06 June 2013
Biotic-abiotic coupling in arctic and alpine environments
Dr Marc Macias-Fauria
Department of Zoology
Biotic and abiotic processes in arctic and alpine environments are strongly coupled. Besides climatic factors, the physical characteristics of the landscape – resulting from the geological history of a given region plus landscape evolution processes (e.g. erosion and uplift) – create an intricate matrix of habitat suitability that determines the chances of successful dispersal, recruitment, establishment, and growth of plant (or animal) individuals. This matrix has dynamics of its own linked to changes in climate and/or biotic processes (e.g. differential pressure of herbivory).
The spatial and temporal scales of landscape processes are generally longer/larger than those of ecological ones. Moreover, many ecological studies stem from site-based (i.e. points or transects) research. Consequently, arctic and alpine plant ecology has often treated the highly dynamic landscape as a uniform and/or static neutral background. Results from site-based studies have often been up-scaled without accounting of how representative they are of the area where they were conducted. In all, and although qualitatively recognized, the role of landscape heterogeneity and evolution is very rarely quantified in impact assessment under climate change scenarios.
This talk will describe two research projects in which the strength and spatial structure of the coupling between biotic and abiotic processes in arctic and alpine environments is quantified and partitioned, and will discuss how their results fundamentally modify predicted climate change impacts under warmer scenarios. These are:
1) The role of climate and geomorphology in controlling the position of the alpine treeline in the Canadian Rocky Mountains.
2) The differential effects of climate, geomorphology, and herbivory pressure in the observed increase of Eurasian tundra shrub productivity, size and extent (known as the ‘Greening of the Arctic’).
30 May 2013
The path to commercial lignocellulosic biofuels
Professor Ian Dobson
BP Biofuels
Lignocellulose deconstruction to simpler constituents such as sugars or syngas and subsequent conversion to liquid fuel molecules has been an ongoing focus of research for decades. That Lignocellulose derived liquid fuels are always five years away has been a hollow joke for some time now. Recently this has changed as several parties, including BP, now have technology in demonstration. The beginnings of a new industry are close. The seminar looks at what the practical options are, what is catalysing commercialisation now and what challenges still remain.
23 May 2013
The mechanism and evolution of vegetative phase change in flowering plants
Professor Scott Poethig
University of Pennsylvania
Scott’s primary interest is the mechanism the transition from the juvenile to the adult phase of shoot development (vegetative phase change). These studies led to the discovery that vegetative phase change is controlled by the evolutionarily conserved microRNAs, miR156 and miR157. He is currently studying how the temporal expression pattern of miR156/miR157 is regulated, the specific functions of these miRNAs during shoot development, and their role in the evolution of vegetative phase change in the Acacieae. This pan-tropical tribe of nitrogen-fixing trees includes many strongly heteroblastic species, as well as species that undergo relative minor changes in leaf morphology during shoot development, and is therefore an excellent model for the evolution and functional significance of vegetative phase change in flowering plants.
Blackman Lecture 2013
There will be a drinks reception in the Common Room, Plant Sciences at 5.00pm.
16 May 2013
Nitrification in acid soils: solving the paradox, possibly
Professor Jim Prosser
University of Aberdeen
Ammonia oxidation in soil was, until recently, thought to be dominated by autotrophic, chemolithotrophic proteobacteria. These organisms gain energy from oxidation of ammonia to nitrite and perform the first step in nitrification. All cultivated ammonia oxidising bacteria show no or very poor growth in liquid batch culture below pH 7. Paradoxically, nitrification occurs in acid soils at rates that are often faster than those in apparently more favourable neutral and alkaline soils.
Understanding acidophilic ammonia oxidation is important globally and economically. Approximately 30% of the world’s soils are acidic (pH<5), including 50% of arable soils, and up to 70% of ammonia-based nitrogen fertiliser is lost through nitrification and leaching or denitrification of nitrate.
Potential mechanisms for acidophilic ammonia oxidation include urea hydrolysis, protection in biofilms and aggregates and heterotrophic nitrification, but could also be due to acidophilic or acidotolerant ammonia oxidisers. Assessment of selection for such groups in acid soils was impossible using traditional techniques and acidophilic ammonia oxidising bacteria have never been isolated. Molecular techniques enable cultivation-independent analysis of ammonia oxidisers and recently led to the discovery that archaea can also oxidise ammonia.
This talk will describe how a combination of molecular and cultivation-based techniques have identified a novel ammonia oxidiser that provides a solution to the paradox of nitrification in acid soils that applies at local, regional and global scales. It will also consider the degree to which niche specialisation, exemplified in these studies, can explain soil microbial community composition.
09 May 2013
Driving genes through mosquito populations to curb human disease
Professor Charles Godfray
Department of Zoology
Infectious diseases such as malaria that are vectored by mosquitoes and other insects remain very major scourges for humanity. Control is difficult in poor countries, and the problems may get worse as the pathogen and vector evolve resistance to drugs and insecticides. But there are new ideas about how these diseases can be controlled that involve drive genes through vector populations that reduce their fitness or capacity to transmit disease. In this talk I’ll explore recent ideas and progress in this field of applied evolutionary biology, concentrating in particular on how a class of genes called homing endonucleases may be used.
02 May 2013
The hidden depths of Rab GTPase regulation during membrane traffic
Professor Francis Barr
Department of Biochemistry
01 May 2013
Transposon demethylation in Arabidopsis; gametophytic companion cells preserve gamete genome integrity
Dr Xiaoqi Feng
University of California at Berkeley
Sexual reproduction in flowering plants involves the generation of gametophytes containing gametes and their companion cells, followed by double fertilization. The Arabidopsis thaliana male gametophyte comprises two sperm cells and a companion vegetative cell, and the female gametophyte contains an egg cell and a companion central cell. The two sperm cells fertilize the egg and central cells, respectively, to generate a diploid embryo and a triploid endosperm. Previous studies discovered that A. thaliana endosperm is extensively hypomethylated, and that this process is at least in part dependent on the DNA glycosylase DEMETER. To further understand the extent and significance of DNA demethylation during plant sexual reproduction, we examined the methylomes of A. thaliana sperm, vegetative cells, and the paternal and maternal genomes of the endosperm and embryo in wild-type and dme mutant backgrounds by bisulfite sequencing. We find that DNA demethylation of small euchromatic transposons is a common feature of central and vegetative cells, and entirely dependent on DEMETER. We also showed that lack of DEMETER in vegetative cells reduces small RNA-induced methylation of transposons in sperm. The data thus suggest that demethylation of companion cells, which are genetically identical to the gametes, reinforces transposon silencing in plant gametes and serves to protect the genome integrity of the next generation.
