3649-08 IICB.indd - Faculty of Biological Sciences - University of ...

Institute of Integrative 

& Comparative Biology 

FACULTY OF BIOLOGICAL SCIENCES

Institute of Integrative 

and Comparative Biology 

Welcome to the Institute’s brochure. Its purpose is to provide an introduction to our research 

activity – what we do and why we do it. The brochure is intended for a broad spectrum of 

readers – for those considering studying at the University, or for experts wishing to benefit 

from our research or invest in it. The Institute has two main reasons for existence – to educate 

and to discover through research. This brochure focuses on our research. However, we also 

have extensive undergraduate and postgraduate education programmes running in parallel. 

These programmes are not separate from our research but inter-woven with it. Research informs our teaching and causes it to be 

revised annually. It also provides a rich and cutting-edge experience in research discovery for undergraduates and postgraduates 

through projects in our research laboratories. We should also not forget that research is a central platform for the reputation of our 

University, which will influence the lives of most who study at it. 

Organisms are integrated systems that have evolved to function in their natural environment. Through the process of 

development, genetic and environmental information is integrated into a functioning organism, with the phenotype being the 

interface between the organism and its environment. The focus of the Institute of Integrative and Comparative Biology is to 

understand how organisms “work” within their environments (from genetics, through development, cellular biology, physiology, 

life history and ecology to evolution). In a rapidly changing world, with ever greater demands on resources, there are numerous 

scientific problems that demand our attention. How can we grow sufficient crops to feed a growing population, and can we 

do this in a way that is sustainable for the environment? Can we understand the biology of disease vectors – like malarial 

mosquitoes – with a view to their control and reduction in the million or so people killed by the disease each year? The rise 

of genome-sequencing begs important questions about the functioning of those genes that have been sequenced, and the 

translation of genetic information into the functional phenotype. These are the sort of topics you will see from the following 

pages that are being addressed within the Institute. 

The Institute consists of approximately 45 academic staff, grouped within two research groups: the Centre for Plant Sciences, 

and Genetics, Ecology and Evolution. The overall aim of the Institute is to foster an environment where research can flourish 

because it is the focus of our activities, and where staff and students can interact in an intellectually stimulating and supportive 

environment. The Institute fits within the Faculty of Biological Sciences at Leeds and alongside the other research institutes. 

Collaborations between members of the different institutes are common and encouraged, so “Integrative and Comparative 

Biology” is part of the larger biological enterprise at Leeds. Collaborations outside the faculty are also common. For example, 

the University Interdisciplinary Institute, the Earth & Biosphere Institute (http://earth.leeds.ac.uk/ebi/) is a grouping of 

scientists with interests in the effects of biotic and environmental changes on a spectrum of time and space scales, from short 

term to geological, and from nano-scale to global. The Astbury Centre for Structural Molecular Biology is another University 

Interdisciplinary Institute with links into the Institute. 

The University of Leeds recognizes the international excellence of our research endeavours as the majority of staff members 

are linked to one (or more) “peaks of excellence”: the Astbury Centre, the Centre for Plant Sciences and Evolutionary Ecology 

(as part of a broad Earth and Environmental Systems Science peak). Wherever you are in the world – for example at a school in 

Leeds, in a biotech firm or from a city on the other side of the globe, if you are interested in our research areas, please consider 

visiting us, joining us or investing in us. You would be most welcome. We are an ambitious, productive and open research 

centre in a big cosmopolitan city adjacent to some of the most beautiful countryside on the planet. You can contact any of 

our academics directly through e-mail. For enquiries about our undergraduate and postgraduate programmes, please see 

information on our web pages and make contact accordingly http://www.fbs.leeds.ac.uk/. 

Professor Helen Miller 

Director, IICB 

Email: diriicb@leeds.ac.uk 

Tel: +44 (0)113 343 2842

Group 

Research 

Centre for 

Plant Sciences 

The CPS was founded in 1990 as 

a cross-faculty, multidisciplinary 

research unit and became recognised 

by the BBSRC as one of its top funded 

departments; rewarded with its own 

quota of PhD studentships. Current 

research income of £11M, derives 

from Research Councils, Charities, 

EU, and Industry. CPS staff have a 

strong publication record, publishing 

in high-impact general and specialist 

journals. The CPS recently won a 

national competition to provide the 

GATSBY Foundation training in 

Plant Sciences, including running a 

residential Summer School for 100 

top UK science undergraduates. 

CPS research is spread across the 

range of plant sciences, from basic 

to applied. Outside the “core” CPS 

staff we have strong formal and 

informal research links to other 

researchers within Leeds (GEE, 

textiles and food science, chemistry), 

nationally and internationally. The 

CPS is an international organisation 

with PIs postdocs and PhD students 

from around the world. 30% of 

our publications are with overseas 

collaborators. Our international outlook 

is also demonstrated by our current and 

past success in EU funding. The CPS 

has also co-founded an International 

Joint Laboratory of Plant Sciences 

with the Institute for Genetics and 

Development Biology of the Chinese 

Academy of Sciences (www.JLPS.org). 

With the benefit of externally awarded 

investment in our science, infrastructure 

and facilities we have created a 

research group with the facilities to work 

from the basic molecular level through 

analysis of transgenic plants to field 

trials and environmental assessment. 

Plant Science has the potential to 

contribute enormously to our future 

health and wealth and the CPS aims to 

contribute to developing this potential. 

The CPS is committed to the 

commercialisation of research, which 

is essential given the potential for 

plant science to deliver real industries 

in the future. We have a number of 

spin-outs arising from research in the 

CPS and other groups have licensed 

distinct patented technologies to major 

biotech companies. An example of our 

success at doing science that matters is 

provided by the highlighting of the GM 

crop nematode resistance technologies 

in both the GM Science Review Report 

and the Prime Minister’s Strategy Unit 

Report. This work is also the principal 

GM-based research of DFID www.dfidpsp.org 

being donated to subsistence 

farmers worldwide. 

www.plants.leeds.ac.uk

Group 

Research 

Genetics, Ecology 

and Evolution 

The Genetics, Ecology and Evolution 

Group at Leeds is one of the largest 

whole organism-centred research 

groups in the UK, with 30 full-time 

academic staff, 18 postdoctoral 

research fellows/research assistants and 

around 80 postgraduate researchers. 

One of the particular strengths of the 

Group is our success in integrating 

research across a broad spectrum 

of interests from post-genomics to 

ecosystem processes, which we have 

achieved via studies of gene action and 

regulation, development, functional 

design and adaptation, behaviour, life 

histories, epidemiology, population 

genetics and dynamics, and species 

interactions. We are at the forefront 

of a number of integrative research 

initiatives crossing traditional subject 

boundaries. These include a recent 

Systems Biology initiative involving 

collaboration with computer scientists 

to study the neuronal control of 

locomotion. We are also members of 

the Earth and Biosphere Institute 

http://earth.leeds.ac.uk/ebi/news.htm 

through which we have strong research 

links with staff in Geography, Earth 

Sciences and Environmental Biology 

tackling broader research topics in the 

arena of Earth Systems Science. 

In addition to multi-disciplinary research 

programmes within the University of 

Leeds, staff in GEE are also founding 

partners of the UK Population Biology 

Network, which enables collaborative 

research projects between some of 

Britain’s leading genetics and ecology 

research groups. We are unique in 

hosting two Marie Curie European 

Centres of Excellence for research and 

teaching; one in Advanced Genetic 

Analyses (http://www.fbs.leeds.ac.uk/ 

agape/) and the other in Biodiversity 

and Conservation (http://www.leeds. 

ac.uk/european/information/marie_ 

curie/ training_sites/ biodiversity/ 

overview.html). Group members have 

also had notable recent success in 

the commercial development of their 

research and in Knowledge Transfer, 

for example through the commercial 

development of a sonic walking 

stick based on principles developed 

through work on echo-location in bats 

and through the recently-established 

National Pig Development Centre at 

Leeds, which is the largest facility 

for pig research, development and 

knowledge transfer in the country. 

Current research grant income of 

group members is over £5m, including 

support from BBSRC, NERC, MRC, 

Department of Health, DEFRA 

(including the Darwin Initiative), joint 

research council initiatives and the 

EU. The group has an outstanding 

track-record of publications in the top 

journals within our research field (e.g. 

Ecology Letters, American Naturalist, 

Proceedings of the Royal Society, 

Molecular Microbiology, Molecular 

and Cellular Proteomics and American 

Journal of Human Genetics) in addition 

to exceptionally high-profile publications 

in Nature, Science, PNAS, PLoS and 

Cell (average of more than two per year 

since 2001). These achievements have 

enabled us to form a large part of the 

University Centre of Excellence in Earth 

and Environmental Systems Science, 

one of 12 such centres of excellence 

across the university.

Dave G. Adams 

BSc (Liverpool); 

PhD (Liverpool); 

Lecturer in Microbiology, University of Leeds (1985 – 1995); 

Senior Lecturer in Microbiology, University of Leeds (1995 - ) 

Contact: d.g.adams@leeds.ac.uk 

Cyanobacteria: gliding motility, 

plant symbiosis and bloom formation 

My research interests encompass many 

aspects of cyanobacteria and include 

studies on the mechanism of gliding 

motility, the formation of cyanobacteriaplant 

symbioses and the prevention of 

toxic cyanobacterial bloom formation. 

Cyanobacteria are the largest group of 

nitrogen-fixing bacteria on earth. Many 

are filamentous and develop several 

cell and filament types, including 

the heterocyst (Figure 1), which is 

specialised for nitrogen fixation, 

and filaments known as hormogonia 

which are motile by gliding and which 

serve both as a means of dispersal 

and as the infective agents in plantcyanobacteria 

symbioses. 

The mechanism of cyanobacterial 

gliding motility is unknown. Beneath 

the outer membrane of motile 

cyanobacteria we have identified arrays 

of parallel protein fibrils (Figure 2) 

that we believe act as novel molecular 

motors that provide the motive 

force for gliding. To determine the 

mechanism of gliding we are taking two 

approaches. In the first we are isolating 

and characterising the fibrils and fibril 

structural proteins in wild-type and 

mutant cyanobacteria. In the second 

we hope to visualise motor function by 

using Atomic Force Microscopy of live, 

immobilised cyanobacteria. 

Figure 2 

As a model for our studies on symbiosis 

we use the association between 

cyanobacteria and the liverwort 

Blasia. We are currently examining 

the importance of chemotaxis to 

the establishment of symbiosis by 

using insertional mutagenesis of 

genes involved in the formation and 

function of pili which are external 

protein fibres thought to be involved 

in motility, adhesion and chemotaxis 

of cyanobacterial hormogonia, all of 

which are crucial to the establishment 

of symbiotic colonies such as that seen 

fluorescing red in Figure 3. 

Figure 3 

We have recently started a project, 

in collaboration with Yorkshire Water, 

to examine the use of rotting barley 

straw to control cyanobacterial bloom 

formation in local reservoirs. 

Funding for these projects has 

come from NERC, BBSRC, The 

Leverhulme Trust and most recently 

Yorkshire Water. 

More information: 

http://www.fbs.leeds.ac.uk/staff/profile. 

php?staff=DGA 

Representative Publications 

Read, N, Connell, S & Adams, DG (2007). 

Nanoscale visualization of a fibrillar array in the 

cell wall of filamentous cyanobacteria and its 

implications for gliding motility. J. Bacteriol. 

189 (20), 7361-7366. 

Duggan, PS, Gottardello, P & Adams, DG 

(2007). Molecular analysis of genes in Nostoc 

punctiforme involved in pilus biogenesis and 

plant infection. J. Bacteriol. 189, 4547-4551. 

Adams, DG, Bergman, B, Nierzwicki-Bauer, SA, 

Rai, AN, Schussler, A (2006). Cyanobacterial- 

Plant Symbioses, in The Prokaryotes. A 

Handbook on the Biology of Bacteria, third 

edition. Volume 1: Symbiotic Associations, 

Biotechnology, Applied Microbiology, eds. 

M. Dworkin, S. Falkow, E. Rosenberg, K.-H. 

Schleifer and E. Stackebrandt. Springer, New 

York, pp 331-363. 

Goddard, VJ, Baker, AC, Davy, JE, Adams, DG, 

De Ville, MM, Thackeray, SJ, Maberly, SC & 

Wilson, WH (2005). Temporal distribution of 

viruses, bacteria and phytoplankton throughout 

the water column in a freshwater hypereutrophic 

lake. Aquatic Microbial Ecology 39, 211-223. 

Phoenix, VR, Konhauser, KO & Adams, DG, 

Bottrell, SH (2001). Role of biomineralization 

as an ultraviolet shield: Implications for 

Archean life. Geology 29, 823-826. 

Figure 1

John Altringham 

BA (York); 

PhD (St. Andrews); 

Lecturer, Senior lecturer and Reader, University of Leeds (1989-1999); 

Professor of Biomechanics University of Leeds (1999-) 

Contact: j.d.altringham@leeds.ac.uk 

Animal mechanics: 

The biology and conservation of bats 

I am interested in how evolution shapes 

the form and physiology of animals for 

locomotion, in particular for swimming 

and flying. To catch food, avoid 

becoming food, to find a mate or to 

migrate, animals must be able to move 

effectively and efficiently if they are to 

be successful in the evolutionary race. 

Integrating studies on muscle function 

with whole animal movement has been 

the major theme of my research. 

More recently I have become interested 

in bats, with the aim of relating their 

ability to fly and echolocate to their 

behaviour, ecology and ultimately, 

population biology. Despite their small 

size, bats have a life history strategy 

of low fecundity and longevity and 

through their ability to fly, they utilise 

the landscape on a large scale. Given 

these factors, and bats’ enormous 

diversity, they have considerable 

potential as a model group for studying 

mammalian ecology. Much of my work 

on bats is driven by a concern for their 

conservation: the very features which 

make them interesting also make 

them vulnerable in an ever more 

fragmented landscape. 

Figure 2: Brown long-eared bat 

Our research is multi-faceted, using 

a variety of field and lab-based 

techniques. In field studies, the foraging 

and social behaviour of bats is related to 

the distribution of their resources (e.g. 

food, roosts, mating and hibernation 

sites) and to the mating systems that 

have evolved within the constraints of 

the system. In the lab, in collaboration 

with Prof. Roger Butlin, molecular 

genetic approaches are used to probe 

mating systems and to study the effects 

social structure, migration and mating 

patterns have on population structure. 

Some of our research has more 

immediate practical goals, for example 

we are currently investigating new 

techniques for identifying bats in the 

field from their echolocation calls, 

assessing the effects on bat behaviour 

of protective grilles at hibernation sites 

and surveying and monitoring mating 

and hibernation sites in need 

of protection. 

Funding for our work comes from 

the BBSRC, NERC and a number of 

conservation agencies and charities 

including Natural England and the 

Yorkshire Dales and North York Moors 

National Park Authorities. 



php?staff=JDA 


Rivers NM, Butlin RK and Altringham JD. 

2006. Autumn swarming behaviour of 

Natterer’s bats in the UK: population size, 

catchment area and dispersal. Biological 

Conservation 172: 215-226. 

Rivers NM, Butlin RK and Altringham 

JD. 2005. Genetic population structure 

of Natterers bats explained by mating at 

swarming sites and philopatry. Molecular 

Ecology 14: 4299-4312. 

Senior P, Butlin RK and Altringham JD. 

2005. Sex and segregation in temperate bats. 

Proceedings of the Royal Society B 272: 

2467-2473. 

Harwood CL, Young IS and Altringham JD 

2002. How the efficiency of rainbow trout 

(Oncorhynchus mykiss) ventricular muscle 

changes with cycle frequency. Journal of 

Experimental Biology 205: 697-706.

Graham Askew 

BSc (Leeds); 

PhD (Leeds); 

Lecturer, University of Leeds (2001-) 

Contact: g.n.askew@leeds.ac.uk 

Muscle physiology 

and biomechanics 

My research is primarily aimed at 

understanding how the mechanical 

properties of skeletal muscle determine 

the biomechanics and energetics of 

animal movement. 

Mechanical function of muscles 

during locomotion 

Our work integrates a variety of 

techniques that enable us to measure 

muscle length, activity pattern and 

force during locomotion. Current 

research projects are examining muscle 

performance during all of the major 

modes of locomotion: flight, running 

and swimming. Recent work has 

examined how small birds modulate 

pectoral muscle power production 

across a range of flight speeds. Many 

vertebrates possess muscles with 

mixed fibre types having a range 

of mechanical properties. In these 

species, muscle power output can be 

modulated by varying the degree to 

which different types of motor unit are 

recruited. As a consequence of the fact 

that their pectoral muscles contain a 

single muscle fibre type, many small 

birds are unable to vary muscle power 

output by recruiting motor units with 

different intrinsic properties. We found 

that power output of the pectoralis 

can be modulated by changing strain 

trajectory and the relative timing and 

intensity of muscle activity. 

