final level biol units - by unit number code title biol30111

FINAL LEVEL BIOL UNITS - BY UNIT NUMBER

Code Title

BIOL30030 Projects

BIOL30111 Analysis of Organismal Form

BIOL30112 Neuroinflammation in Health and Disease

BIOL30121 How Cells Sense & Respond to their Environment…

BIOL30142 Biochemical Basis of Disease

BIOL30152 Bioethics

BIOL30161 Cell Signalling

BIOL30191 Glycobiology – Glycan Functions in Health and Disease

BIOL30252 Oil and Metal Pollution in Water

BIOL30262 Applications of Plant Biotechnology

BIOL30271 Protein Sorting and Organelle Biogenesis

BIOL30291 Trees and Forests

BIOL30302 Advanced Developmental Biology

BIOL30311 Advanced Neuropharmacology

BIOL30322 Advanced Parasitology

BIOL30331 Current Trends in Human Anatomy for Clinical & Research Perspectives

BIOL30342 Bacterial Infections of Man

BIOL30351 Advanced Behavioural Neurobiology

BIOL30362 Cardiovascular Systems in Health and Disease

BIOL30371 Cell Adhesion: the Molecular Biology of Cell-Matrix & Cell-Cell Interactions

BIOL30381 Channels & Transporters: Molecule to Function

BIOL30401 Chemical Communication in Animals

BIOL30441 Clinical Endocrinology

BIOL30452 Clinical Genetics

BIOL30471 Control of Cell Division

BIOL30491 Post-Genome Biology

BIOL30501 Evolution of Animal Behaviour

BIOL30541 Hormones and Behaviour in Animals

BIOL30551 Human Reproductive Biology

BIOL30561 Channels & Transporters: Health & Disease

BIOL30582 Molecular Biology of Cancer

BIOL30592 Current Topics in Microbiology

BIOL30602 Molecular Toxicology

BIOL30631 Pollution, Plants and Ecosystems

BIOL30681 Immune Response and Disease

BIOL30801 Advanced Immunology

BIOL30931 Stem Cells

BIOL31031 Developmental Neuroscience

BIOL31042 Conservation Biology

BIOL31051 Programming for Biologists

BIOL31072 Cognitive Neuroscience

BIOL31101 Imaging Living Systems: Molecules to Man

BIOL31181 Gene Regulation & Disease

BIOL31191 Protein Assembly, Dynamics & Function

BIOL31241 Macromolecular Recognition in Biological Systems

BIOL31431 Chronobiology

FINAL LEVEL BIOL UNITS - BY UNIT NAME

Code Title

BIOL30351 Advanced Behavioural Neurobiology

BIOL30302 Advanced Developmental Biology

BIOL30801 Advanced Immunology

BIOL30311 Advanced Neuropharmacology

BIOL30322 Advanced Parasitology

BIOL30111 Analysis of Organismal Form

BIOL30262 Applications of Plant Biotechnology

BIOL30342 Bacterial Infections of Man

BIOL30142 Biochemical Basis of Disease

BIOL30152 Bioethics

BIOL30362 Cardiovascular Systems in Health and Disease

BIOL30371 Cell Adhesion: the Molecular Biology of Cell-Matrix & Cell-Cell Interactions

BIOL30161 Cell Signalling

BIOL30561 Channels & Transporters: Health & Disease

BIOL30381 Channels & Transporters: Molecule to Function

BIOL30401 Chemical Communication in Animals

BIOL31431 Chronobiology

BIOL30441 Clinical Endocrinology

BIOL30452 Clinical Genetics

BIOL31072 Cognitive Neuroscience

BIOL31042 Conservation Biology

BIOL30471 Control of Cell Division

BIOL30592 Current Topics in Microbiology

BIOL30331 Current Trends in Human Anatomy for Clinical & Research Perspectives

BIOL31031 Developmental Neuroscience

BIOL30501 Evolution of Animal Behaviour

BIOL31181 Gene Regulation & Disease

BIOL30191 Glycobiology – Glycan Functions in Health and Disease

BIOL30541 Hormones and Behaviour in Animals

BIOL30121 How Cells Sense & Respond to their Environment…

BIOL30551 Human Reproductive Biology

BIOL31101 Imaging Living Systems: Molecules to Man

BIOL30681 Immune Response and Disease

BIOL31241 Macromolecular Recognition in Biological Systems

BIOL30582 Molecular Biology of Cancer

BIOL30602 Molecular Toxicology

BIOL30112 Neuroinflammation in Health and Disease

BIOL30252 Oil and Metal Pollution in Water

BIOL30631 Pollution, Plants and Ecosystems

BIOL30491 Post-Genome Biology

BIOL31051 Programming for Biologists

BIOL30030 Projects

BIOL31191 Protein Assembly, Dynamics & Function

BIOL30271 Protein Sorting and Organelle Biogenesis

BIOL30931 Stem Cells

BIOL30291 Trees and Forests

PROJECTS BIOL30030 Unit Coordinator(s): Dr Liz Sheffield ([email protected])

Semester 1 & 2 Credits 30

See also information on Projects under Section 33 i n this handbook and on the Intranet.

You should have registered the type of project that you would like to undertake. These include Laboratory or Field-based (includes Data-analysis and Bioinformatics) or Public Understanding and Communication of Science (includes eLearning, Science and Education in schools or projects supervised by the Centre for the History of Science, Technology and Medicine or an Enterprise Project). You will be informed of the name of your supervisor early in the first semester of the final year. You should contact your allocated supervisor as soon as possible in the new semester, he/she will discuss the type of project with you and offer some "starter" references so that you can begin background reading (if you are doing a literature review, you should have started work by week 6).

Library Session for Literature Searching

Sessions will be arranged for you during week 6 on Literature Searching for Research. These will take place in the John Rylands Library, User Education Room.

This is relevant to all types of final year project and you should attend. Helen McEvoy (Faculty Librarian) will give instruction on how to undertake an effective literature search and to be critical of the sources used. He will cover literature and bibliographic databases and help you identify an effective search strategy.

You will be informed of the date and time of the sessions via the intranet Announcements Service.

Literature Reviews A 10 credit literature review (BIOL30101) is completed in semester 5 by most students. ‘With Language’ students undertake a 30 credit project BIOL30040.

The deadline for handing in the literature review is given on the front page of this handbook.

Project Write-up Please see Section 33.5. See also the Guide for Writing Literature Reviews and Projects on the intranet www.intranet.ls.manchester.ac.uk/public/downloads.aspx?AliasId=UG-LitReviewGuidelines.

Two hard copies of the project report and an electronic copy should be handed in. The deadline for handing in the project report is given on the front page of this handbook.

Feedback Students completing a literature review or draft introduction can expect to receive formative feedback on an outline. When a literature review or introduction has been read or marked, feedback should be sought on the review itself, from supervisors.

All student can expect to receive formative feedback on a first draft of their project write-up (but this will only forthcoming if dates for submission are agreed with supervisors and met!).

ANALYSIS OF ORGANISMAL FORM BIOL30111 Unit Coordinator(s): Dr Chris Klingenberg (cpk@manc hester.ac.uk) Semester 1

Credits 10

Aims

The main aim of the unit is to provide an introduction to morphometrics - the quantitative analysis of organismal size and shape. The unit gives a survey of methods for data acquisition and analysis as well as applications in diverse fields of biology. Examples will include studies on diverse organisms in the context of different research fields (basic biology as well as medical and other applications).

Intended Learning Outcomes

Students should be enabled to read and understand the current literature in the field and to conduct simple morphometric studies themselves, from the design of the study through data collection to the analysis and interpretation of results.

Lecture Content

The unit is taught primarily via the web to students on campus and from around the world. In addition to ‘lecture’-style material, the course will also offer practical applications of the methods (example data, software and guidance are provided). To enhance interactions, participants work in small groups to prepare blogs featuring specific examples. For students in Manchester, the web content is augmented with weekly meetings for face-to-face discussion and feedback.

• Data acquisition: the kinds of data and the equipment used to collect them. • Statistics of variation, scatter plots, basic multivariate statistics • Definitions of size and shape (distance measures) • Geometric methods to measure shape from a configuration of landmark points • Shape transformations and 'warping' • Analysis of outline shapes • Distinguishing between groups (taxonomy, clinical diagnosis, etc.) • Influence of external factors on shape (ecomorphology, dose-response studies) • Symmetric forms and measurement of asymmetry. • Morphometric inferences about developmental processes, morphological integration,

modularity • Genetics of shape: analyses of resemblance between relatives, QTL analyses. • Phylogeny: reconstructing the evolution of shape

Assessment Two online tests during the course - 10% each. Final exam of 2 hours and consisting of problem questions - 80%.

Feedback The unit has an online discussion forum and there are weekly meetings on campus for discussion and feedback. The instructor will comment on the group work (blogs), and feedback on the test performance is provided as marks.

Prerequisites - None. Familiarity with basic statistical analysis is an advantage, but all necessary material is presented as part of the course unit.

Teaching Staff - Dr Chris Klingenberg

NEUROINFLAMMATION IN HEALTH AND DISEASE BIOL30112 Unit Coordinator(s): Dr Emmanuel Pinteaux ([email protected])

Semester 2 Credits 10

Aims To provide an extensive knowledge of the role of inflammation in nervous system health and disorders. Inflammation is involved in many CNS-regulated physiological processes (including energy balance, sleep, memory and synaptic plasticity) and is a key host defence response to acute and chronic peripheral and central disorders. Research into neuroinflammation is a major field which aims to develop new therapeutic interventions to treat all major nervous system disorders including stroke, brain trauma, epilepsy, Alzheimer’s and Parkinson’s diseases, obesity and neuropathies (for which there is currently no/limited treatments). This unit will cover the important role of inflammatory molecules as key mediators of CNS functions and will provide basic knowledge of pathogenesis and inflammatory responses to acute and chronic nervous system disorders.

Intended Learning Outcomes Students will be able to:

• acquire basic knowledge of CNS-regulated physiological functions that are mediated by inflammatory mediators, and pathogenesis and inflammatory responses to acute and chronic central and peripheral nervous system injuries.

• use intellectual skills (combining established knowledge acquired during previous lectures with cues identified during GBL-based sessions) to address specific questions associated to the group of lectures. E-learning will be created (through Blackboard) to generate an interactive environment that will allow the students to study learning objectives and to further explore the subjects studied.

• present and debate on GBL-cases. • attend 1-2 Neuroscience lectures on related matters, & subsequently write up of 1-2 assays.

Lecture Content Lectures will provide an overview of each aspect of inflammatory mediators in nervous system functions and disorders. This will include:

• biology of the major inflammatory molecules families (including their ligands, receptors, cell targets, signalling pathway, downstream cellular effect & secondary inflammatory mediators).

• the role of inflammatory mediators in neuro-immune interaction (HPA axis), sleep, memory and synaptic plasticity, regulation of energy balance.

• the role of inflammatory mediators in acute (stroke, brain trauma, epilepsy) and chronic (Alzheimer’s, Parkinson’s diseases, multiple sclerosis) brain disorders.

• the role of inflammatory mediators in peripheral neuropathies. • inflammatory mediators as early biomarkers, markers of inflammation in diagnosis including

recent advances in brain imaging.

In addition, there will be 4 group-based learning activities (GBL/eGBL cases related to 4 themes of lectures). Students will search on cases (enquiry-based learning, E-learning), and present/feedback/debate to the rest of the group. There will be 1-2 Neuroscience seminars to attend.

Assessment - 2 hour examination (80%), 1 hour presentation and debate on GBL cases (10%), essay on attended seminar(s) (10%)

Feedback - Students may receive immediate feedback on their activity and performance during the GBL sessions by talking to staff. Students will also receive feedback on their answers to short answer questions and/or MCQs. In addition, students will receive feedback on overall performance in the form of the final mark for the unit and will receive individual feedback from their advisor.

Prerequisites - BIOL10832 (Compulsory); BIOL20761 (Recommended)

Teaching Staff - Stuart Allan, Dave Brough, Natalie Gardiner, Cath Lawrence, Jaleel Miyan, Emmanuel Pinteaux, Craig Smith

HOW CELLS SENSE & RESPOND TO THEIR ENVIRONMENT: LESSONS FROM EUKARYOTIC MICROBES

BIOL30121

Unit Coordinator(s): Dr Sue Crosthwaite ([email protected])


Aims The ability of cells to monitor and react appropriately to their environment is crucial for the survival of both unicellular and multicellular organisms. This unit will focus on the mechanisms employed by a variety of eukaryotic microbes to sense their environment and will show how they make use of this information to organize cellular and developmental processes. Students will be encouraged to think beyond the lecture material and to critically review and interpret experimental data in primary research papers. Through analysis and debate of primary literature students will acquire the skills to formulate their own short research proposal (an example research proposal can be found in associated course material on blackboard, 1000 word limit). The research proposal will build on writing skills developed in the second year RSM and will test and reinforce students understanding of material covered during the course. A prize will be awarded for the best research proposal.

Intended Learning Outcomes Students will be able to:

• describe in detail the strategies employed by a range of eukaryotic microbes to sense and respond to changes in light and nutrient availability

• give examples of mechanisms employed by eukaryotic microbes to sense each other, invading viruses and potential hosts, including humans

• describe how information about the environment is used to promote survival and to orchestrate complex developmental programs

• illustrate how model eukaryotic microbes can be used to study fundamental problems in biology

In addition, students will have developed their ability to critically evaluate published data and to communicate science and scientific ideas both orally and in writing.

Lecture Content There will be 12 lectures plus a one-hour workshop to teach the do’s and don’ts of grant writing. Lectures will be interspersed with student-led seminars (one student seminar associated with each of the five main topics). Students will work in groups to discuss and present a primary research paper to their peers.