ANNALS OF BOTANY SPECIAL SEMINAR 2013
25 April 2013
Rethinking carbon fixation
Dr Ron Milo
Weizmann Institute, Israel
Carbon fixation is the main pathway for storing energy and accumulating biomass in the living world. It is also the main reason for humanity’s usage of land and water resources. Under human cultivation, where water, light and nutrients can be abundant, it is the rate of carbon fixation that significantly limits growth. Hence increasing the rate of carbon fixation is of major importance in the path towards agricultural and energetic sustainability.
Are there design principles that limit the rate of such central metabolic pathways? Recent attempts to improve the rate and specificity of Rubisco, the key enzyme in the Calvin-Benson cycle, have achieved only limited improvement.
In this lecture we consider options to overcome this bottleneck by systematically exploring the space of carbon fixation pathways that can be assembled from all ~4000 metabolic enzymes known in nature. We computationally compare all possible metabolic pathways based on kinetics, energetics and topology. Our initial analysis suggests a new family of synthetic carbon fixation pathways that utilize the most effective carboxylating enzyme, PEP carboxylase. I will describe how our lab approaches synthetically implementing carbon fixation within bacteria.
16 April 2013
Syngenta Vegetables Trait Research
Dr Charlie Baxter
Syngenta
All welcome.
14 March 2013
‘Being a metabolism geek’
Dr Lee Sweetlove
Department of Plant Sciences
9th Week Seminar
07 March 2013
‘Population genetics of wild tomatoes: population divergence, seed banks, and molecular signatures of adaptation‘
Professor Wolfgang Stephan
LMU München
Wild tomato species, native to western South America and the Galapagos Islands, are an evolutionary plant model system. Although the extant wild tomato species are morphologically distinct, studies of molecular variation suggest that these species are relatively young. This allowed us to use a population genetic approach to examine the role of demography, population structure and seed banks in the origin and divergence of the tomato species. Furthermore, wild tomatoes exhibit considerable morphological and functional variation, much of which is thought to be adaptive. For instance, they dwell in a variety of habitats, spanning a wide range of temperatures and water availability and are therefore exposed to different abiotic stress regimes. We have used a series of “candidate genes” influencing two stress responses, cold adaptation and drought tolerance, to elucidate the molecular signatures of positive selection.
28 February 2013
‘Why there is more to gene evolution than protein function: splicing and dual-coding sequence’
Professor Laurence Hurst
University of Bath
There is considerable variation in the rate at which different genes evolve. Why is this? Classically it has been considered that the density of functionally important sites must predict rates of protein evolution. Likewise, amino acid choice is usually assumed to reflect optimal protein function and codon choice is random. Here I present evidence suggesting that this view is too simplistic. In particular I concentrate on how selection acting during the protein’s production history can also affect gene evolutionary rates as well as amino acid and codon choice. Exploring the role of selection at the RNA level, I specifically address how the need to specify exonic splice enhancer motifs in pre-mRNA impacts amino acid choice, codon choice and rates of evolution at both synonymous and non-synonymous sites. Moreover, I show that as regards splicing, selection is stronger, not weaker, when population sizes are small in opposition to the nearly neutral theory of molecular evolution.
27 February 2013
‘Will Agriculture Destroy the World before It Saves It?’
Jack A. Bobo, JD, MS
United States Department of State
Agriculture lies at the crossroads of many global challenges, including food security, climate change, and biofuels. The world needs to increase food production by 60 to 70 percent by 2050, and it needs to do so using less land, less water, less fertilizer and less pesticides. The challenges faced by mankind have never been greater. Fortunately, the tools available to scientists to address these challenges have also never been greater. Over the last one hundred years, technology has consistently delivered on its promise of improved yields and a cleaner environment, year after year, decade after decade.
In many ways, the question is not, can technology achieve the improvements necessary to get the world where it needs to be by 2050, but whether governments will allow the needed technologies to find their way to market. The obstacles to bringing products to market are increasing and putting at risk international trade in the food and commodities that feed the world. They are also undermining the ability of scientists to achieve the sustainable intensification of agriculture that is needed to save our soil, water ways and air for future generations.
27 February 2013
Scanning functional diversity in conifer trees
Professor John MacKay
Université Laval, Québec, QC, Canada
Studying species with life habits and evolutionary histories that are distinct from model organisms may uncover unique adaptations or novel mechanisms, in addition to broadening our understanding of evolutionary processes. Our research uses spruce trees (Picea spp.) as representatives of the conifers, which also include pines, firs, and other northern hemisphere forest trees. Conifers are long-lived and outbred species, which dominate many terrestrial ecosystems. They are evolutionary ancient and have among the largest genomes (18 to 30 gigabases). We have applied large-scale transcriptome profiling methods to study the evolution of gene families, naturally-occurring expressional diversity and adaptive mechanisms.
We present an approach that enables genetic analyses of expression variation based upon the segregation in haploid meiotic products of single diploid individuals (Verta et al., 2013 Mol. Ecol). We found abundant Mendelian variation in gene expression, which was more abundant among environment interaction genes and duplicated genes. Our results suggest that analyses of wild species such as P. glauca may reveal new parameters that affect the nature of genetic variation in gene expression networks.
Transcriptome profiling was also utilized to study a naturally-occurring resistance phenotype for a major defoliating insect, the spruce budworm Choristoneura fumiferana (Clem.). Resistant trees accumulate two phenolic compounds that are toxic to the insect while non-resistant trees accumulate glycosylated forms (Delvas et al. 2011 Entomol. Exper. Applic. 141:35). Transcripts encoding a putative glycosyl hydrolase accumulated to high levels specifically in resistant trees and appears to be required resistance. To date, the tree’s defense mechanisms were unknown owing to the cyclical nature and variable spatio-temporal scale of insect outbreaks. Our discovery of a novel insect resistance mechanism directly in a wild population of trees broadens the application chemical ecology.
