

they might be used in the natural environment for communication between organisms. The metabolic

pathways for natural products are often related to primary metabolic pathways and we have learnt how to

manipulate these pathways to change the chemistry of the final product; a useful approach to generating

novel products that might be more effective as drugs. The targets for antibiotics have been the focus of

study with a view to understanding how antibiotics work and designing new drugs.

In this module we will consider where our antibiotics have come from in the past and look to where they

might come from in the future.

LEARNING OUTCOMES:

The students should:

Understand what an antibiotic is, how they were discovered during the ‘Golden Age’, and how bio-prospecting continues today

Understand how certain classes of antibiotics are made in microorganisms by studying their biosynthesis.

Appreciate how modifications of antibiotic structures can be made by modifications to biosynthetic pathways, using genetic manipulation.

Understand that antibiotic biosynthesis is controlled by many environmental and physiological signals

Understand the mode of action of some antibiotics at the molecular level

Know the principles of structure-based drug design

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BIO00044H: CHROMOSOME DYNAMICS

ORGANISER: Prof Peter McGlynn

RECOMMENDATIONS/PREREQUISITES: BIO00004C Molecular Biology and Biochemistry

SUMMARY:

The maintenance and copying of the genetic material within a cell is one of the fundamental features

of life. But no metabolic process occurs in isolation and genome duplication must be coordinated with

many other reactions that occur simultaneously. This module investigates the problems that genome

duplication faces when operating inside complex intracellular environments and the multiple enzyme

systems that minimise the risk of incomplete or inaccurate DNA replication. These topics will be

illustrated using systems that are well-characterised at the mechanistic level, primarily those found in

bacteria and yeast, but comparisons will be made with other systems.

The module will centre on recent research papers in this field, using seminars to discuss each paper in

detail. Both the biology and the experimental techniques used will be covered in these seminars,

deconstructing each paper to probe each research topic. Additionally, the first session of the course

will provide lecture material summarising the more advanced experimental approaches employed in

the research, facilitating initial reading of the papers. Review papers will also be given as background

reading to provide wider perspectives of the field, allowing the research papers to be viewed within a

broader context.

This module is designed for biochemists, molecular biologists and geneticists who wish to learn more

about genome duplication and the complex interplay between multiple aspects of nucleic acid

metabolism inside

LEARNING OUTCOMES:

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

understand how the requirement for genome stability shapes chromosome structure

discuss the problems associated with duplicating a genome inside the complex environment of a cell

appreciate how damaged replication complexes can be repaired and the importance of these repair mechanisms

understand and illustrate the importance of coordination in replication, repair and recombination

understand the links between recombination, replication repair and genome rearrangements

discuss the biochemical and genetic techniques commonly used to study replication, repair and recombination mechanisms

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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.

BIO00001H: 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 of development.

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

BIO00003H: ADVANCED TOPICS IN IMMUNOLOGY

ORGANISER: TBC

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.

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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 an immune response are beneficial, and can even be life threatening.

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

BIO00004H: 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 enzyme catalysis and improve/alter enzyme activity and specificity.

An understanding of how ‘random mutagenesis’ or ‘in vitro’ evolution experiments can be used to improve 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 to generate novel RNA catalysts

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BIO00005H: 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 be found 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.

BIO00006H: BIOFUELS & BIOTECHNOLOGY

ORGANISER: Dr Gavin Thomas

RECOMMENDATIONS/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 of energy and how biomass currently contributes to this.

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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 the long-term viability of biofuels.

BIO00007H: 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.

BIO00010H: 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

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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.

BIO00012H: ECOLOGICAL GENETICS

ORGANISER: Kanchon Dasmahapatra

RECOMMENDATIONS/PREREQUISITES: Stage 2 BIO00017I Evolutionary and Population Genetics

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.

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.

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BIO00013H: EPIGENETICS IN DEVELOPMENT & DISEASE

ORGANISER: Dr Louise Jones

RECOMMENDATIONS/PREREQUISITES: Stage 2 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.

BIO00016H: 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

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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.

BIO00018H: HUMAN MOLECULAR PARASITOLOGY

ORGANISER: Prof Paul Kaye (and Dr Walrad)

RECOMMENDATIONS/PREREQUISITES: BIO00002I Immunology and BIO00007I From gene to

function

SUMMARY:

Understanding how eukaryotic parasites infect and survive in their human host and current strategies to

prevent this happening provides the context for this module. The burden of disease caused by parasitic

protozoa and helminths remains high in many parts of the world, especially the tropics and sub-tropics

where prevailing climatic conditions favour transmission. Parasites have large and complex genomes,

allowing them to deploy sophisticated immune evasion strategies which are underpinned by unusual and

evolutionarily-refined molecular and biochemical pathways. In the area of drug development, research on

new chemotherapeutic agents of low toxicity and high efficacy has been limited, while drug resistance is

on the increase in many regions. The current options for effective therapies against these infections are

poor. However recent genome sequencing projects are revealing many surprises in how parasites

organise and express their genes, providing potential new strategies to combat these ancient ailments.

LEARNING OUTCOMES:

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

The major protozoan (Plasmodium, Trypanosoma, Leishmania) and helminth (Schistosoma, filarial nematodes) parasites causing disease in humans, their complexity, the most significant recent findings in the field and the difficulty of identifying drug targets and/or protective antigens.

The way in which parasites survive and cause disease in the human host, often by manipulating the host immune system to their advantage. The way in which parasites, particularly those that inhabit the bloodstream, can evade host immune defenses, so hindering vaccine development.