• Overview of eukaryotic microbes and the importance of model organisms. • Adaptive responses of Chlamydomonas to environmental stress: Responses to nutrient stress -

metabolic and molecular responses to nutrient deficiency. Responses to light stress - light sensing and mechanisms of phototaxis in response to excess light

• Circadian orchestration of gene expression and development with a focus on light and temperature sensing and the circadian clockwork of Neurospora crassa.

• For Dictyostelium, terminal differentiation is a life or death decision. These lectures will cover how the timing of this decision is coordinated in response to environmental stimuli and the molecular basis of social interactions between different strains as each tries to avoid death.

• Human gut commensals such as Candida albicans or widespread soil living species such as Aspergillus fumigatus become opportunistic pathogens in response to changes of the host. Pathways underlying opportunistic pathogenicity; virulence factors employed by opportunistic human fungal pathogens and host-pathogen interactions in disease development will be discussed.

• Mechanisms employed by Neurospora to defend its genome against invasion by selfish DNA: Quelling (RNAi), Repeat Induced Point mutation (RIP) and Meiotic silencing of unpaired genes. Implications of these phenomena for genome evolution.

Assessment Short research proposal (20%) Participation in discussion groups and student-led seminars (5%) 2 hour written examination (75%)

Feedback - Feedback provided during and after the student-led seminar sessions. Drafts of research proposals will be peer reviewed, students will then be given the chance to make improvements to the proposal before the final mark is given by a member of staff. Students will be able to gauge their understanding of each topic by completing online multiple-choice questions.

Prerequisites - BIOL10221 (Recommended).

Teaching Staff - Dr Sue Crosthwaite, Dr Christian Heintzen, Dr Jon Pittman, Dr Geoff Robson, Dr Lubomira Stateva, Dr Chris Thompson.

BIOCHEMICAL BASIS OF DISEASE BIOL30142 Unit Coordinator(s): Professor Ray Boot-Handford (r [email protected])


Aims

Major diseases of man such as diabetes, obesity, atherosclerosis, fibrosis and osteoporosis are significant contributors to morbidity and fatality in the western world. Developing treatments for these diseases is a major challenge to the pharmaceutical industry in the 21st century and there is therefore great interest in the biochemistry underlying their pathogenesis. This unit aims to describe the biochemistry of these common diseases and highlight how understanding disease mechanisms is necessary to develop novel rational therapies.


Students should have an understanding of the biochemical basis of a number of major diseases of man, an appreciation of the disease mechanisms being targeted in treatments, and further insights into the tissue-specific biochemical specialisations underlying the functioning of complex organisms such as mammals.

Lecture Content

A significant proportion of this course will be delivered in the form of directed reading supported by lectures and will focus on biochemical aspects of:

• Diabetes: metabolism, secondary complications, beta cells, insulin secretion, Type II diabetes • Obesity and Atherosclerosis: insulin resistance, blood lipids • Fibrosis: TGF beta, wound healing • Angiogenesis: inhibitors and promoters as therapeutic tools • Stroke and Haemoglobinopathies: biochemical basis of platelet aggregation and oxygen

transport in blood • Amyloid diseases: Alzheimer's and protein folding/misfolding diseases • Osteoporosis: imbalances in bone homeostasis

Assessment

2 hour essay-based exam (100%).

Feedback

Bulletin board; feedback session on self-directed learning component of course.

Prerequisites

BIOL20112 (Recommended)

Teaching Staff

Dr David Boam; Professor Ray Boot-Handford; Professor Paul Brenchley; Dr Ann Canfield; Dr Richard Kammerer

BIOETHICS BIOL30152 Unit Coordinator(s): Dr Caroline Bowsher ([email protected])


Aims

To provide a stimulating, structured logical approach to ethical issues and to provide a context for practising this. To allow students to appreciate the importance of the public’s perceptions; to be aware of scientific investigations of impacts, to relate knowledge of modern biology to wider issues, and to apply good thinking and grasp ethical principles.

NOTE: All students must have registered by the 2nd week of semester 5. No-one can transfer onto this unit after this date.


A greater ability to think in a structured way. Knowledge of the different ethical principles with which different people may approach the same issue and ability to use these to provide a basis for understanding current issues and novel issues of the future.

Lecture Content

An informal, seminar type approach forms the bulk of the unit; students are given reading to do before each session and criticise, discuss material and ask questions during the seminar.

The examples and topics covered will depend to some extent on current areas of interest in the field of bioethics. Some topics are expected to cover the following which should give an idea of the likely scope and type of material:

• Introduction to ethics and bioethics - The ethical basis of science

• Ethical issues in agriculture and food production - GM crops and food - Patenting of genes for agricultural biotechnology

• Ethical issues in biomedical science - reproductive technologies - genetic information: use and abuse

Assessment

Group oral presentations on specific topic, essay on topic of student’s choice, short answer questions on a topic requiring application of the principles of ethics.

• 15% of marks allocated to an oral presentation • 55% of marks allocated to an essay • 30% of marks to a short question examination

Feedback - The oral presentation will receive peer evaluation, verbal generic feedback and written feedback on individual group performances. The proposed essay titles identified by individuals will receive written comments. The final essays will receive written feedback.

Prerequisites - None.

Recommended Reading • Harris, J Enhancing Evolution: The ethical case for making better people 2007 Princeton • Bryant J, et al Introduction to Bioethics 2005 Wiley • Harris, J The Value of Life 2003 Routledge

Teaching Staff - Dr Caroline Bowsher; Professor Terry Brown; Dr Sarah Chan; Dr Charles Erin; Professor John Harris; Dr Dean Jackson; Dr Liz Sheffield; Dr Cathy Walton

CELL SIGNALLING BIOL30161 Unit Coordinator(s): Dr Alan Whitmarsh ([email protected])


Aims • To provide an understanding of the molecular mechanisms by which cells communicate. • To illustrate the commonality of mechanisms using examples of various types of signalling

molecules. • To provide a basis for the understanding of disease processes in which signalling is

compromised. • To give insight into the experimental methods used for studying cell signalling.

Intended Learning Outcomes To:

• be able to describe the various types of signalling molecules including receptors, adapter proteins, second messengers, kinases, and phosphatases;

• have an understanding of how the physical properties of signalling molecules influence their behaviour;

• be able to describe the major intracellular signalling pathways in cells and have an understanding of their complexity and the interactions between them;

• have an understanding of the link between extracellular signals and intracellular events, including the regulation of gene expression;

• be able to discuss the relevance of cell signalling in a variety of physiological and pathological situations;

• appreciate the experimental methods associated with the study of cell signalling;

Lecture Content • Introduction to cell signalling: types of signalling systems, protein-protein interactions, protein

phosphorylation/de-phosphorylation. • Receptors: types of receptors (receptor protein kinases, cytokine receptors, GPCRs), their

mechanism of action, and their function in cells. Regulation of receptor activity and numbers. • Second messengers, calcium signalling and phospholipid signalling. • Intracellular signalling pathways: covers the major pathways in cells, their components

including protein kinases and phosphatases, and the role of multisite phosphorylation and signal integration.

• Transcriptional regulation by signalling pathways: including signal-responsive promoter regulatory elements and the phosphorylation/de-phosphorylation of transcription factors.

• Techniques for the analysis of cell signalling.

Assessment - 2 hour essay-based examination (100%)

Feedback - Feedback may be given in one or more of a range of methods. Contact Unit Coordinator for further details.

Prerequisites BIOL10212 (Recommended); BIOL10232 (Recommended); BIOL20141 (Recommended); BIOL20161 (Recommended)

Suitable for students with some background in eukaryotic molecular and cellular biology e.g. those who have taken the prerequisite units listed.

Recommended Reading • Hancock, J.T. Cell Signalling (2nd edition) 2005 Oxford University Press • Gomperts B.D. et al Signal Transduction 2002 Elsevier Academic Press

Teaching Staff - Dr Cathy Tournier; Dr Alan Whitmarsh; Dr Gino Poulin, Dr Lindsay MacDougall; Dr Katherine Hinchcliffe

GLYCOBIOLOGY – GLYCAN FUNCTIONS IN HEALTH AND DISEASE

BIOL30191

Unit Coordinator(s): Dr Dave Thornton ([email protected])


Aims Glycans provide important mechanisms for cell recognition, cell adhesion, growth factor signalling and extracellular matrix organisation. The overall aim of this unit is to introduce students to the biology and pathobiology underlying these processes. The unit will introduce students to the cellular mechanisms of synthesis and assembly of glycans and an understanding of the range of biological roles they play in cell and tissue functions.


To have a clear understanding of: • The molecular diversity and widespread expression of glycans • Structure and biosynthesis of the major groups of glycans • How glycosylation modulates the structure, properties and functions of proteins • The concept that glycans are key factors in biological recognition • The critical role glycans play in many fundamental cellular processes

Problem solving sessions will enhance the students analytical skills.

Lecture Content • Structural diversity in glycans, oligosaccharides, glycoproteins, proteoglycans. • Mechanisms of biosynthesis • The range of biological functions to which glycosylation contributes. • Mucosal protection (innate immunity) • Trafficking of immune cells to sites of injury/infection and migration of tumour cells • Cellular action, location and organization of glycosyltransferase enzymes for O-linked and N-

linked glycan biosynthesis. • Disease models involving gene mutation and knockout in the N-linked glycan biosynthesis

pathway • Critical function of co-translational glycosylation on protein folding and secretion. • Specificity in glycosaminoglycan biosynthesis • Generation and identification of selective protein binding sequences in glycosaminoglycans • Roles in growth factor signalling • Lessons to be learnt from knockouts and mutations in the developmental biology of humans,

mice and fruit flies

An online problem solving session on glycan structure determination is included as part of the self-directed learning aspect of the course.

Feedback - One lecture will be used to feedback on the self-directed learning aspect of the course; other issues can also be discussed during this session. A bulletin-board is also available.

Assessment - 2 hour written examination (100%)

Prerequisites – None. However, students should note that this course deals mainly with the molecular details of glycan function.

Recommended Reading No text book covers the entire unit. However, 'Introduction to Glycobiology' provides a good general background to many aspects of Glycobiology.

• Taylor, Maureen E Introduction to Glycobiology 2003 Oxford University Press

Teaching Staff - Professor John Aplin; Professor Tony Day; Dr Sally Stringer; Dr Dave Thornton

OIL AND METAL POLLUTION IN WATER BIOL30252 Unit Coordinator(s): Dr Keith White (keith.white@ma nchester.ac.uk) Semester 2

Credits 10 Aims

To provide an understanding of:

• The sources, behaviour in the hydrosphere, fate and impact of trace metal and oil pollutants of marine and freshwater.

• The efficacy and environmental impact of strategies and methods of preventing pollution of waters by oil and trace metals, and clean up should pollution occur.


Knowledge and understanding of:

• The sources, characteristics and behaviour in water of oil and trace metals and why these factors influence the environmental impact of these two groups of pollutants

• Why and how trace metals and oil damage marine and freshwaters ecosystems, fisheries and adversely affect the use of water for recreation and abstraction.

• The efficacy of methods to reduce or prevent the entry of trace metals and oil to marine and freshwaters

• The methods and environmental impact of removing trace metals or oil released to marine and freshwaters

Lecture Content

• Introduction: what is pollution? Characteristics oil and trace metals and how these influence their environmental impact.

• Sources and fate of trace metals in the environment : sources and pathways of trace metals to the aquatic environment.

• Mine Pollution - a case study of Parys Mountain, No rth Wales: generation of acid mine drainage. Behaviour of trace metals in acidic and neutral freshwaters. Behaviour of trace metals in estuaries. Methods of removal of trace metals from water.

• Bioavailability and toxicity of trace metals: the importance of chemical speciation in the bioavailability and toxicity of trace metals. Mechanisms of toxicity of trace metals. Storage and detoxification of trace metals by aquatic organisms.

• Case studies of environmental impact of trace metal s: production, use, transport and environmental impact of mercury, lead and cadmium in the aquatic environment.

• Sources and fate of oil in the environment: sources of oil arising from operational and accidental discharge. Methods of reducing contamination and their efficacy in practice.

• Environmental impact of oil pollution: impact of acute and chronic oil pollution on fisheries, seabirds and mammals.

• To clean or not to clean? - The environmental impac t of removing oil: strategies for the removal of oil, contingency planning. Environmental impact of methods of removing oil at sea and from the shore. Impact on amenity.

Assessment – Two hour examination (100%)

Feedback – verbal feedback throughout the course, guidance on key subject areas to be examined during the final unit-round-up session

Prerequisites - None

Recommended Reading • Mason, CF Biology of Freshwater Pollution (4th edition) 2001 Longman • Clark, RB Marine Pollution (5th edition) 2001 Clarendon Press

Teaching Staff - Dr Amanda Bamford; Dr Keith White

APPLICATIONS OF PLANT BIOTECHNOLOGY BIOL30262 Unit Coordinator(s): Dr Jon Pittman ([email protected])


Aims With a changing climate there are increased pressures to feed a growing world population. Plant biotechnology offers significant potential to increase crop productivity to meet food demands and can provide benefits to the environment. Plant biotechnology can also provide solutions to energy and health challenges, such as with the generation biofuels or the production of vaccines in plants. In this course you will learn how the versatility of plants can be exploited for a wide range of applications, including those relevant to the agricultural, pharmaceutical, food science and chemical industries.

