Biology Issue Two | 2013 News www.biology.ox.ac.uk

Department of Plant Sciences Department of Zoology 2 Biology News, University of Oxford I Issue Two I 2013

Liam Dolan Head of Plant Sciences Department Plant Science (Botany, Agriculture and appointment who will take up a University Forestry) is undergoing a quiet revolution. Lectureship and Tutorial Fellowship at

There is growing recognition of the central John Baker The Queen’s College, will investigate how importance of plants in the production genetic mixtures of crops can enhance yield. of food and the inherent value of plant These research programs demonstrate how diversity for the health of the planet. diversity and food production need not necessarily be mutually exclusive and may The public appreciation of the importance in fact act in synergy. of plant science stems in part from the food commodity price spikes of 2008 The recognition of the importance and their subsequent upward trajectory. of plants in these global challenges Furthermore the world population will has not been missed by Oxford under- increase by approximately 2 billion to 9 graduates. The second year Plants and billion by 2050 and there is a consensus People course teaches plant science from that food production will have to increase. the crop’s point of view. Furthermore Previously yield increases were driven by the Soils Food and Food Security course the availability of cheap fertilisers with often of Africa and has enormous potential to is proving to be immensely popular catastrophic impacts on ecosystems. This contribute to the calorific intake of people with almost 50% of third year students approach is no longer an option. We need on low incomes. The Gates Foundation taking the course. This recent upsurge to be creative. Plants that produce more is also funding Steve to understand the in interest is reflected in an increase in yield from less fertiliser and water without infection of cassava by a trypanosome charitable giving to DPhil scholarships in causing ecosystem catastrophe are needed. parasite of this crop. the area of crops and food security. This enables Oxford to play its part in rising to The pivotal position of plant sciences The tension between food production the challenges of the next 30 years. has been recognised by organisations and conservation of biodiversity is to such as the Bill and Melinda Gates be seen in many parts of the world. These undergraduates and postgraduates Foundation which funds two research Andy Hector, a new professor joining will change the world by developing projects in the Department. Jane Langdale the Department from the University cultivars, technologies and discoveries and Steve Kelly are part of a global network of Zürich, is pioneering approaches to that will help to feed 9 billion without of scientists who are engineering rice to optimise food production and biodiversity devastating the planet that we call home. increase its photosynthetic capacity. Cassava conservation in dipterocarp forests in It is a very exciting time to be a plant on the other hand is the food of the poorest Borneo. Lindsay Turnbull, another new scientist.

Graduate student projects Keeping apart Getting to the root of evolution Discovering plant species Owen Osborne (Queen’s) Thomas Tam (Christ Church) Zoë Goodwin (Wolfson)

What are the Water and Our ability to genomic changes nutrients are understand, John Baker John Baker that underlie absorbed by root measure and evolutionary hairs that form Chris Jeffree evaluate the processes such at the interface extent of as speciation between the the current and adaptation? plant and the soil, ‘biodiversity My research making this cell crisis’ is addresses these type a promising hampered by questions in two target for crop our lack of species of ragwort improvement. knowledge found on Mount Etna. These species have My research aims to discover the gene of how many species there are on recently diverged from a common ancestor network responsible for building root hairs. Earth. Even for relatively well-known and are under on-going selection that I discovered that key components of this groups such as the flowering plants, maintains their integrity in the face of gene network are found in all groups of the inventory of all species is yet to be ongoing hybridisation. I use computational land plants (even in mosses!), where they completed. I am analysing the process techniques to detect ‘molecular signatures’ perform similar rooting functions. This of species discovery to develop a of evolutionary processes in the genomes indicates that the mechanisms controlling novel approach to rapidly revise large of these species and then link these the development of cells at the plant- groups of poorly known plants which ‘signatures’ to ecological and morphological soil interface are ancient. By tracing the contain the majority of species that diversification. This is providing insights into evolution of a gene network, I aim to remain to be discovered. I am using this how evolution works at the fundamental discover fundamental genetic mechanism ‘Foundation Monograph’ approach and level of the hereditary material itself, and have brought about morphological and the large pantropical Drypetes as how this relates to morphological and physiological changes in plants over the past my model. physiological adaptation. 500 million years.

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Peter Holland Head of Zoology Department Welcome to Issue 2 of the newsletter about but it is important to note that increased fees Biology at Oxford, bringing you news from the simply replace what has been removed by cuts Departments of Zoology and Plant Sciences. in government spending on Higher Education.