Energetics of locomotion 

An ongoing interest in my lab is trying 

to understand the basis for the energy 

cost of locomotion. In the past, a 

major obstacle has been the inability 

to measure energy expenditure at the 

muscle level. A recently developed 

technique based on measurement 

of regional blood flow to individual 

muscles and other tissues and has 

overcome this problem, opening 

up the possibility for significant 

advances in our understanding of 

energy use during locomotion. We are 

currently measuring metabolic energy 

expenditure of the muscles and other 

physiological systems in birds flying at 

a range of speeds to separate out the 

factors that determine the overall cost 

of locomotion. The energy usage by 

the flight muscles is being examined 

in relation to their mechanical power 

output. These data will provide the 

first detailed investigation to examine 

the link between the mechanical and 

metabolic energy expenditure 

of muscles. 

Funding from the research in my 

laboratory typically comes from the 

BBSRC. 



php?staff=GNA 

Figure 1: In vivo zebra fi nch pectoralis fascicle strain and 

EMG activity at 10 m s-1. Fascicle length was measured 

by sonomicrometry. Muscle activity was measured using 

a bipolar EMG electrode. 


James, RS, Wilson, RS Askew, GN. (2004) 

Effects of caffeine on mouse skeletal muscle 

power output during recovery from fatigue. 

Journal of Applied Physiology 96: 545-552. 

Askew, GN and Ellerby, DJ (2007) The 

mechanical power requirements of avian flight. 

Biology Letters 3: 445-448. 

Askew, GN and Marsh, RL. (2001) The 

mechanical power output of the pectoralis 

muscle of blue-breasted quail (Coturnix 

chinensis): the in vivo length cycle and its 

implications for muscle performance. Journal 

of Experimental Biology 204: 3587-3600. 

Askew, GN, Marsh, RL and Ellington, CP. 

(2001) The mechanical power output of 

the flight muscles of blue-breasted quail 

(Coturnix chinensis) during take-off. Journal 

of Experimental Biology 204: 3601-3619.

Howard Atkinson 

PhD University of Newcastle-Tyne 1972; 

Formerly Lecturer, Senior Lecturer and Reader, University of Leeds; 

Personal Chair in Nematology; 

Research group; Centre for Plant Sciences, University of Leeds 

Contact: h.j.atkinson@leeds.ac.uk 

Nematode-resistant 

crops 

Plant parasitic nematodes cause losses 

to world agriculture of 125 billion dollars 

annually. Their control in agribusiness 

often depends on pesticides that harm 

the environment. In the developing 

world many growers are unaware of 

these pests and the losses they cause. 

The Plant Nematology lab. improves 

fundamental knowledge of these pests. 

We use the information gained to 

develop new technology and test both 

its efficacy and biosafety. Our recent 

research effort extends from the UK 

to the USA, S. America, Africa, India 

and China. 

Nematode/plant interactions 

Some nematodes alter plant gene 

activity locally when they modify plant 

cells at their feeding sites (Figure. 1). 

We have used microarray analysis to 

define the changes that occur. We also 

study the proteins nematodes secrete 

that control this process. Their roles are 

being defined using RNA interference. 

This causes targeted loss of expression 

of individual proteins enabling the role 

of each in plant parasitism to 

be defined. 

Figure 2: Migratory nematode parasites of banana roots 

(Radopholus similis) are less than 1mm in length. When 

numerous, they cause roots to rot. 

Improving nematode control 

We use the new knowledge we gain 

to devise novel control of nematodes. 

This effort spans from gene discovery 

and plant transformation to trials 

and biosafety assessment. Cysteine 

proteinases are important nematode 

digestive enzymes. Expression by 

crops of specific protein inhibitors of 

these proteinases confers resistance 

to nematodes. The presence of the 

inhibitors can be restricted to roots 

(Figure 1). They are inherently safe 

proteins. They are not new to our diet 

and are harmless when ingested. They 

occur naturally in our saliva and foods 

like rice. The nematode-resistant plants 

do not harm non-target organisms and 

have the potential to displace harmful 

pesticides. We have devised further 

approaches that enhance control levels 

and help ensure nematodes will not 

overcome the new resistance. 

Donation to the 

developing world 

We adapt our approaches for 

developing world needs and donate 

them to subsistence farmers worldwide. 

We collaborate with Ugandan scientists 

to protect the cooking bananas from 

nematode losses (Figure 2). We 

consider all scientific aspects of future 

deployment of our resistance. For 

example, we made a detailed study 

of issues surrounding its future use in 

potato in the Central Andes where many 

wild relatives of this crop occur. 


http://www.biology.leeds.ac.uk/nem/ 


Celis C, Scurrah M, Cowgill SE, Chumbiauca 

S, Franco J, Main G, Keizenbrink DT, Green 

J, Visser RG and Atkinson HJ. (2004) 

Environmental biosafety and transgenic potato 

in a centre of this crop’s diversity. Nature 43: 

222-225. 

Atkinson, HJ, Grimwood, S, Johnston, K and 

Green, J. (2004) Prototype demonstration 

of transgenic resistance to the nematode 

Radopholus similis conferred on banana by a 

cystatin. Transgenic Research 13: 135-142. 

Cowgill, SE, Wright, C and Atkinson, HJ. 

(2002) Transgenic potatoes with enhanced 

levels of nematode resistance do not have 

altered susceptibility to nontarget aphids. 

Molecular Ecology 11: 821-827. 

Urwin, PE, Lilley, CJ and Atkinson, HJ. 

(2002) Ingestion of double-stranded RNA by 

preparasitic juvenile cyst nematodes leads to 

RNA interference. Molecular Plant Microbe 

Interactions 15 (8): 747-752. 

Figure 1: The swollen female of potato cyst nematode 

(Globodera. pallida) is about 0.7mm in diameter. The 

plant cells it has modifi ed are stained blue. Antinematode 

defences can be restricted to these modifi ed 

plant cells.

Alison Baker 

BA (Cambridge); 

PhD (Edinburgh); 

Assistant Lecturer/Lecturer University of Cambridge (1989-2004); 

Lecturer/Senior Lecturer, University of Leeds (1995-2004); 

Reader Plant Cell and Molecular Biology (2004-2008); 

Professor in Plant Cell and Molecular Biology (2008-) 

Contact: a.baker@leeds.ac.uk 

Cell Biology, Biochemistry 

and Functional Genomics of Peroxisomes 

The development and function of 

eukaryotic cells requires the accurate 

delivery of proteins to subcellular 

organelles. The consequence to 

the organism when these systems 

malfunction can be catastrophic. 

Our principal interest is in the 

biogenesis of peroxisomes and the 

targeting and import of peroxisomal 

proteins. In humans the failure of these 

mechanisms results in a debilitating 

and eventually fatal group of diseases, 

the peroxisome biogenesis disorders. 

In plants they have far ranging effects 

on seed viability, germination and 

the ability to withstand stress; all 

agronomically important traits. 

Our goal is to understand the molecular 

mechanism by which proteins enter 

peroxisomes and the contribution 

of peroxisomes to plant growth and 

development. This is done using a 

range of biochemical, confocal imaging, 

chemical genetics and functional 

genomics approaches. 

The principal funder of our work is 

the BBSRC but we have also received 

funding from the European Union and 

the Leverhulme Trust. 


http://www.plants.leeds.ac.uk/groups_ 

bak.html 

Figure 1: Peroxisomes in leaf cells visualised by 

confocal laser scanning microscopy. The plant has been 

engineered to express a green fl uorescent protein that 

has been modifi ed to contain a signal that targets it to 

peroxisomes, which appear as bright green dots. This 

allows us to image peroxisomes in different cell types 

and to look at effects of mutations or environmental 

conditions on peroxisome abundance, movement and 

protein uptake. 


Baker, A, Graham, IA, Holdsworth, M, Smith 

SM and Theodoulou FL. (2006) Chewing the 

fat: β-oxidation in signalling and development. 

Trends in Plant Science 11: 124-132. 

Hadden, DA, Phillipson, BA, Johnston, KA, 

Brown, L-A, Manfield, IW, El-Shami, M, 

Sparkes, IA and Baker, A (2006) Arabidopsis 

PEX19 is a dimeric protein that binds the 

peroxin PEX10. Molecular Membrane Biology 

23 (4): 325-336 

Baker A, and Sparkes IA. (2005) Peroxisome 

protein import: some answers, more questions. 

Current Opinion in Plant Biology 8: 640-647. 

Footitt, S, Slocombe, S, Larner, V, Kurup, S, 

Wu, Y, Larson, T, Graham, I, Baker, A, and 

Holdsworth, M. (2002) Control of germination 

and lipid mobilisation by COMATOSE the 

arabidopsis homologue of human ALDP. EMBO 

Journal 21: 2912-2922.

Tim Benton 

BA (Oxford) PhD (Cambridge); 

Lecturer, Senior Lecturer, University of Stirling (1996-2003); 

Senior Lecturer, University of Aberdeen (2003-2005); 

Professor of Population Ecology (2005-); 

Institute Director, Integrative and Comparative Biology (2005-2007); 

Pro-Dean for Research, Faculty of Biological Sciences (2007-) 

Contact: t.g.benton@leeds.ac.uk 

Population, evolutionary 

and conservation ecology 

I am interested in what determines 

the way a population may change in 

size, with much of my interests being 

driven from an underlying conservation 

interest. In a world that is changing 

in so many ways, how can we predict 

population dynamics? Any answer to 

this question involves understanding 

how the environment affects the 

resources individuals can access and 

therefore the life-history choices they 

make (e.g. to have many small rather 

than few large offspring). These lifehistory 

decisions create the changes in 

birth and death rates which determine 

population dynamics. This research 

programme involves empirical work 

(using a laboratory model organism, a 

soil mite) and theoretical work, primarily 

to understand the interaction between 

the way the environment may fluctuate 

over time and the underlying biological 

rules (e.g. deterministic factors such 

as density dependence). There is an 

evolutionary focus to some of our work 

because as life-histories (and their 

plasticity) evolve so do population 

dynamics, and population dynamics 

in turn asserts selection pressures on 

life-histories. 

In related research, it has become 

very apparent that agriculture has 

huge impacts on the biodiversity of 

the farmed landscape. I am interested 

in the relationships between farming 

practice, invertebrates and bird 

populations, specifically in the way 

changing resources (e.g. insects 

= bird food) cause changes in 

bird life histories and therefore the 

population dynamics. Colleagues and 

I are currently working on an interdisciplinary 

project that assesses the 

costs and benefits of organic agriculture 

(relative to conventional agriculture) at a 

range of spatial scales across the UK. 

Funding from these projects typically 

comes from NERC (4 projects), but 

some comes also from BBSRC and 

from joint research council initiative 

(e.g. the NERC/BBSRC/ESRC Rural 

Economy & Land Use programme). 



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Greenman, JV & Benton, TG. (2005) The 

Frequency Spectrum of Structured Discrete- 

Time Population Models: its properties and 

their ecological implications. Oikos 110: 

369-389 

Benton, TG, Plaistow, SJ, Beckerman, 

AP, Lapsley, CT & Littlejohns, S. (2005) 

Maternal effects can have population dynamic 

consequences. Proceedings of the Royal 

Society B 272: 1351-1356 

Benton, TG & Beckerman, AP. (2005) 

Population dynamics in a variable world: 

Lessons from a mite experimental system. 

Advances in Ecological Research 37: 143-181 

Benton, TG, Vickery, JA, Wilson, JD (2003) 

Farmland biodiversity: is habitat heterogeneity 

the key? Trends in Ecology & Evolution 18: 

182-188

Steve Compton 

BSc (Zoology) and PhD Hull; 

Lecturer and Senior Lecturer, Rhodes University, South Africa (1984-1992); 

Lecturer and Senior Lecturer, University of Leeds (1992-2005); 

Reader in Entomology (2005-) 

Plant-Animal 

Interactions 

My research concentrates on how 

plants and animals interact with each 

other, with a particular emphasis on 

pollination biology and the conservation 

of plant-feeding insects. 

Many main study systems over the 

years have been fig trees and their 

associated animals, particularly the 

fig wasps that pollinate them. This 

has taken me to the Namib Desert 

(to study long distance pollen flow) to 

the volcanic island of Anak Krakatoa 

in Indonesia (to study how rainforest 

recolonisation is speeded up by the 

animals that feed on figs and disperse 

seeds) and to Hyde Park in Leeds, 

where our ‘captive’ population of fig 

trees and fig wasps is the only such 

facility world wide. 

Our conservation studies have centred 

on rare UK beetles, including the 

unique situation on Lundy in the 

Bristol Channel, where an endemic 

plant is host to two beetles known 

from nowhere else. 

The potential role of hybridisation in 

the evolution of fig trees and their 

pollinators is one of our current 

research themes, along with studies 

of the mechanics of how these small 

wasps manage to use their very 

long ovipositors. 

Funding sources have included English 

Nature, BBSRC and NERC 


www.fbs.leeds.ac.uk/staff/profile. 

php?tag=Compton 


Shanahan M, So, S, Compton, SG and Corlett, 

R. (2001) Fig-eating by vertebrate frugivores: a 

global review. Biological Reviews 76: 529-572 

Compton SG. (2002) Sailing with the wind: 

dispersal by small flying insects. Pp.113-133 

in Dispersal Ecology (ed D. Bullock) British 

Ecological Society. Blackwells 

Moore JC, Dunn AM, Compton SG, and 

Hatcher MJ. (2003) Re-emergence and fig 

permeability in fig tree-wasp mutualisms. 

Journal of Evolutionary Biology 16: 1186- 

1195 

Zavodna, M, Compton, SG, Biere, A, Gilmartin 

PM, and van Damme J. (2005) Putting your 

sons in the right place: the spatial distribution 

of fig wasp offspring inside figs. Ecological 

Entomology 30: 210-219.

Stephen Cornell 

MA, DPhil (Oxford); 

Postdoctoral research fellow, Universities of Cambridge, Manchester, Guelph, Geneva (1990-2001); 

Wellcome Trust Junior Research Fellow, University of Cambridge (2001-2004); 

University Research Fellow (2004-) 

Contact: s.j.cornell@leeds.ac.uk 

Dynamics of 

interacting populations 

I’m interested in the way that biological 

populations fluctuate over time and 

space. The study of population 

dynamics is fundamental to (i) ecology, 

which is primarily concerned with the 

patterns of abundance of species; 

(ii) epidemiology, where the impact 

of a pathogen is determined by its 

ability to colonise and spread through 

host populations; and (iii) evolution, 

where a successful phenotype is one 

which is able to increase in number 

relative to its peers. The underlying 

demographic mechanisms of birth, 

death, and immigration, together with 

genetic processes such as mutation 

and recombination, can be formulated 

mathematically, but these processes 

interact in a highly complex manner 

to produce emergent biological 

phenomena. 

The goal of my research is to 

understand the role played by 

interactions – between individuals of 

the same or different species, and over 

space – in determining the dynamics of 

populations. One very theoretical aspect 

to my research is the development 

of new methods for analysing the 

`interacting particle systems’ that 

underpin demographic processes 

– recent work on metapopulations 

represents the first mathematically 

exact analysis of nonlinear spatial 

population dynamics. We are currently 

extending these methods to other 

ecological scenarios such as a spatial 

Lotka-Volterra system and a neutral 

model of tree community dynamics. 

Work on nematode parasites has 

pointed to the importance of spatial and 

stochastic processes in determining 

the frequency of epidemics and the 

emergence of drug resistance. 

More empirically-driven research 

projects include the community 

dynamics of parasites of rabbits, where 

the seasonal patterns of the hosts’ 

immune response play a crucial role, 

and the within-phagocyte dynamics 

of salmonella in mice, where a simple 

model of bacterial proliferation and cell 

lysis explains the observed distribution 

between cells. I also have some more 

applied research interests: recent 

work has suggested a framework for 

reconciling the competing demands 

of agricultural production and 

conservation, and I am modelling 

the response of biodiversity to land 

use as part of a consortium studying 

sustainable management of uplands in 

the UK. 

Funding for these projects has come 

from a variety of sources, including 

the Wellcome Trust, Royal Society, 

Leverhulme Trust, and the Rural 

Economy and Land Use Programme 

(NERC/BBSRC/ESRC). 



php?staff=bgysc 


Ovaskainen, O, and Cornell, SJ. (2006) 

Asymptotically exact analysis of stochastic 

metapopulation dynamics with explicit spatial 

structure, to appear in Theoretical Population 

Biology (published online at http://www. 

sciencedirect.com/science/article/B6WXD- 

4HD8B4S-1/2/ 38e98f0a3b83e6e66e998bb 

6251440e8) 

Green, RE, Cornell, SJ, Schnarlmann, JPW and 

Balmford, AP. (2005) Farming and the fate of 

wild nature. Science 307: 1257-1258 

Cornell, SJ, Isham, VS and Grenfell, BT. 

(2003) Spatial parasite transmission, drug 

resistance, and the spread of rare genes. 

Proceedings of the National Academy of 

Sciences USA 100: 7401-7405 

Ovaskainen, O and Cornell, SJ. (2003) Biased 

movement at a boundary and conditional 

occupancy times for diffusion processes. 

Journal of Applied Probability 40: 557-580

Andy Cuming 

BA (Oxon); 

PhD (Cantab); 

Genetics Degree Programme Manager; 

Senior Lecturer in Genetics 

Contact: a.c.cuming@leeds.ac.uk 

Plant Molecular 

Genetics 

We work with the model moss 

Physcomitrella patens: the first nonflowering 

land plant to be selected for 

genome sequence analysis. Occupying 

a basal position in the land plant 

phylogeny, its genome represents a 

“missing link” between those of the 

green alga Chlamydomonas and the 

flowering plant Arabidopsis thaliana. 