21 February 2013
‘Kinesins, dyneins and the evolution of the eukaryotic cytoskeleton’
Dr Bill Wickstead
University of Nottingham
The cytoskeleton plays critical roles in DNA segregation, cytokinesis and cell shape determination in bacteria, archaea and eukaryotes. In eukaryotes, cytoskeletal function has been hugely elaborated through gene duplication/specialization and by the addition of motors – myosins, dyneins and kinesins. It is likely that the advent of these motor superfamilies was essential for the genesis of much of the cellular compartmentalization that defines eukaryotes. Using genomic sequence from multiple diverse lines, we have analysed the evolution of ancient paralogues and domain architectures in the kinesin and dynein superfamilies. We show that a minimum of 11 kinesin families and all 9 dynein types were present in the last eukaryotic common ancestor (LECA). However, since that time, all families have experienced multiple losses, with the result that no kinesin or dynein family is ubiquitous and at least three lineages now entirely lack dynein motors. Unlike motor families, which are typically ancient, domain architectures are surprisingly ephemeral with only 3 kinesin domain combinations persisting since LECA. Our analyses provide molecular evidence for the existence of key cellular functions in LECA, and show that a large proportion of motor family evolution had already occurred before this ancient cell. Such complexity highlights the evolutionary gulf between the first proto-eukaryote and LECA. In spite of this, motor phylogenies constrain the likely evolutionary path by which some cellular features formed prior to the emergence of LECA – in particular arguing against widely-held assumptions about the formation of the cilium. The distribution of cytoskeletal filaments also puts constraints on the likely prokaryotic line that made the leap of eukaryogenesis.
19 February 2013
A future for forests in the Anthropocene
Dr David Coomes
Forest Ecology and Conservation Group University of Cambridge
The planet's forests continue to be cleared for agriculture, exploited for timber and modified by introduced species. However, researchers are only just starting to understand the implications of these anthropogenic impacts on climate and biodiversity. I shall illustrate ways in which novel computational and remote sensing approaches are changing the way that ecologists think about forests, providing fresh insights into fundamental processes and system dynamics. I shall then discuss how these approaches can be used to make informed decisions about the conservation management of forests.
14 February 2013
'Evolutionary genomics and species diversification’
Professor Christian Lexer
University of Fribourg, Switzerland
Understanding the processes that facilitate the origin, functioning and maintenance of biological diversity is of great interest to the fundamental and applied life sciences. My group`s research interests revolve around the use of novel laboratory and computational tools for studying adaptive evolutionary responses, speciation, and species radiations in plants. To achieve these goals, we make use of Northern hemisphere ‘model’ taxa (Populus spp., Salix spp.) for which extensive genomic and biological resources are available, and we have initiated the transfer of knowledge gained from this work to other plant radiations in highly structured and species-rich environments in South America, Southern Africa and Southeast Asia. I will highlight the basic concepts underlying our work and recent progress by my group.
07 February 2013
‘Cellular and regulatory basis of early plant organ growth’
Dr Robert Sablowski
John Innes Centre, Norwich
A general question in developmental biology is how patterning genes are linked to the cellular activities that regulate tissue and organ growth. During flower development, different combinations of floral organ identity genes direct the development of each of the four types of floral organs (sepals, petals, stamens and carpels). Work in our lab and others’ has shown that the gene network controlled by the floral organ identity genes includes general regulators of of organ growth, such as JAGGED (JAG). To understand what cellular processes are regulated by JAG during organ growth, we combined quantitative, 3D analysis of cell geometry and DNA synthesis. JAG was required for the transition from meristem to primordium growth parameters, including a shift from isotropic to anisotropic growth, enhanced cell growth and division, in addition to loss of coordination between cell volume and DNA synthesis. De-coupling of cell size from cell cycle in emerging primordia was associated with increased cell size heterogeneity, which may be related to accelerated growth and the onset of cell differentiation. Current work aims to analyse quantitatively the role of other regulators of early organ growth and to reveal the molecular basis for the co-ordination between cell growth and cell cycle during plant organogenesis.
31 January 2013
‘Elucidating stress signalling response pathways in Arabidopsis and crops’
Professor Marc Knight
Durham University
My group is interested in the pathways leading from stress perception, through signal transduction, to stress gene expression and altered tolerance, as well as in the fundamental basis of stress tolerance itself. Our most recent work has focussed upon three areas (1) the role of calcium in mediating appropriate patterns of stress gene expression; (2) the mechanisms of drought tolerance in Sorghum bicolor; (3) investigating genetic components of freezing tolerance in Arctic plant species. In the first project, we have taken a transcriptomic approach not only to define the specific transcription factor systems that are regulated by calcium, but also to begin to understand how calcium encodes information that specifies the correct pattern of gene expression. In the second project, we have focussed upon Sorghum bicolor with the aim of uncovering potentially novel drought-tolerance pathways/mechanisms. This species is highly drought-adapted compared to other crops, and extremely drought tolerant “stay-green” Sorghum lines have been isolated, and the genetic loci responsible have been mapped by our collaborators. We have undertaken a transcriptomic approach to describe the fundamental processes underlying the stay-green phenomenon to help us understand why these lines are particularly drought tolerant and allow us to exploit this information. Finally, the last project, still relatively new, involves working on plants whose freezing tolerance is profound i.e. plants from the Arctic where a temperature of -40oC is not unusual in winter. By cloning and functionally testing alleles of genes known to be key genetic determinants in freezing tolerance, we hope to start to understand how the proteins involved have evolved to enhance freezing tolerance in these species. Understanding how such proteins from Arctic plants are able to mediate much greater levels of freezing tolerance will allow us to breed more freezing-tolerant crops.
24 January 2013
‘On mutation: Darwin's 'whatever the cause ...' '
Professor Nick Harberd
Department of Plant Sciences
It has long been known that DNA sequence mutation is fundamental to biological evolution. However, mutation remains a mysterious phenomenon. This is because mutation is a relatively infrequent event, rendering attempts to understand it on a systematic basis problematic. As a result, we have until recently known little of how mutations originate on a genome-wide basis. However, whole-genome DNA sequence analysis now enables sampling of new mutations in sufficient numbers to enable meaningful analysis. Using the genetic model plant Arabidopsis thaliana, I will first show that exposure of plants to ionising fast-neutron irradiation generates a specific spectrum of mutations that differs substantially from that characteristic of mutations accumulating spontaneously in laboratory 'mutation accumulation' (MA) lines. Next, I will show that the intriguing phenomenon of 'somaclonal variation' (the heritable variation characteristic of plants regenerated from in vitro cultured plant cells) is in part explicable by specific classes of de novo DNA sequence mutation. Finally, I will address the question of whether or not 'natural' environments are mutagenic? I will show that plants growing in experimental 'stressful' environments (e.g. on saline soil) accumulate a spectrum of mutations that differs from that seen in MA lines (which are grown in benign environments). Interestingly the mutational spectrum of single nucleotide polymorphisms found in wild Arabidopsis populations reflects more closely the 'stressed' spectrum than the benign MA line spectrum. Does this mean that growth in nature is detectably mutagenic to plants? And that environmental factors induce many of the mutations that fuel the evolution of flowering plants?