In this issue we showcase selected research Amanda Holland It is also worth remembering that Oxford has highlights, tell you about some improvements one of the most extensive bursary schemes of to our facilities, and provide a glimpse of any UK University. We know that students a few research projects undertaken by our today, perhaps more than ever, expect a undergraduate and graduate students. very high quality education and superb facilities. We are confident that the Biological In the Department of Zoology, we have Sciences course already offers this, and in appointed several new academic staff. In 2012 we improved facilities even further September 2012, Aziz Aboobaker arrived by building an impressive new IT suite for with his research team working on genomics, teaching quantitative biology and data analysis. development and regeneration in flatworms; in January 2013, distinguished evolutionary I am always delighted when our academic ecologist Tim Coulson joined the Department staff and students win prestigious awards and Kayla King who has research interests for their research, and this year has been in the evolution of parasitism will join us prestigious Royal Society University Research no exception. A few examples include the later in 2013. Dora Biro and Ashleigh Fellowships in the Department. Marie Curie Prize for Promising Research Griffin will join us as University Lecturers Talent to Gkikas Magiorkinis, the Institute I must mention the retirements of Sarah in Behaviour and Evolutionary of Ecology and Environmental Management Randolph and David Rogers, who have Biology respectively, and Pat Nuttall has Medal to Bob May, the Royal Geographical each given an impressive four decades to joined us as Professor of Arbovirology. The Society Back Award to Simon Hay, the UFAW Zoology in Oxford. Both Sarah and David department has long focussed on supporting Medal for Outstanding Contributions to have made important contributions in the early career research fellows, and into this Animal Welfare Science to Marian Dawkins fields of spatial ecology, vector biology and growing fold this year we have been fortunate and the George Stephenson Award to Nathan entomology; they have each influenced to recruit (amongst others) William Durham, Phillips. In October we also received the literally thousands of students (including me!) Stuart Wigby, Bridget Penman, Laura Ross momentous news that the 2012 Nobel Prize and Jarrod Hadfield. Tobias Uller, well In October 2012 our new intake of UK for Physiology or Medicine had been awarded known to recent undergraduates through undergraduates were the first to be charged the to Sir John Gurdon for research that was the animal diversity practical course, increased tuition fee. This has been a topic of undertaken in the Department of Zoology in has become one of the eleven holders of much debate inside and outside the University, Oxford in the 1960s.

Graduate student projects Malaria vectors Asymmetry in Beehive fences Danica Fabrigar (Jesus) Nathan Kenny (St Cross) Lucy King (Balliol) With the support Left/right How can farmers of the Sir Richard asymmetries prevent African Southwood DPhil – such as the elephants raiding Scholarship, I am Namigai Erica positioning their crops? It is

Andrew Hammond Andrew able to pursue of the liver a tough problem, Save the Elephants Save research on predominantly because elephants the population on the right of do not respect structure of humans – are fences and can African malaria found across the rapidly destroy vectors. One issue animal tree of life. an entire crop. concerns whether Only recently has My research as the long-term indoor use of insecticides it been suggested that these asymmetries a DPhil student in Zoology showed that and bed nets is generating an evolutionary are patterned by similar genes in organisms elephants can be deterred by the sound of selective pressure favouring outdoor, as diverse as snails, mice and sea urchins. honeybees, and furthermore that ‘Beehive rather than indoor, biting behaviour. I have With the help of a Clarendon Studentship, Fences’ can be built incorporating live been collecting mosquito samples in the my work has focused on comparing beehives at regular intervals to protect small Gambia and will be using next generation the underlying mechanisms controlling farms. I am now working with the charity DNA sequencing technologies to test for the establishment and maintenance of Save the Elephants, and in partnership with evidence of selection. Identifying such asymmetry in diverse animals. I am using Disney Worldwide Conservation Fund, to roll changes will be crucial to successful malaria genome sequencing and analysis of gene Beehive Fences out across several African control. activity in embryos of limpets and worms countries for the benefit of elephants and to get new insights into how asymmetry is farmers. My DPhil work was awarded the controlled, and how it evolved. UNEP/CMS Thesis Award by the United Nations, and in 2013 I won the Future for Nature Award.

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Field course news Oxford Biology undergraduates and visiting scientists and students, and teaching staff met the Duke and Duchess learning about the research underway of Cambridge during last September’s there. Following a short trek in the forest Tropical Forest Ecology field course in and a climb into the rainforest canopy, Borneo. Prince William and Katherine they visited the field station’s teaching were visiting Sabah as part of their laboratory and chatted to Oxford

Diamond Jubilee tour of South East Asia students and staff about the field Sabah group Yayasan Samson Lawrence, and the South Pacific. After a helicopter course and rainforest conservation. flight over the largest remaining areas of primary forest on the island, the Royal Owen Lewis couple spent the morning at the Danum The Duke and Duchess of Cambridge at Valley field station meeting local and Danum Valley field station, Sabah

The space in the Department of Zoology individual study and research. Starting The Elton Room that housed the library collections of with ‘Quantitative Methods’ in the first Charles Elton, one of the founders of year and continuing on to a wide range ecology, has a new use. The books, of advanced second and third year journals and reprints have been moved modules, the new teaching suite will