The first draft of the genome sequence 

was recently released. 

The International Physcomitrella 

Genome Programme is a collaboration 

between laboratories in the US, Japan, 

Germany and Leeds. Our contributions 

are the establishment of a BBSRC 

sponsored EST collection and a genetic 

linkage map based on molecular 

markers, supported by the Gatsby 

Charitable Foundation and BBSRC. 

Recombination 

Physcomitrella displays some other 

traits generally absent from flowering 

plants. Most strikingly, it undergoes 

the integration of transforming 

DNA predominantly by homologous 

recombination – the targeting of the 

transforming fragment to homologous 

sequences within the genome. This has 

been exploited for functional genomic 

analysis: creating targeted disruptions 

in endogenous genes in order to 

determine their function. The processes 

by which homologous recombination 

occurs in plants are unknown, largely 

because the favoured (flowering) plant 

models are entirely incompetent to carry 

out this process. By contrast, the moss, 

which exhibits rates of gene targeting 

similar to that in yeast (i.e. up to 100%) 

provides an ideal system in which to 

unravel the mechanism of this process, 

which we have been characterising with 

the support of EU funding. 

Stress tolerance 

Another remarkable feature of 

Physcomitrella, indeed of the mosses in 

general, is its ability to withstand high 

levels of dehydration. As all gardeners 

know, most flowering plants will not 

survive dehydration, whereas the 

mosses, the extant relatives of the first 

plants to colonise a terrestrial habitat 

some 450million years ago, are highly 

tolerant of stresses. We have identified 

many of the genes that respond 

to the imposition of water stress in 

Physcomitrella. By using a highdensity 

microarray we have identified 

genes that are induced in response to 

dehydration, salt stress, osmotic stress 

and to the plant hormone abscisic 

acid (ABA). Remarkably, many of these 

genes have been conserved throughout 

land plant evolution, being similarly 

induced in higher plants. However, 

in the flowering plants the expression 

of these genes is often restricted to 

the developing seed: the only stage 

of the life cycle in which these plants 

exhibit true desiccation tolerance. 

Interestingly, both mosses and flowering 

plants use similar machinery in order 

to switch these genes on. How these 

genes have become restricted in their 

developmental pattern of expression 

during evolution remains an 

outstanding question. 


www.plants.leeds.ac.uk/groups_cum. 

html 


Kamisugi, Y, Cuming AC. (2005) The 

evolution of the Abscisic acid-response in land 

plants: comparative analysis of Group 1 LEA 

gene expression in moss and cereals. Plant 

Molecular Biology 59: 723-737 

Kamisugi, Y, Cuming, AC, Cove, DJ. (2005) 

Parameters determining the efficiency of 

homologous recombination mediated gene 

targeting in the moss Physcomitrella patens. 

Nucleic Acids Research 33: e173 

Kamisugi, Y, Schlink, K, Rensing SA, 

Schween, G, von Stackelberg, M, Reski, R, 

Cuming, AC, Cove DJ (2006) The mechanism 

of gene targeting in Physcomitrella patens: 

homologous recombination, concatenation and 

multiple integration. Nucleic Acids Research 

34: 6205-6214 

Cuming, AC, Cho, SH, Kamisugi, Y, Graham, 

H Quatrano RS (2007) Microarray analysis of 

transcriptional responses to abscisic acid and 

osmotic, salt, and drought stress in the moss 

Physcomitrella patens. New Phytologist 176: 

275-287

Brendan Davies 

BSc (UCL) PhD (Imperial Cancer Research Fund); 

Reader in Plant development (2004-2006); 

Professor in Plant development 2006-) 

Contact: b.h.davies@leeds.ac.uk 

Plant Development 

Laboratory 

My laboratory is interested in 

understanding plant development. 

Unlike animals, plants develop 

continuously in response to their 

environment. This developmental 

plasticity comes about, at least 

partly, because plant organs are 

constantly produced from a pool of 

undifferentiated stem cells which is 

found at the tip of the shoot. Plants 

need to accomplish at least three 

things to convert undifferentiated 

cells in this pool into lateral organs 

such as leaves and petals. Firstly the 

pool of stem cells needs to be able 

to maintain itself, so that the rate of 

generation of new stem cells is equal 

to the rate of differentiation of the old 

cells. Secondly the position of the newly 

formed organ needs to be defined and 

its boundaries established. Finally the 

newly developing organ needs to adopt 

a specific tissue and cell identity – the 

cells need to know whether they are to 

become hairs or stomata, petals 

or ovules. 

Using the model plants Antirrhinum 

and Arabidopsis we are investigating 

the mechanisms controlling these 

developmental changes. We use a 

combination of genetics, using mutants 

in which these processes are disrupted, 

and molecular biology, to identify genes 

which act within these processes. 

The following projects are being 

followed in the laboratory: 

● Analysis of genes controlling stem 

cell maintenance, lateral organ 

boundaries and organ identity. 

● Functional analysis of the MADSbox 

family of transcription factors in 

Arabidopsis and Antirrhinum. 

● Signalling to the cytoskeleton and its 

organisation (a collaboration with Prof. 

Patrick Hussey, Durham). 

● Comparative genome oganisation in 

Arabidopsis and Antirrhinum. 

● Nonsense mediated mRNA decay 

in plants. 

Funding for these projects comes 

from the BBSRC, Leverhulme Trust 

and the EU. 



dav.html 


Causier, B, Castillo, R, Zhou, J, Ingram, 

R, Xue, Y, Schwarz-Sommer, Z, Davies, B. 

(2005) Evolution in action: following function 

in duplicated floral homeotic genes. Current 

Biology 15:1508-1512 

de Folter, S, Immink, RG, Kieffer, M, 

Parenicova, L, Henz, SR, Weigel, D, Busscher, 

M, Kooiker, M, Colombo, L, Kater, MM, Davies, 

B., Angenent GC. (2005) Comprehensive 

interaction map of the Arabidopsis MADS Box 

transcription factors. Plant Cell. 17:1424- 

1433 

Deeks, MJ, Kaloriti, D, Davies, B, Malho, 

R, Hussey, PJ. (2004) Arabidopsis NAP1 Is 

Essential for Arp2/3-Dependent Trichome 

Morphogenesis. Current Biology 14: 1410- 

1414 

Weir, I, Lu, J, Cook, H, Causier, B, Schwarz- 

Sommer, Zs. and Davies, B. (2004) 

CUPULIFORMIS establishes lateral organ 

boundaries in Antirrhinum. Development 131: 

915-922 

Arciga-Reyes, L., Wootton, L., Kieffer, M. and 

Davies, B. UPF1 is required for nonsensemediated 

mRNA decay (NMD) and RNAi in 

Arabidopsis. The Plant Journal (2006) 47: 

480-489. 

Kieffer, M., Stern, Y., Cook, H., Clerici, E., 

Maulbetsch, C., Laux, T., Davies, B. Analysis 

of WUSCHEL and its functional homologue in 

Antirrhinum reveals a potential mechanism for 

their roles in meristem maintenance. Plant Cell 

(2006) 18: 560-573.

Jurgen Denecke 

BA, MSc (Brussels); 

PhD (Ghent); 

Lecturer, University of York (1994-1999); 

Senior lecturer, School of Biology (1999-2005); 

Reader of Plant Cell Biology and Biotechnology (2005-2007) 

Professor of Plant Cell Biology and Biotechnology (2008-) 

Contact: J.denecke@leeds.ac.uk 

The functioning of the 

plant secretory pathway 

My research team aims at 

understanding the secretory pathway 

in plants (Figure 1) and asks how this 

network of membrane compartments 

synthesizes proteins, how it discards 

them when they are incorrectly 

folded and how it packs correctly 

folded products into the appropriate 

transport vesicles for delivery to their 

final destination. 

Many of the genes controlling these 

steps have been discovered and the 

field is well aware of sorting signals and 

receptor molecules that recognize these 

signals. What is much less clear is how 

receptors find their way in the secretory 

pathway and which bio-molecular 

interactions lead to the specificity of 

membrane fusion in vesicle traffic. 

Many of the transport steps are bidirectional, 

to allow recycling of 

transport machinery. To close the cycle 

of events, we need to fully understand 

how such recycling pathways are 

regulated and how this is achieved in 

an energy-efficient manner within the 

mini-ecosystem of a living cell. It is this 

kind of subcellular ecology that interests 

us and requires us to take the next step 

beyond functional genomics and gene 

knockouts: the actual experimentation 

with the gene products themselves! 

Figure 2: vacuolar dynamics 

The challenge will be to discover how 

proteins act, how and with which 

molecules they interact, and how this 

influences bio-molecular interactions 

leading to changes in shape and 

affinity. To achieve these aims, my 

team uses a wide range of disciplines 

including genetics, protein engineering, 

quantitative biochemical in vivo 

transport assays, live fluorescence 

microscopy (Figure 2: vacuolar 

dynamics) and mathematical modeling. 

We use the model plants Arabidopsis 

thaliana for genetic approaches and 

Nicotiana tabacum for most postgenomic 

approaches to address protein 

function. Current projects address the 

process of quality control in protein 

production, ER export and vacuolar 

sorting. A particular focus is given to 

the mechanisms by which transport 

machinery is recycled and where 

energy is dissipated to keep circular 

events running smoothly. 


comes from the BBSRC (currently 

1 project) and the EU (currently 2 

projects) but my team regularly 

hosts PhD students and postdocs, 

mostly from abroad, who bring their 

own fellowships and enrich the 

research group. 



den.html 


Pimpl, P, Taylor, JP, Snowden, CJ, Hillmer, S, 

Robinson, DG, and Denecke, J. (2006) Golgimediated 

vacuolar sorting of the ER chaperone 

BiP may play an active role in quality control 

within the secretory pathway. The Plant Cell 

18: 198-211 

daSilva, LLP, Taylor, JP, Hadlington, JL, 

Hanton, SL, Snowden, CJ, Fox, SJ, Foresti, O, 

Brandizzi, F, and Denecke, J. (2005) Receptor 

salvage from the prevacuolar compartment 

is essential for efficient vacuolar protein 

targeting. Plant Cell 17: 132-148 

Pimpl, P, Hanton, SL, Taylor, JP, daSilva, LLP, 

and Denecke, J. (2003) The GTPase ARF1p 

Controls the Sequence-Specific Vacuolar 

Sorting Route to the Lytic Vacuole. Plant Cell 

15, 1242-1256 

Phillipson, BA, Pimpl, P, daSilva, LLP., Crofts, 

AJ, Taylor, JP, Robinson, DG, and Denecke, J. 

(2001) Secretory bulk flow of soluble proteins 

is COPII dependent. Plant Cell 13: 2005- 

2020 

Figure 1: The secretory pathway in plants

Alison Dunn 

BA (Pembroke College, Oxford); 

PhD (University of Leeds); 

Post Doc (Imperial College at Silwood Park); 

NERC Post Doctoral Research Fellow, University Research Fellow, Lecturer, Senior Lecturer, 

University of Leeds (1992-2005); 

Reader in Evolutionary Ecology (2005-) 

Contact: a.dunn@leeds.ac.uk 

Parasites, sex 

and invasions 

I am interested in the effect of parasites 

on host ecology and evolution. I 

am looking at the evolution and 

mechanisms of parasitic sex ratio 

distortion, the effect of parasites on host 

behavioural ecology and the impact of 

parasites on biological invasions. 

Parasitic sex ratio distorters are 

vertically transmitted from host 

mother to offspring. Only females 

transmit the parasite. By distorting 

host sex ratios towards females, these 

parasites increase their spread. We are 

interested in the evolution of vertical 

transmission and feminisation in the 

Microspora (a phylum of eukaryotic 

parasites). Phylogenetic analyses 

reveal that vertical transmission 

occurs in all major lineages and that 

feminisation has arisen more than once. 

We demonstrated that microsporidia 

feminise the crustacean Gammarus 

duebeni by impeding the development 

of the gland controlling male sexual 

differentiation. 

In theory, feminisers should spread 

rapidly. But prevalence stays fairly 

constant in the field. We have 

demonstrated that host behaviour 

controls the spread of the parasite; 

males prefer uninfected mates and 

donate fewer sperm to infected females. 

Biological invasions pose a major 

threat to biodiversity and economics. 

The spread of new parasites can 

devastate native biota, whilst escape 

from parasites may benefit an invader. 

Recently we have demonstrated that 

parasites can mediate predation 

between native and invading species, 

and influence the success of an 

invasion. Currently we are using 

theoretical and empirical approaches 

to study the role of parasites in 

invasion success. 

Research funded by NERC, BBSRC 

and The Leverhulme Trust. 



php?staff=AD 


Dunn, AM, Andrews, T, Ingrey, H, Riley, J, 

Wedell, N. (2005) Strategic sperm allocation 

under parasitic sex ratio distortion. Biology 

Letters 2: 78-80 

Slothouber-Galbreath, JGM, Smith, JE, Terry, 

RS, Becnel, JJ, Dunn, AM. (2004) Invasion 

success of Fibrillanosema crangonycis, 

n.sp., n.g.: a novel vertically transmitted 

microsporidian parasite from the invasive 

amphipod host Crangonyx pseudogracilis 

International Journal for Parasitology 34: 

235-244 

MacNeil, C, Dick, JTA, Johnson, MP, Hatcher, 

MJ, Dunn, AM. (2004) A species invasion 

mediated through habitat structure, intraguild 

predation and parasitism. Limnology and 

Oceanography 49: 1848-1856 

MacNeil, C, Dick, JTA, Hatcher, MJ, Terry, 

RS, Smith, JE, Dunn A.M. (2003) Parasite 

mediated predation between native and 

invasive amphipods. Proceedings of the Royal 

Society B. 270: 1309-1314

Simon Goodman 

BSc (Sheffield); 

PhD (Cambridge); 

Postdoctoral research assistant at Edinburgh; 

Research Fellow (Institute of Zoology, London); 

Lecturer in Evolutionary Biology (2004–) 

Contact: s.j.goodman@leeds.ac.uk 

Evolutionary and conservation genetics, 

conservation biology, disease ecology 

My research focuses on investigating 

how patterns of genetic variation relate 

to disease susceptibility, and the 

mechanisms by which disease acts as 

a major conservation threat. Pathogens 

are a major driving force in evolution 

and are intimately linked with much of 

the biological diversity we see around 

us. However, the impact of disease is 

now also of concern at a global scale for 

the conservation of biodiversity. Work 

in my group deals with investigating 

both the underlying evolutionary 

genetic interactions between hosts and 

pathogens, and developing ways to 

manage real-world conservation 

disease threats. 

We use a combination of theoretical 

and empirical approaches, for example 

by using theoretical models to test 

hypotheses about the evolution of 

disease resistance, and comparative 

genomic techniques to examine genetic 

variation in host candidate genes in 

relation to specific wildlife diseases, e.g. 

Phocine distemper virus in seals, or 

links between the population genetics 

of vector populations and their ability to 

act as vectors for different diseases (e.g. 

mosquitoes in Galapagos). We recently 

showed that evolutionary feedback due 

to acquired immunity and stochasticity 

in epidemic intervals can impede the 

evolution of disease resistance, which 

may have important implications for 

epidemiological models of disease. 

Together with Ecuadorian partners we 

recently established the first molecular 

genetic and pathology laboratory in 

the Galapagos islands. Many endemic 

species in the Galapagos archipelago 

are vulnerable to introduced diseases, 

or changes to native-disease ecology. 

We use genetic and pathology methods 

to determine current and future disease 

threats, and to develop diseasemitigation 

strategies. Our research here 

has already guided plans to reduce the 

risk of introduction of West Nile Virus to 

the archipelago. 

Figure 1: Caspian seal (photo courtesy of Agip KCO). 

Figure 2: Assessing the health of Galapagos 

giant tortoises. 

We are also working with institutions 

in the five Caspian states to develop 

solutions for conservation of the Caspian 

seal, which we recently demonstrated to 

have declined by more than 90% since 

the start of the 20th century. 

Funding: Darwin Initiative, the Caspian 

Environment Programme, Agip 

KCO, BBSRC and Marie Curie PhD 

studentships 



php?staff=bgysjgo 


Kilpatrick, AM, Daszak, P, Goodman, SJ et al. 

(2006) West Nile virus threatens Galápagos 

through tourism. Conservation Biology 20: 

1224-1231 

Schaschl, H, Suchentrunk, F, Hammer, S & 

Goodman, SJ (2005) Recombination and the 

origin of sequence diversity in the DRB MHC 

class II locus in chamois (Rupicapra spp). 

Immunogenetics 57: 108–115. 

Harding, KC, Hansén, BJ & Goodman, SJ 

(2005) Acquired immunity and stochasticity 

in epidemic intervals impede the evolution of 

host disease resistance. American Naturalist 

166: 722–730. 

Goodman SJ, Tamate, HB, Wilson, R et al. 

(2001) Bottlenecks, drift and differentiation: 

the population structure and demographic 

history of sika deer (Cervus nippon) in the 

Japanese archipelago. Molecular Ecology 10: 

1357–1370.