Intended Learning Outcomes • To understand the potential applications of new technologies in the exploitation of plants • To understand how the knowledge of fundamental plant processes can be applied to drive

biotechnological developments • To learn how to develop a proposal for a plant biotechnology project • To understand various aspects of commercialisation of plant biotechnology

Lecture Content The lectures will examine the approaches used to manipulate plants for biotechnological applications. The lecture content will use case studies which illustrate the major advances that are being made in some of these areas. Some topics to be covered include:

• Non-food uses of plants: biofuels and pharmaceutical production • Drought and salt stress tolerance: engineering plants to grow in a changing climate • Considerations for commercialisation: risk assessment, environmental impact and legislation • A guide to plant biotech start-ups • Improving carbon fixation: can genetic engineering do better than evolution? • Impacts of altered metabolism: quantity versus quality

Assessment - 1 hour examination essay question (45%) and a coursework case study on the development of a hypothetical plant biotechnology project of the student’s choice (55%).

Feedback - Individual written feedback and guidance will be available to each student on a plan of the coursework prior to submission.

Prerequisites - BIOL10212 (Recommended); BIOL10221 (Recommended)

Recommended Reading Students will be provided with reference lists of review and research papers from the primary literature. The listed texts provide useful background reading:

• Slater A, Scott N & Fowler M Plant Biotechnology: The Genetic Manipulation of Plants 2003 Oxford University Press

• Buchanan BB, Gruissem W & Jones RL Biochemistry and Molecular Biology of Plants 2000 American Society of Plant Physiologists

• Bowsher C, Steer M & Tobin A Plant Biochemistry 2008 Garland Science

Teaching Staff - Dr Caroline Bowsher; Dr Anil Day; Dr Patrick Gallois; Dr Jon Pittman; Prof Simon Turner

PROTEIN SORTING & ORGANELLE BIOGENESIS BIOL30271 Unit Coordinator(s): Dr Blanche Schwappach ([email protected])


Aims Eukaryotic cells are characterised by specialised sub-cellular compartments. This compartmental organisation demands that newly synthesised proteins are accurately and efficiently targeted to their appropriate sub-cellular locations. Compartmentalisation also ensures that unique post-translational modifications can occur to a subset of synthesised proteins. The aim of this unit is to examine the molecular mechanisms of organelle biogenesis and protein sorting in eukaryotes, and will review recent data demonstrating that some of these processes are fundamental to all living cells. A substantial part of the course will involve discussion of recently published papers.

Intended Learning Outcomes To understand the mechanisms which target proteins to a number of compartments, the major post-translational modifications occurring throughout the secretory pathway, and the basis of the molecular specificity of vesicular transport. The biogenesis of lipids will be examined together with a review of their role in protein sorting. Lectures will emphasise the applications and limitations of specific experimental approaches. The problem sessions are designed to enhance cognitive skills, and to develop the ability to assess and critically interpret experimental data.

Lecture Content

Protein targeting to the nucleus: • The nature of nuclear localisation signals and nuclear pores. • The role of soluble factors in nuclear import.

Protein targeting to mitochondria: • Mitochondrial targeting signals. • Sorting of proteins to specific compartments within the mitochondrion.

The secretory pathway:

• Protein targeting to the endoplasmic reticulum. • Protein translocation across the ER membrane. • Post-translational modification and folding of secretory proteins. • Global changes to the secretory capacity during differentiation and stress

Mechanisms of vesicular transport: • Formation of transport vesicles • Targeting and fusion of transport vesicles

The endocytic pathway: • Receptor-mediated endocytosis. • Ubiquitin-dependent receptor downregulation

Assessment Assessment is by a written examination (2hrs) that includes both short essay answers and data interpretation (100%).

Feedback - This will be via the bulletin board.

Prerequisites - None necessary but BIOL20161 would be helpful.

Recommended Reading Alberts et al. Molecular Biology of the Cell as a basis. Reference lists will be given in lectures.

Teaching Staff - Dr Blanche Schwappach; Professor Stephen High; Professor Philip Woodman

TREES AND FORESTS BIOL30291 Unit Coordinator(s): Dr Roland Ennos ([email protected])


Aims

Trees include the largest and most familiar of all organisms, and forests cover 30% of dry land, yet despite this many questions about trees remain unanswered or even unconsidered. This unit aims to shed light on the scientific process by examining both what we know about trees and forests and how we know it. But most importantly it will also unearth what we don’t know or are unsure about and try and work out why this is the case.


The unit is in two parts. The first part will be a straightforward account of the current state of our knowledge about trees and forests and will be taught in lectures. The second part will use this background to inform in-depth discussions of topics that are starting to come under scientific investigation and debate. For this part students will be given papers to read and the sessions will be run as informal seminars.

Lecture Content

Part 1 1. The selective advantages of the tree form. 2. The evolutionary history of trees. 3. The hydraulics of trees. 4. The mechanics of wood and trees. 5. The ecology of trees and forest succession. 6. Climate and the global distribution of trees. 7. Was post-glacial Europe covered by forest? 8. The uses and exploitation of trees.

Part 2 1. Why did leaves evolve so late? 2. What limits tree height? 3. Why do some trees' leaves go red in Autumn? 4. Why are tropical rainforests more diverse than other forests? 5. Why does bracken invade deforested land?

Assessment

One essay in exam (50%) on part 1. Long essay on a topic of students' choice (50%) for part 2.

Feedback

Feedback on students' long essays is available on request.

Prerequisites

None.

Recommended Reading

• Ennos AR Trees 2001 Natural History Museum, London • Thomas P Trees: their natural history 2000 Cambridge University Press

Teaching Staff - Dr Roland Ennos; Dr Giles Johnson; Dr Liz Sheffield

ADVANCED DEVELOPMENTAL BIOLOGY BIOL30302 Unit Coordinator(s): Dr Andreas Prokop ([email protected])


Aims

To obtain a clear understanding of how multiple developmental mechanisms regulate the stepwise and reproducible formation of specific body parts, such as the limb and head.


An appreciation of how a single fertilised egg cell develops gradually into a complex, 3D, multicellular organism composed of highly organised tissues, such as bone, cartilage, skin, muscles, nerves, and blood vessels. An understanding of how the concepts of developmental biology, such as pattern formation, positional information, induction and cytoplasmic determinants, can be used to explain the specification and positioning of different cell types within tissues and organs. Knowledge of the key signalling proteins, such as growth factors, which control animal development. An appreciation of the value of model organisms for the investigation of developmental principles, and of common and divergent concepts between animals and plants.

Lecture Content

Part 1: How to make a limb? An integrated view How does a limb bud know where to form? How are the axes of the limb determined? How does the limb acquire its appropriate size? How do skin appendages form? How can formation of skin appendages be modelled? How do skeletal muscles, cartilage and bone, blood vessels, nerve cells and functional synaptic contacts?

Part 2: How to make a head? Specific apects of cran ial development How do head specific features, such as head skeleton, ears and teeth develop?

Part 3: How to make internal organs? How do tubular organs, such as lung and kidney, develop? How are glandular organs, such as pancreas, mammary and salivary glands, formed?

Part 4: How to make a plant organ? How is growth coordinated to shape a leaf? How are specialised organs such as petal and reproductive organs formed? How is the vascular network formed?

Assessment - 2 hour essay-based written examination

Feedback - Written feedback via bullet-point answers to mock questions.

Prerequisites - BIOL20192 (Strongly Recommended)

Recommended Reading The course will utilise reviews and research papers from the primary literature. However the listed texts provide useful background:

NOTE: The 3rd edition of Principles of Development is recommended, if available. • Wolpert, L Principles of Developmental Biology (3rd edition) 2007 Oxford University Press • Gilbert, SF Developmental Biology (8th edition) 2006 Sinauer • Arias A M, Stewart A Molecular Principles of Animal Development 2002 Cambridge University

Press • Larsen WJ Human Embryology (3rd Edition) 2001 Churchill Livingston

Teaching Staff - Professor Enrique Amaya; Dr Denis Headon; Dr Minsung Kim; Dr Kimberly Mace; Dr Andreas Prokop

ADVANCED NEUROPHARMACOLOGY BIOL30311 Unit Coordinator(s): Dr Owen Jones; Dr Jon Turner [email protected]; j.turner-2@mancheste r.ac.uk


Aims The aim of this unit is to present, in depth, key topics at the forefront of modern neuropharmacology. The emphasis of this unit is on the major excitatory, inhibitory and modulatory neurotransmitter receptor systems, focusing on how such systems function in healthy nervous tissues, how they contribute to some of the most prevalent pathophysiological conditions in society and how their actions can be targeted therapeutically.

Intended Learning Outcomes To recognize key concepts, strategies and techniques in modern neuropharmacology. Specifically, to understand how neurotransmitter receptors work at the molecular and cellular level, their roles in healthy excitable cells, their contribution to the generation and therapy of diverse psychiatric and neuropathological disorders, with the successes achieved, and challenges faced, in designing drugs to tackle such disorders. Lecture Content For most areas, there will be two lectures detailing the basic principles. The topicality and importance of these areas will then be underscored by a third lecture designed to be stimulating and foster critical thinking.

• Ligand-gated ion channel receptors • Structure and function of G-coupled receptors • Glutamate receptors and excitotoxicity • GABA and disease • Serotonin • Dopamine • Cytokines and growth factors

Assessment 2 hour examination (100%) consisting of: Section A (1 hour) - answer 4 out of 6 short questions (15mins each) Section B (1 hour) - answer 1 essay question from choice of 6 Feedback - Feedback may be given in one or more of a range of methods. Contact Unit Coordinator for further details.

Prerequisites BIOL20782 (Recommended) Recommended Reading

• E.J. Nestler, S.E. Hyman, R.C. Malenka. Molecular Neuropharmacology: A foundation for Clinical Neuroscience.

Teaching Staff Dr Stuart Allan; Dr Owen Jones; Dr Simon Luckman; Dr Richard Prince; Dr Jon Turner

ADVANCED PARASITOLOGY BIOL30322 Unit Coordinator(s): Professor John Hyde ([email protected])


Aims

Parasitic infections cause some of the most prevalent and pathological diseases world-wide and have a major effect on the socio-economic status of affected countries. This unit (i) aims to build upon the information received in the second year unit 'Parasitology' (BIOL20432) and provide an understanding of the complex relationships between parasites and their hosts. In addition it (ii) aims to illustrate by experimental examples, the ways in which the study of parasitic organisms have provided fundamental insights into the fields of molecular biology, immunology and cell biology, and (iii) to address in detail important aspects of the molecular biology of selected parasites, how such organisms can respond at the molecular level to challenges by the immune system or chemotherapy, and how novel approaches to disease prevention might be developed.


Students will gain an appreciation of the ways in which parasites have evolved for survival in their hosts; understand how the host immune response can results in immune pathology; acquire knowledge of the complex molecular mechanisms of evasion of the host immune response and of the development of resistance to antiparasitic drugs; understand the use of parasites as experimental tools to answer fundamental biological questions, and gain an appreciation of the value of recently mapped parasite genomes and proteomic studies.

Lecture Content

Immunoparasitology • Polarisation of the T helper cell response: Leishmania, Trichuris • Immunity to human schistosomes • Intracellular parasitism – the macrophage as a habitat: Leishmania, Trypanosoma cruzi • Effector mechanisms: malaria, Toxoplasma gondii • Immunosuppression in filariasis • Immunopathology : schistosome egg granuloma, Wolbachia in filarial pathology

Molecular parasitology • Malaria: antigen genes, protein structure, immune responses, vaccine studies • Drug resistance and drug development in protozoa • Molecular biology of trypanosomes and their unorthodox gene expression • Toxoplasma gondii as a genetic tool, drug resistance, subversion of host behaviour • Parasite genomes • Parasite proteomics

Assessment - 2 hour examination (100%)

Feedback

Feedback will comprise an element of the revision session, which is held after the lectures, in the last one-hour scheduled period of the course.

Prerequisites

BIOL20141 (Recommended); BIOL20221 (Recommended); BIOL20432 (Recommended)

Recommended Reading

No text book covers the course. Reference lists will be given in lectures.

Teaching Staff - Dr Kath Else; Professor John Hyde; Dr Paul Sims

CURRENT TRENDS IN HUMAN ANATOMY FROM CLINICAL & RESEARCH PERSPECTIVES

BIOL30331

Unit Coordinator(s): Dr Niggy Gouldsborough ([email protected])


Aims The unit aims to build on the students existing knowledge of human anatomy and allow them to apply this knowledge to clinical and research settings. Clinicians lecturing on this unit will demonstrate the relevance of anatomy in modern clinical practice. Alongside this, students will be exposed to current research methodology in the field of Human Anatomy.


• Describe the anatomy of the upper & lower limbs, thorax, abdomen and head & neck • Discuss current clinical and research trends in the above anatomical fields • Explain how knowledge of anatomy is utilised in the clinical and research settings • Name and identify the important anatomical structures (and their relations) of the upper limb, lower

limb, thorax, abdomen and head & neck on prosections and models • Utilise relevant scientific literature to enhance their knowledge of the lecture topics and further

develop critical thinking skills

Lecture Content The unit will cover a number of anatomical themes. Both research and clinical aspects will be studied and these will be underpinned by a practical session in the dissecting room. The practical session aims to reinforce the student’s anatomical knowledge in preparation for the research and clinical lectures.

Each week students will study one of the following themes; upper limb, lower limb, thorax, abdomen and head & neck. The week will consist of three 1 hour sessions as stated below:

1. Practical session covering the anatomy of the relevant theme 2. Research lecture highlighting current studies in the relevant area (please note that anatomical

research tends to have a clinical basis) 3. Clinical lecture highlighting clinical aspects associated with the relevant anatomy

Assessment - 2 hour written examination (100%): Section A: 4 short answer questions (40%), Section B: 1 essay (1 from a choice of 3) (60%)

Feedback - Ongoing informal feedback given during weekly dissection room sessions and on blackboard.