Peter Holland Peter to the Radcliffe Science Library, as part enable students to develop their skills for of a re-structuring of Oxford libraries, interrogating large data sets – ranging giving an opportunity to update further the from whole genome sequences, to images teaching facilities for Biological Sciences. from microscopy or satellites, to ecological The newly refurbished ‘Elton Room’, meta-data. Purchase of the computer officially opened on the 2012 Alumni equipment, an interactive lectern and three Day, now accommodates a state-of-the-art simultaneous projectors was made possible computer suite for teaching quantitative by a generous donation from the E. P. biology. Individual desks with client Abraham Cephalosporin Fund. terminals for 56 students permit class The new Elton Room teaching, plus a facility is provided for Rosalind Harding

Undergraduate student projects The cleaner fish market Senescence in a potential Malaria vaccines Laura Voak (New) model organism Katrina Spensley (St Catherine’s) Lauren Sumner-Rooney (St Anne’s) Two months, Malaria vaccine 60 dives and I investigated design is 2 underwater complicated

Kristen Nehr Kristen the effects of cameras into my by parasite

Peter Ward Peter vitamin B12 project, I was on senescence Society of Biology protein sequence still in awe of my in the fish variability. The subject – Labroides Nothobranchius project explored dimidiatus, the furzeri, which the possibility bluestreak cleaner was proposed of finding wrasse – running as a new model immune selection a business. The organism for signatures using cleaner fish mutualism is analogous to a ageing studies. computer analysis of publicly-available human economic market, with ‘clients’ To detect age-associated changes, PfAMA-1 protein sequence data instead queuing at cleaning stations to be serviced. I video-tracked subjects’ motor activity, of established laboratory methods. New I travelled to Indonesia to film thousands of and tested their ability to solve a maze, at programs had to be written to handle the interactions and analyse why some client both young and advanced ages. I found that volumes of data involved, and positive species were given a higher quality service the B12-deficient subjects were initially results suggest that this approach is viable. than others. Remarkably, transient species much less active than the controls, but For me, the project was a fascinating (whose home range included >1 cleaning that this reversed as ageing progressed. glimpse into leading-edge scientific station) received the highest quality service The autonomy granted by having my own research. My project was awarded the and were even allowed to jump the queue, project was a rewarding experience, and ZSL Charles Darwin Award and Marsh together with piscivorous species which gave me a valuable insight into the exciting Prize from the Zoological Society of posed a threat to the cleaner. Queues world of scientific research, inspiring me to London, and I was shortlisted for a SET were also much longer at sunrise (when begin a PhD. award for the work. the cleaners begin their day) and in more polluted locations. www.biology.ox.ac.uk Biology News, University of Oxford I Issue Two I 2013 5

Undergraduate student projects

One of the undoubted highlights of but those leaving Oxford often use part of Biological Sciences at Oxford is the Honours their summer vacation as well, as long as Project (also known as a dissertation in they are able to raise the funds for travel

the outside world). Every student does one and subsistence. Both Departments run Martin Speight and most find it both fun and intellectually small bursary schemes to help support some challenging. Most members of academic student travel, primarily funded by donations staff in Plant Sciences and Zoology are keen made by former academic staff and students. to supervise at least one or two students As with all research, success (measured in per year, and undergraduates either join an terms of new, significant results) cannot be existing research group as a team member, guaranteed, and the experience is just as or carry out their project on their own but much about learning the process of planning with the advice of a member of academic and conducting scientific research, and staff. The practical work for the Honours analysing data. Project can be carried out in the labs, fields, rivers or woods of Oxford, or students Some projects are phenomenally successful, can choose to visit other institutions and however, resulting in peer-reviewed scientific organisations within the UK, or indeed papers that make a real contribution to further afield in Europe or the rest of the knowledge and stand the test of time. This world. Here coral reefs, rainforests and year for example, Katrina Spensley’s project even the deepsea can provide habitats on malaria proteins was judged one of the to investigate. Choosing the topic for a best three student biology projects across research project is not trivial to say the Europe in the Science, Engineering and least. All academic staff provide details of Technology Student of the Year Awards. their research allowing students to gain a One day, if the Biological Sciences degree good idea of what may be available, so any at Oxford is extended to a fourth year, subject within the hugely broad spectrum even more emphasis will be placed on of interests across both Departments (and the Honours Project; for now, it is an sometimes in the wider university) is undergraduate’s first real chance to see what potentially a possibility. This amounts to research is like, and for many, to decide if this is the career they’ve been looking for. pretty much the whole of biological sciences! Pitfall trap and temperature/humidity data Students normally do their practical work logger on a student project on insects in in the Trinity Term of their second year, Martin Speight meadows, Oxfordshire