John Grahame 

BSc (University of the West Indies); 

PhD (Wales); 

Senior Lecturer 

Contact: j.w.grahame@leeds.ac.uk 

Variation, adaption 

and evolution 

I work on rough periwinkles – a group 

of intertidal snails – investigating the 

extent and likely significance of natural 

variation in these animals. 

There are two main areas of interest: 

in one species (Littorina saxatilis) there 

is a sharp gradient of variation from 

high to low water, associated with 

this is a partial barrier to gene flow. 

I am collaborating with Roger Butlin 

(Sheffield) on this study. We know 

that the barrier is much stronger for 

some parts of the genome than for 

others, and current effort is focused 

on investigating these more strongly 

affected regions to discover what genes 

are involved and how they vary. 

This work is especially exciting since 

the organism may represent an 

instance of speciation driven by 

ecological processes. 

More widely I am working on shell 

variation in Littorina saxatilis and two 

closely related sister species. This is 

directed at describing and quantifying 

shell variation, divergence and 

convergence, on a biogeographical 

scale, it is therefore an exercise in the 

evolution of form. 

These projects have recently been 

extended in collaboration with Geoffrey 

Trussell, Northeastern University 

(Mass.); collaborations are being 

developed with Emilio Rolàn-Alvarez 

(Spain) and Kerstin Johannesson 

(Sweden) which bring a broader 

biogeographic dimension to the work 

which has been in progress here. 


from NERC, BBSRC, EU 


http://www.fbs.leeds.ac.uk/staff/ 

grahame/ 


Backeljau, T, Frias Martins, AM, Gosling, 

E, Grahame, J, Mill, P, Brito, C, Clarke, A, 

Medeiros, R, Small, M, Wilding, C, Wilson, I, 

Winnepenninckx, B, Clarke, R, and De Wolf, H. 

2001. Periwinkles (Gastropoda, Littorinidae) 

as a model for studying patterns and dynamics 

of marine biodiversity. Bulletin de L’Institut 

Royal des Sciences Naturelles de Belgique, 

Biologie 71: 43-65 

Simpson, RJ, Wilding, CS, and Grahame, 

J. 2005. Intron analyses reveal multiple 

calmodulin copies in Littorina. Journal of 

Molecular Evolution 60: 505-512 

Wilding, CS, Grahame, J, and Mill, PJ. 

2001. Correlation of morphological diversity 

with molecular marker diversity in the rough 

periwinkle Littorina saxatilis (Olivi). Journal of 

Shellfish Research 20: 501-508 

Wilding CS, Grahame J, and Mill PJ. 2002. 

A GTT microsatellite repeat motif and 

differentiation between morphological forms 

of Littorina saxatilis: speciation in progress? 

Marine Ecology Progress Series 227: 195-204

Henry Greathead 

BSc Animal Science; 

PhD (University of Nottingham); 

PGCLTHE (University of Leeds); 

Research Assistant, University of Nottingham (1990-1996); 

Study Manager, Life Sciences (1997-1998); 

Lecturer in Animal Production Science, University of Leeds (1998-) 

Contact: H.M.R.Greathead@leeds.ac.uk 

Animals are 

what they eat! 

How does what an animal eats effect 

its performance? This is of both 

fundamental and applied interest. 

Plants produce an immense diversity of 

plant secondary metabolites, the nonubiquitous 

products of plant secondary 

metabolism. Many of these compounds 

are bioactive. It is of fundamental interest 

to understand how these compounds 

interact with living organisms, from 

a molecular level (nutrigenomics) 

right through to the whole organism 

itself. Why? – because it will improve 

our understanding of how common 

chemicals in the diets of animals 

affect their performance. The applied 

interest is being driven by the growing 

legislation against the prophylactic use 

of performance enhancing medicinal 

feed-additives for which bioactive plant 

secondary metabolites are a potential 

and sustainable alternative. 

Research over the last six years, aimed 

at identifying novel strategies to enhance 

dairy cow performance by modifying 

the rumen microflora, has identified 

individual plant extracts, namely eugenol 

and cinnamaldehyde, that have potential 

to enhance the efficiency of protein and 

energy metabolism in the rumen. The 

rumen bacteria and Archaea involved in 

these effects are under investigation. 

A project investigating the use of plant 

secondary metabolites as anticoccidial 

feed additives in broiler chickens has 

shown that while thymol and carvacrol 

appear to have no negative impact on 

the E. acurvulina parasite itself, thymol 

may have a role to play in controlling 

coccidiosis through its ability to limit the 

pathological impact of the disease. 

Future work will strive to understand 

how plant secondary metabolites elicit 

their effects. In particular how they 

might interact with genes expressed 

in enterocytes. 

Sources of funding include the EU, 

BBSRC and industry. 



php?staff=HMRG 

Figure 1: The effect of feeding thymol and carvacrol (1:1 

combination) at a range of diet inclusion levels (0, 125, 

250, 500, 1000 and 2000 ppm) to broilers infected (I) 

with 500,000 sporulated E. acervulina oocysts on live 

weight versus uninfected/untreated (U0) birds. The error 

bar is the standard error of the difference (n=6). 


Greathead, HMR, Dawson, JM, Craigon, J, 

Sessions, VA, Scollan, ND and Buttery, PJ. 

(2005). Fat and protein metabolism in growing 

steers fed either grass silage or dried grass 

over a range of ME intakes. British Journal of 

Nutrition 94: 1-13 

Ilsley, SE, Miller, HM, Greathead, HMR 

and Kamel, C. (2003). Plant extracts as 

supplements for lactating sows: effects on 

piglet performance, sow food intake and diet 

digestibility. Animal Science 77: 247-254 

Greathead, HMR. (2003) Plants and plant 

extracts for improving animal productivity. 

Proceedings of the Nutrition Society 62: 

279-290 

Greathead, HMR, Dawson, JM, Scollan, ND, 

and Buttery PJ. (2001) In vivo measurement of 

lipogenesis in ruminants using [1-14C]acetate. 

British Journal of Nutrition 86: 37-44

Keith Hamer 

BSc (Manchester); 

PhD (Glasgow); 

Lecturer, Senior Lecturer, University of Durham (1993-2002); 

Senior Lecturer (2002-2004); 

Ecology and Evolution Group Leader (2003-); 

Reader in Animal Ecology (2004-) 

Contact: k.c.hamer@leeds.ac.uk 

Population and behavioural ecology; 

conservation biology 

The main theme of my research is life 

history-environment interactions: how 

the life histories of different species are 

shaped by features of their environments, 

and how life history in turn determines 

the ability of different species to respond 

to changing environments. My interests 

in this field span a wide range of 

organisms from sap-sucking plant-lice in 

sub-Artic Norway to dipterocarp trees in 

Bornean rainforest. However most of this 

work focuses on two organisms, seabirds 

and tropical butterflies. 

My work on seabirds is particularly 

concerned with foraging and food 

provisioning. For instance, several 

current projects are examining the 

different foraging strategies employed by 

male and female parents, and how these 

affect their contributions to biparental 

care. I’m also very interested in the 

reproductive strategies of parents, in 

particular how parents regulate their 

reproductive effort and adjust the sexes 

of their offspring so as to maximise their 

lifetime reproductive success. My work 

also has a number of more applied 

themes, including interactions between 

seabirds and fisheries, and impacts of 

climate change on seabird demography. 

My work on tropical butterflies 

focuses mainly on how species’ life 

histories determine their responses to 

disturbance. I’m also very interested 

in how disturbance affects species 

richness, community composition and 

the abundance, distribution and genetic 

diversity of species at different spatial 

and temporal scales. 

Funding for these projects comes from a 

wide variety of sources including NERC, 

the European Commission and DEFRA’s 

Darwin Initiative. 



php?staff=KCH 


Hamer, KC, Quillfeldt, P, Masello, JF & 

Fletcher, KL. (2006) Sex differences in 

provisioning rules: responses of Manx 

shearwaters to supplementary chick-feeding. 

Behavioral Ecology 17: 132-137 

Votier, SC and 12 others. (2004) Changes 

in fisheries discard rates and seabird 

communities. Nature 427: 727-730 

Hill, JK & Hamer, KC. (2004) Determining 

impacts of habitat modification on diversity of 

tropical forest fauna: the importance of spatial 

scale. Journal of Applied Ecology 41: 744-754 

Lewis, S, Hamer, KC, Money, L, Redman, 

KK, Griffiths, R, Wanless, S & Sherratt, TN. 

(2004) Brood neglect and contingent foraging 

behaviour in a pelagic seabird. Behavioural 

Ecology and Sociobiology 56: 81-88

Ian Hope 

BA (Oxford); 

PhD (Edinburgh); 

Postdoctoral Research Associate, Harvard Medical School (1984-87); 

Junior Staff Scientist, MRC Laboratory of Molecular Biology (1987-91); 

Lecturer and Senior Lecturer (1991-2008); 

Professor of Invertebrate Development Genetics (2008-) 

Contact: i.a.hope@leeds.ac.uk 

Caenorhabditis elegans 

developmental genomics 

The nematode worm, Caenorhabditis 

elegans, is a key model system in 

modern biological research. We are 

investigating how its genome is controlled 

to allow development from fertilization 

to the mature adult animal. (Figure 1, 

shows a C. elegans embryo at the one-, 

two- and four-cell stage. The embryo is 

50 µm long.) 

Figure 1 

C. elegans was the first animal for which 

the whole genome was sequenced 

and has led the way in genomics 

research. Its invariant, fully described, 

developmental cell lineage provides 

a unique framework through which 

the control of the expression of this 

genetic information can be understood. 

Gene expression patterns provide a 

direct link between the DNA sequence 

and the development we can observe 

using a microscope. We generate gene 

expression pattern data using green 

fluorescent protein (GFP) reporter gene 

fusions. Complete transparency of the 

animal allows observation of GFP through 

all developmental stages. (Figure. 2, 

shows constitutive GFP expression 

driven by a PHD zinc-finger transcription 

factor gene’s promoter. The adult is 1 

mm long.) 

Developmental expression of the 

genome is controlled by a complex 

regulatory network. To understand 

this control we must study the entire 

system, representing that system using 

computer models. The core of such 

models will be transcription factors, 

sequence specific DNA binding proteins 

that control the expression of target 

genes. We have re-analysed the genome 

sequence data annotation to identify all 

C. elegans transcription factor genes. 

Reporter fusions have been constructed 

for most of these, for expression pattern 

determination in transgenic C. elegans. 

Our data, with protein–protein and 

protein–DNA interaction data from 

collaborating laboratories, will be used 

to generate models of the regulatory 

circuitry. (Figure 3, shows nuclearlocalized 

GFP in the embryo, driven by 

a C2HC zinc-finger transcription factor 

gene’s promoter.) 

Biological processes are remarkably 

conserved at the molecular genetic 

level. Discoveries made with this small 

nematode worm have been and will 

continue to be of great importance in 

advancing our understanding of animal, 

including human, biology. 

Funding: Wellcome Trust, NIH, MRC, 

BBSRC 


http://bgypc059.leeds.ac.uk/~web 

Figure 3 


Reece-Hoyes, JS, Deplancke, B, Shingles, 

J, Grove, CA, Hope, IA & Walhout, AJM. 

(2005) A compendium of C. elegans 

regulatory transcription factors: a resource for 

deciphering transcription regulatory networks. 

Genome Biology 6: R110 

Hope, IA, Stevens, J, Garner, A et al. (2004) 

Feasibility of genome-scale construction of 

promoter: reporter gene fusions for expression 

in Caenorhabditis elegans using a MultiSite 

Gateway recombination system. Genome 

Research 14: 2070–2075 

Reece-Hoyes, JS, Shingles, J, Dupuy, D et 

al. (2007) Insight into transcription factor 

gene duplication from Caenorhabditis elegans 

Promoterome-driven expression patterns. BMC 

Genomics 8: 27 

Dolphin, CT & Hope, IA. (2006) 

Caenorhabditis elegans reporter fusion genes 

generated by seamless modification of large 

genomic DNA clones. Nucleic Acids Research 

34: e72 

Figure 2

Bill Hughes 

BSc (Bangor); 

MSc (Imperial College); 

PhD (Southampton); 

Research Fellow, University of Copenhagen (2001-2003); 

Honorary Visiting Scholar, University of Sydney (2004-2005); 

Marie Curie Research Fellow, University of Sheffield (2004-2006); 

Lecturer, University of Leeds (2006-) 

Evolutionary ecology 

of social insects 

My research uses social insects as 

model systems for investigating a range 

of general questions in ecology and 

evolution. One of my main areas of 

interest is host-parasite interactions. 

Social insects are particularly interesting 

because their colonies are in many ways 

ideal for the survival and transmission of 

parasites, yet they appear to suffer much 

less from disease than we would expect. I 

use primarily leaf-cutting ants and fungal 

pathogens to investigate the diversity and 

impact of parasites upon social insects, 

their defences against parasites, and 

general host-parasite questions such as 

within-host competition and the evolution 

of virulence. On the other side of the 

symbiosis-spectrum, I am also interested 

in the fascinating agricultural mutualism 

between leaf-cutting ants and their 

fungal food. 

Another subject that links several of my 

research questions is the implications 

of within-group genetic diversity. The 

division of labour and morphological 

castes of many social insect colonies 

represent some of the most extreme 

examples of phenotypic diversity and we 

have recently shown in leaf-cutting ants 

that genetics can influence which caste 

a larva develops into. We have also found 

that more genetically diverse groups of 

ants are more resistant to disease. These 

results suggest that leaf-cutting ant 

queens may improve both their colonies’ 

resistance to disease and division of 

labour by increasing their colonies’ 

genetic diversity, providing some 

explanation for the perplexing question 

of why females of many species engage 

in the costly behaviour of mating with 

multiple males. Current work combines 

a comparative approach with targeted 

experimental and molecular studies 

in order to develop a more complete 

understanding of the overall trade-offs 

underlying mating strategies. 

My research involves field and lab based 

studies on a range of social insects, with 

leaf-cutting ants and honeybees being 

my main model systems, and utilises 

a mix of behavioural, chemical and 

molecular techniques. 

Recent funding for my research has 

come from the EC, NERC, BBSRC 

and the Carlsberg Foundation 


Hughes, WOH, & Boomsma, JJ. (2006) Does 

genetic diversity hinder parasite evolution in 

social insect colonies. Journal of Evolutionary 

Biology 19: 132-143 

Sumner, S, Hughes, WOH, Pedersen, JS & 

Boomsa, JJ. (2004) Social parasite queens 

abandon multiple mating. Nature 428: 35-36 

Hughes, WOH, Sumner, S, van Borm, 

S & Boomsma JJ. (2003) Worker caste 

polymorphism has a genetic basis in 

Acromyrnex leaf-cutting ants. Proceedings of 

the National Academy of Sciences USA 100: 

9394-9397 

Hughes, WOH, Eilenerg, J & Boomsma, JJ. 

(2002) Trade-offs in group-living: transmission 

and disease resistance in leaf-cutting ants. 

Proceedings of the Royal Society of London B 

269: 1811-1819

David Iles 

BSc Microbiology, University College London; 

PhD Catholic University of Nijmegen (KUN), The Netherlands, specialising in Molecular Neuroendocrinology 

and Medical Parasitology; 

Department of Cell Biology and Histology, KUN, awarded a Doctorate in Medical Sciences for work on the molecular 

genetics of neuromuscular disease; 

Member of the Human Genome Organisation (HUGO) and the European Malignant Hyperthermia Group; 

Senior Lecturer in Human Genetics 

Molecular genetic basis of 

malignant hyperthermia (MH) 

MH is an autosomal dominant disorder 

of skeletal muscle that manifests as 

a potentially life-threatening adverse 

reaction to volatile anaesthetics. Since 

MH results from an anaesthetic-induced 

breakdown in calcium homeostasis, 

my work has in the past focused on 

establishing the relationships between 

susceptibility to MH (MHS) and genes 

encoding skeletal muscle Ca2+ channels 

and their regulatory subunits. To date, 

6 MHS loci have been identified, but by 

far the most important of these is RYR1, 

the gene encoding the skeletal muscle 

isoform of the ryanodine receptor. 

Future work will focus on the functional 

consequences of missense mutations in 

the RYR1 gene. 

Idiopathic male factor infertility 

The male is the infertile partner in 

approximately half of the 15% of 

couples who seek help from assisted 

conception clinics. Of particular interest 

to us are the reasons underlying male 

factor infertility in otherwise healthy, 

normozoospermic men. We are currently 

seeking to identify chromosomal domains 

that are preferentially histone packaged 

in spermatozoa and establish whether 

or not normal boundaries of histone/ 

protamine packaging are disturbed in 

spermatozoa from infertile men and if 

these domains are more susceptible to 

DNA damage than protamine-bound 

domains. This work is being carried 

out in collaboration with Dr David 

Miller, Department of Obstetrics and 

Gynaecology, Leeds General Infirmary. 

Collaborations 

Functional analysis of mutations in the 

human RYR1 gene associated with 

malignant hyperthermia susceptibility. 

With Professor Paul Allen, Brigham and 

Women’s Hospital, Harvard Medical 

School, Boston MA. 