Prerequisites - BIOL10811 (essential); BIOL20711 (essential); Human Anatomy RSM (recommended) or years 1 & 2 M.B & Ch.B

Recommended Reading • Snell, R.S. Clinical Anatomy by Regions (8th Edition) Lippincott, 2008 Williams & Wilkins • Moore & Dalley Clinically Orientated Anatomy, 5th edition, 2007 Lippincott, Williams & Wilkins

Teaching Staff - Dr Bip Choudhury and Dr Niggy Gouldsborough; plus a selection of invited lecturers

BACTERIAL INFECTIONS OF MAN BIOL30342 Unit Coordinator(s): Professor Ian Roberts ([email protected])


Aims The aim of this unit is to provide students with an in depth, up to date understanding of the molecular biology of bacterial infections of man. Specifically, the mechanisms by which bacteria are able to colonise and establish infections will be addressed as well the bacteria/host interactions that subvert/modify the ability of the host to respond to infections. These processes will be illustrated by studying selected infections in details that will serve as paradigms to illustrate the principles of microbe/host interactions.


To understand in detail: • The mechanisms by which pathogens colonise and subsequently establish invasive infections

of man • The strategies used by bacteria to circumvent host defences by modification of the host's

cellular physiology • The role of bacterial products (such as exotoxins, endotoxin, teichoic acid, peptidoglycan) in the

pathology of selected diseases including-cholera, diptheria, tetanus & botulism • The mechanisms used by pathogens to survival inside host-cells • The impact of genomics on the treatment and prevention of bacterial infections • The epidemiology of infectious diseases and public health • The problem of multiple antibiotic resistance and nosocomial infections

Lecture Content • Introduction to the concepts of infectious diseases. • Bacterial attachment-the first step in any infection The detailed molecular mechanisms by

which bacteria adhere to and colonise host epithelial surfaces. Urinary tract infections and STD will be used as paradigms.

• Survival strategies in the host-resistance to host defences. The role of the cell surface in conferring resistance to host defences

• Survival strategies in the host-acquisition of nutrients. The ability of bacteria to acquire nutrients in hostile environments, with an emphasis on Fe uptake.

• Survival strategies in the host-intracellular survival The ability of bacteria such as Listeria and Salmonella to survive inside host cells.

• Communication between pathogens and the host-subversion of cellular physiology. The ability of bacteria to inject effector molecules directly into epithelial cells and thereby alter their response to pathogens will be discussed with emphasis on Yersinia and Salmonella infections.

• The impact of genomics on the treatment and prevention of bacterial infections. • Epidemiology of infectious diseases & public health. The spread of disease & the acquisition of antibiotic

resistance will be described with an emphasis on nosocomial infections. • The use of pathogens as bio-warfare agents.

Assessment - 2 hour written examination (90%) and a 10 minute oral presentation on a selected topic related to the course (10%).

Feedback. The students will receive feedback on their oral presentations both in terms of the content and the presentational skills.

Prerequisites - BIOL20461 (Recommended)

Recommended Reading • Salyers A, Whitt D Bacterial Pathogenesis : A Molecular approach (2nd ed.) 2001 ASM Press

Teaching Staff - Dr Jen Cavet; Professor Sarah O'Brien; Professor Ian Roberts

ADVANCED BEHAVIOURAL NEUROBIOLOGY BIOL30351 Unit Coordinator(s): Dr Hugh Piggins ([email protected])


Aims The main purpose of this unit is to provide students with an advanced overview of the neural mechanisms of behaviour in many species. The course will use examples from model organisms to demonstrate the divergence and convergence in the evolution of neural systems underpinning behaviour.

Intended Learning Outcomes Through a combination of lectures and self-directed learning, students will be able to critically evaluate major current studies on the neural basis of behaviour across a range of species. By the end of the course, the students will have knowledge of the key problems and leading researchers in behavioural neurobiology.

Lecture Content Theme A: Reinforcement, motivation, and addiction

• Rodent models of substance abuse • Invertebrate models of substance abuse

Theme B: Sensory Strategies, (sensory filtering and communication) • What is communication? • Auditory communication in insects, frogs and bats • Echolocation in mammals • Circuits in the avian brain for production and learning of song

Theme C: Sleep and Arousal • Sleep - what is it? • Neural basis of sleep and arousal I: brainstem and thalamic mechanisms • Neural basis of sleep and arousal II: hypothalamic circuits • Sleep and arousal in non-mammalian species: invertebrates to vertebrates

Theme D: Orienting to space • Simple (kinesis vs taxis) • Complex (migration, allocentric vs egocentric spatial representation) • Visual cues - sun, stars, landmarks, route-following • Magnetic cues - earth’s magnetic field • Chemical cues - olfaction in fish migration • Electrical cues - electrolocation in fish

Theme E: Learning and Cognition • Recording electrical rhythms from large populations of neurons • The importance of synchronized electrical rhythms to cognition • Neural bases for navigation and route learning in mammals • Neuromodulation of memory • Sleep and memory consolidation

Assessment - Essay-based written examination - answer to 2 out of 4 questions.

Feedback - learning modules; Bulletin Board; post-exam guidance.


Recommended Reading • Alcock J Animal Behaviour: An Evolutionary Approach (7th edition) 2001 Sinauer Associates • Carew T J Behavioral Neurobiology: The cellular organization of natural behavior 2001

Sinauer Associates • Kandel ER, Schwartz JH & Jessel TM Principles of Neural Science (4th edition) 2000

McGraw-Hill

Teaching Staff - Dr Enrico Bracci; Dr John Gigg; Dr Hugh Piggins

CARDIOVASCULAR SYSTEM IN HEALTH & DISEASE BIOL30362 Unit Coordinator(s): Dr Nick Ashton ([email protected])


Aims To provide an understanding of the normal physiology of the cardiovascular system and the mechanisms underlying its major pathologies.

Intended Learning Outcomes Students will have gained an understanding of (i) the complex control processes which regulate the cardiovascular system in health and disease and (ii) the major diseases of the cardiovascular system, including heart failure, stroke and hypertension.

Lecture Content

Introduction to Unit • Overview of cardiovascular system

Electrophysiology of the heart • Cardiac action potential • Excitation-contraction coupling • Cardiac inotropy • Heart failure, ageing and arrhythmias • Ventricular hypertrophy

Blood vessels • Control of vascular tone • Atherosclerosis – pathology & clinical approaches to treatment

Hypertension • Epidemiology, risk factors and socio-economic costs of hypertension • Secondary hypertension - renal, adrenal and other rare forms of hypertension • Primary hypertension - vascular hypertrophy, the kidneys & the renin-angiotensin system • Developmental origins of cardiovascular disease

Stroke • Cerebral ischaemia and neuronal death

Assessment 2 hour examination (100%).

Feedback Feedback will be provided verbally in lectures, in response to email enquiries and via comments posted on the bulletin board for the unit.

Prerequisites BIOL10811 (Strongly Recommended); BIOL20122 (Recommended), BIOL20802 (Recommended)

Recommended Reading Review and primary research papers will be recommended by individual lectures. The following textbooks will provide helpful background material.

• Katz A.M., Physiology of the Heart, 2005, Lippincott Williams & Wilkins • Swales, J.D., Manual of Hypertension, 1995, Blackwell Science

Teaching Staff - Dr Stuart Allan; Dr Nick Ashton; Dr Cathy Holt; Dr Andrew Trafford; Dr Luigi Venetucci; Professor Arthur Weston

CELL ADHESION: THE MOLECULAR BIOLOGY OF CELL-MATRIX AND CELL-CELL INTERACTIONS

BIOL30371

Unit Coordinator(s): Professor Charles Streuli ([email protected])


Aims Cell adhesion is critical for all aspects of cell function in multicellular organisms. Cell interactions with the extracellular matrix and with each other are required for building patterned tissues, maintaining their architecture, and regulating their differentiation and behaviour. Alterations in normal adhesion mechanisms are also central in the progression of many of the major diseases affecting mankind, including inflammation and cancer. The aim of this unit is to consider the molecular details of how different classes of adhesion receptors work, to explore established concepts (as well as the latest advances) of how they control basic cellular functions, and to examine what happens when adhesion systems become defective.

Intended Learning Outcomes Students should acquire a detailed understanding of: the molecular biology of cell adhesion systems; how adhesion links to cell migration, proliferation, apoptosis, differentiation, and to development; how these controls break down in disease.

Lecture Content

Introduction: Adhesion in cell function, development, tissue maintenance and differentiation, regeneration and wound healing.

The key adhesion components and how they work at th e molecular level: Structure and function of extracellular matrix proteins, integrins, and transmembrane proteoglycans; integrin activation mechanisms; formation of adhesion complexes and how they transmit intracellular signals; composition of cell-cell adhesion complexes.

Adhesion and cell migration: Integrin-directed organisation of the cytoskeleton; matrix deposition and remodelling in cell migration; wound healing; adhesion in directed cell migration, eg neural crest, leukocytes, axon guidance; cancer metastasis.

Cell-matrix interactions in cell and tissue functio n: How adhesion receptors signal to control cell cycle, apoptosis, and differentiation; molecular mechanism of adhesion at muscle and skin attachment sites; integrins in platelet activation and T-cell function; diseases to illustrate the importance of adhesion to extracellular matrix in cell regulation, eg skin and inflammatory disorders, cancer.

Cell-cell interactions in cell and tissue function: Molecular mechanisms of how cell-cell adhesion is mediated; adhesion junctions as sites for controlling transcription, eg wnt-catenin signalling; intercellular ligand-receptor systems in tissue patterning; neuronal and immunological synapses; diseases to illustrate the importance of intercellular adhesion in cell behaviour, eg hearing and immune defects, cancer.



Prerequisites - A solid grounding in cell & molecular biology at the 2nd year level will be an advantage

Recommended Reading • Lodish, H. et al., Molecular Cell Biology (6th edition), 2007, Freeman • Lewin, B. et al. Cells, 2007, Jones & Bartlett • Alberts, B. et al., Molecular Biology of the Cell (5th edition), 2008, Garland

Teaching Staff - Dr Andrew Gilmore; Professor Martin Humphries; Dr Andreas Prokop; Professor Charles Streuli

CHANNELS & TRANSPORTERS: MOLECULE TO FUNCTION

BIOL30381

Unit Coordinator(s): Dr Liz Fitzgerald ([email protected])


Aims Ion channels and transporters are ubiquitous membrane proteins that transport ions and other small molecules in cells. They are crucial to cellular definition and function. This unit will explore how these proteins are studied, explain their structural diversity and illustrate their importance in electrically active and non-electrically active cells.

Intended Learning Outcomes The student should understand how ion channels and transporters are assembled into unique complexes and control functional niches. The student will have developed transferable skills in evaluating published material, information gathering, communication and problem solving.

Lecture Content

Ion channels and transporters - Introduction - the advanced principles of ion (Ca2+, Cl-, Na+ and K+) and solute transport through these proteins and the techniques that are used to study them; from electrophysiology to informatics. The general structures and properties of these proteins will be described.

Ion Channel Trafficking - The advanced principles of ion channel biosynthesis, assembly, trafficking, degradation and targeting/distribution will be described using voltage-gated K+ and Ca2+ channels as examples.

Voltage-gated ion channels - A description of basic structures of membrane potential sensitive channels will be exemplified by a review of voltage-gated Ca2+ and K+ channels. Their roles in controlling cell function will be addressed by specifying examples in neuronal, cardiovascular and endocrine cells.

Ligand-gated ion channels - Ligand-gated channels are key proteins in the conversion of chemical signals into immediate responses. The families of ligand-gated channels will be reviewed and their roles and pharmacological regulation discussed.

Transporters and aquaporins - The structures, functions and regulation of acid-base transporters, solute transporters and aquaporins will be addressed through specific examples of physiological systems. The co-operative interactions of channels and transporters in epithelial ion transport will be evaluated at an advanced level.

Feedback - Verbal feedback during lectures


Prerequisites - BIOL10832 (Strongly Recommended); BIOL20122 (Strongly Recommended)

Recommended Reading Specific references for individual lectures will also be recommended by the lecturers.

• Ashcroft, FM Ion Channels and Disease 2003 Academic Press • Alberts B, Johnson A, Lewis J, Raff M, Roberts K & Walter P Molecular Biology of the Cell (4th

edition) 2002 Taylor & Francis

Teaching Staff - Professor Mark Dunne; Dr Gillian Edwards; Dr Liz Fitzgerald; Dr Owen Jones; Dr Richard Prince; Dr Craig P Smith; Dr Martin Steward; Professor Arthur Weston; Dr Paulo Tamarro

CHEMICAL COMMUNICATION IN ANIMALS BIOL30401 Unit Coordinator(s): Dr Matthew Cobb ([email protected])


Aims To study the mechanisms, functions and consequences of chemical communication in a range of animals in order to provide students with a full understanding of this fundamental mode of communication, with particular emphasis on a critical understanding of the primary research literature.


1. understand the key concepts underlying the detection and processing of chemical signals in a range of biological systems - from receptor cell biology to the function of insect societies

2. be able to critically evaluate published research 3. have developed their ability to discuss research in both oral and written form

Lecture Content The unit combines three forms of teaching; traditional lectures, three seminar-style discussions of research papers and a "virtual seminar" in which students have to contribute via Blackboard to a discussion of a research paper. The unit will cover five key aspects:

Peripheral processing: Chemical signals and their receptors. Processes that take place external to the cell membrane, at the membrane and within the receptor leading to the response of the receptor neuron. Receptor structure, receptor-ligand relations, the number of receptor molecule types per receptor neutron, and the distribution and phylogeny of receptor genes. Smell vs Taste. Recent discoveries that challenge the accepted view of chemo-receptors as G-protein coupled receptors.

