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Michaelmas term modules 2013-14

 

M1 Topics in vertebrate evolution

Module organiser: Prof Jenny Clack

The course introduces the history and evolution of non-mammalian vertebrates, emphasising questions that are the subject of current debate and controversy. Palaeontology is the only means of discovering the anatomy and biology of extinct forms and is central to understanding evolutionary patterns, the assembly of extant body plans, and the history of life on earth.

We integrate studies of fossil and living vertebrates to examine major events in evolution. These variously include the relationships of gnathostomes to jawless fishes; the interrelationships of gnathostomes and the evolution of their distinguishing features; the early evolution of tetrapods and the transition to land-dwelling; the origin and radiation of stem tetrapods and amphibians; the diversification of amniotes and the subsequent evolution of the diapsids into lepidosaurs and archosaurs, including dinosaurs and birds. Building on the evolutionary relationships of these groups, we draw implications for their biology in several areas. These include topics such as the origin and development of fins and limbs, the evolution of terrestrial hearing, the evolutionary radiation and biogeography of lizards, and the origin of snakes and turtles, the mechanics of locomotion and feeding among dinosaurs, and the origins of avian biology. Case examples are used to highlight analytical approaches to interpreting fossil data such as morphometrics.

An important component of the course are the demonstration practicals, which give "hands-on" experience of actual fossil material, including some type and figured specimens. Practical and theoretical approaches to systematics including computer-based methods are dealt with.

 

M2 Conservation Science

Module Organiser: Prof Andrew Balmford 

(Inter-departmental Course)

This interdepartmental course, taught by the Departments of Zoology and Plant Sciences, aims to provide an understanding of why wild nature is currently in decline, why this matters, and how biology coupled with other disciplines, can be harnessed to identify potential solutions.

The course begins by explaining the distribution and importance of biodiversity, and the evidence that it is currently being lost. It then examines in detail the immediate threats to wild populations and their habitats, and the underlying drivers of those threats. The final section of lectures explores potential solutions, combining socioeconomic as well as biological insights to take a constructively critical look at approaches ranging from sustainable harvesting and ecosystem restoration to agrienvironment schemes and the marketing of ecosystem services.

Core lectures are supplemented by case studies given by outside experts on policy, economics, and conservation practice. There is also a field trip, a careers session, and a visit to a local conservation organisation.

 

M3 Population biology

Module Organiser: Dr Andrea Manica 

This course aims to provide an integrated understanding of key issues in population biology, spanning population dynamics, population genetics and evolutionary dynamics.

The course begins with six lectures outlining the basic concepts of population dynamics. In particular, Andrea Manica assesses how basic population processes such as competition, predation and parasitism influence the persistence and dynamics of real populations in time and space. Recent theoretical and empirical work on spatial heterogeneity is introduced. The focus of the last 2 lectures is on methods for explaining spatial processes at different scales (notably the metapopulation concept), the effects of spatial dynamics on population persistence and the tradeoff between competition and dispersal-colonization. The next three lectures, given by Colin Russell, further develop the concept of metapopulations with several applications to diseases.

The next six lectures explore two major groups (diseases and plants) that have been the subject of a large body of research in population biology. Derek Smith looks at the ecology and management of diseases in animals and humans. David Coomes provides an overview on plant population dynamics. Plants are a great study system to quantitatively test both simple and complex theories in population biology, and David highlights both successes and short-comings of the current framework.

The next four lectures introduce basic concepts of molecular ecology. After a lecture on the use of genetic markers, Bill Amos describes the application of molecular ecology to analyse the interaction between population genetics and population dynamics in a range of systems.

The final four lectures explore the relationship between population dynamics and tradeoffs in life history traits. Rufus Johnstone introduces basic ideas of co-evolutionary ecology and in particular the application of game theory to explore evolutionary dynamics.

 

M4 Neural mechanisms of behaviour

Module Organiser: Dr Berthold Hedwig

This course examines a central problem in animal biology: how does the nervous system gather information about the environment, process it, and then produce an appropriate behavioural response? The lectures cover most major aspects of this problem and place a strong emphasis on understanding the neural mechanisms underlying behaviour. We cover a very wide range of species and many patterns of behaviour, from the sky-compasses of bees to olfactory learning in mammals. These examples are chosen to illustrate the fundamental organisational principles of neuronal processing. Adaptation of structure to function is analysed at a number of levels of organisation, from protein sequences to the evolution of behaviour. Our approach exploits the unrivalled opportunities that nervous systems offer to relate the proximate molecular and cellular mechanisms of behaviour, to their ultimate function in promoting the fitness of the whole organism.

The first lectures show how an animal's sensory capabilities are linked to its ecology and lifestyle and demonstrate how neural systems are adapted to enlarge behavioural repertoires and optimise performance. We then consider how analyses of the properties of individual nerve cells and their patterns of connection to one another can explain the control of motor patterns and how hearing and auditory processing is adapted to the lifestyle in insects. Next we demonstrate how neuronal systems undergo plasticity, which allows animals to learn from their experiences and adapt their behaviour to changing circumstances. Finally we ask how information from an animal's genes is combined with information from its environment to construct neural circuits that are capable of producing behaviour.

 

M5 Behaviour

Module organiser: Dr Nicholas Mundy

Individual variation is the raw material for evolution. This course examines the evolution of animal behaviour by focusing on how individual differences in behaviour arise.