Identifying the molecular components 

of the carotid body oxygen sensor. With 

Professor Chris Peers (Cardiovascular 

Medicine, University of Leeds). 

Funding sources: 

Department of Health, BBSRC, MRC 


Kemp, PJ, Peers, C, Riccardi, L, Iles, DE, 

Mason, HS, Wootton, P, Williams, SE. (2006). 

In search of the acute oxygen sensor: 

functional proteomics and acute regulation 

of large-conductance, calcium-activated 

potassium channels by hemeoxygenase-2. Adv 

Exp Med Biol. 580:137-46 

Williams, SE, Wootton, P, Mason, HS, Bould, 

J, Iles, DE, Riccardi, R, Peers, C and Kemp, 

PJ. (2004). Hemeoxygenase-2 Is an Oxygen 

Sensor for a Calcium-Sensitive Potassium 

Channel. Science 306: 2093-2097 

Snoeck, M, Sengers, R, Iles, DE, ter Laak, H, 

Robinson, R, Padberg, G. (2004) Investigation 

of a Family Following Fulminant Malignant 

Hyperthermia. J Clin Neuromusc Dis. 5: 122- 

128 

Williams, SE, Wootton, P, Mason, HS, Iles, 

DE, Peers, C, Kemp, PJ. (2004). siRNA 

knock-down of gamma-glutamyl transpeptidase 

does not affect hypoxic K+ channel inhibition. 

Biochem Biophys Res Commun 314: 63-68

R Elwyn Isaac 

BSc (University College Cardiff); 

PhD (University College Cardiff); 

Postdoctoral research at Liverpool, Texas A&M University and at the Department díEtudes et díIngÈniÈrie des 

ProtÈins, Gif-Sur-Yvette, France; Visiting Lecturer, University of Lancaster; 

Professor of Comparative Biochemistry 

Contact: r.e.isaac@leeds.ac.uk 

The role of neuropeptides and peptidases 

in development and reproduction 

Our research exploits the amenable 

genetics and the sequenced genomes 

of the fruit fly Drosophila melanogaster 

and the nematode Caenorhabditis 

elegans to understand biochemistry 

of behaviour, development and 

reproduction. We are particularly 

interested in the role of neuropeptides 

and peptidases and the development 

of novel strategies to control parasitic 

nematodes and insect pests. 

We have characterized the genes for 

proctolin, the first insect neuropeptide 

to be sequenced, and a family of 

tachykinin peptides (Dtk) related to 

human tachykinins. We are currently 

using P-element mutants, conditional 

gene silencing and ectopic expression 

to study their role in development, 

behaviour and gut physiology. 

Figure 1: A nematode with two coats. Inactivation of the 

C. elegans ACE gene prevents shedding of the old cuticle 

during moulting and leads to eventual death 

Neutral endopeptidases are zinc 

peptidases that include mammalian 

neprilysin (NEP) and endothelinconverting 

enzyme (ECE), both of 

which can switch peptide signals on/off 

at the cell surface. We have recently 

identified a novel NEP with roles in 

renal function and reproduction in 

Drosophila. Other zinc peptidases that 

process and inactivate neuropeptides 

are the angiotensin-converting enzymes 

(ACEs). We have exploited the genomes 

of Drosophila, Caenorhabditis and 

Anopheles gambiae (mosquito) to 

study invertebrate ACE gene families 

and their physiological roles. Of the six 

D. melanogaster ACE genes, only two 

are enzymically active. There are nine 

ACE genes in the A. gambiae genome, 

three of which are upregulated after a 

blood meal, and we have shown that 

ACE inhibitors block egg-laying. Our 

work on ACE genes in the mosquito 

and fruit fly validate ACEs as exploitable 

targets for insect control. In C. elegans, 

ACE controls the expression of genes 

required for periodic moulting of the 

cuticle. Nematodes with an inactive 

ACE gene fail to moult properly and die 

wrapped in two or more cuticles. 

Peptidases in male reproductive 

tissues are important for reproduction. 

We have used proteomics to identify 

new peptidases in accessory-gland 

secretions of Drosophila and are 

currently investigating their roles 

in fertility. 

Funding: BBSRC, DEFRA, 

Wellcome Trust 


http://bgypc059.leeds.ac.uk/~elwyn/ 


Thomas, JE, Rylett, CM, Carhan, A et al. 

(2005) Drosophila melanogaster NEP2 is a 

new soluble member of the neprilysin family 

of endopeptidases with implications for 

reproduction and renal function. Biochemical 

Journal 386: 357–366. 

Taylor, CAM, Winther, AME, Siviter, RJ, 

Shirras, AD, Isaac, RE & Nassel, DR. (2004) 

Identification of a proctolin preprohormone 

gene (Proct) of Drosophila melanogaster: 

expression and predicted prohormone 

processing. Journal of Neurobiology 58: 

379–391. 

Brooks, DR, Appleford, PJ, Murray, L & 

Isaac, RE. (2003) An essential role in 

molting and morphogenesis of Caenorhabditis 

elegans for ACN-1, a novel member of the 

angiotensin-converting enzyme family that 

lacks a metallopeptidase active site. Journal of 

Biological Chemistry 278: 52340–52346.

Stefan Kepinski 

RCUK independent research fellow (2006-); 

Bsc.Hons (Liverpool); 

PhD. (Liverpool) 

Contact: s.kepinski@leeds.ac.uk 

Auxin and 

plant development 

I am interested in understanding how 

the plant hormone auxin operates 

throughout plant development to 

shape the plant and control important 

traits. Auxin is a fascinating signalling 

molecule because of the sheer diversity 

of plant developmental processes in 

which it is involved. 

At the cellular level, auxin can regulate 

cell division, cell expansion and can 

trigger specific differentiation events. 

In addition, auxin is unique among 

plant hormones in that its transport 

is both tightly regulated and polar, 

allowing auxin to carry directional 

intercellular and long distance signals, 

and thus act as a regulator of pattern 

formation. A central component of 

this developmental control is the 

transcriptional regulation of hundreds 

of genes and we are focussing 

on precisely how auxin regulates 

gene expression. Using a range of 

biochemical and genetic techniques we 

have recently made significant progress 

in understanding the early events 

of auxin signalling by identifying the 

receptor for this response and thereby 

completing a basic signal transduction 

cascade from auxin to changes in gene 

expression. As well as understanding 

better the biology of auxin perception, 

we are also studying how this entire 

mechanism is then used throughout 

the plant to regulate a range of very 

different developmental processes. 

This addresses the apparent paradox 

of how the perception of auxin as a 

single signalling molecule can generate 

diverse response outputs, specific to 

particular developmental contexts. 

This work involves a systematic 

analysis of the auxin signalling 

components in hand coupled to 

novel genetic and chemical genetic 

screens to identify new components 

modulating auxin response. 

Funding for this work comes from the 

BBSRC and Umeå University, Sweden 



php?tag=Kepinski_S 


Kepinski, S. (2006) Integrating hormone 

signalling and patterning mechanisms in plant 

development. Current Opinion in Plant Biology 

9: 28-34 

Kepinski, S and Leyser, O. (2005) The 

Arabidopsis F-box protein TIR1 is an auxin 

receptor. Nature 435: 446-451 

Kepinski, S and Leyser, O. (2004) Auxininduced 

SCF TIR1 -Aux/IAA interaction involves 

stable modification of the SCF TIR1 complex. 

Proceedings of the National Academy of 

Science, USA 101: 12381-12386 

Gray, WM†, Kepinski, S†, Rouse, D, Leyser, 

O, and Estelle, M. (2001) Auxin regulates 

SCF TIR1 -dependent degradation of Aux/IAA 

proteins. Nature 414: 271-276

Jerry Knapp 

BSc (Hull); 

PhD (Wales); 

Lecturer in Microbiology (1981–1997); 

Senior Lecturer in Microbiology (1997–) 

Contact: j.s.knapp@leeds.ac.uk 

Environmental microbiology, 

bioremediation and effluent treatment 

My main interest is in how 

microorganisms degrade environmental 

pollutants, especially those produced 

during the manufacture and use of 

synthetic chemicals. The increasing use 

of such organic chemicals has caused 

many environmental problems. Microbes 

have always had a role in ‘cleaning up’ 

our environment but their task in recent 

years has been considerable because 

the structures of many new, xenobiotic, 

chemicals make them very difficult 

to degrade. 

I am interested in how microbes 

develop the ability to degrade xenobiotic 

chemicals, many of which bear little 

resemblance to natural chemicals, 

and the mechanisms by which these 

chemicals are broken down. I have 

researched the biodegradation of 

structurally diverse compounds by 

a range of microbes. Recently my 

research has focused largely on the 

biodegradation of benzothiazoles 

(sulphur-containing aromatics used 

in the rubber industry) by bacteria in 

the genus Rhodococcus and on the 

problems of pollution by coloured 

effluents. Work on benzothiazoles 

has used classical biochemical and 

microbiological methods, together with 

state-of-the-art analytical techniques, 

genomics and proteomics. 

Coloured effluents are commonly 

produced during the manufacture and 

use of dyes. Our research has included 

the use of bacteria under anaerobic 

conditions and of white rot fungi, e.g. 

Coriolus versicolor. Research has 

involved optimization of conditions 

for degradation and studies of the 

biochemical mechanisms by which 

complex azo dyes are degraded. We have 

developed a range of novel reactors and 

demonstrated the robustness of white 

rot fungi grown in such bioreactors for 

prolonged periods. 

Recently I have been involved in 

research into the problems caused by 

textile-dyeing effluents in Bangladesh. 

This work has involved monitoring of 

pollution problems and investigation of 

effluent treatment processes used locally. 

Many industrial effluents are of high and 

variable salinity and I am also interested 

in the biodegradation of industrial 

effluents and xenobiotic chemicals under 

highly saline conditions. Other interests 

include the role of microbes in deposition 

of minerals and the development and 

use of novel disinfectants. 

Funding for these projects has typically 

come from industry but some has come 

from DFID and the EU. 



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Akhtaruzzaman, M, Clemett, A, Knapp, J, 

Mahmood, MA & Ahmed, S. (2005) Choosing 

an Effluent Treatment Plant. Stockholm 

Environment Institute, Stockholm and 

Bangladesh Centre for Advanced Studies, 

Dhaka 

Knapp, JS & Bromley-Challenor, KA. (2003) 

Recalcitrant organic chemicals. In Handbook 

of Water and Wastewater Microbiology (eds 

Mara, DD & Horan, NJ), pp. 501–536. 

Academic Press, London 

Haroune, N, Combourieu, B, Besse, P, et 

al. (2002) Benzothiazole degradation by 

Rhodococcus pyridinovorans strain PA: 

evidence of a catechol 1,2-dioxygenase 

activity. Applied and Environmental 

Microbiology 68: 6114–6120 

Knapp, JS, Vantoch-Wood, EJ & Zhang, 

F. (2001) Use of wood-rotting fungi for 

the decolourisation of dyes and industrial 

effluents. In Fungi in Bioremediation (ed. 

Gadd, GM), pp. 242–304. Cambridge 

University Press, Cambridge

Celia Knight 

BSc (Bristol); 

PhD (Leeds); 

Lecturer Leeds (1994); 

Senior Lecturer Leeds (2001); 

University Teaching Fellow (2003-4); 

Academic Coordinator for Gatsby Plants (2004-); 

Director of the Undergraduate School (2006-); 

Director of the Institute of Life Science Education (2006-) 

Contact: c.d.knight@leeds.ac.uk 

Plant Developmental 

Biology 

I am interested in plant development, 

particularly at the level of the cell and 

the relatively simple decisions that the 

cell makes. For most of my career I 

have studied development in the moss 

Physcomitrella patens because it has 

simple cell structures and yet these 

respond to light, gravity and hormones 

as angiosperms do. I have published on 

gravitropism and jointly published the 

first report of stable transformation of 

P.patens in 1991. I co-ran the BBSRCfunded 

Physcomitrella EST Programme 

(PEP) from 1999-2002 (with David Cove 

and Andrew Cuming, Leeds), being 

responsible for the transformation and 

training service involving 5 international 

training workshops on moss techniques. 

PEP was part of an international effort 

which has resulted in the complete 

sequencing of the Physcomitrella 

genome (draft sequence recently 

released) as the first non-angiosperm 

land plant. I am currently editing a book 

on Physcomitrella to be published by 

Blackwell in 2008. 

Plant-Microbe Interactions 

I am also interested in the ways that 

plants and microbes produce and 

perceive chemical signals, having 

previously worked and published on 

Rhizobium spp. nodulation. Working 

with David G Adams (Leeds), I published 

a method to detect chemotaxis in the 

symbiosis between nitrogen-fixing 

cyanobacteria and liverworts. This 

has potential for the identification and 

characterisation of plant compounds 

from a range of host species, including 

cereals, that are perceived by soil 

nitrogen-fixing microbes. 

Communicating Science 

I am committed to developing ways 

to inspire and inform students about 

Biology, as well as assisting academics 

to teach manageably within a research 

environment. The Gatsby Plants project 

runs an annual summer school for 

high-achieving undergraduates from 

UK Universities as well as developing a 

web-based teaching resource. As part 

of my teaching fellowship I have 

developed an undergraduate e- 

journal (Biolog-e) to showcase and 

reward undergraduate research and 

have established the first national 

undergraduate research journal, 

Bioscience Horizons, as part of a UK 

University consortium and Oxford 

University Press. 

Funding for these projects has been 

from BBSRC, NERC, EU and Gatsby. 


Lee, KJD, Sakata, Y, Mau, S-L, Pettolino, 

F, Bacic, A, Quatrano, RS, Knight, CD, and 

Knox, JP. (2005) Arabinogalactan Proteins 

Are Required for Apical Cell Extension in the 

Moss Physcomitrella patens. Plant Cell 17: 

3051-3065 

Knight, CD, Cove, DJ, Cuming, AC and 

Quatrano, RS. (2002) Moss Gene Technology. 

In: Plant Molecular Biology – a practical 

approach. Eds. Gilmartin PM and Bowler C. 

IRL Press. 

http://www.gatsbyplants.leeds.ac.uk 

http://www.biolog-e.leeds.ac.uk 

http:www.biohorizons.oxfordjournals.org

Paul Knox 

Professor of Plant Cell Biology (2005-); 

Lecturer, Senior Lecturer, Reader, Professor, University of Leeds (1991-); 

BSc (Newcastle), PhD (Wales) 

Contact: j.p.knox@leeds.ac.uk http://www.plantcellwalls.net 

Plant 

cell walls 

Cell walls are fundamental to processes 

that underpin plant growth and 

development and also impact greatly 

on the properties of plant materials 

with industrial or food uses. We are 

interested in the biology of plant cell 

walls and how the components of these 

complex polysaccharide-based fibrous 

composites function in diverse cell types 

and in processes such as cell expansion 

and cell adhesion. In addition, we are 

also interested in how changes in cell 

wall polymer structure and function has 

related to plant evolution. 

Our work focuses on the polysaccharide 

components of primary and secondary 

cell walls. In particular we are exploring 

the structure-function relations 

of the complex galacturonan sets 

of pectic polymers and the class 

of plant proteoglycans known as 

arabinogalactan-proteins in a range of 

developmental systems including the 

Arabidopsis seedling root. Current work 

has also focused on the xylan set of cell 

wall polysaccharides that are abundant 

in the secondary cell walls of xylem 

elements and plant fibres. 

One of our major strategies to explore 

plant cell wall functions is by the 

generation and use of defined molecular 

probes to cell wall polysaccharide 

components. These probes, such as 

monoclonal antibodies, are invaluable 

tools to uncover the spatial- and 

developmental-regulation of cell wall 

polymers and for the imaging of cell wall 

architectures. Moreover, such probes 

can define alterations to cell walls in 

response to environmental or genetic 

impacts or during the processing or 

use of plant materials. We have also 

extended the range of molecular probes 

for cell wall polymers by adapting 

carbohydrate-binding modules (CBMs, 

protein modules from microbial 

glycoside hydrolases) that have the 

capacity to bind polysaccharides 

including cellulose for use as probes. 

Our extending sets of molecular tools 

are useful for the analysis of plant cell 

walls in all contexts. 


Blake AW, McCartney L, Flint JE, Bolam DN, 

Boraston AB, Gilbert HJ, Knox JP (2006) 

Understanding the biological rationale for the 

diversity of cellulose-directed carbohydratebinding 

modules in prokaryotic enzymes. 

Journal of Biological Chemistry 281, 29321- 

29329 

McCartney L, Blake AW, Flint J, Bolam DN, 

Boraston AB, Gilbert HJ, Knox JP (2006) 

Differential recognition of plant cell walls by 

microbial xylan-specific carbohydrate-binding 

modules. Proc. Natl. Acad. Sci. USA 103, 

4765-4770 

Lee KJD, Sakata Y, Mau S-L, Pettolino F, 

Bacic A, Quatrano RS, Knight CD, Knox 

JP (2005) Arabinogalactan-proteins are 

required for apical cell extension in the moss 

Physcomitrella patens. Plant Cell 17, 3051- 

3065 

Carafa A, Duckett JG, Knox JP, Ligrone R 

(2005) Distribution of cell-wall xylans in 

bryophytes and tracheophytes: new insights 

into basal interrelationships of land plants. 