17 January 2013
‘Brown algae, a different way of looking at life’
Dr J. Mark Cock
Roscoff
The brown algae are members of the supergroup chromalveolata, and as such are very distantly related both to animals and to green plants. This group of seaweeds evolved complex multicellularity independently of the plants and animals and is one of only a small number of eukaryotic groups that has acquired this level of developmental complexity1. Analysis of the genome sequence of the model brown alga Ectocarpus has revealed a number of features that may be linked to the emergence of complex multicellularity in this lineage, including a family of membrane-localised receptor kinases that evolved independently in brown algae but strongly resemble the receptor kinases of green plants and animals2. Genome analysis has therefore provided some clues about the molecular mechanisms that underlie multicellular development in the brown algae but more meaningful comparisons with other multicellular lineages will only be possible if we can obtain a deeper, experimental understanding of these molecular mechanisms. To address this problem, we have proposed and are developing the filamentous brown alga Ectocarpus as a model system for the brown algae3 and are using this system to investigate the genetic basis of specific developmental processes. This work currently focuses on two key aspects of this organism's reproductive biology, life cycle regulation and sex determination.
The life cycle of Ectocarpus involves an alternation between two independent multicellular organisms, the sporophyte and the gametophyte. We have shown that the identities of the two generations are not determined by ploidy, but rather are determined genetically. Several life cycle mutants are currently being studied4,5, including the ouroboros mutant, which exhibits complete conversion of the sporophyte generation into a gametophyte. The ouroboros mutation not only identifies a key developmental regulator in Ectocarpus but also represents a new class of homeotic mutant in which there is a switch between developmental programs at the level of the whole organism rather than at the organ or tissue level.
Brown algae exhibit a broad diversity of mating systems, ranging from isogamy to oogamy. Sex determination in Ectocarpus is particularly interesting because of the minimal level of sexual dimorphism (near-isogamy and very similar male and female gametophytes) and because sex is genetically determined in the haploid phase of the life cycle (i.e. a UV system rather than the well known XY or WZ systems). We have identified the sex chromosome in Ectocarpus and current work is aimed both at exploring the evolutionary history of this locus and investigating how the sex-determining region orchestrates sexual differentiation.
06 December 2012
‘Roots: past, present and future’
Professor Liam Dolan
Department of Plant Sciences
The appearance of multicellular plants with differentiated organs systems on land over 475 million years ago led to the development of the first complex terrestrial ecosystem in the history of the planet. Our research has focused on the development of specialised filamentous cells on the root surface that play critical roles in the uptake of these essential nutrients from the soil. The discovery of the mechanism underpinning the growth and development of cells at the plant-soil interface provides insight into fundamental mechanisms of development and evolution. It also provides tools that can be used to develop technologies for the generation of crops with enhanced nutrient uptake capacity. Such yield-enhancing technologies can contribute to the sustenance a growing world population once there are regulatory mechanisms in place that ensure access to technology and food, irrespective of income or geography.
References from our research:
1. Jang G, Pires N, Keke Y, Menand B, Dolan L 2011 RSL genes are sufficient for rhizoid system development in early diverging land plants Development 138, 2273-2281.
2. Keke Y, Bell E, Menand B, Dolan L 2010 A basic helix loop helix transcription factor controls cell growth and size in root hairs Nature Genetics 42, 264-267.
3. Menand B, Keke Y, Jouannic S, Hoffmann L, Ryan E, Linstead P, Schaefer DG, Dolan L 2007 An ancient mechanism controls the development of cells with a rooting function in land plants Science 316, 1477-1480.
4. Lenton, T, Crouch M, Johnson M, Pires N, Dolan L 2012 First plants cooled the Ordovician Nature Geoscience 5, 86-89.
9th Week Seminar
22 November 2012
Making new molecules
Professor Anne Osbourn
John Innes Centre, Norwich
Plants produce a huge array of natural products, many of which are specialised metabolites associated with particular species. These secondary metabolites often have important ecological roles, facilitating pollination and seed dispersal and/or providing protection against attack by pests and pathogens. Although the ability of plants to perform in vivo combinatorial chemistry by mixing, matching and evolving the genes required for different secondary metabolite biosynthetic pathways is likely to have been critical for survival and diversification of the Plant Kingdom we know very little about the mechanisms underpinning this process. This talk will focus on plant natural product function and synthesis, the origins of metabolic diversity and potential for metabolic engineering, drawing on our research on terpene synthesis in crop and model plants.
16 November 2012
‘ANALYSIS OF NATURALLY OCCURRING GENETIC VARIATION IN PLANTS: BUILDING COMPREHENSIVE CATALOGUES OF VARIATION’
Michele Morgante
Universita' di Udine, Italy
The genomics revolution of the last 15 years has improved our understanding of the genetic make up of living organisms. Together with the achievements represented by complete genomic sequences for an increasing number of species, high throughput and parallel approaches are available for the analysis of DNA sequence variation, transcripts, proteins. The use of genomic tools has allowed us to start to unravel the genetic make up of traits that are relevant to adaptation. At the same time a deeper understanding of what natural variation is at the sequence level has also been achieved, allowing us to realize that nature can sometime have much greater fantasy and inventiveness than any laboratory scientist and that genetic variation is continuously created in plant species. The pace at which we can analyze natural sequence variation has recently been greatly accelerated thanks to the advent of new DNA sequencing technologies.