The classical way to study animal behaviour separates questions concerned with function (what is the adaptive value of the behaviour? what is its evolutionary history?) from those focused on causation (how is the behaviour controlled? how does it develop during a lifetime?). The aim of this course to show that recent research is sweeping aside these traditional distinctions in two different ways:

  • The mechanisms that cause animal behaviour, and the way that it develops, generate the individual variation upon which selection acts. Therefore, we cannot understand the evolution of behaviour without some consideration of the genetics, neurobiology and psychology of the animals involved.
  • At the same, the mechanisms controlling behaviour and its development are themselves subject to natural selection. This means that we can predict the particular mechanisms involved in behavioural development, as well as an animal’s specific cognitive and sensory capacity, from aspects of its ecology.

The first half of the course focuses on the genetic foundations of behaviour. We begin by considering how behaviour develops during a lifetime before examining the evolutionary genetics of behaviour and sensory systems in vertebrates and invertebrates. In the second half of the course, the emphasis is on cognitive and sensory function, with blocks of lectures on sensory ecology and imprinting, early learning and recognition memory. We conclude by considering animal cognition, focusing particularly on natural populations.

 

M6 Cell assembly and interactions

Module Organiser: Dr Howard Baylis

(Inter-departmental Course)

Cells are highly organised and dynamic structures. In this module we will explore how the architecture of the cell is constructed and how cells interact with each other and their environment. Our current knowledge of these vital topics in cell biology will be presented in depth, with a focus on the molecular mechanisms that regulate cell behaviour. In addition to establishing basic cellular mechanisms, we will also examine how cells use these mechanisms in complex activities within organisms such as development and key physiological functions in the adult.

The module will begin with a discussion of the interplay between sub-cellular structures and cellular function. We will focus on the establishment of the different membrane compartments in the cell and the regulated transfer of molecules between them. We will then turn to how cells integrate and respond to the vast array of diverse information arriving at their surface. The emerging theme that the control of the location of signalling molecules has a profound influence on the nature of signalling will be discussed. The first half of the course will culminate in exploring how trafficking of signalling molecules between membrane compartments is an essential element of signalling pathways.

In the second half of the module we describe the interplay between plasma membrane receptors and the cytoskeleton in a variety of processes: 1) the establishment of cell polarity, 2) mediation of adhesion between cells to form higher order multicellular assemblies, 3) specifying the shape of cells and 4)   promoting cell and tissue movement.

This is an interdepartmental course (with PDN). In addition to lectures there are six journal club sessions in which there will be an interactive discussion of topical references.

 

M7 From genome to proteome

Module organiser: Dr Torsten Krude

This course aims to introduce and discuss the regulation of gene expression using a wide range of examples and different model organisms, and to introduce you to the range of methodology that is used in such studies. This course aims to take you from the level of familiarity with textbooks and reviews up to the level of reading, understanding and critically evaluating original research papers.

Control of gene expression is a fundamental topic for the understanding of cellular and developmental biology. A key question in this field is: what are the principles and rules of regulation that ensure that only a specific subset of genes are expressed in a given cell at a given time, and how all other genes are kept silenced? The main focus of this course, therefore, is a discussion of molecular mechanisms controlling the expression of selected genes in a eukaryotic cell. These mechanisms operate at many levels in the cell, beginning with RNA synthesis, i.e. transcription, moving on to the levels of RNA splicing and modification, RNA localisation and finally to the level of translation. An additional level of control is provided by non-coding small RNAs such as microR NAs. Due to the recent impact of genome projects, emphasis will also be given to higher level patterns of gene expression in different cells and organisms. Aspects of nuclear structure, such as the packing of genomic DNA into chromatin, are part of this regulation of gene expression and will be discussed as well.

This course is interdepartmental and the first 9 lectures are given in the Department of Zoology. The subsequent 15 lectures are also taken by students reading Part II Biochemistry and these are given in the Department of Biochemistry.

 

M8 Development: Patterning the embryo

Module Organisers: Dr Isa Palacios

(Inter-departmental Course)

This course is the first of two complementary modules (with L6), which can also be taken on their own. Our aim is to explore a fascinating biological question: how does a single cell, the fertilized egg, have all the information to make an animal? Our current knowledge of the underlying molecular mechanisms that create cell diversity and pattern in the early embryo will be examined in depth. We will discuss how the experimental advantages of different model organisms have aided the discovery of the principles of development, and the insights provided by comparing the developmental strategies of vertebrates and invertebrates. In this first module we will address key aspects of early development, including how development is regulated, how the patterning of spatial information is established and how morphogenetic mechanisms shape the embryo. At each stage we will discuss the cellular mechanisms required and the molecular networks that drive them. By comparing the development of different animals we aim to come to an understanding of conserved strategies of animal development.

These themes will be covered from the establishment of polarity in the egg, and its elaboration after fertilisation, to a consideration of how these events set the body axes. We will then see how axial patterning direct the morphogenetic movements of gastrulation and the grouping of cells into segments with differing identities.

This interdepartmental course (with PDN) will consist of three lectures per week with six one hour journal club sessions, in which we will aim for interactive sessions discussing key references.

Our aim is to provide a course that is accessible to anyone doing Part II Zoology and we hope that you will consider doing this course whatever your previous background.