Undergraduate student projects Immune response in plants Bird malaria Space use by Mary Tetlow (Brasenose) Philip Birget (St Peter’s) Tom Williams (St Anne’s) My research My Honours In July 2012, project was carried project considered I travelled to

out during the the influence of Ben Evans a dry forest in Ana Mendes Summer of 2011 natural disease North-western in collaboration Linda Nell’Angela occurrence Madagascar in with the University (malaria) on order to study of Warwick, the size of the two species under the joint badge of male of Malagasy supervision of house sparrows. snakes Professor Sarah I also integrated (Leioheterodon). Gurr in Oxford a measure of These snakes are and Professor Jim Beynon in Warwick. testosterone exposure (bird digit ratios) unusual in both the ecology and physiology. I investigated the role of three genes during the egg stage to control for potential I spent two months in the field individually potentially key to the immune response maternal effects. This work was carried out marking animals, monitoring individual of Arabidopsis thaliana using microarray in two regions, an insecticide treated region movements and species occurrences. I analysis. This identified interesting roles in and a region with no mosquito control. then used this data to examine the effects the coordination of immunity for two of The main result was that birds with bigger of both intraspecific and interspecific these genes. Future research will define the digit ratios were more likely to be infected, competition on space use, using ArcGIS, precise molecular function of these genes. but more molecular work with Oxford occupancy modelling and randomisation Working in the lab gave me insight into researchers is required to confirm that methods. I was able to statistically how discoveries are made and I have also finding. demonstrate the second ever example of gained valuable experience in a wealth of territoriality in snakes, and this suggests molecular techniques. territoriality is more widespread in snakes than previously thought.

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Evolution, ecology, organismal biology and bacterial pathogens of humans

Since 1997 my group has been working to cause disease) than others. Our experi- in the Department on the evolution of mental work, combined with theoretical genetic diversity in bacterial pathogens studies conducted in collaboration with and its consequences for human health, Sunetra Gupta, is providing explanations concentrating on Neisseria meningitides Hammond Andrew for this and has led to a vaccination (the meningococcus, a global cause approach currently in phase I trials in of meningitis and septicaemia) and collaboration with Andrew Pollard in Campylobcter jejuni and Campylobacter Paediatrics. coli, collectively the most important causes of bacterial gastroenteritis. Although the most likely reason for someone in the UK having bacterial At first glance, a group studying bacterial gastroenteritis in the UK, Campylobacter diseases of humans in a Zoology Department infection of humans is also incidental seems incongruous, but the non-medical and accidental. With genetic characteris- approach that we take to studying human ation studies of Campylobacter isolates disease makes the Department a very suitable The meningococcus – an electron micrograph of an accidental killer from a range of sources, including human home, and one in which we have thrived. disease from the John Radcliffe Hospital, Rather than taking the diseased patient as The meningococcus has a fearsome we have helped to establish that retail the starting point for our studies, our first reputation as a highly aggressive pathogen poultry meat is a major cause of human questions about the pathogens we study are which can kill children in hours; however, disease. Working with Marian Dawkins founded in organismal biology, ecology and, examination of its evolution and ecology and the Food Animal Initiative in above all, evolution: what is the lifestyle of the reveals a very different story. A large Wytham we have uncovered possible links bacterium in question, how has this evolved proportion of people, especially young between animal welfare and infection and what is the role of human pathogenesis adults (and particularly undergraduates!) with Campylobacter that may help reduce in these processes? By addressing these carry the meningococcus harmlessly in the burden of this unpleasant and costly questions, we aim to obtain insights into their throats and disease, when it does human disease. Collaboration with Andy how the burden of the human disease cause occur, is an accident that is as bad for the Gosler in the EGI also helped to indicate can be reduced. For both organisms we bacterium as it is for the human host as that wild birds are not a likely source of have taken a multidisciplinary approach, disease is ends host-to-host transmission. Campylobacter infection for humans (or, collaborating with other members of the Intriguingly, meningococci are highly indeed, chickens). department and including high-throughput diverse and paradoxically some persistent genomic techniques. strains are very much more invasive (likely Martin Maiden

Infectious disease Catherine Moyes epidemiology mapping

Estimated global distribution of Plasmodium falciparum malaria endemicity in 2010

Nearly 1500 pathogens have been recorded Alarmingly, so far only 3% of these (7 With the support of the Wellcome ‘making a living’ on or in humans, and diseases) have satisfactory maps produced. Trust, Simon Hay and colleagues have together they cause ~350 infectious spent much of the last decade mapping diseases recognised by physicians. Many of This leaves a considerable blind spot in detail the worldwide distribution of these infectious diseases have a ubiquitous in international biosurveillance. It also malaria (see www.map.ox.ac.uk), still global presence in human populations, presents an obstacle for those wishing one of the biggest infectious disease albeit at very different prevalence levels. to measure the health impact of infectious killers of children globally. These data Researchers in the Department of Zoology diseases. Perhaps most worryingly, it are now being used by agencies in many identified a list of 174 diseases with more also impairs our ability to infer what countries to help in critical decision limited geographical spread, for which might happen to the infectious disease making, for example in deciding where there is a good public health rationale to landscape under the many forces of limited public health resources should make accurate distribution and risk maps. environmental change. be spent. www.biology.ox.ac.uk Biology News, University of Oxford I Issue Two I 2013 7

Trees for tomorrow

In my own research group we are currently trying to understand how and why disease