The comparative sequencing of several plant genomes revealed that, in addition so single nucleotide polymorphisms (SNPs), transposable elements are largely responsible for extensive variation in both intergenic and local genic content not only between closely related species but also among individuals within a species. In addition larger structural variants can be detected, similar to the copy number variants identified in the human genome and involving hundreds of Kbp of DNA and tens of genes. A single genome sequence may therefore not reflect the entire genomic complement of a species and prompted us to introduce in plants the concept of the pan-genome, which includes core genomic features common to all individuals and a dispensable genome composed of non-shared DNA elements that can be individual- or population-specific.
We will describe the variation that can be detected among plant genotypes not only as SNP but also and especially as structural variants due either to simple transposable element insertions or to insertions/deletions of large genomic regions using next generation sequencing methodologies. We will particularly focus on how to create either horizontal catalogues of genetic variation, i.e. looking at the variation in a limited number of very interesting genes in a very large number of individuals or vertical catalogues, i.e. looking at the variation in the entire genome of a limited number of very interesting individuals and provide examples of how to make use of such catalogues to address specific biological questions.
Keywords: next-generation sequencing technologies; structural variation; transposable elements.
15 November 2012
POSTPONED DUE TO ILLNESS
On Mutation: Darwin's 'whatever the cause'...
Professor Nick Harberd
Plant Sciences
It has long been known that DNA sequence mutation is fundamental to biological evolution. However, mutation remains a mysterious phenomenon. This is because mutation is a relatively infrequent event, rendering attempts to understand it on a systematic basis problematic. As a result, we have until recently known little of how mutations originate on a genome-wide basis. However, whole-genome DNA sequence analysis now enables sampling of new mutations in sufficient numbers to enable meaningful analysis. Using the genetic model plant Arabidopsis thaliana, I will first show that exposure of plants to ionising fast-neutron irradiation generates a specific spectrum of mutations that differs substantially from that characteristic of mutations accumulating spontaneously in laboratory 'mutation accumulation' (MA) lines. Next, I will show that the intriguing phenomenon of 'somaclonal variation' (the heritable variation characteristic of plants regenerated from in vitro cultured plant cells) is in part explicable by specific classes of de novo DNA sequence mutation. Finally, I will address the question of whether or not 'natural' environments are mutagenic? I will show that plants growing in experimental 'stressful' environments (e.g. on saline soil) accumulate a spectrum of mutations that differs from that seen in MA lines (which are grown in benign environments). Interestingly the mutational spectrum of single nucleotide polymorphisms found in wild Arabidopsis populations reflects more closely the 'stressed' spectrum than the benign MA line spectrum. Does this mean that growth in nature is detectably mutagenic to plants? And that environmental factors induce many of the mutations that fuel the evolution of flowering plants?
08 November 2012
Linking HIV immunology and Epidemiology
Professor Angela McLean
Department of Zoology
Studies of the natural history of HIV infection within infected individuals show how the virus evolves to escape from the selection pressures imposed by immune responses. Carefully interpreted, such data can teach us about the strength of those immune responses. Data on the within-host evolutionary dynamics of HIV is hard to gather and contingent on having samples from the precise weeks and months when new variants are growing out. It is much easier to gather data on the population-level prevalence of immune escape mutants. I will present a mathematical model that allows us to "integrate up" the impact of many within-host events to find the expected epidemiological patterns of escape mutant prevalence, both in hosts of different types and changing through time. This is a model that lets us make inferences about the rate of evolutionary change within individuals from data on the prevalence of escape mutants within populations.
01 November 2012
Establishing beneficial interactions with the symbiosis signalling pathway
Professor Giles Oldroyd
John Innes Centre, Norwich
The establishment of rhizobial and mycorrhizal symbioses requires the common symbiotic signalling pathway that utilises oscillations in calcium as a secondary messenger. Despite commonalities in signalling, it is clear that differential outputs occur from the signalling pathway, which coordinate specific aspects of each symbiosis. Calcium oscillations are perceived by a calcium and calmodulin dependent protein kinase (CCaMK) and gain-of-function mutations in this protein autoactivate both nodulation and mycorrhizal responses. Downstream of CCaMK are a suite of GRAS-domain transcription factors, with NSP2 having dual roles in nodulation and mycorrhization, but NSP1 and RAM1 functioning specifically in nodulation or mycorrhization respectively. NSP2 interacts with both NSP1 and RAM1 and this suggests that the specificity of symbiosis signalling may be defined by the specific formation of one or the other transcription factor complex. NSP1 can bind the promoters of Nod factor inducible genes and of particular importance is the activation of the NIN and ERN1 transcription factors. These are necessary for activation of nodulation and bacterial infection. In contrast, RAM1 binds the promoters of mycorrhizal induced genes, including RAM2 a protein that functions in the promotion of mycorrhizal colonisation. While we now have a grasp on the nature of specific downstream responses, the precise mechanisms that ensure the appropriate activation of mycorrhizal or rhizobial-specific responses remains unclear.
25 October 2012
Quantitative systems modelling of the stomatal guard cell with real predictive power
Professor Mike Blatt
University of Glasgow
Stomatal guard cells play key roles in gas exchange for photosynthesis and in minimizing transpirational water loss by opening and closing the stomatal pore. The dynamics of stomatal movements have long been incorporated into mathematical models, but few of these have been developed from the ‘bottom-up’ and none are sufficiently generalised to predict stomatal behaviour at a cellular level. Over the past four years my laboratory developed a dynamic computational model for cellular physiology building on the wealth of biophysical and kinetic knowledge available for guard cell transport, signalling and homeostasis. The Onguard software and model incorporate explicitly all of the fundamental properties for transporters at the plasma membrane and tonoplast, the salient features of osmolite metabolism, cytosolic-free Ca2+ and pH buffering. The model integrates the kinetics of transport and metabolism and has proven remarkably robust in recapitulating physiologically complex behaviours, including those of oscillations in membrane voltage and cytosolic-free Ca2+ concentration previously reported in vivo. The predictive power of the OnGuard model is evident in its ability to generate a number of unexpected and counterintuitive outputs of physiological relevance without ad hoc assumptions or additional regulatory networks. It led to the uncovering of a previously unrecognised homeostatic network exposed by slac1, an anion channel mutant of Arabidopsis. Similar results have now come from studies of transporter mutants associated with the tonoplast. Thus, the OnGuard model sets out a framework for the systems biological analysis of stomatal guard cells, and it offers a powerful new tool that should find applications in addressing the previously intractable problem of tonoplast transport in vivo.