Central Processing: How does the brain form a molecular "image" of an odour, a taste or a pheromone? We will examine and contrast the two major approaches: combinatorial models vs synchronic neuronal activity. Examples will be taken from a range of model organisms (C.elegans, Drosophila, locust, rodents).

Pheromones: Sex, aggregation and social pheromones in invertebrate and vertebrate systems, including humans. Emphasis will be put on the biological context in which these pheromones function, and the way in which they may have evolved. The key example of social insects will be the focus of a separate lecture.

Chemical ecology: The role of chemical communication within and between species. Striking examples of inter-specific communication will be discussed, as will the effect of chemical communication on phenotypic plasticity in a number of species.

Modelling the nose: "Electronic noses" and the various approaches used in developing artificial sensors and sensory networks. The way in which these systems mimic organic systems and the insight artificial detection and processing systems can provide for models of animal communication.

Assessment 1 hour 30 min examination (60%) and 2000-word extended essay to be handed in during the course (36%). There will also be compulsory participation in an online discussion of a research paper (4%).

Feedback – Seminars (face-to-face and electronic), marked essay


Recommended Reading • Wyatt TD Pheromones and Animal Behaviour 2003 Cambridge University Press • Bradbury J W, Vehrencamp S L Principles of animal communication 1998 Sinauer Associates

Teaching Staff - Dr Matthew Cobb; Dr Krishna Persaud

CLINICAL ENDOCRINOLOGY BIOL30441 Unit Coordinator(s): Dr Donald Ward ([email protected])


Aims To gain an understanding of the principal diseases of the human endocrine system, and the advances that cellular and molecular techniques have facilitated in diagnosing and managing such conditions.

Intended Learning Outcomes To have:

• an appreciation of the defects in molecular and cellular processes and control mechanisms that underlie the development and progression of endocrine disease;

• an awareness of current strategies for surgical, pharmacological and molecular intervention in the clinical management of endocrine malfunction.

Lecture Content • The principal pathologies of the pituitary gland and their molecular basis; the clinical and

surgical management of pituitary tumours. • Growth hormone and prolactin; the molecular basis of peptide production, secretion and

actions. The biology and physiological role(s) of Growth Hormone: interaction with the IGF-I axis.

• Disorders of growth hormone action; the clinical role of growth hormone replacement therapy. Disorders in the control of IGF bioavailability, & their clinical consequences.

• Thyroid adenomas and carcinogenesis: underlying mechanisms, diagnosis & management. • Thyroid hyperplasia and goiter – diagnosis and management. • Autoimmune thyroid disease – Graves’ Disease and Hashimoto’s thyroiditis. • Clinical consequences and management of diabetes mellitus and hyperinsulinism of infancy. • Endocrine control of extracellular calcium homeostasis: PTH, vitamin D3 and calcitonin:

production, roles and control. • Receptors for PTH, Ca2+ and 1,25(OH)2 vitamin D3. Proteins involved in calcium homeostasis:

Ca2+ channels, exchangers and pumps and FGF23/klotho. • Clinical abnormalities of calcium metabolism: Hyperparathyroidism, hypoparathyroidism,

osteoporosis, rickets, mutations of the calcium receptor and PTH receptor, Paget's disease. • Pituitary-adrenal control; laboratory and clinical investigations. • The principal diseases and disorders of the pituitary-adrenal axis – underlying causes. The

diagnosis and management of adrenal pathologies. • Disorders of glucocorticoid signalling; their consequences, diagnosis & management • CLINICAL CASE PRESENTATION: the interactive roles of the patient, clinician and clinical

biochemist in the clinical diagnosis and management of an endocrine disorder.



Feedback - Via Bulletin Board and ad-hoc contact with unit Lecturers

Recommended Reading Directed reading (examinable) to be assigned in the areas of thyroid, pituitary, GH/IGF axis, adrenal, diabetes mellitus and calcium homeostasis.

Teaching Staff - Dr Steve Bidey; Dr Karen Cosgrove; Professor Julian Davis; Professor David Ray; Dr Donald Ward; Dr Melissa Westwood; Dr Andrew Whatmore; Professor Anne White

CLINICAL GENETICS BIOL30452 Unit Coordinator(s): Dr Tao Wang (Tao.Wang@manchest er.ac.uk) Semester 2

Credits 10

Aims

To study the roles of genes in human disease, and the use of genetic techniques in clinical research and management of families. To examine how DNA sequence changes cause inherited diseases and cancer (molecular pathology), the strategies for molecular diagnosis, and the issues in population genetic screening.


Students should appreciate the nature and general causes of three categories of genetic conditions: Mendelian, chromosomal and multifactorial. They should have an understanding of how loss-of-function and gain-of-function mutations cause Mendelian diseases and cancer; of the general types of DNA sequence change that can lead to such loss or gain of function of a gene; and of how such changes can be detected in the laboratory. Students should appreciate the issues involved in translating this scientific knowledge into diagnostic and population screening services, and the roles of clinicians and counsellors in the process. This unit will not involve any contact with patients.

Lecture Content • The overall impact of genetic diseases • Genetic laboratory diagnosis: methods for detecting mutations, direct testing and gene

tracking • Molecular pathology of selected diseases, e.g. Duchenne and Becker muscular dystrophy,

collagen diseases. • Unstable expanding nucleotide repeats and their role in genetic disease • Cancer genetics • Polygenic and oligogenic disease • Diseases caused by chromosomal abnormalities • Epigenetic effects and genetic imprinting • Issues in population genetic screening • Estimating genetic risks (Mendelian risks, empiric risks) • The role of the clinician in genetics • The aims and process of genetic counselling • Gene therapy

Feedback Topic-related questions in various forms will be discussed during some of the lectures and verbal feedback will be provided.

Assessment 2 hour examination (100%)

Prerequisites No formal prerequisites, but students who have not covered basic human genetics and basic DNA techniques in another course will need to do some extra reading.

Recommended Reading • Read, A & Donnai, D New Clinical Genetics 2007 Scion Publishing • Strachan T & Read A P Human Molecular Genetics (3rd edition) 2003 Bios Scientific

Publishers

Teaching Staff Dr Yvonne Alexander, Dr Brian Bigger, Ms Lauren Kerzin-Storrar, Dr William Newman, Dr May Tassabehji, Prof Dorothy Trump, Dr Gillian Wallis, Dr Tao Wang, Dr Michelle Webb

CONTROL OF CELL DIVISION BIOL30471 Unit Coordinator(s): Professor Andrew Sharrocks ([email protected])


Aims

The aim of the unit is to provide an insight into the complex and highly co-ordinated events that result in the correct duplication of a cell. Students will be introduced to the different experimental approaches used to study these events and will learn why correct control of the cell division cycle is essential for preventing the formation of cancers in mammalian cells.


To understand the molecular mechanisms controlling cell cycle progression and how directionality can be imposed upon an otherwise fully reversible set of complex biochemical reactions. Students will appreciate how internal and external factors can disturb the normal cell cycle, the mechanisms that cells have developed to deal with such disturbances and how inability to deal with disturbances can lead to diseases such as cancer. Finally, they will recognise how these key questions have been addressed using genetic, biochemical and molecular approaches in different model systems to give a unified view of highly complex biological process.

Lecture Content

• Background, conceptual problems, approaches to studying the cell division cycle • The G2/M transition; genetic and biochemical analysis, phosphorylation and proteolysis • Mitosis; structural rearrangements, microtubule structure, dynamics and function, kinetochores,

MAPS, motor proteins, phosphorylation cascades and proteolysis, cohesins, spindle checkpoint

• START; controls acting at START, identification of START, regulation of START • DNA replication; ARS binding proteins, ORC components and function, co-ordination with

mitosis, dependency • Checkpoints; DNA synthesis and DNA damage checkpoints, detectors, transducers, effectors • Cancer and the cell cycle

The course will consist of 15 lectures interspersed with 3 'journal clubs'. In these sessions groups of students will be given a research article and asked to give a presentation to their peers. In the presentation they will summarise the context in which the paper was written, the methodology of the paper the finding of the paper and lead a general discussion about research.



Prerequisites - BIOL10232 (Compulsory); BIOL20141 (Recommended); BIOL20161 (Recommended)

Recommended Reading • Morgan, DO The Cell Cycle 2007 New Science Press Ltd • Hunt T, Murray A An Introduction to the Cell Cycle 1993 Oxford University Press

Teaching Staff - Dr David Hughes; Dr Janni Petersen; Professor Andrew Sharrocks

POST-GENOME BIOLOGY BIOL30491 Unit Coordinator(s): Dr Simon Hubbard ([email protected])


Aims Well over 400 completed genome sequences are now available for the biologist to study. So what exactly can we learn from them, and how do we do it? The aim of this unit is to introduce you to the fast moving world of post-genome science, which involves bioinformatics, functional genomics, transcriptomics, proteomics, structural biology and systems biology - key concepts in these disciplines and show how they can be used to address the latest biological research questions.

Intended Learning Outcomes A knowledge of the application of bioinformatics methods to genome sequencing and (comparative) analysis, transcriptomics, proteomics and systems biology, as well as function prediction and protein structure. The self-directed learning will help develop critical analysis in these areas – reviewing the latest developments in the field.

Lecture Content Teaching will be by a mixture of lectures (18 hours), seminars and self-directed learning (4-6 hours).

Genomics: Basic strategies for genome sequencing and bioinformatic requirements. Taking case studies from the current literature, topics will include:

• Gene prediction methodologies • Genome Annotation strategies • Comparative genomics

Transcriptomics: This section will focus on the challenges of capturing, interpreting and exploiting microarray data. Case studies will be taken from existing research projects.

• Transcriptome platforms (Affymetrix, 2 colour etc.) and basic theory. • Data analysis of microarray experiments • Applications in gene function discovery and cancer diagnostics

Proteomics: An overview of proteomic methods including bioinformatics, which will cover:

• Mass spectrometry-based protein and peptide identification • Applications in target discovery and protein:protein interactions

Systems biology: An introduction to this expanding area, which integrates transcriptomics, proteomics and metabolomics and generates predictive models of biological pathways.

Structure and Function: This section will provide an overview of methods in prediction of biological function and structure. Topics covered will include:

• Prediction of protein function from sequence and structure • Predicting protein structure and functional properties

Feedback - This is provided in the self-directed learning and seminars. You are given key research articles to read and present to your colleagues. These reinforce major themes in the unit. You will receive direct feedback on your knowledge of the field from staff and your colleagues.

Assessment - 2 hour essay-style examination (100%). Answer 2 from 5.

Prerequisites - None – although this unit builds on the bioinformatics practicals in the 2nd year LSMs

Teaching Staff - Dr Casey Bergman; Professor Andrew Doig; Dr Simon Hubbard; Dr Simon Lovell; Dr. Jean-Marc Schwartz, Dr Jim Warwicker

EVOLUTION OF ANIMAL BEHAVIOUR BIOL30501 Unit Coordinator(s): Dr Matthew Cobb ([email protected])


Aims To introduce students to concepts and approaches used in the modern study of the evolution of animal behaviour. Topics will focus around the adaptive value of animal behaviour, and the genetic influences and types of selection acting on behaviour. A second aim is to expose students to current literature in animal behaviour and to develop the ability to evaluate the revelant primary literature critically. This will be done through seminars, both on-line (Blackboard) and face-to-face

Intended Learning Outcomes • Develop reasoning skills. • Critically evaluate approaches to studying animal behaviour. • Evaluate the value of animal behaviour research. • Learn to evaluate published research critically. • Develop verbal skills and ability to discuss research.

Lecture Content Traditional lectures are combined with assigned reading and discussions of published research papers.

To include topics such as: • Researching animal behaviour; thinking about animal behaviour research. • The nature/nurture debate. • Learning. • Consciousness and morality • Behaviour genetics. • Animal communication. • Reproduction. • Sexual selection. • Parental care. • Social behaviour.

All topics will be accompanied by a discussion of a current research paper in the field.

Assessment 1 hour 30 min examination (60%) and 2000-word extended essay to be handed in during the course (36%). There will also be compulsory participation in an online discussion of a research paper (4%).


Feedback - This will be provided through the seminars, both on-line and face-to-face

Recommended Reading • Alcock, J Animal Behaviour: An Evolutionary Approach (8th or 7th edition) Sinauer Associates

Teaching Staff - Dr Matthew Cobb; Dr Reinmar Hager

HORMONES AND BEHAVIOUR IN ANIMALS BIOL30541 Unit Coordinator(s): Professor Andrew Loudon ([email protected])


Aims

To introduce students to the subject of behavioural endocrinology and neuroendocrinology, focussing on mechanisms driving complex behaviours, including substrates, genes and neural pathways. Themes include sexual behaviour and aggression, fidelity monogamy and polygamy, maternal behaviour and offspring recognition, stress and memory systems. Examples will be drawn from across the animal kingdom, including man. Contributions from clinical scientists at Manchester will also elucidate the relevance of these systems to man.


Students should understand: • Brain structures involved in regulation of mammalian behaviour; • Mechanisms of action of hormones and their metabolism at target sites; • The role of genetics and evolution in driving behavioural mechanisms in mammals • Implications for the study of behaviour in man and primates

Lecture Content Introduction: Principles of hormone action and neuroendocrine pathways. Steroids and peptide hormones and mechanisms of action. Anatomy of the hypothalamus and ancient control centres.

Sexual Behaviour: Sexual differentiation of the brain and action of sex steroids. Central control of sexual behaviour and role of GnRH. The endocrinology of love and pair bonding, monogamy and polygyny. Secondary sexual characteristics and their hormonal control.

Parental behaviour, developmental and environmental control of behaviour: Parent-offspring behaviour in mammals: behavioural imprinting and role of hormones. Pre and post-natal programming influences on behaviour – hormonal mechanisms. Opioids, reward behaviours, tolerance and dependence.