Kevin Tuck Kevin resistance breaks down, and how pathogens acquire the ability to infect previously resistant plants. This may help us to assess whether plant varieties and species that are currently resistant to pathogens are likely to retain this resistance in the future. We have also been studying how environmental factors such as soil nutrients can tip the balance between infection and immunity. Researchers have speculated that climate change, extreme weather, and other environmental changes associated with agriculture, industry and development have opened the door to new diseases by reducing the ability of trees to resist infection, but further research is needed Ash copse to assess these possibilities. The arrival of ash dieback in the UK, homes, but a single shipment can carry In the case of ash dieback, we are fortunate along with the recent emergence of diseases a lethal legacy for native plants. that ash exhibits a high degree of genetic such as horse chestnut bleeding canker, diversity, and that trees have already been acute oak decline, Phytophthora ramorum Genome sequence analysis of multiple identified that appear to be resistant to the in larch, and Dothistroma (red band) needle strains of the pathogen Pseudomonas disease, providing optimism that durably blight in pine, has brought new attention syringae pv. aesculi, the causal agent of horse resistant lines can be found or bred, and that to the challenges facing plant pathologists chestnut bleeding canker, has shown that some mature trees will survive the current world-wide. Trade and traffic in plants all the strains isolated from infected trees outbreak. The University of Oxford is likely and plant products are enabling pathogens across the UK are nearly identical, suggesting to make an important contribution to this (disease-causing microorganisms) to that they originate from a single, recent research due to the work of local researchers move from country to country with introduction. New disease outbreaks have such as David Boshier in analysing the unprecedented speed. As a nation that is also arisen from changes in the behaviour of genetic diversity, reproductive biology and passionate about plants and gardening, existing pathogens. Phytophthora ramorum local adaptation of ash in Britain and Europe we take pleasure in bringing plants from was originally reported in the UK in 2002 together with partners across the EU. around the world into our gardens and in plants and shrubs such as rhododendron, viburnum and camellia, but in 2009 emerged So, although the newspaper headlines are in as a lethal pathogen of Japanese larch trees many respects justifiably bleak, the horizon (Larix kaempferi), the first time it had been holds some hope. Detailed understanding reported as pathogen of an economically of the biology of these pathogens and A challenge for the next decade important conifer. the trees they infect, along with better is to streamline methods and scale-up management practices, disease resistant this work, to consider a much broader In a world focused on short term impact, plants, increasingly sensitive disease suite of infectious disease pathogens tree diseases illustrate the need to take detection methods and better import control of public health significance: all 174 a long term view. Plants, unlike humans, measures may all help to ensure we do have of them. lack adaptive immunity, the ability to trees for tomorrow. dynamically modify their immune system One strategy, which has a great to recognise and resist new pathogens. Gail Preston heritage in epidemiology, is to exploit Instead, they possess innate immunity, advances in ecology, particularly a form of disease resistance in which developments in ‘species niche years of natural selection have driven the modelling’, allowing prediction

evolution of surveillance systems that Gail Preston when data are scarce. A second recognise and respond to commonly method is to collaborate with computer encountered pathogens. As a result, native scientists developing systems to plants often have little or no ability to resist extract information on infectious exotic pathogens. In trees this problem is diseases from the deluge of digital particularly acute, for while arable farmers information on the internet. We hope can select and sow a new cereal variety each this mix of ecology and informatics year, trees can only play the genetic hand will help us rise to these Big Data they have been dealt. One of the major challenges in mapping and make challenges facing plant pathologists is the significant in-roads into the spatial challenge of identifying or breeding trees epidemiology of infectious disease. and crops with durable resistance, which can endure in the face of successive waves Simon Hay of pathogen attack. Bleeding symptoms on horse chestnut

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Cooperation and conflict: from bee-eaters to bacteria

