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Department of Zoology

 

Modules available in Lent Term:

 

ZL1 Evolution and Comparative Anatomy of Mammals

Module Organiser: Dr Robert Asher

Also available as a BBS minor.

Beetles are more numerous, and cartilaginous fish are geologically older. However, no other animal group rivals the Mammalia in terms of size and, some would say, adaptive variability. In this module, we examine the evolution of ourselves and our closest relatives, from an ancestor that existed over 300 million years ago to the diversity of bats, whales, lemurs, rabbits, elephants, sloths, koalas, echidnas and many other living species. Using evolution, the Tree of Life and comparative anatomy as our guides, we will explore how mammals adapt and thrive everywhere, from deserts to oceans and from poles to tropics. We note how genomics have revolutionized our understanding of Life's evolutionary tree, yet also confirmed basic ideas about this Tree outlined in the 19th century. We explore links between DNA and development, and consider how genomes can exhibit their own fossil record. We will observe the extraordinary commonalities shared by animals as diverse as blue whales and tarsiers, and the major differences between animals that at first glance appear to be similar, such as talpid and afrotherian moles. We furthermore consider the general theme of extinction. During the "Ice Age" we note key lines of evidence that document climate variability and the responses of species to repeated changes in ice cover and sea levels, fluctuations which help explain, among many other phenomena, the distinctive yet essentially European identity of the British Isles.

Biological natural science students taking this course will recognize themes from their first two years, such as development, reproduction and ecology. Vets and medics will already be familiar with anatomical concepts, tomographic, and histological methods used in our course. All students will appreciate how the anatomy of humans, their livestock and pets exhibit commonalities and contrasts with non-model species, from armadillos to Thrinaxodon. Ecologists, cell-biologists and any other Part II student will recognize topics concerning our own biology and place in the Tree of Life. This is an independent, self-contained module and there are no first, second, or third year courses that are prerequisites to do well in ZL1.

In addition to standard lectures, students in ZL1 have extensive access to the collections in the Museum of Zoology. These museum specimens comprise a hands-on resource to help illustrate relevant points from lectures and readings. For students particularly keen on comparative anatomy, ZL1 offers the "assessed practical", a two-hour exam based on identifications of museum specimens that takes place in early Easter term and replaces one short project. All students will find the demonstrations of use and during term students have swipecard access to a reserved part of the museum (the "dem room"). Self-explanatory stations showing these specimens are available Monday-Friday during business hours; lecturers and demonstrators affiliated with ZL1 are generally available from 12noon following most lectures (and at other times upon request).

ZL2 Responses to global change

Module Organisers: Dr David Aldridge (Zoology), Dr Johannes Kromdijk (Plant Sciences)

(Inter-departmental Course, with Plant Sciences)

Also available as a BBS minor.

Global temperature is on the increase, extreme climatic events are increasing, and the sustainability of agricultural land use and vegetation cover is being challenged; pest and pathogen impacts are exacerbated in a warming world and their spread accelerated by human interactions. The scientific challenges underpinning these dramatic changes, and our collective response,  will shape your future, and that of a growing global population. The module provides a generic background to climate change adaptation and mitigation, before considering a succession of timely issues in depth.

  • Global limits to growth: planetary boundary layers and their impacts in key areas of water resources, ecosystem fertilisation and greenhouse gas emissions
  • Impacts of seasonality and phenological mismatch on bird population dynamics in a changing world and development of appropriate conservation practices  (James Pearce-Higgins, British Trust for Ornithology)
  • Use of modelling to scale physiological limitations on plant growth from leaf, via canopy, to ecosystem (Wanne Kromdijk)
  • Modelling epidemiology and plant pathogen distribution in a changing world (Nik Cunniffe)
  • The “Madingley Model” of ecosystems and biodiversity: development of policy from projections of biodiversity change under different scenarios of human development (Mike Harfoot, UNEP-WCMC)
  • Evidence-based analyses of insect declines and invasive species: how should society respond to the need for sustainability in the face of climate change? (Lynn Dicks)
  • Impacts of disturbances on ecosystem functioning and the potential for their management to combat climate change (Adam Pellegrini)

 

ZL3 Evolution and behaviour: populations and societies

Module Organiser: Prof Rufus Johnstone

This module aims to provide a functional interpretation of variation in animal social behaviour and inter-species interactions. The underlying theme is that individuals will behave in ways that promote their genetic contribution to future generations. The way in which they do so is constrained by their ecology and by social interactions with members of their own and other species.