Social Behaviour: Vasopressin/oxytocin and the central regulation of social behaviour. Eusocial mammals: the case of the naked mole rat. Social rank, status and its hormonal control in primates and other mammals.

Aggressive and violent behaviour: The trouble with testosterone – mechanisms of action and aromatization. Genetic models for studies of aggressive behaviour. Genomic imprinting in man. Anabolic steroids: use and abuse and secondary effects on behaviour.

The behavioural biology of stress: Stress pathways in the brain. Effects of stress hormones on learning and memory.


Feedback - Feedback will be via use of Blackboard & a question/answer session.

Prerequisites - BIOL20421 (Recommended); BIOL20811 (Recommended)

Recommended Reading • Breedlove, M, Crews, D, McCarthy, M.M, Becker, J.B Behavioural Endocrinology (2nd Edition)

2002 MIT Press

Teaching Staff - Professor Andrew Loudon

HUMAN REPRODUCTIVE BIOLOGY BIOL30551 Unit Coordinator(s): Professor John Aplin ([email protected])


Aims This is an integrative biology unit open to students from a wide range of backgrounds. Man has acquired the knowledge to manipulate reproduction, and environmental and social changes may have an incidental impact on fertility. The unit explores recent discoveries about how reproduction is controlled in males and females, how it is affected by disease and how reproductive processes can be changed by medical and pharmacological intervention. In addition it examines recent findings that indicate an important relationship between events in fetal life and health in the adult.

Intended Learning Outcomes Through the lecture course and guided outside reading, students will gain a broad knowledge of human reproduction and its associated technologies. This will include an understanding of steroid hormone receptors and how steroids act to control the reproductive cycle. Students will appreciate the mechanisms of action of steroidal and other contraceptives. They will have a broad knowledge of the biology of human pregnancy including the pre-implantation embryo, implantation, placental function and parturition. They will gain some knowledge of how imaging techniques can reveal embryonic and fetal growth. They will understand selected drug actions and applications in assisted reproduction and pregnancy. They will gain an appreciation of the technologies associated with assisted reproduction and reproductive cloning and some insight into the future uses to which these developing technologies may be put.

Lecture Content

Reproductive hormones and receptors: the menstrual cycle, steroids and their receptors, contraception.

Fertilisation, assisted reproduction and the embryo : spermatogenesis, fertilisation and IVF, pre-implantation development.

Embryo cloning: the biology, technology and impact of cloning.

Early pregnancy: implantation, imaging, placental development, ectopic pregnancy, miscarriage.

Pregnancy and parturition: placental transport, fetal growth and nutrition, vascular tone in the uterus, endocrine signals for parturition, pre-eclampsia and fetal growth restriction.

Fetal programming : how fetal growth and development programmes metabolism and influences disease risk in adults.




Recommended Reading • Johnson M Essential Reproduction (6th edition) 2007 Blackwell Science • Knobil E and Neill J D (eds) Encyclopaedia of Reproduction 1998 Academic Press • Knobil E & Neill J The Physiology of Reproduction (2nd edition) 1994 Raven Press • Jones R Human Reproductive Biology (2nd edition) 1991 Academic Press

Teaching Staff - Professor John Aplin; Dr Rebecca Jones; Dr Sue Kimber; Dr Clare Tower; Dr Melissa Westwood

CHANNELS & TRANSPORTERS: HEALTH & DISEASE BIOL30561 Unit Coordinator(s): Dr Gillian Edwards ([email protected])


Aims Ion channels and transporters have important roles in the control of cellular activity. This unit aims to acquaint students both with drugs which selectively target these proteins (and their therapeutic potential) and also with clinical conditions (such as deafness or diabetes) which occur when ion channels and transporters malfunction (e.g. due to genetic defects).

Intended Learning Outcomes The student should understand how drugs may influence the activity of ion channels and transporters and the physiological consequences of this; the student will have developed skills in information gathering and evaluation of published material.

Lecture Content

Pharmacology of plasmalemmal potassium and calcium channels: Site of action and physiological effects of drugs which modify the selective modulation (ie. stimulating opening or inhibiting) of specific potassium or calcium channels the therapeutic use/potential of such drugs. Cardiac ion channels: Following an overview of the ion channels and transporters involved in the cardiac action potential, the benefits and hazards of modifying their activity will be highlighted. Channels involved in signalling: Both the role of intracellular calcium channels (inositol trisphosphate and ryanodine receptors) involved in the release of calcium from intracellular stores and the mechanisms for refilling the stores will be described. The concept of channels as sensors for pH, temperature, taste or mechanical stress will be introduced. Crosstalk involving ion channels and transporters: The importance of crosstalk between vascular endothelial cells and smooth muscle which plays a role in the regulation of vessel tone and which involves potassium channels, gap junctions and Na+/K+-ATPase will be described. This will provide revision of the pharmacology of some channels and transporters already encountered in the module and will demonstrate how channels and transporters interact within cellular microdomains. Anion channels and transporters: physiological role and regulation of channels and transporters involved in the movement of chloride ions across plasma membranes. Therapeutic use/potential of drugs which modify chloride channel activity. Channelopathies: throughout the module, diseases caused by gene mutations which modify ion channel or transporter activity will be described.


Feedback - Verbal feedback during lectures

Prerequisites BIOL10832 (Strongly Recommended); BIOL20122 (Strongly Recommended); BIOL20922 (Compulsory); BIOL20932 (Compulsory); BIOL20942 (Compulsory); BIOL30381 (Compulsory)

Any of the RSM units is compulsory for this unit - i.e. BIOL20922, BIOL 20932 or BIOL20942.

Recommended Reading - All background: specific references for individual lectures will also be recommended by the lecturers.

• Rang HP, Dale MM, Ritter JM & Flower, R Rang & Dale's Pharmacology (6th Edition) 2007 Churchill Livingstone

• Boron, WF & Boulpaep, EL Medical Physiology (2nd edition) 2009 Saunders • Alberts B, Johnson A, Lewis J, Raff M, Roberts K & Walter P Molecular Biology of the Cell (4th

edition) 2002 Taylor & Francis

Teaching Staff - Dr Peter Brown; Dr Jason Bruce; Dr Gillian Edwards; Dr Liz Fitzgerald; Professor Alison Gurney; Dr Paolo Tammaro, Professor Arthur Weston

MOLECULAR BIOLOGY OF CANCER BIOL30582 Unit Coordinator(s): Professor Andrew Sharrocks ([email protected])


Aims To provide students with a general understanding of the molecular events which lead to cancer.


1. have an understanding of the specific molecular events leading to the formation of specific tumours

2. be able to relate the processes of apoptosis, cell cycle and signal transduction to tumorigenesis

3. be acquainted with the latest developments in basic cancer research

Lecture Content Tumour formation

• Overview of lecture course. Introduction to cancer and its molecular causes. Concept of multi-step progression and the multiple-hit hypothesis.

• Introduction to the cellular changes and the stages in cancer progression. • Chemical carcinogenesis and DNA repair • Cell cycle and checkpoints • Mechanisms and detection of genetic instability • Translocations and cancer. • Viruses & cancer. DNA viruses, Retroviruses, tumour suppressor genes & oncogenes. • Predisposition to cancer. e.g. in retinobastomas and breast cancers.

Molecular basis • Tumour suppressor proteins including p53 and RB and relationship to cell cycle • Introduction to MAP kinase signal transduction pathways • Nuclear targets of MAP kinase signal transduction pathways. e.g. c-Fos and c-Jun. • Transcriptional regulation of the c-fos gene. • Relationship to oncogenes and signal transduction pathways. • Other signal transduction pathways and relationship to tumourigenesis. • Apoptosis and its relationship to cancer. • Tissue invasion and metastasis.

Therapies • Cancer cures and possible therapies.

Self-directed learning • Research into specific cancers and identification of specific molecular changes associated with

individual tumours. • Research into the following topics; Telomeres and cancer, Cancer Stem Cell Hypothesis,

Tumour Angiogenesis, additional signalling pathways disrupted in Cancers.




Recommended Reading • Weinberg, RA The Biology of Cancer 2006 Garland Science • Blasco, M (Ed. Pelengaris, S & Khan, M) The Molecular Biology of Cancer 2006 Blackwell

Publishing • Pecorino, L Molecular Biology of Cancer: Mechanisms, Targets, and Therapeutics 2005

Oxford University Press • Macdonald, F., Ford, C.H.J. and Casson, A.G. Molecular Biology of Cancer BIOS

Teaching Staff - Dr Claudia Wellbrock; Professor Andrew Sharrocks; Dr Paul Shore; Professor Charles Streuli

CURRENT TOPICS IN MICROBIOLOGY BIOL30592 Unit Coordinator(s): Dr Nicola High (nicky.high@man chester.ac.uk) Semester 2

Credits 10

Aims

The overall aim of this unit is to provide an insight into the most recent advances in Microbiology. Emphasis will be placed upon the mechanisms used by microorganisms to adapt to changing environmental stimuli and to evade host immune defences during infection. The course will also focus on the most recent techniques such as metagenomics and the generation of artificial microorganisms, pioneered by Craig Venter, and their role in studying bacteria and bacterial ecosystems.


To understand:

• The molecular mechanisms underlying phase and antigenic variation and the role of these processes in immune evasion.

• How bacteria sense and respond to changing host environment conditions encountered during the disease process.

• The role of horizontal gene transfer in the adaptation of microorganisms to ecological niches within the host. .

• The use of modern genomic techniques to advance our understanding of bacteria and bacterial ecosystems.

Lecture Content

• Molecular mechanisms of phase and antigenic variation. • How bacteria sense and respond to changing environmental stimuli • Quorum sensing – density dependent gene regulation; its role in pathogenesis and biofilm

formation. • Horizontal gene transfer in the evolution and adaptation of bacterial pathogens • Advances in genomics: Mining hidden microbial communities and the analysis of the minimum

genomic component required for bacterial life

Assessment

100% examination


Prerequisites

BIOL20141 (Recommended); BIOL20551 (Recommended)

Teaching Staff

Dr Nicola High; Professor Ian Roberts

MOLECULAR TOXICOLOGY BIOL30602 Unit Coordinator(s): Dr Mauro Esposti ([email protected])


Aims

• To appreciate the relevance of poisons and toxins to research, healthcare and society and learn their molecular aspects.

• To understand how chemicals and drugs are, or become toxic to cells, humans and animals.


• To be able to integrate knowledge of biochemistry, cell biology, genetics and pharmacology for understanding the toxicity mechanisms of current and future drugs.

• To form an educated attitude for analysing the complexity of drugs effects and the relationships between toxins and the pathogenesis of important diseases like cancer and neurodegenerative conditions.

Lecture Content

• Overview of poisons and natural toxins and their molecular action • Xenobiotic transformation • The toxicity of common drugs • Mechanism of cell death - focus on stress and drug-induced effects • Mitochondrial toxins and reactive oxygen species (radicals) • Neurotoxins and neurodegenerative diseases • DNA damage, mutation and cancerogenesis • Toxicogenomics • Membrane toxins, anthrax and socio-political aspects of toxicology • Risk assessment • Other areas of toxicology chosen by the students for student-led activities

Assessment

2 hour examination (100%).


Prerequisites

None.

Recommended Reading

A recommended text for basic aspects of toxicology is listed below, however, no textbook covers all aspects of the course – handouts of all lectures will be made available in the intranet and appropriate references provided

• Ling L, Clark R, Erickson T, Trestrail J Toxicology Secrets 2001 Hanley & Belfus, Inc.

Teaching Staff Dr Mauro Esposti; Dr Andrew Gilmore; Professor Ian Kimber

POLLUTION, PLANTS AND ECOSYSTEMS BIOL30631 Unit Coordinator(s): Dr Amanda Bamford ([email protected])


Aims • To survey the main sources of air pollutants, their emissions and concentrations in the

atmosphere. • To promote an understanding of the biological effects of pollutants on plants, agriculture and

ecosystems. • Develop the ability to gather and process information from a wide range of sources, • Read critically and discuss a paper in the field of air pollution. • Encourage independent thinking & an analytical approach to environmental issues

Intended Learning Outcomes Students will have an understanding of the sources and impacts of atmospheric pollutants on terrestrial ecosystems and their biological effects on plants. Students will be able to read critically, appraise and discuss a journal paper in the field of air pollution.

Lecture Content A combination of lectures, videos and discussions will form the basis of this course. Sessions will involve lectures and then an informal session involving a detailed discussion of a journal paper. The critical analysis of papers will play an important role in this course and students will be encouraged to appraise methods and results, interpret data and summarise the scientific content. Occasionally, videos on a particular subject under discussion will be included. Questions addressed will include; what are the main problems affecting the atmosphere today? What is meant by the greenhouse effect? Is the ‘ozone hole’ real? What is ozone pollution? How will agriculture cope with global climate change? What environmental problems result from nitrogen oxide pollution? Subjects covered include:

• Pollutant sources, emission levels and atmospheric concentrations – how much is in our air? • Biological impacts of atmospheric pollutants, such as ozone & nitrogen-containing pollutants,

on vegetation and ecosystems. • Ozone layer thinning, UV-B radiation, and CFCs - causes and biological impacts on plants and

crops. • Global climate change - what is it and how will it affect plants?

Assessment 2 hour written examination (85%) at the end of the semester (consisting of two short essay questions to be selected from a list of 5 topics) and coursework which will consist of a critical review of a paper of students’ choice (15%).

Feedback - Feedback is via coursework, informal question sets, and during discussions in lecture sessions

Prerequisites - None except an interest in pollution issues.

Recommended Reading Journal papers will be the main source of reading for this unit, however, the following texts are recommended for background reading.