At the peaceful end, natural history move around as a collective group. Kevin documentaries have made famous how Foster and his collaborators showed that meerkats live in cooperative groups, where while these secretions improve the fitness Erik Svensson members babysit and feed pups that are not of all of the bacteria, strains that do not their own. Several research groups at Oxford produce the secretion can also make use the are trying to make sense of this variation, secretions made by other, more cooperative, as well testing how social behaviours can be cells. What then prevents the lazy non- harnessed to help us control pathogens. producers from taking over? It turns out that the cooperators only produce the secretions Some birds and mammals live in when they have more resources than they cooperative groups such as bee eaters, need to grow. This prudent behaviour allows where individuals care for young that are them to compete well against strains that do not their own. One example is the meerkats not invest in the cooperative good and helps mentioned above, but another from the to explain how cooperation can be stable UK is the family groups of long-tailed tits over evolutionary time. that move noisily between trees. However, White-fronted bee eaters many birds and mammals do not live in Our understanding of social behaviours cooperative groups. For example, all the can also be put to applied use. Bacterial other non-human birds and mammals in pathogens appear to rely on cooperative the UK! How can we explain this variation? behaviours to grow and hence damage Kevin Foster Kevin their hosts. For example, they release Ashleigh Griffin and her collaborators a range of molecules that act as toxins, found that a major factor was the sex life scavenge nutrients and break down host of females. If females are promiscuous, tissue. Furthermore, bacteria signal to each the chicks in her nest will be half-siblings other to coordinate these behaviours, only with the same mother but different fathers. switching them on when they have reached If she is monogamous, the chicks in her sufficient density to swamp their hosts. nest will have the same father and be full siblings. Helping full siblings to breed is Consequently, if we can learn to manipulate twice as effective as helping half siblings cooperative behaviours, then this could at transmitting genes to future generations, provide a tool for helping us reduce the and so cooperation is more likely to evolve virulence and even eliminate infections. in species where females are relatively Stuart West and collaborators found that Social interactions between bacteria in a petridish monogamous, such as meerkats and if you add non-cooperative ‘cheats’ to a long-tailed tits. bacterial infection that this reduces the The interactions between organisms can lie rate at which bacteria grow and more anywhere on a continuum from extreme Cooperation isn’t the preserve of higher than halves the death rate in hosts. We conflict to peaceful cooperation. At the animals. Over the last 20 years it has been are currently investigating the extent to extreme end, males of some insects have found that bacteria engage in a range of which this could be exploited clinically. huge jaws that they use to chop off each cooperative behaviours. For example, others heads in competition for females. bacteria use secretions to help them to Stu West

Nobel Prize for Oxford research

Everyone connected with biology in ‘for the discovery that mature cells can be Oxford was delighted to hear the reprogrammed to become pluripotent’. news that Sir John Gurdon had been The Nobel Prize recognized John’s work awarded the Nobel Prize in Physiology on cloning in Xenopus (clawed toads) or Medicine for 2012. John was a conducted in Oxford in the 1960s. John undergraduate and graduate student in Gurdon’s experiments demonstrated that the Department of Zoology, Oxford, and cells do not lose genes as they become then an Assistant Lecturer, before moving specialised, thereby opening the way to to Cambridge in 1972. John shares the stem cell research and potential therapies prize with Shinya Yamanaka from Kyoto, using cellular reprogramming.

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Using genomes to study animal diversity and evolution

Genome sequencing is playing an increasing role in many areas of our research, enabling new projects and allowing previously intractable questions Holland Peter Helen Thompson to be tackled So pervasive is ‘genome biology’ that it is easy to forget that it is only a little over a decade ago that the sequence of the human genome was first revealed. Until recently the massive cost of such projects kept them the preserve of giant international consortia, focussed on model species such as mouse and fruit fly. However, new inexpensive and efficient DNA sequencing technologies mean that genome biology now penetrates many areas of research. Twenty years ago, a single researcher might spend a year to obtain a few thousand nucleotides of MartinKyle David Ferrier DNA sequence, but today it is straightforward to determine tens of billions of nucleotides in a few months. It is even possible for a single postgraduate student to sequence the complete genome of their ‘own’ study organisms, whatever they may be. In the Department of Zoology, many researchers are using genome sequencing to investigate topics including animal phylogeny, the origin of particular sets of genes, the embryonic development of neglected groups of organisms, mechanisms of mutation and the effect of the environment on Some species for which Department of Zoology researchers have recently determined genome evolution and development. sequences. Clockwise from top left: larva of the common limpet, comma butterfly, African butterfly fish and keelworm Genome resources, to tolerate extreme stress, and the way in Planning for the future neglected taxa and the which early cell divisions are organised. evolution of development As genome-level sequencing spreads Mollusc and annelid embryos undergo a through zoological research and Genome sequencing, coupled with process known as spiral cleavage, where with the increasing involvement of sequencing the entire messenger RNA embryos going from four to eight cells postgraduates and undergraduates, content of particular cells and tissues, twist the axis of cell division to the left new challenges have arisen. Managing now provides the bedrock for studying or the right. This creates a spiral stacking and manipulating the data needs groups of animals that have been largely of cells that directly determines whether significant computational power and bypassed by modern biology. Molluscs adult features such as the spiral of a snail’s data storage, as well as requiring students and annelids, for example, comprise shell are left-handed or right-handed. By to develop bioinformatic skills. We roughly 100,000 and 12,000 described integrating genome and RNA sequencing have invested in new computational species respectively, yet we know very with gene expression studies and live infrastructure to support this, as well little about their development, genome embryo imaging, we are investigating as adapting graduate training and organisation or genomic adaptations. how such asymmetries form, propagate undergraduate teaching to promote Developing genome sequences and RNA and relate to asymmetries in other animals. bioinformatics: skills we think catalogues for species such as the common Most surprisingly, it seems as though will become ever more valuable as limpet is enabling deeper study of their some aspects of this process are the same the genomic revolution spreads. evolution, development and physiology. as those that control the asymmetric Here the development of pivotal structures organisation of our own heart and guts, Seb Shimeld such as the mollusc shell form a focus, as hinting at ancient mechanisms for does the ability of shore-dwelling species making left and right different.