18 October 2012
The Arabidopsis plant at night
Professor Alison Smith
John Innes Centre, Norwich
Plants acquire carbon for growth and maintenance through photosynthesis, in which carbon dioxide from the air is converted into carbohydrates. However, photosynthesis is possible only in the light. At night, Arabidopsis growth and maintenance is dependent on consumption of starch reserves built up by photosynthesis during the previous day. Starch is consumed at a linear rate so that reserves are almost entirely exhausted at dawn. This pattern is maintained when plants are grown in different day/night regimes and – remarkably – when plants are subjected to an unexpectedly early night. Thus when night falls, the rate of starch degradation is set by a mechanism that uses the circadian clock to anticipate the time until the next dawn and measures leaf starch content, then operates an arithmetic division to set the appropriate rate of degradation. Adjustment of starch degradation is coordinated with a massive shift in the pattern of metabolism and growth of the plant between the day and the night.
Mary Snow Lecture 2013
15 October 2012
The Resilience and Rescue of Critically Endangered Trees
Professor Jaboury Ghazoul
ETH Zurich, Switzerland
Many tree species, particularly on oceanic islands, are now considered to be critically endangered, often persisting only in tiny and isolated populations. Such species include the jellyfish tree and the coco-de-mer palm, among the most fascinating and charismatic of plants – the tigers and pandas of the plant world. More importantly, they include many species of the great Asian tropical tree family, the Dipterocarpaceae. Although many are now afforded some degree of protection, they remain vulnerable to the insidious loss of population and genetic viability through Allee effects and genetic erosion. Are these species a lost cause, irretrievably trapped within the Extinction Vortex? Or do they have sufficient resilience to enable our efforts at genetic rescue and ecological restoration to be applied to good effect? Our work on critically endangered plants in the Seychelles, India and Malaysia seeks to provide the scientific basis for practical conservation action that will allow us to save these wonderful species.
11 October 2012
[THIS SEMINAR HAS BEEN POSTPONED]
Population genetics of wild tomatoes: population divergence, seed banks, and molecular signatures of adaptation
Professor Wolfgang Stephan
LMU München
21 June 2012
C4 Rice - what, why and how?
Professor Jane Langdale
Department of Plant Sciences
Ninth week seminar
14 June 2012
'Traits, Trade-offs and Tropical Forest Diversity'
Dr David Burslem
University of Aberdeen
According to niche theory, resource partitioning by competing plant species contributes to the maintenance of species richness in plant communities. Hyper-diverse tropical lowland rain forest tree communities present a challenge to this theory because ecologists have difficulty defining sufficient distinct niches to accommodate the large number of competing species. Trade-offs among multiple resource axes may help to resolve this problem, especially when biotic interactions are considered. In this seminar I discuss mechanisms of coexistence among competing species of Dipterocarpaceae, which is the dominant family of trees in Southeast Asian rain forests. Among dipterocarps, per capita seed production appears to be equalised across species despite orders of magnitude variation in flower production among species. This equalization of seed production can be interpreted as contributing to an equalization of fitness among species that, all else being equal, would aid the coexistence of multiple competing species. Our data suggest that this equalization of per capita seed production among species is determined by interactions of flower size, pollinator body size, pollination success and pollen dispersal distance. Maximum flower production was two orders of magnitude greater in small-flowered than large-flowered species of Dipterocarpaceae, but small-flowered species also had smaller-sized pollinators, lower average pollen dispersal distances and lower mean pollination success than large-flowered species. Paternity analysis revealed that mating between related individuals was more frequent in a smaller-flowered species. We conclude that a trade-off embedded in the relationship between flower size and pollination success contributes to equivalence of fruit production among species. Our findings also demonstrate the potential for differential vulnerability of species to the deleterious ecological and genetic consequences of forest fragmentation. They have clear implications for forest restoration, as seed collection from small-flowered species may be especially vulnerable to cryptic genetic erosion. Our interpretation highlights the importance of maintaining pollinator communities and gene flow in order to sustain the species richness of tropical tree communities.
07 June 2012
'The endodermis – how plants build their inner skin'
Professor Niko Geldner
University of Lausanne
My lab investigates the establishment of endodermal structure and polarity. The endodermis is an invariable barrier within the root of vascular plants. Its barrier function is mediated by the Casparian Strips, ring-like hydrophobic cell wall thickenings that are coordinated between cells and form a supracellular network. Casparian Strips effectively blocks passage of nutrients and pathogens through the extracellular space, while still allowing for signal perception and nutrient uptake. This very much resembles the dual, protective/uptake function of polarised gut epithelia in animals, for example. The molecular players and mechanisms that underlie this intricately structured cell layer have remained obscure. Our group has recently described the developmental events leading to a differentiated endodermis and visualised a strict polarity within this cell layer. We found that the two polar domains in the endodermis are separated by a central membrane diffusion-barrier and identified an unknown protein family that forms this barrier and predicts the site of Casparian Strip formation. Mutants in these CASP genes display disorganized deposition of Casparian Strips. In addition, we have obtained a number of mutants in Casparian Strip development, by forward and reverse genetic approaches, which display interrupted, or strongly delayed, deposition of Casparian Strips, some by interfering with CASP localization. These mutants now provide the unprecedented opportunity to directly test the many supposed roles of the Casparian Strips and I will report on our latest results from our mutant analysis.
31 May 2012
'Analysis of the allohexaploid bread wheat genome (Triticum aestivum) using comparative whole genome shotgun sequencing'
Professor Mike Bevan
John Innes Centre, Norwich
The large 17 Gb allopolyploid genome of bread wheat is a major challenge for genome analysis because it is composed of three closely- related and independently maintained genomes, with genes dispersed as small “islands” separated by vast tracts of repetitive DNA. We used a novel comparative genomics strategy to identify 88,854 wheat genes with associated sequence polymorphisms and assigned a significant proportion to the component A, B and D genomes. Our analysis reveals a highly dynamic genome, with rapid and extensive loss of gene family members upon polyploidization, and an abundance of gene fragments forming a potential reservoir for rapid gene evolution. Several classes of genes involved in energy harvesting, metabolism and growth are among expanded Triticeae- specific gene families, consistent with the high productivity of the wheat crop. Our genome analysis, coupled with the identification of extensive genetic variation, provides an important new resource for accelerating gene discovery and improving this centrally important crop.