New Phytologist 168, 231-240

Jens Krause 

BA (Berlin); 

MPhil & PhD (Cambridge); 

Lecturer, Leeds University (1996-2002); 

Senior Lecturer, Leeds University (2002-2004); 

Reader, Leeds University (2004); 

Professor of Behavioural Ecology (2004-) 

Contact: J.Krause@leeds.ac.uk 

Behavioural ecology, social networks, 

collective behaviour 

My research interest is focused on 

the mechanisms and functions of 

group-living in animals. Group-living 

has a wide range of potential benefits 

and costs which can be investigated 

experimentally both in the field and/or 

the laboratory. 

We use social network theory to 

study details of the social structure 

of free-ranging fish populations. This 

approach has the potential to go well 

beyond conventional analysis of social 

interactions in the behavioural sciences, 

providing quantitative predictions 

regarding important issues such as 

reciprocal altruism and the transmission 

of information and diseases. Our main 

study system is the Trinidadian guppy, 

Poecilia reticulata, which we found to 

have a complex and highly structured 

social network, exhibiting features that 

fulfil the pre-requisite for the evolution 

of reciprocal altruism. This work is done 

in collaboration with Dr. Dick James 

(Bath University). 

More recently we have also started 

looking at other species such as red 

deer, lemon sharks in the Bahamas and 

various species of domestic animals 

(such as cows and sheep). 

In the context of social networks we are 

very interested in social recognition in 

fish and familiarity preferences. Several 

fish species have been reported to 

prefer familiar fish with whom they had 

experiences in the past to unfamiliar 

ones. This has been a particularly 

important point regarding models of the 

evolution of reciprocal altruism between 

unrelated individuals in the context 

of predator inspection behaviour. 

Another challenge is to relate individual 

personality traits of fish to their position 

in the social network (see figure). 

We have found that fish differ in 

boldness and shoaling tendency and 

currently explore the consequences of 

such traits for diffusion of information 

in social networks. 

Funding for these projects comes from 

the EPSRC and The Leverhulme Trust. 



php?staff=JK 


Couzin, ID, Krause, J, Franks, NR & Levin, SA. 

(2005) Effective leadership and decisionmaking 

in animal groups on the move. Nature 

433: 513-516 

Croft, DP, James, R, Ward, AJW, Mawdsley, D 

& Krause, J. (2005) Assortative interactions 

and social networks in fish. Oecologia 143: 

211-219 

Ward, AJW, Hart, PJB & Krause, J. (2004) 

The effects of habitat- and diet-based cues 

on association preferences in three-spined 

sticklebacks. Behavioural Ecology 15: 

925-929 

Ward, AJW, Thomas, P, Hart, PJB & Krause, 

J. (2004) Correlates of Boldness in Three- 

Spined Sticklebacks (Gasterosteus aculeatus). 

Behavioural Ecology and Sociobiology 55: 

561-568

Bill Kunin 

AB (Princeton) MPP (Harvard) PhD (Washington); 

Postdoctoral researcher, Centre for Population Biology, Imperial College at Silwood Park (1992-1995); 

Director, European Centre for Biodiversity & Conservation Research; 

Senior lecturer in Ecology (at Leeds since 1996) 

Contact: w.e.kunin@leeds.ac.uk 

Spatial aspects of population and 

community ecology and conservation biology 

I am interested in rare species and the 

factors that influence their populations: 

their interactions with their environment 

and with the species that compete 

with them and feed upon them. I 

focus particularly on plant populations, 

and on their interactions with insect 

herbivores and pollinators. Much of 

my work has relied on manipulative 

field experiments in which I have set 

up controlled populations of plants and 

investigated the effect on pollination 

and herbivory. These experiments 

have highlighted strong positive effects 

of population density on pollination, 

while effects on herbivores varies 

greatly, raising interesting questions 

for future research. 

Natural populations tend to be spatially 

complex, with individuals patchily 

distributed across a wide range of 

spatial scales. One aspect of my recent 

work has been the application of 

fractal and other multi-scale models 

to describe and predict the spatial 

and temporal dynamics of such 

populations. Modelling work suggests 

that autocorrelation in dynamics and 

disturbance may be key in predicting 

the probability of extinction. More 

generally, I have begun work on species 

distributions, and in particular of the 

dynamics of populations at the margins 

of a species’ range. Some of this recent 

work has included collaborations with 

molecular geneticists to examine the 

factors limiting populations in these 

marginal areas. 

A third key research area is biodiversity: 

its maintenance and conservation. 

I have conducted research on the 

role of dispersal across environmental 

boundaries on diversity (spatial mass 

effects), one of a range of mechanisms 

which may help maintain diverse 

natural communities. We will soon 

begin work on the role of surrounding 

landscapes in explaining local 

biodiversity in agricultural and 

upland landscapes, in the UK 

and across Europe. 

My research has been funded by 

NERC (including a large collaborative 

Postgenomics project), the EU (as part 

of the ALARM consortium), the US 

Forest Service and the interdisciplinary 

Rural Economy and Land Use 

programme. 



php?staff=WEK 


Biesmeijer, JC, Roberts, SPM, Reemer, 

M, Ohlemüller, R, Edwards, M, Peeters, T, 

Schaffers, AP, Potts, SG, Kleukers, R, Thomas, 

CD, Settele, J, Kunin, WE. (2006) Parallel 

Declines in Pollinators and Insect-Pollinated 

Plants in Britain and the Netherlands. Science 

313(5785): pp.351 - 354 

Wilson, RJ, Thomas, CD, Fox, R, Roy, DB. & 

Kunin, WE. (2004) Spatial patterns in species 

diversity reveal biodiversity change. Nature 

432: 393-396 

Hartley, S, Kunin, WE, Lennon, JJ and Pocock, 

MJO. (2004) Coherence and discontinuity in 

the scaling of species distribution patterns. 

Proceedings of the Royal Society B. 271: 

81-88 

Hartley, S and Kunin, WE. 2003. Scale 

dependency of rarity, extinction risk, and 

conservation priority. Conservation Biology 17: 

1559-1570 

Thomas, CD and Kunin, WE. (1999) Spatial 

structure. Journal of Animal Ecology 68: 

647-657 

Kunin, WE; (1998) Extrapolating species 

abundance across spatial scales. Science 281: 

1513-1515

Peter Meyer 

PhD (Cologne); 

Post Doc, Max-Planck-Institute for Breeding Research, Cologne (1985-1989); 

Group Leader, Max-Delbrueck-Laboratory of the Max-Planck-Society (1989-1994); 

Heisenberg Fellow of German Research Society, DFG (1994-1995); 

Professor of Plant Genetics (1995-) 

Contact: p.meyer@leeds.ac.uk 

Plant 

epigenetics 

Epigenetic effects are phenomena that 

alter the expression profile of a gene in 

a heritable way, without any affect on 

the DNA sequences. These heritable 

but reversible effects occur at two 

different levels: 

(i) The competence of a gene to 

be accessible for the transcription 

machinery is determined by its 

chromatin structure. Many transposable 

elements and transgenes are packaged 

into a repressive chromatin state 

that prevents their transcription. In 

transgenes, this can lead to tissue 

sectors where an intact transgene 

has been switched off, while in other 

regions, the trangene is still functional. 

(ii) The transcripts of individual genes 

can be selectively degraded, a process 

often associated with the formation of 

double strand RNA for the affected 

gene. The degradation products 

(small RNAs) can guide a chromatin 

remodeling mechanisms to the 

homologous DNA, where these impose 

a repressive chromatin structure. Plants 

apply this mechanism to package 

repetitive regions into heterochromatin 

to ensure efficient genome organization. 

We are interested to identify target 

genes for epigenetic processes and 

molecular functions that regulate 

silencing events. 

The role of natural antisense 

transcripts in plants 

In related research, we study the 

role of natural antisense transcripts. 

In textbooks, individual genes are 

often depicted as independent units 

that consist of a promoter, a coding 

region and a polyadenylation unit. In 

reality, however, there is a surprisingly 

high number of genes that partially 

overlap with other genes in antisense 

orientation. Many of these convergently 

overlapping genes are co-expressed 

in the same tissue, which implies 

that expression of one gene may be 

involved in the regulations of the other. 

We are using a number of such senseantisense 

gene pairs to evaluate the 

molecular effects of antisense gene 

expression on the sense transcript. 


comes from the EU and from BBSRC. 


http://www.fbs.leeds.ac.uk/staff/pm/ 


Depicker, A, Sanders, M and Meyer, P. (2005) 

Transgene silencing. In: Annual Plant Reviews: 

Plant Epigenetics, ed P Meyer, Blackwell 

Publishing, Oxford, p 1-32 

Jen, C-H, Michalopoulos, I, Westhead, DR and 

Meyer, P. (2005) Natural antisense transcripts 

with coding capacity in Arabidopsis may have 

a regulatory role that is not linked to dsRNA 

degradation. Genome Biology 5/6/6/R51 

Zubko, E and Meyer, P. (2007) A natural 

antisense transcript of the Petunia hybrida 

Sho gene suggests a role for an antisense 

mechanism in cytokinin regulation. Plant 

Journal 52: 1131-1139 

Mueller, A, Marins, M, Kamisugi, Y and Meyer, 

P. (2002) Analysis of hypermethylation in the 

RPS element suggests a signal function for 

short inverted repeats in de novo methylation. 

Plant Molecular Biology 48: 383-399

Helen Miller 

BSc (Edinburgh); 

MAgrSc (Reading); 

PhD (Alberta); 

Senior Lecturer/Lecturer in Nutritional biochemistry (1996-2006); 

Director National Pig Development Centre (2006-); 

Professor of Pig Science (2007-); 

Institute Director, Institute of Integrative and Comparative Biology (2008-) 

Contact: h.m.miller@leeds.ac.uk 

Nutrition of pigs and poultry with particular 

emphasis on health, feed intake and nutrient 

partitioning for production 

The overall aim of my research is 

to develop feeding systems which 

enhance animal health, performance 

and meat quality in a sustainable 

manner. This research requires a 

fundamental understanding of the 

underlying physiological, metabolic and 

genomic responses to nutrients so that 

mechanisms already existing within the 

animal may be triggered to respond in 

an optimal way. Two critical periods 

in the pig’s life are immediately after 

birth and immediately after weaning. 

The latter is of particular importance 

at present following the recent ban on 

in-feed antibiotic growth promoters 

which were used routinely in weaner 

feeds prior to 2006. This research 

involves defining fundamental changes 

in the pig that help it to be successful 

and how these may be stimulated by 

nutrition. A number of factors influence 

piglet success following weaning: 

Comparing piglets produced in our 

indoor versus our outdoor facilities we 

found that rearing environment affects 

both survival and performance. 

Can we use nutrition to equalise 

environment effects? 

Certain feed additives e.g. zinc oxide, 

help pigs to resist disease. Can we 

create a similar response without using 

a heavy metal? 

Another area we are investigating is the 

voluntary feed intake of the weaned 

animal since, unsurprisingly, pigs which 

eat well post weaning do better than 

those which do not, but what makes 

some pigs eat more than others at 

this time? We have developed a group 

feeding recording system to help us 

answer this question. 

Other areas currently under 

investigation are: 

• Role of butyrate in stimulating 

gut development 

• Mode of action of ZnO in controlling 

pig diarrhoea 

• Developing sustainable alternatives 

to therapeutic use of heavy metals 

in pig diets 

• Feeding for enhanced meat quality 

(with University of Bristol) 

• Genomics of gut development 

Funding for these projects currently 

comes from DEFRA, BBSRC, HGCA, 

MLC and industry. 



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Ilsley, SE, Miller, HM, Kamel, C. (2005) 

Effects of dietary quillaja saponin and 

curcumin on the performance and immune 

status of weaned piglets Journal of Animal 

Science 83: 82 – 88 

Ilsley, SE; Miller, HM, (2005) Effect of dietary 

supplementation of sows with quillaja saponins 

during gestation on colostrum composition and 

performance of piglets suckled Animal Science 

80: 179 – 184 

Barkley, GR; Miller, HM; Forbes, JM, 

(2004) The ability of laying hens to regulate 

phosphorus intake when offered two feeds 

containing different levels of phosphorus 

British Journal of Nutrition 92: 233 – 240 

Miller, HM; Foxcroft, GR; Aherne, FX, (2004) 

Increasing feed intake in late gestation does 

not affect plasma progesterone concentration 

in the sow. Theriogenology, 62: 1618 – 1626

Lesley Morrell 

BSc (UEA); 

PhD (Glasgow); 

PDRA, Leeds University (2005-6); 

NERC Postdoctoral Fellow, Leeds University (2006-) 

Contact: l.j.morrell@leeds.ac.uk 

Behavioural ecology: 

aggregation and predator avoidance 

In general, I am interested in 

behavioural interactions between 

animals, how they are affected by the 

physical and social environment, and 

the effect of individual behavioural 

decisions at the level of the group or 

the population. I am particularly 

interested in the evolution of aggregation 

as an anti-predator response in animals, 

and use a combination of theoretical 

and experimental approaches in 

my research. 

Current projects: 

Animal aggregation: mechanisms for 

the selfish herd 

When animals are frightened, perhaps 

because they detect a predator, they 

often group closely together, forming 

what is known as a ‘selfish herd’. But 

how does the group go from being a 

loose collection of individuals to a tight 

cluster? My current work investigates 

how well different movement rules 

reduce an individual’s risk of falling prey 

to the predator, and how the benefits 

of the different rules are influenced by 

ecological conditions such as population 

size and density, and the time it takes 

a predator to attack after it has been 

detected by the prey. 

Colour and shoaling in 

western rainbowfish 

The ‘oddity effect’ predicts that 

predators can combat the problem of 

attacking a single prey animal within 

a group by targeting ‘odd’ individuals 

(those that differ in appearance from 

the rest). In shoaling fish, predation 

risk is generally higher for animals that 

are different in size or colour to the 

rest of the group. However, studies 

of colour have considered artificially 

selected strains, rather than drawing 

on the natural variation found in the 

wild. In collaboration with Jenny Kelley 

(University of Western Australia) I am 

investigating shoal assortment by colour 

in natural populations of the western 

rainbowfish (Melanotaenia australis) 

and linking this with experimental 

analysis of the role of colour variation in 

group choice. 


NERC, Royal Society, Association for 

the Study of Animal Behaviour, British 

Ecological Society and the Company 

of Biologists. 



php?tag=Morrell 

Figure 1. What is the best way for an animal to minimise 

its ‘Domain of Danger’? The individual in the centre (red) 

is well protected. 


Morrell, LJ, Hunt, KL, Croft, DP & Krause, J. 

(2007) Diet, familiarity and shoaling decisions 

in guppies. Animal Behaviour 74: 311-319 

Kokko, H, López-Sepulcre, A & Morrell, 

|LJ. (2006) From hawks and doves to 

self-consistent games of territorial behavior. 

American Naturalist 167: 901-912 

Morrell, LJ, Lindstrom, J & Ruxton, GD (2005) 

Why are small males aggressive? Proceedings 

of the Royal Society of London Series B 272: 

1235-1241 

Morrell, LJ & Kokko, H (2004) Can too strong 

female choice deteriorate male ornamentation? 

Proceedings of the Royal Society of London 

Series B 271: 1597-1604

David Pilbeam 

BSc (London); 

PhD (London); 

Lecturer in Applied Biology (1979-1993); 

Senior Lecturer in Applied Biology (1993-) 

Contact: d.j.pilbeam@leeds.ac.uk 

Plant Nutritional Physiology, 

Farm Woodlands and Novel Crops 

We have known which nutrients are 

essential for plant growth since the 

middle of the nineteenth century, and 

since that time we have worked out the 

ideal ratios to supply nutrients at for 

optimum crop growth. However, we are 

still not well informed about how nutrient 

supply influences metabolic processes 

and the development of plants. The 

supply of nutrients has a direct effect on 

partitioning of resources into different 

processes and different organs in plants, 

and this plasticity in plant processes and 

structures in turn has a direct influence 

on nutrient availability. 

This research programme involves 

research at all levels, from laboratory 

studies (in particular on the influence of 

nutrient supply on metabolic processes 

and root:shoot partitioning) to field 

studies on the relationship between 

nutrient supply and plant growth. This is 

particularly studied in our experimental 

agroforestry plots, where cereal and 

oilseed crops compete with trees for 

nutrients and water, as well as for 

light (Figure 1). Recent work has lead 

to production of a model of tree/crop 

interactions that has helped determine 

future subsidy regimes for farm 

woodlands. Production of novel crops, 

such as short rotation coppice willow 

(Figure 2), is also studied with an aim to 

improve yields and crop quality. 

Figure 1 

A recent project on intercropping maize 

and beans in the UK has demonstrated 

potential for improved protein content of 

silage whilst maintaining high yields. 

Funding from these projects has 

recently come from the EU and the 

Yorkshire Agricultural Society. 



php?staff=pls6djp 


W Van der Werf, K Keesman, P Burgess, 

A Graves, D J Pilbeam, L D Incoll, K 

Metselaar, M Mayus, R Stappers, H van 

Keulen, J Palma and C Dupraz. (2007) Yield- 

SAFE: a parameter-sparse process-based 

dynamic model for predicting resource capture, 

growth and production in agroforestry systems. 