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Using natural diversity to feed the future

It is predicted that by 2050 we will need C4 photosynthesis into non-C4 crops such to increase food production by at least ©IRRI as rice (http://c4rice.irri.org). 50%. At the same time, improvements in farm yields of our major crops has In our work, which is a collaborative slowed down. This is clearly a serious effort linking Universities in Cambridge, global problem that needs to be addressed. Toronto, Alberta and the International There are few examples of inventions Rice Research Institute in the Philippines, in the natural world that could produce we are trying to learn from evolution such large increases in our domestic how it is that C4 plants (like corn, sugar crops, but one that has this potential is cane and millet) evolved from their known as C4 Photosynthesis. You can non-C4 ancestors. One way in which think of C4 photosynthesis as the plant we are currently doing this is by using equivalent of ‘division of labour,’ the idea new sequencing technologies to read that kick-started the industrial revolution. and quantify the genes of more than By dividing up the tasks of capturing 40 different C4 plants and their closest non-C4 relatives. Our discoveries are CO2 from the atmosphere and storing it Sorghum seedlings in C4 screenhouse as sugars into two different cells within revealing the extent to which different species have used the same genes to the leaf, C4 plants essentially invented different families of plants. What’s more, achieve C4 photosynthesis and how many the production line and dramatically it’s so efficient that although C4 plants different ways evolution has found of increased their overall efficiency. This only make up 3% of plants on earth they reaching the same solution. We hope to saving allows them to grow more quickly are responsible for 20–30% of all CO 2 use this information to engineer these and store more carbon in their leaves, capture by plants. The sheer number of changes into rice and thereby use natural seeds and fruits. Perhaps unsurprisingly times that C4 photosynthesis has been diversity to feed the planet into the future. given the advantage that this optimisation re-invented in nature combined with the can confer, C4 photosynthesis has evolved urgent need to improve crop yields has led at least 62 different times in at least 18 to international efforts to engineer Steve Kelly ©IRRI

Harvesting rice

John Baker The Department of Plant Sciences Herbarium

When the University’s herbarium, a Plants gathered in gene banks and culture collection of flattened dried plants, was stocks are familiar to researchers working established in 1621, biology as a discipline with model species, searching for gene did not exist. Our knowledge of how plants function or breeding disease-resistant crops. worked was based on the experiences However, the pedigree of scientific plant of foresters, farmers and physicians. collections extends beyond the last century Naturalists were concerned with ordering to the European Renaissance, when herbaria plant diversity, and identifying plants that first became fundamental botanical tools. could feed, kill or cure us. Fundamental Herbaria record the physical evidence plant functions, which we take for granted, of the diversity and spatial and temporal were unappreciated, including sexual distribution of the planet’s plant life. Today, reproduction, light for plant growth and herbarium specimens, prepared using basic anatomy. fifteenth-century technology, are being used Specimen of Sturt’s pea (Swainsona formosa) to investigate twenty-first-century problems. collected by the privateer William Dampier in August 1699 in Western Australia and The University’s herbarium (c. 1,000,000 housed in Oxford University Herbaria specimens), packed into two rooms in www.biology.ox.ac.uk Biology News, University of Oxford I Issue Two I 2013 1 1

Peculiar plant sex chromosomes

Most plant species do not have separate sexes - male and female organs develop on the same individual or even in the same flower. This can have advantages; for example a plant separated from other individuals of the same species can still reproduce via self- fertilisation. On the other hand, the ability to self-fertilise may lead to inferior progeny because of inbreeding depression. Many plant

groups developed a variety of mechanisms Groutidos & Constantinos Dmitry Filatov that prevents self-fertilisation, with some plants going as far as evolving separate males and females. These plant species have evolved sex chromosomes that control whether an individual develops as a male or a female, just like animals. This process has occurred Closely related Silene latifola (white) and Silene dioica (pink) species grow side by side (and form many times and quite recently in some plant hybrids) all over Europe. Both of these species have separate male and female individuals, which is determined by sex chromosomes. Similar to humans XX individuals of these species develop as females, groups. For example, Silene latifolia (white while XY individuals become males campion) evolved sex chromosomes as recently as 5 to 10 million years ago, from To discover how sex chromosomes marks along the chromosomes. Interestingly, ancestors that had neither separate sexes originated in S. latifolia we compared this pattern has been found in many different nor sex chromosomes. This provides an the location of genes in S. latifolia and animal species with sex chromosomes, opportunity to study how separate sexes and S. vulgaris genetic maps. The latter species so the evolutionary processes shaping sex sex chromosomes form and evolve. has no separate male and female individuals chromosomes are similar in both kingdoms. and no sex chromosomes, so it effectively The identification of a sufficient number of shows us how the S. latifolia genome may However, unlike the sex chromosomes of genes that are located on sex chromosomes have looked like before sex chromosomes animals, we see little evidence of gene loss (sex linked genes) has been a significant evolved. This analysis revealed that from the Y-chromosome in S. latifolia. This hurdle for understanding sex chromosome S. latifolia sex chromosomes correspond difference between the kingdoms may, at evolution in plants. Fewer than 12 sex- to a single pair of chromosomes (autosomes) least partly, be due to fundamental difference linked genes had been identified until the in S. vulgaris. in plant and animal life cycles. In plants advent of high-throughput sequencing. a significant proportion of the genome is We have now identified several hundred In order for the sex chromosomes to evolve actively expressed at the haploid stage of life sex-linked genes from the S. latifolia from autosomes, recombination between the cycle, while in animals the genome is mostly genome in the last three years. This revealed proto-X and –Y chromosomes must have inactive at this stage. a dynamic picture of sex chromosome stopped. We discovered that this happened in evolution in S. latifolia. at least three distinct steps leaving distinctive Dmitry Filatov