24 May 2012
'Plant diversity provides new genetic tools for management of insects and weeds in sustainable food production'
Professor John Pickett
Rothamsted Research
Sustainability in food production, because of the high energy inputs involved, requires minimisation of losses after crops have been sown and nutrition for growing plants has been delivered. In the search for methods to reduce losses due to pests, plant secondary metabolites, particularly those acting by regulatory and signalling mechanisms, are being targeted and developed by new routes, including GM. The diverse genetics of the plant kingdom, and specifically crop plant ancestry, are providing a range of options for crop protection, including against parasitic weeds, in both developed and developing countries.
GE Blackman Lecture
17 May 2012
'Science Online: Tools, Data, Crowds, Collaboration, and Science in a Digital World'
Dr Eric T Meyer
Oxford Internet Institute
The internet is transforming all aspects of modern life, from how we communicate with each other and form and maintain relationships, to how we work and learn. Scientific uses of the internet have been at the leading edge since the first networks that would eventually become the internet were established. This talk will discuss some of the ways that moving science online opens up both the results of science, but also the process of science. From engaging the public to help classify astronomical data, as in the Galaxy Zoo project, to efforts to use the internet to engage the public with science and understand the science behind the news headlines, science is less mediated than ever. However, what does this disintermediation mean for scientists? This talk will address these issues.
10 May 2012
‘Developmental timing in plants: seasonal regulation of flowering’
Professor Caroline Dean
John Innes Centre, Norwich
The correct timing of flowering is crucial for reproductive success. Genetic analysis in Arabidopsis has identified an integrated regulatory network that controls the timing of this developmental switch. This network has provided the basis to understand how multiple environmental and endogenous cues influence flowering and how relatively minor changes in predominance of different pathways can explain the diversity of reproductive strategies seen in nature.
In recent years the Dean lab has focused on how prolonged cold promotes flowering. This process is known as vernalization and it aligns flowering with spring. We have dissected the mechanistic basis of vernalization in Arabidopsis through identification of mutants, analysis of the corresponding genes, chromatin biochemistry and more recently, computational modelling. Central to vernalization in Arabidopsis is the epigenetic silencing of a floral repressor gene, FLC, by a conserved Polycomb mechanism. The talk will describe our understanding of this process and the sequential steps involved: the transcriptional silencing of FLC by cold; the cold-induced nucleation of modified Polycomb complexes at a specific site in FLC; their spreading yet spatial restriction to FLC upon return of the plants to warm conditions. We are currently exploring the role of non-coding RNAs in this process and the basis of the quantitative response to cold exposure.
This mechanistic understanding is being linked with evolutionary and ecological analyses to fully understand how different Arabidopsis accessions have adapted to different climates. Our data shows that differences in the epigenetic silencing of FLC are an important component of the natural variation in vernalization response. Cis polymorphism in FLC itself quantitatively modulates the chromatin silencing. We are now investigating the structure/function relationship of different FLC alleles in Arabidopsis accessions in both lab and field conditions.
Jenkinson Lecture. A drinks reception will be held in the Plant Sciences Common Room following this lecture.
03 May 2012
'Making oil in plants and algae: insights from metabolic flux analysis'
Professor Yair Shachar-Hill
Plant Biology Department, Michigan State University
Growth and production by photosynthetic organisms is powered by the flow of huge quantities of energy and substrates through a core network of metabolism. These flows make precursors, reductant, and free energy available for biosynthesis and work. Research in our group focuses on describing and understanding these flows, which we believe are at the heart of biological functional phenotypes. Using the tools of metabolic flux analysis we strive for insights into the functioning of metabolic networks in plant systems. Our practical aim is to learn enough about core metabolism and transport to allow rational genetic engineering and management of plant systems for practical benefits such as making plant based biofuels and chemicals and improving food crops.
As an example, the genetic engineering of altered oil, protein and starch levels in crop seeds has met with limited success due to our limited understanding of metabolic fluxes and their regulation in vivo. Mapping the metabolic flows through central metabolism during seed development in oilseed rape, soybean, maize, sunflower, and Camelinahas yielded insights into the routes and rates of carbon flow, the sources of biosynthetic reductant, carbon and energy use efficiency, and the metabolic role of light in green seeds. A second area of interest is algal lipid production, where technical challenges for flux analysis come together with opportunities for integrating multiomic data-sets.
26 April 2012
'Studying the genotype-phenotype map in Arabidopsis'
Dr Magnus Nordborg
GMI, Vienna
Making sense of natural variation remains one of the greatest challenges in biology. Understanding how genetic variation translates into phenotypic variation, and how this translation depends on the environment is fundamental to our understanding of evolution, and has enormous practical implications for medicine, agriculture and energy production.
We are attempting to tackle this problem using Arabidopsis thaliana as a model. Because it is highly self-fertilizing and naturally exists as inbred lines, A. thaliana can be brought into the laboratory and grown, in replicate, under different environmental conditions, in order to explore how the genotype-phenotype map works and has been molded by evolution. The presence of inbred lines, coupled with its compact, 120 Mb genome, also makes A. thaliana useful as a model for genomic approaches that will soon be possible in others organisms. As part of the 1,001 Genomes Project, we are sequencing well over 1,000 inbred lines, and are complementing these data with other kinds of “-omic” information, such as DNA methylation patterns and transcriptome measurements in large numbers of lines under multiple environmental conditions. For example, we are currently analyzing the data from a study that involved flowering time and multiple other phenotypes in a sample of 200 Swedish lines grown at two different temperatures. These data have been complemented with transcriptome (via mRNA-seq) and DNA methylation (via bisulfite sequencing) measurements of all lines under both temperatures. By supplementing the genome-wide associations between genotype and phenotype with the “in-between-ome”, we hope to gain insight not only in which genetic polymorphisms are associated with phenotypic variation, but why.
By carrying out these kinds of studies in A. thaliana, which can be grown in replicate under controlled conditions, we also hope to gain insight into the limitations of these “brute force” genomic approaches, which are rapidly becoming economically feasible for a broad range of species, but may not be practicable from a biological point of view. In particular, we have learned much about the difficulties involved in identifying causal genetic polymorphisms through genome-wide association studies.