Ecological Engineering 29: 419-433 

M I Dawo, J M Wilkinson, F E Sanders and 

D J Pilbeam. The yield and quality of fresh 

and ensiled plant material of maize (Zea mays) 

and beans (Phaseolus vulgaris). Journal of the 

Science of Food and Agriculture 87: 1391- 

1399 (2007)) 

M I Dawo, F E Sanders and D J Pilbeam. 

Yield, yield components and plant architecture 

in the F3 generation of common bean 

(Phaseolus vulgaris L.) derived from a cross 

between the determinate cultivar ‘Prelude’ 

and an indeterminate landrace. Euphytica 

156: 77-87 (2007). 

J M Wilkinson, E J Evans, P E Bilsborrow, 

C Wright, W O Hewison and D J Pilbeam. 

Yield of willow cultivars at different planting 

densities in a commercial short rotation 

coppice in the north of England. Biomass 

and Bioenergy 31: 469-474 (2007). 

Figure 2

Rupert Quinnell 


DPhil (Oxford); 

Postdoctoral fellow, London School of Hygiene & Tropical Medicine (1990-97); 

MRC Career Development Fellow (1997-2001); 

Lecturer in Biology (2001-2008); 

Senior Lecturer in Biology (2008-) 

Contact: r.j.quinnell@leeds.ac.uk 

Epidemiology, genetics and 

control of parasitic infection 

I am interested in the factors that 

determine the severity of parasitic 

infection in an individual, and in 

the control of parasitic infection at a 

population level. This research focuses 

on two medically important host-parasite 

systems: human hookworm infection 

and visceral leishmaniasis. Hookworms 

are parasites of the small intestine, 

which infect more than 1 billion people 

worldwide, and are an important cause 

of iron-deficiency anaemia. Within 

an infected population, only a few 

individuals have heavy infections and 

severe disease. These heavily infected 

individuals may have greater exposure 

to infective stages, or a more effective 

immune response due to their genetic 

background. Using data from large 

field studies in Papua New Guinea 

and elsewhere, I am interested in 

such questions as: What is the relative 

role of exposure and host genetics 

in determining hookworm burdens? 

What genes are involved in controlling 

hookworm infection? What immune 

responses protect against hookworm 

infection, and do hookworms subvert 

these responses to aid their survival? 

These studies involve a combination of 

field, laboratory and theroretical work. 

Visceral leishmaniasis is a vector-borne 

disease for which dogs are the main 

reservoir host in South America. Human 

disease could be controlled by reducing 

transmission from dogs. Current control 

programmes are ineffective, so we are 

investigating the effectiveness of treating 

dogs with long-lasting insecticide as 

a control measure in Amazon Brazil, 

in collaboration with the University 

of Warwick and the Instituto Evandro 

Chagas, Brazil. Related projects build 

on previous research which has shown 

that only a proportion of dogs develop 

severe disease and are important for 

disease transmission. Currently, we are 

investigating the effect of dog genetics 

and immune responses on the outcome 

of infection, in collaboration with the 

Universities of Manchester and Warwick. 

Funding for these projects has come 

from the Wellcome Trust and MRC. 



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Quinnell, RJ. (2003) Genetics of susceptibility 

to human helminth infection. International 

Journal for Parasitology 33: 1219-1231 

Quinnell, RJ, Pritchard, DI, Raiko, A, Brown, 

AP & Shaw, M-A. (2004) Immune responses 

in human necatoriasis: association between 

interleukin-5 responses and resistance to 

reinfection. Journal of Infectious Diseases 

190: 430-438 

Quinnell, RJ, Kennedy, LJ, Barnes, A, 

Courtenay, O, Dye, C, Garcez, LM, Shaw, M-A, 

Carter, SD, Thomson, W & Ollier, WER. (2003) 

Susceptibility to visceral leishmaniasis in the 

domestic dog is associated with MHC class II 

polymorphism. Immunogenetics 55: 23-28 

Courtenay, O, Quinnell, RJ, Garcez, LM, 

Shaw, JJ & Dye, C. (2002) Infectiousness in 

a cohort of Brazilian dogs: why culling fails to 

control visceral leishmaniasis in areas of high 

transmission. Journal of Infectious Diseases 

186 : 1314-1320

Martin Richards 

BSc Genetics (Sheffield); 

PhD (Manchester); 

Wellcome Trust Bioarchaeology Research Fellow, University of Oxford (1996-1999); 

Research Fellow in Human Evolutionary Genetics, UCL (1999-2000); 

Senior Lecturer in Biology, University of Huddersfield (2000-2004); 

Senior Lecturer in Human Genetics, University of Leeds (2004-2007); 

Professor of Archaeogenetics (2007-) 

Contact: m.b.richards@leeds.ac.uk 

Archaeogenetics 

My group is interested in the 

geographic distribution of modern 

human genetic variation, with the 

aim of addressing questions from 

archaeology, anthropology and history, 

an approach termed ‘phylogeography’. 

Our main focus has been mitochondrial 

DNA, which is inherited without 

recombination down the female 

line of descent, allowing us to make 

inferences from estimates of the human 

maternal genealogy. We are increasingly 

also applying the phylogeographic 

approach to Y-chromosome variation, 

which traces the male line of descent, 

and hope in the future to study 

non-recombining blocks of the X 

chromosome and the autosomes in a 

similar fashion. 

Our principal avenue of research in 

the past few years, with initial funding 

from the British Academy, has been 

the prehistory of Southeast Asia, where 

we have challenged the consensus 

view of archaeologists and linguists 

concerning the history of the region, in 

which expanding farming communities 

from South China play the major role. 

This parallels our earlier research on 

the prehistory of Europe where we 

have shown that the demographic 

contribution of pre-farming huntergatherer 

populations to the modern-day 

gene pool has been under-estimated 

in the past. This work has continued 

with an active collaboration between 

ourselves and archaeologists, 

exemplifying the group’s philosophy 

of a harmonious marriage between 

archaeology and genetics. 

We have also worked with pre-historians 

on the reconstruction of human 

dispersals in Africa, and with historians 

on the Atlantic slave trade. 

Some of our more recent research, 

funded by the Royal Society and the 

Discovery Channel, has focused on 

the process of the initial dispersal of 

modern humans out of Africa and 

peopling of the world and, with funding 

from the Bradshaw Foundation, we 

are now exploring the possible role 

of the eruption of the super-volcano 

Toba about 75,000 years ago on the 

dispersal process. 



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Macaulay, V, Hill, C, Achilli, A, Rengo, C, 

Clarke, D, Meehan, W, Blackburn, J, Semino, 

O, Cruciani, F, Scozzari, R, Taha A, Shaari, 

NK, Raja, J.M, Ismail, P, Zainuddin, Z, 

Goodwin, W, Bulbeck, D, Oppenheimer, S, 

Torroni, A, Richards, M. (2005) Single, rapid 

coastal settlement of Asia revealed by analysis 

of complete mitochondrial genomes. Science 

308: 1034–1036 

Gamble, C, Davies, W, Pettitt, P, Hazelwood, 

L, Richards, M. (2005) The archaeological 

and genetic foundations of the European 

population during the Lateglacial: implications 

for ‘agricultural thinking’. Cambridge 

Archaeological Journal 15: 193–223 

Bandelt, H.–J., Macaulay, V., Richards, M. 

(eds) (2006) Mitochondrial DNA and the 

evolution of Homo sapiens. Springer–Verlag, 

Berlin 

Hill, C., Soares, P., Mormina, M., Macaulay, 

V., Clarke, D., Blumbach, P.B., Vizuete- 

Forster, M., Forster, P., Bulbeck, D., 

Oppenheimer, S., Richards, M. (2007) A 

mitochondrial stratigraphy for Island Southeast 

Asia. American Journal of Human Genetics 

80:29–43

Steven Sait 

BSc (Nottingham); 

PhD (Liverpool); 

PGRA, University of Bristol (1987-1988); 

PDRA, University of Liverpool (1992-1995); 

Higher Scientific Officer, NERC CEH-Oxford (1995-1997); 

NERC Advanced Fellow, University of Liverpool (1997-2002); 

University Research Fellow (2002-2007) 

Contact: s.m.sait@leeds.ac.uk 

Population, community 

and evolutionary ecology 

I am interested in insect population 

and community ecology and evolution, 

with an emphasis on natural enemies 

(predators, parasitoid wasps and 

parasites). Major themes focus on 

mechanisms underlying patterns in 

abundance, species co-existence and 

community structure, predator-prey 

interactions and the co-evolution of 

host resistance and parasite virulence. 

I use simple laboratory systems as 

biological analogues of the real world. 

Coupled with mathematical modelling, 

this approach represents a powerful 

tool for dissecting the mechanisms 

underpinning interactions within 

and between species. Using various 

combinations of species in the lab., 

we construct simple communities and 

explore a wide range of contemporary 

questions. Can a natural enemy enable 

competing prey species to co-exist? 

What happens when two natural 

enemies compete for the same prey? 

Do some combinations of species 

co-exist whilst others don’t? As well 

as being of interest in ecology and 

evolution, we also learn more about the 

biological control of pest species, the 

management of diseases, the effects 

of species invasions on communities 

and the impact of climate change on 

species distributions and extinction. In 

future, this approach will be adapted 

to other systems, including mosquitomalaria 

interactions and the evolution of 

senescence in a nematode worm. 

The principles that we investigate in 

the laboratory are also being explored 

in the natural world. I am currently 

investigating the ecology and molecular 

biology of viruses in Lepidoptera and 

the relative role of horizontal and 

vertical transmission strategies. I am 

also exploring interactions between 

biotic factors (resource limitation, 

natural enemies) and abiotic factors 

(environmental variation, land use) that 

affect lepidopteran ecology, such as the 

magpie moth, on the Orkney Islands. 

This pest species is a problem when it 

destroys the habitat of sensitive groundnesting 

birds. Colleagues and I are also 

working on a multi-disciplinary project 

that assesses the costs and benefits of 

organic agriculture at a range of spatial 

scales across the UK. 

Funding from these projects comes from 

NERC, a joint research council initiative 

(the Rural Economy & Land Use 

programme) and The Leverhulme Trust. 



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Cameron, T.C., Metcalfe, D., Beckerman, A.P. 

& Sait, S.M. (2007) Intraspecific competition: 

The role of lags between attack and death 

in host-parasitoid interactions. Ecology 88, 

1225-1231 

Wearing, HJ, Rohani, P, Cameron, TC & Sait 

SM. (2004) The dynamical consequences of 

developmental variability and demographic 

stochasticity for host-parasitoid interactions. 

American Naturalist 164: 543-558. 

Rohani, P, Wearing, H, Cameron, TC & Sait, 

SM. (2003) Natural enemy specialisation 

and the period of population cycles. Ecology 

Letters 6: 381-384 

Bjørnstad, ON, Sait, SM, Stenseth, NC, 

Thompson, DJ & Begon, M. (2001) The impact 

of specialised enemies on the dimensionality 

of host dynamics. Nature 409: 1001-1006

Mahesh Sankaran 

MSc (Pilani, India); 

MS (Auburn, USA); 

PhD (Syracuse, USA); 

Postdoctoral Research Associate, CPB, Imperial College, Silwood Park (2001-2002); 

Research Scientist, NREL, Colorado State University, USA (2002-2006); 

Lecturer, Integrative and Comparative Biology (2006-) 

Contact: m.sankaran@leeds.ac.uk 

Community, ecosystem 

and conservation ecology 

My research addresses central 

questions in ecosystem ecology 

concerning the role of large herbivores 

in influencing patterns of energy 

and nutrient cycling. 

I am particularly interested in 

tropical savanna systems where large 

mammals are important regulators of 

community structure and function. 

Despite the apparent simplicity of 

these biomes, understanding how 

different components interact to 

function as an integrated whole remains 

a challenge. My research combines 

empirical and theoretical approaches 

to ask how interactions and feedbacks 

between herbivores, fire, climate and 

biogeochemistry influence energy and 

nutrient cycling, and the composition, 

structure and stability of savannas. 

I am also intrigued by the role 

of species diversity in regulating 

the functioning of communities 

and ecosystems. Understanding 

consequences of changes in 

biodiversity that result from species 

loss, introduction of exotic species and 

alteration of biogeochemical cycles by 

humans represents one of the most 

challenging problems facing ecologists 

today. Does biodiversity act as a buffer 

to counteract anthropogenic changes to 

the global environment? Does species 

loss within communities affect their 

subsequent ability to function, recycle 

nutrients and water, and withstand 

future disturbances? In the face of 

these changes, will species rich systems 

necessarily fare better than species 

poor ones? 

Funding for these projects has typically 

come from the National Science 

Foundation (USA), NERC, Wildlife 

Conservation Society (India) and the 

World Bank (FREEP-India) 



php?tag=Sankaran_M 


Cardinale, BJ, Srivastava, DS, Duffy, JE, 

Wright, JP, Downing, AL, Sankaran, M, 

Jouseau, C. (2006) Effects of biodiversity 

on the functioning of trophic groups and 

ecosystems. Nature 443: 989 - 992 

Sankaran, M., et al. (2005) Determinants of 

woody cover in African savannas. Nature 438: 

846 - 849 

Bunker, DE, De Clerck, F., Bradford, JC, 

Colwell, RK, Perfecto, I, Phillips, O, Sankaran, 

M, Naeem, S. (2005) Species Loss and Aboveground 

Carbon Storage in a Tropical Forest. 

Science 310: 1029-1031 

Sankaran, M, Ratnam, J, Hanan, NP. (2004) 

Tree grass coexistence in savannas revisited 

– insights from an examination of assumptions 

and mechanisms invoked in existing models. 

Ecology Letters 7: 480-490

Marie-Anne Shaw 

BSc (London); 

PhD (London); 

Postdoctoral research at Cambridge, London School of Hygiene and Tropical Medicine and University of London 

Lecturer/Senior Lecturer in Human Genetics (1995–) 

Contact: genmas@leeds.ac.uk 

Genetic susceptibility 

to infectious disease 

My primary interest is genetic control 

of susceptibility to infectious diseases 

and accompanying immune responses. 

To what extent does human genetic 

variation contribute to susceptibility? 

What genes are responsible for 

development of clinical disease? 

The most interesting questions relate 

to severity of disease and 

responsiveness to therapy. 

The diseases I investigate are prevalent 

in the tropics and field work is carried 

out in several South American and 

African countries. Studies are carried 

out both at a population level and using 

multicase families. 

I have a long-standing interest in 

diseases caused by pathogens invading 

macrophages, such as tuberculosis 

and leprosy. Another such disease 

is cutaneous leishmaniaisis, which is 

caused by several species of parasite 

including Leishmania braziliensis. A 

spectrum of immune responses among 

individuals is associated with different 

clinical manifestations of the disease. 

Mathematical analysis of population 

data suggests that there is genetic 

control of susceptibility to cutaneous 

leishmaniasis. A study looking at 

severe and disfiguring mucocutaneous 

leishmaniasis, which develops in fewer 

than 10% of patients who have suffered 

from cutaneous leishmaniasis, has 

identified a gene which predisposes to 

this particular type of disease. 

Helminth infections are also associated 

with high morbidity worldwide. Different 

T-cell subsets are beneficial in defence 

against cutaneous leishmaniasis 

and helminth infections. The same 

genes as those studied for cutaneous 

leishmaniasis are being examined 

in helminth-infected populations. 

An ultimate goal of these studies is 

to address how one infection may 

influence the severity of a second 

disease. My interests also include 

gaining a more complete picture by the 

study of pathogen genetic variability, 

alongside the study of genetic variability 

in humans and domestic species. 

Figure 1: Mucosal Leishmaniasis 

In addition to infectious disease 

susceptibility, I work on the anaesthetic 

disorder malignant hyperthermia. 

An adverse response to inhalational 

anaesthetics can cause death. This 

is a disorder of Ca2+ homeostasis in 

skeletal muscle. The largest collection 

worldwide of DNA from patients and 

family members is held at Leeds, and 

use of this material is revealing the 

genetic and functional complexity of 

the condition. 

Funding: Wellcome Trust, 

Department of Health 



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Carpenter D., Abushama H., Bereczky S., 

Farnert A., Rooth I., Troye-Blomberg M., 

Quinnell R., Shaw M.-A. (2007). Genetic 

control of malaria induced antibody responses. 

Human Immunology 68, 165-169. 

Robinson R., Carpenter D., Shaw M.-A., 

Halsall J., Hopkins P. (2006). Mutations in 

RYR1 in malignant hyperthermia and central 

core disease. human mutation 27, 977-989. 

Booth M., Shaw M.-A., Carpenter D., Joseph 

S., Mwatha J., Kabatereine N., Jones F., 

Macbeath R., Ouma J., Dunne D. (2006). 

Carriage of HLA-DRB1*13 is associated with 

higher IgE responses, and lower re-infection 

levels, after praziquantel treatment for 

Schistosoma mansoni infection. 

J. Immunology 176, 7112-7118. 

Quinnell, RJ, Pritchard, DI, Raiko, A, Brown, 

AP & Shaw, M-A (2004) Cytokine responses in 

human necatoriasis: interleukin-5 responses 

are associated with resistance to reinfection. 