• Bell JNB & Treshow M Air pollution and plant life 2002 J. Wiley & sons Ltd. • Wellburn A Air pollution and climate change. The biological impact 1994 Oxford University

Press

Teaching Staff - Dr Amanda Bamford

IMMUNE RESPONSE AND DISEASE BIOL30681 Unit Coordinator(s): Dr Peter Wood ([email protected])


Aims To apply knowledge of basic immunology to the understanding of diseases involving the immune system. Students will be introduced to contemporary approaches to manipulating the immune system which are of relevance to the pharmaceutical and biotechnology industries.

Intended Learning Outcomes To know about various diseases in which the immune system is involved, including allergy, autoimmunity, congenital and acquired immunodeficiency and transplantation. Students should understand how immune responses are normally regulated and how knowledge of this regulation can be utilised to increase, decrease or change the nature of immune responses in the context of disease, vaccination and tumours.

Lecture Content Lectures will be based around the following themes:

Immune related diseases: immunological basis of allergy; autoimmunity; congenital and acquired immunodeficiency, transplantation.

Manipulation of the immune response: immune regulation; manipulation of the immune response using drugs, antibodies and peptides.

Vaccines: conventional and new generation vaccines against infectious agents; tumour vaccines and passive tumour immunotherapy.

Assessment - 2 hour examination (100%).

Feedback - Question and answer session during course.

Prerequisites - BIOL20221 (Strongly Recommended); BIOL30801 (Recommended)

Recommended Reading There are no recommended texts. Students are given a reading list consisting primarily of reviews at the beginning of the module.

Teaching Staff - Dr Peter Wood

ADVANCED IMMUNOLOGY BIOL30801 Unit Coordinator(s): Professor Richard Grencis ([email protected])


Aims The immune system evolved to protect us from infection. The most primitive mechanisms (phagocytes, complement, inflammation) constitute innate immunity and these are magnified and focussed by the more recently evolved adaptive/ acquired immune system (T cell, B cells and antibodies). Knowledge of the immune system has advanced rapidly in the last decade. This unit aims to build on knowledge presented in Introduction to Immunology or in the Preclinical Science course, highlighting the modern view of the immune system.

Intended Learning Outcomes To know about: the cells and molecules of the innate immune system (phagocytes, NK cells, complement, cytokines and non-specific recognition of 'dangerous' foreign material); the genes and molecules of the major histocompatibilty complex and their role in presenting antigen for T cell recognition; the role of T cells and B cells in specific immune response; Tolerance and how the immune response is regulated.

Lecture Content The innate immune system, inflammation, the major histocompatibility complex, MHC molecules, antigen processing and presentation, T cell receptors, development of T cells, molecular events in T cell activation, T cell phenotype and function, antibody genes and molecules, antibody-producing cells, tolerance, immunodeficiencies.


Feedback - Feedback will be provided via an online Blackboard self-assessment module emphasising key concepts from different lectures of the course, highlighting the important facts required for understanding.


Recommended Reading Additional reading material will be recommended by individual lecturers, some of which will be posted on the School teaching intranet.

• DeFranco AL, Locksley RM & Robertson M Immunity. the Immune Response in Infectious & Inflammatory Disease. Primers in Biology (1st edition) 2007 New Science Press Ltd

• Janeway CA, Travers P, Walport M & Shlomchik M Immunobiology: The Immune System in Health & Disease (6th edition) 2004 Churchill Livingstone

• Kuby J, Goldsby RA, Kindt TJ & Osborne BA Immunology (5th edition) 2002 Freeman

Teaching Staff - Professor Richard Grencis; Dr Douglas Millar; Professor Werner Muller; Dr Peter Wood

STEM CELLS BIOL30931 Unit Coordinator(s): Dr Sue Kimber ([email protected])


Aims Stem cells are rare cells with unique potential for both self renewal and differentiation into mature cells of one or more lineages. The ability of stem cells to renew tissues has significant therapeutic potential for the regeneration of damaged tissues such as bone marrow, skin, insulin producing cells and neurones. The aim of this unit is to describe the properties of stem cells and to explain the mechanisms underlying the control of self renewal and specific lineage commitment. Recent reports on common pathways in cancer cells and stem cells will be used to illustrate the current thinking on the close association between stem cells and cancer.

Intended Learning Outcomes Students should have acquired a detailed understanding of the features of both embryonic and adult stem cells, how their activity is assayed, the pathways involved in the intrinsic and extrinsic (environmental) control of their activity and the association between stem cells and cancer. As stem cell biology is a rapidly progressing field, any current “hot” areas in stem cell biology will also be covered.

Lecture Content Lectures, supported by a set problem exercise to encourage student-led learning, will focus on:

Introduction to the stem cell and its niche: description of the concepts underlying the definition of a stem cell, and the stem cell niche. Concept: Stem cells are able to give a lifelong reconstitution through self renewal and differentiation. This may be controlled through the stem cell niche.

Adult stem cells: these lectures will describe the stem cell systems that have been well characterised in adult tissues including epidermis and bone marrow. This will lead into descriptions of more recently defined systems such as the neuronal stem cell.Concept: Tissue specific stem cells are capable of lifetime regeneration of specific lineages.

Embryonic Stem cells: these lectures will describe the origins and use of stem cells derived from embryonic tissue and their potential use for regeneration of various tissues. Areas such as nuclear reprogramming and the signalling pathways that control pluripotency will be covered. Concept: Embryonic stem cells are capable of lifetime regeneration of multiple (all?) tissue types.

Controlling stem cell activity: description of the stem cell niche and the pathways known to control stem cell activity including cytokines, transcription factors, activin, FGF, Notch and Wnt signalling. Concept: Stem cells may be controlled both intrinsically and extrinsically.

Stem cells and cancer: stem cells and cancer cells share many similar features - self renewal/Notch/Wnt pathways. Also there are potential problems with stem cells becoming transformed. Concept: Stem cells and cancer cells are closely related.

Assessment - 2 hour examination (100%). A problem will be set at the end of the course which will aid synoptic learning and revision of course material.


Prerequisites - BIOL10232 (Strongly Recommended) - this unit is strongly recommended as you will need a good grounding in basic cell biology.

Teaching Staff - Dr Martin Baron; Dr Anne-Marie Buckle; Dr Rob Clarke; Dr Sue Kimber

DEVELOPMENTAL NEUROSCIENCE BIOL31031 Unit Coordinator(s): Dr Jaleel Miyan (j.miyan@manch ester.ac.uk) Semester 1

Credits 10

Aims

To introduce students to the principles of nervous system development and to provide an understanding of how different regions of the brain are formed and “wired” together. The focus will be on human but important relevant material from other organisms, in particular Drosophila, will be covered. As well as normal development the unit will cover the outcomes when things go wrong.


Ability to describe the origin and process of development of the central nervous system. Detail the important genes and their roles in the development of the CNS. Describe the process of development of the cerebral cortex with reference to both intrinsic and extrinsic mechanisms and including the role of environmental factors contained in the extracellular space and cerebrospinal fluid. Describe the process of neuronal growth, specifically axonal pathfinding including the role of signalling molecules involved in this. Describe potential mechanisms in abnormal development and their outcomes. Compare and contrast mechanisms of neural development in different organisms. Understand the concept of the stem cell, its role in development and its potential use in therapies.

To be able to address key issues in development of the CNS through literature review and discussion. To integrate information from genetics, developmental biology, neurology and physiology in understanding both normal and abnormal processes of development.

Lecture Content

Lecture 1 - Introduction to CNS and development Lecture 2-3 - Concept of the brain stem cell Lecture 4 – Embryological origins of the CNS Lectures 5-7 - Axon guidance Lecture 8-9 - Neuropile organisation Lecture 8-9 - Development of the visual pathways Lecture 10-12 - Development and organisation of visual pathways Lecture 13-15 – Development of the cerebral cortex Lecture 16-17 -The cerebrospinal fluid system and cortical development Lecture 18 - Overview summary and future prospects

Assessment 2 hour examination, 2 essay questions (100%)

Feedback Feedback is provided via a question and answer session in the final lecture and in response to email queries from students.

Prerequisites None.

Recommended Reading • Wolpert, L Principles of Development (3rd edition) 2006 Oxford University Press • Brodal, P The Central Nervous System (3rd edition) 2004 Oxford University Press

Teaching Staff Dr Anne-Marie Buckle; Dr Nicholas Glossop; Dr Jaleel Miyan; Dr Jon Turner

CONSERVATION BIOLOGY BIOL31042 Unit Coordinator(s): Dr Cathy Walton ([email protected])


Aims

The biodiversity of our planet is increasingly at risk due to the activities of man. This unit aims to provide the conceptual background to enable students to understand the main concerns in the loss of biodiversity and how appropriate conservation strategies could help to ameliorate man’s impact. The theoretical basis of conservation biology is multidisciplinary involving population genetics, ecology, evolution, population biology and systematics. Students will be expected to have some basic knowledge in these areas (see prerequisite recommendations) which will be extended and applied to conservation using a wide range of examples of conservation research and management. Lectures will be interspersed with several Case Studies on a topical subject (e.g. the consequences of the fragmentation of tropical forests in Southeast Asia). For this the students will be given papers to read and the sessions will be run as informal seminars.

Intended Learning Outcomes 1. A rational understanding of the importance of conserving biodiversity & current priorities. 2. A conceptual understanding of the broad base of theory and scientific methodology underlying

conservation biology. 3. An appreciation of the ways in which biodiversity can be conserved by the application of

appropriate management strategies and the problems involved in successful implementation.

Lecture Content

Threats to Biodiversity, Conservation priorities: the effects of man on the environment and biodiversity. Conservation priorities. How is biodiversity quantified? The geographical distribution of biodiversity and biodiversity hotspots. Changes in biodiversity over time. The Problems of Small and Fragmented Populations: loss of genetic diversity and inbreeding depression in small populations. Captive breeding programs and reintroduction. Habitat degradation and restoration. Use of phylogeography and population genetics to assess genetic population structure and to infer gene flow particularly in fragmented populations. The management of wild populations to ameliorate the effects of inappropriate gene flow. Local adaptation of populations and outbreeding depression. Non-environmentally related conservation problems: invasive and exotic species. Hybridisation. Disease (in endangered species and zoonoses in humans). Conservation Management and Sustainable Development : the importance of taxonomy in determining management units and implementing legislature for species protection. The importance of species interactions and the preservation of ecosystems. Restoration ecology. The design, establishment and management of conservation areas. The effectiveness of conservation laws and treaties. Rights of native peoples. Farming and conservation. Ecotourism.

Assessment - Final examination (2 hour short answer and essay style paper) - 75% Coursework based on Case Studies - 25%

Feedback - Feedback is provided during the seminar sessions. Students are asked questions (provided in advance) that relate seminar material to lecture material and also have the opportunity to question lecturers and other students.

Prerequisites - BIOL20412 (Compulsory)

Teaching Staff - Dr Richard Preziosi; Dr Cathy Walton

PROGRAMMING FOR BIOLOGISTS BIOL31051 Unit Coordinator(s): Dr Ingo Schiessl ([email protected])


Aims This course aims to introduce students to basic programming techniques and skills in an environment suitable for laboratory based scientists. To get the students writing their own simple programs within the first week and to encourage them to continue to develop their programming skills after this course is concluded.

Intended Learning Outcomes Students should be able to:

• Demonstrate an understanding of the basics of the MATLAB Programming environment. • Demonstrate how to design a computer program. • Solving of biological problems in a computational environment • Finding and removing errors or bugs in computer code • Graphical display of computation results and brain images. • Apply their knowledge to real lab based experimental problems in the life sciences

Lecture Content The course will introduce students to the most important concepts of computer programming using the MatLab Programming Environment.

Syllabus: • An introduction to MATLAB • MATLAB Basics • Branching Statements and Program Design • Loops • User-Defined Functions • Multidimensional Arrays • Sparse Arrays and Structures • Input/Output Functions • Representation of functional brain imaging data

Assessment Biweekly online blackboard assessment (10%) Written exam (90%) Feedback - Feedback may be given in one or more of a range of methods. Contact Unit Coordinator for further details.


Teaching Staff - Dr Ingo Schiessl

COMPUTATIONAL NEUROSCIENCE BIOL31061 Unit Coordinator(s): Dr Marcelo Montemurro ([email protected])


Aims To introduce students to the discipline of computational neuroscience and to the discipline of neural coding, i.e. how neurons compute and transmit information.

Intended Learning Outcomes Students should be able to:

• Define, describe and understand the main models of neuronal activity. • Define, describe and understand biologically plausible neuronal networks models of brain

function. • Define, describe and understand the main models of neural coding: spike counts, spike timing,

neural synchrony, population coding • Describe and explain the rationale of the main mathematical tools needed to study neural

networks and neural coding • Apply the above mathematical tools to the study of neuronal models • Given experimental neuronal responses, analyze them and formulate a simple hypothesis on

how these neurons transmit information.

Lecture Content The course will introduce students to the most important notions of Computational Neuroscience.

Syllabus: • Neuronal codes: spike trains, firing rates, spike counts, spike times, neural synchrony, cell

assemblies, neuronal population codes • Neuronal models: binary neuron, Integrate-and-Fire neuron, Hodgkin-Huxley neuron. • Biologically plausible neural network models. • Mathematical tools for computational neuroscience: numerical differential equations, spike

train analysis, tuning curves, cross-correlograms, and information theory.

Assessment Written exam (8 short questions plus one essay question)



Teaching Staff - Dr Marcelo Montemurro

COGNITIVE NEUROSCIENCE BIOL31072 Unit Coordinator(s): Dr Ken Grieve (ken.grieve@manc hester.ac.uk) Semester 2

Credits 10

Aims

Cognitive neuroscience is the study of the biological underpinnings of complex cognition - the relationship between the structural and physiological mechanisms of the nervous system and the psychological reality of the mind. This vibrant and exciting field has made major advances in the past few years with the explosion of new methods dependent on computers and brain imaging. The aim of this unit is to guide students through the biological basis of complex cognitive behaviour by covering a variety of topics.