the Department of Plant Sciences, is the and are laying unnamed or wrongly of data filed in herbarium cabinets cannot fourth oldest botanical collection in the named in the world’s herbaria. be ignored. Herbarium data, amalgamated world. It is part of a global network of into international databases, are used to approximately 2,600 herbaria, housing DNA extraction and pollen isolation model processes of species introduction or about 300,000,000 specimens. Plant from herbarium specimens has become changes in species’ ranges due to climate collectors have spent their careers and, commonplace giving researchers access change and even the provision of ecosystem in some cases, their lives, combing the to extinct species, or species impossible services. Herbaria have risen to the self- planet for specimens to populate herbaria. to collect for political, conservation, evident challenge of digitising herbarium The global financial investment in herbaria social or financial reasons. Importantly, specimens and abstracting data. However, through specimen collecting, curation the specimen automatically becomes the challenges with amalgamated data sets and premises costs is enormous. evidence (voucher) that a gene or pollen remain including collector and curator grain came from a particular species. biases and the ever-present concern with Traditionally, herbarium specimens are These researchers take advantage of the specimen identification. part of the evidence used to answer often difficult fieldwork undertaken by fundamental botanical questions. What others. Furthermore, the task of specimen Herbaria are facilitators of research, plant is this? How many different plants identification is usually underestimated, where the limitations should be the are there? Where does this plant grow? especially by those working in areas replete imaginations of researchers and the How is this plant distributed globally? with high-quality fieldguides. quality of collections, not the bureaucracies How does this plant’s morphology vary of collection management. However, across its range? To what is this plant As access to herbaria and the manipulation researchers demanding large datasets related? It has been estimated that of large datasets has become easier, must be aware of the limitations inherent approximately 70,000 species of flowering researchers from many disciplines, even in herbarium data. plant remain to be named, of which if they have no direct interest in , about 35,000 have already been collected have recognised that the vast quantities Stephen Harris

www.biology.ox.ac.uk NEWSLETTER FOR BIOLOGY ALUMNI AND FRIENDS

This is the second edition of the Biology at Oxford newsletter. We hope you like it, and we continue to welcome your comments. See our website (www.biology.ox.ac.uk/alumni), and email us on [email protected]

Other websites: www.alumni.ox.ac.uk; www.plants.ox.ac.uk; www.zoo.ox.ac.uk

OXFORD UNIVERSITY ALUMNI WEEKEND SEPTEMBER 2013

The Departments of Plant Sciences & Zoology invite you to our Open Day in the Department of Zoology

SATURDAY 21ST SEPTEMBER 2013 1.00 PM TO 4.00 PM

ATTRACTIONS WILL INCLUDE TALKS: Prof. David Macdonald, Director, WildCRU ‘War and Peace : Living with Carnivores’ Prof. Nick Harberd, Sibthorpian Professor of Plant Sciences ‘Mutation – Darwin’s ‘whatever the cause’ ’ Dr Stephen Harris, Druce Curator of the Oxford University Herbarium ‘Conserving Biodiversity in the Face of Global Change’ Dr Steve Kelly, Systems Biology Research Fellow in Plant Sciences ‘Using Genomics to Feed the World’

LAB TOURS & PRACTICAL DEMONSTRATIONS: Plants Sciences Department: DPhil students & postdocs ‘Roots, Fruits & Shoots: Plant Science & Food Security’ Zoology Department: Prof. Fritz Vollrath ‘Silk – from Webs to Medical Implants’ Dr Theresa Burt de Perera & Dr Graham Taylor ‘Flight and Swimming’

TEACHING DISPLAYS: Dr Martin Speight, Admissions Coordinator for Biological Sciences ‘Teaching Facilities in the Dept. of Zoology, Labs, Livestock & Lecture Courses’

Refreshments will be served TO REGISTER PLACES, PLEASE EMAIL [email protected] Martin Speight Martin Speight Alex Rogers Alex Martin Speight

Front cover: Female mosquito, Anopheles albimanus. Photo by James Gathany CDC