Journal of Infectious Diseases 190: 430–438 

Shaw, M-A, Donaldson, IJ, Collins, A et al. 

(2001) Association and linkage of leprosy 

phenotypes with HLA class II and class III 

genes. Genes and Immunity 2: 196–204

Judith Smith 

BSc (Edinburgh); 

Dip.Nut., PhD (Cambridge); 

Researcher, Imperial College; 

Professor of Parasitology (2005-); 

Director of the Graduate School (2005-) 

Contact: j.e.smith@leeds.ac.uk 

Host: Parasite Diversity, 

Transmission and Pathogenesis 

Parasites have long term evolutionary 

relationships with their host species. 

My interests are in understanding 

host:parasite interactions at both the 

cellular and the population level, in 

particular the relationship between 

transmission and virulence. The 

important zoonotic parasite Toxoplasma 

gondii provides a useful model system 

due to its widespread distribution and 

complex transmission routes. We have 

generated molecular probes to assess 

parasite diversity, and employed them 

to monitor transmission. This reveals an 

important role for vertical transmission 

in sheep. These data support a change 

in husbandry to remove susceptible 

ewes and potentially breed the 

disease out of the national flock. We 

now plan to evaluate the role of host 

and pathogen genotype on parasite 

transmission and disease (abortion) in 

sheep. We are also interested in wider 

projects to map transmission routes of 

toxoplasma and in evaluating the role 

of parasite genotype in AIDS associated 

toxoplasma reactivation in humans. 

The Microsporidia are an ancient and 

diverse group of intracellular parasites 

which infect host species ranging from 

protists to humans. We have used 

molecular techniques to discover new 

microsporidia and to monitor their 

transmission. Phylogenetic analysis 

reveals that vertical transmission of 

ubiquitous importance across this 

parasite phylum and that it is linked 

with sex ratio distortion of invertebrate 

hosts. Although bacterial SRD’s such 

as Wolbachia sp are well known, the 

microsporidia are the first eukaryotic 

SRD’s. Such reproductive parasites 

can have significant impact on 

host populations, we have shown 

an SRD parasite is retained during 

transcontinental invasion and propose 

the feminising affect this parasite may 

directly enhance host invasion success. 

To consider evolutionary interactions 

between microsporidia and their hosts 

we are now looking at co speciation and 

life history interactions in the ancient 

species flocks in the isolated Lake 

Baikal in Siberia. 


from NERC, the Royal Society, the EU 

Marie Curie Programme and the Meat 

and Livestock Commission. 



php?tag=Smith_J 


Hughes, JM, Williams, RH, Morley, EK, Cook, 

DAN, Terry, RS, Murphy, RG, Smith, JE, 

Hide, G. (2006) The Prevalence of Neospora 

caninum and co-infection with Toxoplasma 

gondii in naturally occurring mammal 

populations. Parasitology 132: 29-36 

Williams, RH, Morley, EK, Hughes, JM, 

Duncanson, P, Terry, RS, Smith, JE, Hide, G. 

(2005) High levels of congenital transmission 

of Toxoplasma gondii in longitudinal and crosssectional 

studies on sheep farms provides 

evidence of vertical transmission in ovine 

hosts. Parasitology 130: 301-307 

Terry, RS, Smith, JE, Sharpe, RG, Rigaud, T, 

Littlewood, TDT, Ironside, JE, Rollinson, D, 

Bouchon, D, MacNeil, C, Dick, JTA, Dunn, AM. 

(2004) Widespread vertical transmission and 

associated host sex ratio distortion within the 

eukaryotic phylum Microspora. Proceedings 

of the Royal Society of London. Series B. 

Biological Sciences 271: 1783-1789 

Rodgers-Gray, TP; Smith, JE; Ashcroft, AE; 

Isaac, RE; Dunn, AM (2004) Mechanisms of 

parasite-induced sex reversal in Gammarus 

duebeni International Journal for Parasitology, 

34, 747-753.

P E Urwin 

PhD (University of Durham); 

Postdoctoral Fellow at Centre for Plant Science (CPS), University of Leeds; 

Senior Research Fellow. CPS, University of Leeds; 

University Developmental Fellow. CPS, University of Leeds; 

Reader. CPS, University of Leeds 

Contact: p.e.urwin@leeds.ac.uk 

Nematode-resistant 

crops 

Introduction 

Plant-parasitic nematodes are a major 

biotic cause of world agricultural yield 

loss. Nematicides are often harmful 

to the environment and humans. We 

have advanced a range of novel control 

options from gene discovery to field 

trials and a full biosafety assessment. 

We also carry out fundamental aspects 

of plant nematology. 

Figure 1: Specialised feeding sites of nematodes. 

A, A cyst nematode (cn) feeding from an induced, 

single syncytium (arrowed at either end). B, Root knot 

nematode (rkn) parasitizing a root feeds from 6-8 giant 

cells (two are arrowed) within a gall (open arrow). 

Microarray analysis 

We have used microarrays to compare 

transcript abundance in sections of 

root harbouring the feeding sites of 

either cyst or root knot nematodes with 

similar uninfected material. We are now 

carrying out further characterization 

of the nematode responsive genes. 

We also use transcriptomics to define 

changes in C. elegans as a response to 

exposure to xenobiotic compounds. 

RNAi for defining gene function 

We established RNAi for plant-parasitic 

nematodes to facilitate functional gene 

analysis. Octopamine was used to 

induce dsRNA uptake and different 

genes were targeted to establish the 

general utility of the approach. Delivery 

of dsRNA in planta is being optimized. 

Transgenic proteinase-inhibitorbased 

control 

Cysteine proteinases are important 

nematode digestive enzymes. Their 

activity is inhibited in female cyst 

nematodes after incubation with 

a cystatin. A gene encoding a rice 

cystatin, Oc-I, was engineered for 

enhanced inhibitory activity. Expression 

of Oc-I in Arabidopsis was the first 

transgenic technology shown to 

work against both root-knot and cyst 

nematodes. The work culminated in 

transgenic potatoes with commercially 

useful resistance. Full resistance was 

observed by stacking natural and 

transgenic resistance. Transgenic 

potato plants with cystatin expression 

restricted largely to roots have been 

field-trialled. 

Disruption of chemoreception 

We isolated two different peptides 

that either inhibit acetylcholinesterase 

or bind to nematode nicotinic 

receptors. Both inhibited nematode 

chemoreception. The strategic 

development of this approach 

provided a prototype potato plant that 

expressed the peptide that inhibits 

acetylcholinesterase. Protection levels 

of >80% have been achieved against 

nematodes. 


http://www.biology.leeds.ac.uk/nem/ 

Figure 2: Trials of transgenic plants under challenge from 

the potato cyst nematode, G. pallida. A, Potato fi eld trial 

planted in a cereal fi eld. B, Young potato plants in the 

glasshouse. 


Lilley, CJ, Atkinson, HJ & Urwin, PE (2005) 

Molecular aspects of cyst nematodes. 

Molecular Plant Pathology 6: 577–588. 

Lilley, CJ, Goodchild, SA, Atkinson, HJ & 

Urwin, PE (2005) Cloning and characterisation 

of a Heterodera glycines aminopeptidase 

cDNA. International Journal for Parasitology 

35: 1577–1585. 

Liu, B, Hibbard, JK, Urwin, PE & Atkinson, 

HJ (2005) The production of synthetic 

chemodisruptive peptides in planta disrupts 

the establishment of cyst nematodes. Plant 

Biotechnology Journal 3: 487–496. 

Bakhetia, M, Urwin, PE, McPherson, MJ & 

Atkinson, HJ (2005) RNA interference and 

control of plant parasitic nematodes. Trends in 

Plant Science 10: 362–367.

Dean Waters 

BSc Ecology (UEA); 

PhD (Bristol); 

Lecturer, Senior Lecturer in Zoology (1995-) 

Contact: d.a.waters@leeds.ac.uk 

Bioacoustics and 

bio-inspired engineering 

My research focuses on the way that 

animals, including humans, use sound 

to communicate and to discover 

things about their environment. Much 

of this work involves bats and their 

echolocation system, one of the most 

sophisticated uses of sound in the 

animal kingdom. The way that bats 

process sonar information is of great 

interest to engineers as bats can 

apparently outperform all current sonar 

technology. Studies of the echolocation 

system of bats has inspired recent 

work on sound in virtual reality for 

human use, ultrasonic guide canes for 

the blind, and advances in medical 

ultrasonics, underwater remote vehicles 

and geological surveys. Work on the 

sonar calls of the only genus of fruitbats 

to echolocate has shown them 

to have a unique structure not unlike 

the sonar calls of dolphins. These calls 

appear to be optimally adapted to focus 

energy at specific regions of the bat’s 

auditory system to enhance detection 

and their structure, quite unlike 

those of insectivourous bats, poses 

some interesting questions about the 

evolution of echolocation in bats. 

I am also interested in the role of sound 

in the acoustic war between bats and 

moths. Moths can detect the sonar 

calls of bats and take evasive action to 

avoid being eaten. However, bats have 

evolved countermeasures that make 

their calls less apparent to the moths. 

This cycle of predator and prey leads 

to some very interesting evolutionary 

and neurophysiological questions such 

as the generation of unpredictable 

escape responses and the detection 

of weak signals in noise using 

stochastic resonance. 


the BBSRC and EPSRC. 



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Holland, R.A, Waters, D A & Rayner, J MV 

(2004) Echolocation signal structure in the 

megachiropteran bat Rousettus aegyptiacus 

(Geoffroy, 1810). Journal of Experimental 

Biology 207: 4361-4369 

Waters, DA. (2003). Bats and moths: what is 

there left to learn? Physiological Entomology 

28: 237-250 

Waters, DA & Vollrath, C. (2003) Echolocation 

performance in the fruit-bat Rousettus 

aegyptiacus. Acta Chiroptologica 5: 209-219 

Wong, J & Waters, DA. (2001) The 

synchronisation of signal emission with 

wingbeat during the approach phase in soprano 

pipistrelles (Pipistrellus pygmaeus). Journal of 

Experimental Biology 204: 575-583

Chris West 


PhD (Manchester); 

Postdoctoral research associate, University of Manchester; 

BBSRC David Phillips Fellow (2004–) 

Contact: c.e.west@leeds.ac.uk 

DNA double-strand 

break repair 

I am interested in how plants repair 

DNA damage and maintain the 

integrity of their genetic material for 

future generations. DNA damage 

occurs constantly and is caused by 

environmental and cellular factors. A 

particularly severe form is the DNA 

double-strand break (DSB) – effectively 

a broken chromosome – which can 

result in the loss of large amounts of 

genetic information and ultimately cell 

death. We investigate mechanisms that 

mediate repair of DSBs: higher plants 

usually repair DSBs via non-homologous 

end joining (NHEJ) in which DSBs 

are simply rejoined, end-to-end, 

independent of DNA sequence (Figure 

1). In contrast to NHEJ, homologous 

recombination (HR) rejoins the break 

using an identical or similar DNA strand 

as a template for repair, although this 

is thought to occur infrequently in 

plant somatic cells. The ratio of HR- to 

NHEJ-mediated DSB repair influences 

the way that DNA is integrated into the 

plant genome when it is introduced 

into plant cells in the production of 

genetically modified plants. Through an 

understanding of these recombination 

pathways it may be possible to promote 

HR-mediated transgene integration, 

thus allowing gene targeting in plants. 

Figure 2 

Current studies are investigating the 

mechanism of NHEJ in Arabidopsis 

through the functional analysis of 

DNA-repair genes and corresponding 

proteins. We use complimentary 

approaches including phenotypic 

analysis of T-DNA insertional mutants 

and protein biochemistry to study the 

in vitro activities of DNA-repair proteins. 

Double-strand breaks can be induced 

by treatment of plants with X-rays 

or radiomimetic drugs. Arabidopsis 

mutants in the NHEJ pathway of DSB 

repair are hypersensitive to X-rays, 

resulting in severely reduced growth in 

the NHEJ mutant plants (Figure 2). 

Current projects are investigating 

the effects of NHEJ mutations on 

the frequency of gene targeting in 

Arabidopsis using green fluorescent 

protein as a reporter for HR in individual 

cells (Figure 3). We have identified 

novel components required for DNA 

repair in plants through transcriptomics 

approaches and aim to determine 

the molecular function of these 

recombination proteins. 

Funding: BBSRC (a research fellowship 

and DTA studentship), Royal Society 



php?staff=bmbcew 

Figure 3 


Bray, CM & West, CE. (2005) DNA repair 

mechanisms in plants: crucial sensors and 

effectors for the maintenance of genome 

integrity. New Phytologist 168: 511–528 

Waterworth, WM, Jiang, Q, West, CE, Nikaido, 

M., and Bray, CM. (2002). Characterization of 

Arabidopsis photolyase enzymes and analysis 

of their role in protection from ultraviolet-B 

radiation. Journal of Experimental Botany 53: 

1005-1015 

West, CE, Waterworth, WM, Story, GW, 

Sunderland, PA, Jiang, Q & Bray, CM. (2002) 

Disruption of the Arabidopsis AtKu80 gene 

demonstrates an essential role for AtKu80 

protein in efficient repair of DNA double-strand 

breaks in vivo. Plant Journal 31: 517–528 

Figure 1

Hanma Zhang 

BA (Central China Normal University); 

MSc (Institute of Botany, Academia Sinica); 

PhD (Nottingham); 

Higher Scientific Officer, John Innes Institute (1990-1993); 

Higher Scientific Officer, IACR-Rothamsted (1993-1999); 

University Research Fellow, Lecturer, University of Leeds (1999-) 

Contact: bgyhz@leeds.ac.uk 

Root development 

and its regulation 

The root system of higher plants 

performs vital functions such as 

water and nutrient acquisition and 

physical anchorage and has a great 

biological and agronomic significance. 

My research interests centre on the 

question as to how the root system 

is regulated. The current research 

activities of my group focus on the 

following three areas: 

The effects of nitrogen nutrition 

on root development: The effect of 

nitrogen nutrition on root development 

has been known for many years, but 

the mechanism of this effect is largely 

unknown. Our research focuses on the 

effects of nitrate on lateral roots (also 

known as branch roots) in Arabidopsis 

thaliana. Our contributions in this area 

include the characterisation of the two 

opposing effects of nitrate on lateral 

roots (i.e. a localised stimulatory effect 

and a systemic inhibitory effect); the 

identification of an important regulator 

of the stimulatory effect (ANR1) 

and the discovery that abscisic acid 

(ABA) mediates the inhibitory effect 

(Signora et al., 2001). We are currently 

concentrating on the regulatory pathway 

mediating the inhibitory effect. 

The regulatory role of ABA in 

root development: As a classical 

plant hormone, ABA has attracted 

considerable research interest. 

However, there is very little information 

about its role in root development. Our 

research interest in this area stems 

from the finding that ABA plays a role 

in mediating the inhibitory effect of 

nitrate on lateral root development. We 

have established that ABA inhibits the 

activation of newly formed lateral root 

meristems and that this inhibition is 

not mediated by the characterised ABA 

signalling mechanisms (De Smet et al., 

2003). Our current efforts focus on the 

ABA signalling mechanisms involved in 

this inhibition. 

Histidine homeostasis and root 

development: Histidine is one of the 

essential amino acids required by all 

living organisms, but its role in plant 

development has not been previously 

reported. In collaboration with Professor 

Ping Wu (Zhejiang University), we have 

recently uncovered one such role from 

the characterisation of an Arabidopsis 

mutant, hpa1, which carries a mutation 

in one of the two genes coding for the 

histidinol phosphate aminotransferase 

(which catalyses the 7th step in the 

histidine biosynthetic pathway), and 

has a reduced level of free histidine. 

Although the mutant does not show 

any previously described symptoms of 

histidine starvation, it fails to maintain 

the function of the root meristem and 

has an extremely short root system. We 

have established that the root meristem 

failure is linked to the reduction in free 

histidine content (Mo et al., in press). 

Funding for these projects typically 

comes from BBSRC, The Royal 

Society and Chinese Natural Science 

Foundation. 



php?staff=bgyhz or http://www.plants. 

leeds.ac.uk 


Mo, XR, Zhu, QY, Li, X, Li, J., Zeng, QN, 

Rong, HL, Zhang, H and Wu, P. (2006) The 

hpa1 mutant of Arabidopsis reveals a crucial 

role of histidine homeostasis in root meristem 

maintenance. Plant Physiology 141: 1425- 

1435 

Casimiro, I, Beeckman, T, Graham, N, 

Bhalerao, R, Zhang, H, Casero, P, Sandberg, 

G, Bennett, MJ. (2003) Dissecting Arabidopsis 

lateral root development. Trends in Plant 

Science 8: 165-171 

De Smet, I, Signora, L, Beeckman, T, Inze, D, 

Foyer, CH and Zhang, H. (2003) An abscisic 

acid-sensitive checkpoint in lateral root 

development of Arabidopsis. The Plant Journal 

33: 543–555 

Signora, L, De Smet, I, Foyer, CH and 

Zhang, H. (2001). ABA plays a central role 

in mediating the regulatory effects of nitrate 

on root branching in Arabidopsis. The Plant 

Journal 28: 655-662

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