Knowledge of the basis of cognition, in man and lower animals at currently accepted neuroscience level. Deductive reasoning, application of scientific principles in practice. Reasoning and debate.

Lecture Content

The unit will be entirely lecture based. Lectures will cover a range of current cognitive neuroscience topics, from animal models to man, and include discussion of the methods involved. The course will include guided reading of the current scientific literature.

Topics to be covered will include: • Introduction to Cognitive Neuroscience, history • Methods in Cognitive Neuroscience • Perception, and encoding and higher perceptual functions • Attention, • Language, • Decision making • Action • Conciousness (thalamo-cortical loops, neural Darwinism etc) • Diseases of cognition


Feedback Students are encouraged to discuss questions with the individual lecturers, firstly at the end of lecture periods, otherwise by email. The course coordinator also reinforces this route of contact and acts as overall conduit for course feedback on most of the questions raised. Further, the coordinator will, if requested, organise 1 or 2 short seminar/tutorials for small groups of students with particular questions. In the past this has worked well, for example, with intercalating medical students and students returning form industrial placement, but is open to all.

Prerequisites - BIOL20421 (Strongly Recommended); BIOL20572 (Compulsory); BIOL20591 (Compulsory); BIOL20961 (Strongly Recommended)

Recommended Reading - Most of the course is based on published journal papers and review articles, but students are recommended to read appropriate chapters from the listed texts.

• Purves D, Brannon E, Cabeza R & Huettel SA Principles of Cognitive Neuroscience 2008 Sinauer Associates Inc

• Kandel ER, Schwartz JH & Jessel TM Principles of Neural Science (4th edition) 2000 McGraw-Hill

Teaching Staff - Dr John Gigg; Dr Ken Grieve; Dr Ingo Schiessl

IMAGING LIVING SYSTEMS: MOLECULES TO MAN BIOL31101 Unit Coordinator(s): Dr Ingo Schiessl ([email protected])


Aims To provide students with an understanding of how cutting edge imaging methods are used in Medical and Life Science research. Guided by recent publications the students will learn about the type of research that can be addressed with each of the presented imaging techniques. The course will provide an understanding of the nature of the signal as well as spatial and temporal constraints. Starting at the sub-millimetre scale the course will look at imaging techniques to investigate properties and signals of healthy and diseased cells and tissues. From there, with increasing spatial scale, we will look at imaging of anatomical and functional structures in living systems. The course will finish with imaging methods that look at function and metabolism of the whole brain and the human body. The knowledge provided will form an essential foundation to many of the lab based projects that rely on the imaging of living systems.

Intended Learning Outcomes • understand the differences in functional and anatomical imaging approaches. • be able to describe the nature of the signal and how it is detected and measured with each of

the imaging techniques. • understand the spatial and temporal constraints of different imaging techniques. • appreciate the advantages and drawbacks of different imaging techniques. • be able to discuss which of the imaging methods covered in the course are suitable to address

a given research problem.

Lecture Content • Research that addresses the exploration of anatomy and function at a sub-millimetre scale

through the use of imaging methods like confocal-, two photon - and electron microscopy. • Introduction to anatomical and fluorescence markers used with techniques like calcium

imaging. • Investigating the anatomical and functional structure of healthy and diseased tissue using

imaging methods like radiography and computer tomography. • Exploring the nervous system with optical imaging, functional magnetic resonance imaging

(fMRI) and Magnetoencephalography (MEG). • Imaging metabolic activity in the human body with positron emission tomography (PET).

Assessment - 2 hour examination (100%) - essay questions.

Feedback - Time is provided at the end of each lecture for questions and feedback from students. The final session in the semester is a dedicated question and answer session that wraps up all the lectures and gives the opportunity for exam specific feedback.


Recommended Reading The course will utilise review and research papers but the following texts will provide useful background:

• Guy, C & Ffytche, D An Introduction to the Principles of Medical Imaging (Revised Edition) 2005 Imperial College Press

• Hibbs, AR Confocal Microscopy for Biologists 2004 Plenum • Dhawan, AT Medical Image Analysis 2003 John Wiley and Sons Ltd • Toga, M (eds.) Brain Mapping: The Methods 2002 Academic Press

Teaching Staff - Dr Jose Rodriguez Arellano; Dr Ingo Schiessl

GENE REGULATION & DISEASE BIOL31181 Unit Coordinator: Dr Graham Pavitt ([email protected])


Aims To provide understanding of molecular mechanisms underlying a variety of genetic and infectious diseases. This unit will focus on on specific factors with direct roles in the gene regulation pathways-from chromatin structure, histones and mRNA transcription, to mRNA splicing, stability and translation. Examples will also include basic research into fundamental mechanisms of control, including mouse models, where this enables understanding of the molecular processes underlying the diseases described. The module explores both molecular mechanisms and physiological consequences for gene regulation control and disease in animals and Man. This unit is ideal for Biochemistry, Genetics and Molecular Biology students as well as those taking more medically focussed degrees and options (eg Medical Biochemistry, Biomedical Sciences).

Intended Learning Outcomes Students will be able to:-

• Understand the importance of gene regulation for health and disease. • Be familiar with molecular defects underlying specific diseases and the consequences of these

for cells, tissues and the whole animal? • Discuss the molecular techniques used to uncover these mechanisms.

Lecture Content • The lectures will cover aspects of both common multi-factorial disorders that afflict increasing

numbers in the population (diabetes, obesity , cancer) and several specific 'orphan' genetic diseases selected from the increasing range uncovered as well as common infectious viral diseases .

• The consequences of disease mutations for protein-nucleic acid interactions and functions at the molecular level will be coupled with studies of consequences for tissues, organs and the whole animal.

• The latest research findings will reveal the diversity of control mechanisms uncovered and show common themes where they exist.

• Where available, information concerning therapeutic approaches will be described. • A self-directed eLearning module will supplement lecture material.

Assessment 2 hour examination (100%)

Prerequisites BIOL20141 (recommended) Feedback Provided via (i) review lecture and (ii) an email discussion group for teaching staff and students.

Recommended Reading There is no single recommended textbook. Review and primary research journal articles will be the main sources. References will be given in lectures. Teaching Staff Dr Mark Ashe; Dr Catherine Millar; Dr Raymond O'Keefe; Dr Graham Pavitt; Dr Paul Shore

PROTEIN ASSEMBLY, DYNAMICS & FUNCTION BIOL31191 Unit Coordinator(s): Professor Andrew Doig ([email protected])


Aims The unit aims to provide students with an introduction to modern protein science, covering a representative range of high profile, contemporary topics, from folding and assembly through to dynamics and membrane transport.

Intended Learning Outcomes Students will:

• be able to describe how protein folding is studied in vitro; they should also be able to compare protein folding processes in vitro with those in vivo

• be able to cite examples to show how protein dynamics can be measured and how it plays an important role in function (e.g. catalysis)

• be able to cite examples of the assembly of complex multiprotein complexes. • be able to describe the structure and function of at least two macromolecular machines • be able to describe how knowledge of the structures of membrane transporters and ion

channels has led to the current understanding of their mechanisms. • develop the ability to analyse protein structure and demonstrate how it explains biological

function. • develop the ability to analyse protein structures. • develop organisational and presentational skills, to prepare an assessed essay on a topic

relevant to the unit.

Lecture Content

A) Protein folding: • in vitro: including techniques used to study it. Protein folding landscapes and pathways. • in vivo: misfolding and implications for disease (prions): link with Protein Sorting (BIOL30271) and Biochemical Basis of Disease (BIOL30142)

B) Protein dynamics: methods used to study it, including NMR and simulations. Role in protein function.

C) Protein assembly: • chaperones: proteins which help other proteins to fold • assembly of multiprotein complexes e.g. viruses, ribosome

D) Structures of macromolecular machines e.g. F1F0 ATPase, proteasome, flagellum

E) Structures of membrane protein transporters (link to ion channels BIOL30381 & BIOL30561). Sym and Antiporters. ABC transporters. Ion channels.

Assessment 1.5 hour written examination (80%) 6 page (A4) essay on a current topic relevant to the unit (20%)

Prerequisites BIOL10212 (Compulsory); CHEM10021 (Recommended); CHEM10022 (Recommended)

Teaching Staff Professor Andrew Doig

MACROMOLECULAR RECOGNITION IN BIOLOGICAL SYSTEMS

BIOL31241

Unit Coordinator(s): Dr Paul Sims (paul.sims@manche ster.ac.uk) Semester 1 Credits 10

Aims Accurate molecular recognition is the key to biological chemistry - it is, for instance, what sets the enzymes apart from inorganic catalysts. The aim of this unit is to investigate the molecular basis of specificity for a number of biologically important processes involving protein/protein and protein/DNA protein/RNA and RNA/RNA interactions.

Intended Learning Outcomes • To understand the structural basis of protein/protein interactions. • To be able to effectively use basic molecular modelling computer software. • To understand the molecular basis of protein/DNA recognition, the roles of specific and non-

specific interactions and the structural motifs involved. • To understand the structural diversity of RNA and how this relates to diversity of function

through specific interaction with protein or other RNA molecules. • To be able to describe the structural features of RNA, identify them from a secondary structure

diagram and understand how they can be specifically recognised by certain proteins. • To be able to describe and discuss features of RNA that enable it to act catalytically.

Lecture Content

Protein-Protein interactions: protein crystallography methodology and its limitations, examples of protein-protein interactions and use of molecular modelling software as an aid to understanding macromolecular recognition.

Protein-DNA interactions: methodology and general principles, classification of DNA binding motifs and examples of those found in regulatory and catalytic proteins.

RNA recognition and catalysis: structural and functional diversity of RNA, general aspects of RNA recognition, UIA protein and specific recognition of an RNA hairpin, recognition of tRNA, catalytic RNA, ribosome structure and function.

Assessment Coursework - molecular modelling exercise (5%) and 2 hour written examination (95%).

Feedback - Feedback is provided in the modelling exercise and through annotated scripts, which are returned.

Prerequisites - BIOL10212 (Compulsory); BIOL20851 (Compulsory); CHEM10021 (Recommended); CHEM10022 (Recommended)

Recommended Reading No single text book covers the whole of this unit but the listed titles cover specific areas. In addition, lists of key papers will be prepared and distributed by the lecturer responsible for each of the topics.

• R F Gesteland, T R Cech & J F Atkins The RNA World (3rd ed.) 2005 Cold Spring Laboratory Press

• Liljas, A Structural Aspects of Protein Synthesis 2004 World Scientific Books • Neidle, S Nucleic Acid Structure and Recognition 2002 Oxford University Press • Travers A & Buckle M DNA-Protein Interactions: a practical approach 2000 Oxford University

Press • Branden C & Tooze J Introduction to Protein Structure (2nd ed.) 1999 Garland • R F Gesteland, T R Cech & J F Atkins The RNA World (2nd ed.) 1999 Cold Spring Laboratory

Press • Blackburn, G.M. & Gait, M.J. Nucleic Acids in Chemistry and Biology (2nd ed.) 1996 Oxford

University Press • R F Gesteland, T R Cech & J F Atkins The RNA World (1st ed.) 1993 Cold Spring Laboratory Press

Teaching Staff - Dr Johanna Avis; Dr Jeremy Derrick; Dr Paul Sims

CHRONOBIOLOGY BIOL31431 Unit Coordinator(s): Professor Andrew Loudon ([email protected])


Aims To provide an overview of biological timing systems and biological rhythms, their evolution and the implications of biological clocks in matching the behaviour of animals to daily, tidal and seasonal rhythms in the environment. To emphasise current understanding of physiological and molecular process regulating biological rhythms, as well as how chronobiology is relevant to wild organisms and humans. This is one of the fastest moving and exciting areas of biology, and requires integration of knowledge across different species models and cellular/physiological systems.

Intended Learning Outcomes Students should understand:

• The extent of action of biological clocks and circadian times in regulating cellular, physiological and behavioural rhythms in eukaryotic organisms

• The cellular and genetic mechanisms, neuroanatomical structures and circadian pathways of the nervous system

• The biological and medical significance of circadian dysfunction

Lecture Content

Introduction • Properties of biological clocks and rhythms • Basic responses of clocks to environmental stimuli • Measurement and analysis of biological rhythms

Anatomical Location of clocks • Neuroanatomical aspects of the mammalian circadian system • Photic and non-photic entrainment and role of Photoreceptors • Pharmacological manipulations of clocks • Diurnal vs Nocturnal animals

Clock genes • Clock genes and their actions in the cell • Plant and fungal timers • Molecular genetics of clocks, role of photoreceptors and common themes

Adaptive significance of clocks • Sites of action of clocks, cell cycle and the cancer connection (mammals) • Biological time-keeping in other vertebrate groups and insect clocks • Comparative vertebrate neurobiology, evolution of time-keeping structures • Seasonal and annual cycles and their timing, role of melatonin • Hibernation and torpor - life in cold climates and role of clocks • Navigation and migration in birds, insects and fish

Human Clocks • The human circadian systems and chronopharmacology • When the clocks go wrong


Feedback: This will be offered via Blackboard and a question/answer session


Recommended Reading • Dunlap, Loros, DeCoursey (eds) Chronobiology: Biological Timekeeping 2004 Sinauer Press

Teaching Staff - Dr Susan Crosthwaite; Dr Nicholas Glossop; Professor Andrew Loudon; Professor Rob Lucas; Professor Hugh Piggins

final level biol units - by unit number code title biol30111

Documents