The strengths and weaknesses of current chemotherapeutic treatments. How researchers are attempting to circumvent these obstacles to make progress in the development of new therapies, including vaccines and drugs.

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BIO00022H: NUTRIENT ACQUISITION AND CYCLING IN NATURAL AND

AGRICULTURAL SYSTEMS

ORGANISER: Dr Angela Hodge


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

BIO00024H: 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.

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LEARNING OUTCOMES:

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

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

explain the structural basis of sequence-independent RNA recognition by proteins

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

describe the structural features of E. coli RNA polymerase

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

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

discuss the use of chromatin immuno-precipitation to probe transcription and chromosome organisation in vivo

BIO00026H: SYSTEMS AND SYNTHETIC BIOLOGY

ORGANISER: Dr A Jamie Wood

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

completed the BIO00032I Systems Biology Skills module in Stage 2.

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 of mathematical and experimental study can lead to new biological insights.

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

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

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

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

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BIO00045H: EUKARYOTIC GENE TRANSCRIPTION

ORGANISER: Bob White (RJW)

RECOMMENDATIONS/PREREQUISITES: BIO00007I Gene to Function

SUMMARY:

Transcription is essential for genetic information to become physical reality; as such, it underlies all

biology. Aberrant transcription is a feature of all biological disorders and is responsible for many. This

module is designed for biochemists, molecular cell biologists and biomedical scientists who are interested

in learning more about the mechanisms and control of gene expression in eukaryotic organisms and how

these go awry in human diseases. It will present general principles and key molecules, describing how

they achieve their functions. All stages will be illustrated with examples that are of particular interest and

importance. Transcription and transcription factors will be considered as potential therapeutic targets for

the treatment of diseases such as cancer. Experiments from transcription-related research papers will be

examined in detail to provide training in data interpretation.

LEARNING OUTCOMES:

On completing this module, students should be able to:

describe the key features of nuclear RNA polymerases

explain how transcription complexes assemble and function at distinct types of gene

discuss the impact of chromatin on gene transcription

explain how transcription is regulated

describe examples of regulatory transcription factors and how they function

describe how transcription factors are used by cells to respond to environmental conditions

explain the importance of transcription factors for cancer

discuss the potential of transcription as a target for therapeutic intervention.

identify appropriate experimental controls

Page 51 of 60

Page 52 of 60

SECOND YEAR MODULE CHOICES 2014 – 2015

You must select a 20 credit module – From gene to function or Organisms in their

environment

Your credits for the year must total 120

Student: BIOLOGY

Module No Module name Term taught Credits

BIO00032I Scientific skills and tutorials – please indicate your

preferred choices of skills module overleaf

Aut / Spr / Sum 30

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

Page 53 of 60

BIO00032I Scientific skills choices

You are required to select a practical course from each group. Rank your choices from each

group – 1-6 or 7 with 1 being your preferred choice

BIO00032I

Experimental design and practical skills. Please rank

your choices (1 – 6 or 7 with 1 being your preferred

choice)

Skills Group 1:

Cell imaging

Electrophysiology

GIS

Modeling

PCR


Taxonomy

Skills Group 2:

Bioenterprise

Communicating science

Evolutionary trees

Genomics

Molecular imaging

Systems

Aut, Spr, Sum

30

DEADLINE FOR SUBMISSION TO UNDERGRADUATE OFFICE – MONDAY 4 MARCH

Page 54 of 60


Your compulsory modules are entered below


Student: Biotechnology and Microbiology

Mod No Module name Term taught Credits



Aut / Spr / Sum 30

BIO00007I From gene to function Aut, Spr, Sum 20

BIO00008I Molecular biotechnology Aut 10

BIO00018I Post-genomic biotechnology Spr, Sum 10


Page 55 of 60




BIO00032I



choice)

Skills Group 1:

Cell imaging

Electrophysiology

GIS

Modeling

PCR


Taxonomy

Skills Group 2:

Bioenterprise


Evolutionary trees

Genomics

Molecular imaging

Systems

Aut, Spr, Sum

30


Page 56 of 60




Student: ECOLOGY

Mod No Module name Term taught Credits



Aut / Spr / Sum 30

BIO00036I Organisms in their environment Spr, Sum 20



Page 57 of 60




BIO00032I



choice)

Skills Group 1:

Cell imaging

Electrophysiology

GIS

Modeling

PCR


Taxonomy

Skills Group 2:

Bioenterprise


Evolutionary trees

Genomics

Molecular imaging

Systems

Aut, Spr, Sum

30


Page 58 of 60




Student: GENETICS




Aut / Spr / Sum 30


BIO00033I Mechanisms of genetic change Aut 10

BIO00017I Evolutionary and population genetics Spr 10


DEADLINE FOR SUBMISSION TO UNDERGRADUATE OFFICE –MONDAY 4 MARCH

Page 59 of 60




BIO00032I



choice)

Skills Group 1:

Cell imaging

Electrophysiology

GIS

Modeling

PCR


Taxonomy

Skills Group 2:

Bioenterprise


Evolutionary trees

Genomics

Molecular imaging

Systems

Aut, Spr, Sum

30


Page 60 of 60




Student: Molecular cell biology




Aut, Spr, Sum 30


BIO00034I Metabolism in health and disease Aut 10

BIO00035I Cell biology Spr 10



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BIO00032I

Experimental design and practical skills.

Skills Group 1:

Cell imaging

Electrophysiology

GIS

Modeling

PCR


Taxonomy

Skills Group 2:

Bioenterprise


Evolutionary trees

Genomics

Molecular imaging

Systems

Aut, Spr, Sum

30


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