The course aims to provide you with an understanding of:

  1. the framework of evolutionary theory that is used to explain variation in animal social behaviour;
  2. the way in which ecology and social competition constrain and control evolutionary options;
  3. the empirical evidence that supports functional interpretations of social behaviour and life history (including observation, comparative and experimental studies).

Lecture blocks deal with communication, family life, group living and collective behaviour, coevolution (from mutualism to parasitism) and major transitions in social evolution.

 

ZL4 Applied ecology

Module Organiser: Dr Edgar Turner

All too often, managers of natural resources make ill-informed decisions that can have devastating consequences upon ecosystems and the human populations who depend upon them. This module is about how a sound understanding of ecological processes can greatly improve our ability to manage ecosystems in a desirable way.

The course considers a diverse range of applied applications of ecological knowledge, from understanding disease epidemics, to predicting the future impacts of climate change. It also considers the role of applied ecology in a diverse range of environments, from the world’s most remote island groups and Polar regions, to familiar agricultural landscapes.

Different sections of the course include ecological approaches for the control of influenza, the control of invasive species on islands, the ecology of Antarctic ecosystems in the face on environmental change, applying lessons from palaeobiology to modern changes in species, and ecology in agricultural environments. As well as lectures, the course also includes sessions with applied ecologists from the David Attenborough Building and seminars that enable students to explore aspects of applied ecology in more detail.

Students taking this course will learn how a well-trained and enthusiastic ecologist can apply their scientific knowledge to make a real change to the world around them.

 

ZL5 Evolutionary Genetics and Adaptation

Module Organisers:  (Zoology), Prof Frank Jiggins (Genetics)

(Inter-departmental Course, with Genetics)

Also available as a BBS minor.

Modern evolutionary theory has its roots in the union of Mendelian genetics with Darwin’s theory of evolution, two of the great unifying themes of biology. This course will consider the process of evolution from a genetic perspective, exploring the central topics of natural selection, adaptation and genetic drift, and combining a variety of empirical and theoretical approaches. Alongside this, the course will explore how genomes themselves are shaped by selection, drift and their evolutionary history. This course lies at the interface of whole organism biology and molecular genetics. 

These lectures will begin by introducing the basic principles of population genetics such as selection and drift. It will then illustrate how adaptive thinking can be applied to features of genomes, and explore the different ways in which a geneticist might test adaptive hypotheses. How do genomes evolve?  A large proportion of many genomes consists of repetitive DNA, which replicates itself at the expense of the organism – a form of genomic parasitism.  Other sources of conflict occur between the sexes, and between parents and offspring.  We will look at the genetic basis of sex determination and how this can lead to conflict between chromosomes. How are species and populations related? We look at how we can reconstruct species relationships from DNA sequences, and how this can inform our understanding of traits such as human language. What is the genetic basis of adaptation?  Do we expect evolutionary change to involve few or many genes?  What kinds of genes control recent evolutionary changes? Butterfly wing patterns and many other examples are used ­to illustrate these questions.

 

ZL6 Development: cell differentiation and organogenesis

Module Organiser:

(Inter-departmental Course, with PDN)

This course is the second of two complementary Developmental Biology modules (with ZM8) that can also be taken on their own.  This module examines a second phase of embryonic development, following the initial steps of defining axes, major cell layers, and broad pattern domains that are covered in ZM8. 

This interdepartmental course (with PDN) will consist of three lectures per week, and seven interactive sessions (such as journal clubs) in which we will aim to discuss key references and the concepts presented in the lectures.

A series of topics will be presented, each using particular tissues or organs to highlight individual developmental mechanisms. Thus, the generation of airways and vasculature addresses principles of tubulogenesis; vertebral column and lung illuminate mechanisms of cell allocation and morphogenesis; limb development illustrates how patterning mechanisms are coordinated with cell proliferation; the progressive determination of cell lineages and establishment of stem cells shows how organs are derived; and the development of pharyngeal arches, neural crest cells and craniofacial organizing centres demonstrates how epithelial-mesenchymal interactions instruct cell differentiation and patterning in the head.

A mixture of examples from simpler invertebrate models and vertebrates will show how developmental mechanisms have diversified with increasing cell number.

 

ZL7 Cell cycle, signalling and cancer

Module Organiser:

(Inter-departmental Course, with Biochemistry)

Also available as a BBS minor.

Precise control of cell proliferation is crucial to the normal development and homeostasis of multi-cellular organisms. Failure to accurately regulate these processes can lead to cancer. This course aims to provide a broad molecular understanding of the processes underlying cell proliferation in normal development and disease. It aims to explore experimental systems to study tumour biology, and to critically discuss therapeutic strategies against cancer.

This course will first concentrate on the molecular mechanisms underlying controlled cell proliferation, including cell cycle control, replication of DNA, repair of DNA damage and programmed cell death. It will then apply this fundamental understanding of cell proliferation and homeostasis to explore tumours as aberrantly proliferating tissues, including the interplay between oncogenes and tumour suppressors, and the specific topography of tumour microenvironments. Finally, this course will consider therapeutic anti-cancer strategies, including tumour virus vaccination, small molecule drugs and antibody-based therapies. It further aims to illustrate the experimental approaches used, to highlight important questions that remain to be answered, and to encourage critical evaluation of the scientific literature.

This module is fully interdepartmental and the lectures are also taken by students reading Part II Biochemistry. The lectures are given in the Department of Biochemistry by members of the Departments of Zoology, Biochemistry and the Gurdon Institute, as well as by several external experts.

 

Bioinformatics

Module Organiser: Dr Alexia Cardona

(borrowed module from BBS)

Also available as a BBS minor.

Bioinformatics is an interdisciplinary field that uses computational ways to process  biological data.  With the biological and biomedical sciences becoming more data-driven than ever before, bioinformatics is central to these areas.  This course introduces the fundamental bioinformatic concepts and methodologies used to analyse biological data.  It is structured around 3 main blocks; data science, omics analysis, and network analysis.

In the Data Science for Bioinformatics block, we will introduce programming, data visualisation, data manipulation, statistics and machine learning that are popular in the bioinformatics field.  These topics are fundamental to the analysis of data which are currently in high-demand due to the data-driven approach of answering research questions, driven by the  increasing amount of data becoming available.  Knowledge gained from this set of lectures and practicals can be applied and transferred to different research domains. 

The Bioinformatics Approaches to Omics Analysis, will introduce omics data and bioinformatics workflows used to process omic datasets with hands-on practice on genomic and transcriptomic data.  We will go through the different stages of the omic data workflow, starting from the raw data, quality control, alignment, variant calling and analysis.  Finally, genome-wide association studies are introduced, a popular approach in population studies which allow the identification of associations between single-nucleotide polymorphism (SNPs) loci and traits.

In the last block of the course, Pathway and Network Analysis of Biological Data, we will introduce ontologies and gene set enrichment analysis to link results obtained from the previous analyses back to biology and identify classes of genes or proteins that are over-represented in our results which may have an association with disease phenotypes.  It will also introduce basic concepts of biological networks and their analysis with hands-on practice using Cytoscape, a widely used platform for Network Analysis.

The course is specially designed for students coming from the biological and biomedical sciences.  The course consists of a set of lectures that introduce theoretical concepts, and practicals which provide hands-on practice using real biological datasets.  More information can be found at https://bioinfotraining.bio.cam.ac.uk/undergraduate