01 March 2012
'When should you flower if flowering kills you? Life history evolution in a model system'
Dr Jessica Metcalfe
Department of Zoology, University of Oxford
Some plant species require less than a year to reach maturity. For others, tens or even hundreds of years may be necessary. Here, we use data from a range of species for which flowering is fatal to untangle the evolutionary determinants of timing of reproduction. We introduce models of increasing complexity, exploring how both the biotic and abiotic environment may shape the optimal flowering strategy. We show that where sufficient data is available it is possible to predict evolutionary outcomes in natural systems, both for timing of flowering, and for germination strategies. We conclude by discussing ways in which this body of work could interact with the extraordinary wealth of information on proximate mechanisms underlying timing of flowering in Arabidopsis thaliana. A synthesis between the two fields opens the way to predicting short-term evolutionary outcomes, of particular interest in the context of a changing environment.
Departmental Research Seminar
23 February 2012
'Exploiting natural and induced genetic variation for trait dissection in cultivated barley'
Dr Robbie Waugh
The James Hutton Institute
For several years we have been focused on the goal of developing the resources necessary to enable genetic analysis to single gene resolution in cultivated barley. We have concentrated on three major research elements: assembling germplasm that is suited to trait analysis, developing molecular tools and approaches that facilitate high resolution genetic analysis, and jointly leading international efforts to derive a reference barley genome sequence. In parallel we have been exploring areas of biology that are both academically and practically interesting and have resulted in either historical advances during the process of domestication, cultivation, and breeding and/or offer further potential for improvement in the future. In this presentation I will attempt to illustrate how we have been using the genetic, genomic and informatics resources we now have available, and the how the collision between our analysis of natural and induced genetic variants has proven central to trait gene identification and validation.
Departmental Research Seminar
16 February 2012
'The role of mixing entropy in carbohydrate metabolism'
Dr Oliver Ebenhoeh
Institute of Medical Sciences, University of Aberdeen
The vast diversity of carbohydrates is generated by carbohydrate-active enzymes (CAZymes) accepting many different substrates and catalyzing numerous reactions. This promiscuity is in stark contrast to most enzymes active in central metabolism which are highly specific and catalyze exactly one or a very small number of reactions. The multitude of accepted substrates and catalyzed reactions makes CAZymes har d to characterize in classical enzymological terms. Equilibrium constants and Michaelis constants, which were developed for highly specific enzymes, have no straight forward analogon for CAZymes.
We show how statistical thermodynamics can be employed to concisely describe and explain the action of CAZymes, where the mixing entropy of the reactants emerges as an important state variable of metabolic systems. We can thus correctly predict equilibrium distributions and explain their dependence on the initial conditions, which has not been possible with previous approaches. Experimentally verified stochastic simulations confirm the validity of our approach outside equilibrium.
Our proposed interpretation of polydisperse pools as statistical ensembles facilitates a new perspective to understand many enzymatic processes. With a mathematical model of the turnover of the soluble heteroglycan pool, we illustrate how entropy gradients are exploited constructively in vivo to establish a robust buffering and integrating metabolic function. The latter result motivates a novel interpretation of metabolism as an interplay of energy- and entropy-driven processes and hints at a novel evolutionary design principle.
Departmental Research Seminar
09 February 2012
'The origins of Earth-like planets'
Professor Alex Halliday
Earth Sciences, University of Oxford
Over the past 20 years technological advances have made it possible to accurately determine the time scales of planet formation in the laboratory. The proportions of isotopes in key elements in meteorites and lunar samples provide unique evidence that constrains the ages of the Earth, Moon and Mars, as well as, for example, which light elements have been sequestered into Earth’s metallic core. The Moon is thought to have formed from the debris produced in a collision between Earth and another planet called “Theia”. It can be shown that this Giant Impact took place approximately 100 million years after the start of the solar system. There is evidence that Venus, Earth and Mars started with similar volatile element budgets that were changed by such processes as well as some later additions. The net result is that carbon and nitrogen are actually more depleted in the silicate Earth (that is the whole planet minus its iron core) than any other element, when measured relative to the most primitive meteorites. The little we have may have been added quite late, which is quite significant given the search for habitable planets elsewhere in the galaxy.
Departmental Research Seminar
02 February 2012
'Plant Immunology: Cracking the Redox Code'
Professor Gary J. Loake
Institute of Molecular Plant Sciences, University of Edinburgh, Edinburgh
Changes in redox status are a conspicuous feature of immune responses in a variety of eukaryotes, but the associated signalling mechanisms are not well understood. In plants, attempted microbial infection triggers the rapid synthesis of nitric oxide (NO) and a parallel accumulation of reactive oxygen intermediates (ROIs), the latter of which is generated by NADPH oxidases related to those responsible for the pathogen-activated respiratory burst in phagocytes. Both NO and ROIs have been implicated in immune signalling and the control of the hypersensitive response (HR), a programmed execution of plant cells at sites of attempted infection. Our findings suggest that S-nitrosylation, the addition of an NO moiety to a protein cysteine thiol to form an S-nitrosothiol, is a key regulator of the plant defence response, controlling ROI synthesis, the accumulation of the immune activator, salicylic acid (SA) and cognate SA signalling. We are employing a variety of complementary approaches, including: forward and reverse genetics, Solexa-based gene expression profiling and novel proteomics strategies, to uncover the molecular landscape of S-nitrosylation during plant immune function.
Departmental Research Seminar
19 January 2012
'Where have all the flowers gone: changes in British woodland flora over the last half century'
Dr Keith Kirby
Natural England
The talk would look at changes in the woodland flora as indicated by results from broad-scale distribution studies, from studies of a series of woods across Britain and from individual sites including Wytham Woods; what seems to have driven these changes and the implications for future conservation management.
Departmental Research Seminar
08 December 2011
Coping with stress: a tale of two adaptations
Professor JAC Smith
Department of Plant Sciences
Ninth Week Seminar
01 December 2011
Impacts of global warming on plant biodiversity and ecosystem function: A 200 million year old case study from East Greenland
Dr Jenny McElwain
University College Dublin
The functioning of modern terrestrial ecosystems has been shaped by an evolutionary legacy of four mass extinction events, multiple geologically driven global warming and cooling events, meteorite impacts, the evolution of advanced plant reproductive grades and plant extinction. Studies from the fossil plant record have revealed that global environmental change of a magnitude similar and greater to that predicted by the year 2100, can result in the collapse of terrestrial ecosystems, resulting in high species level turnover and extinction. In the case of the Triassic-Jurassic boundary (~200 million years ago), ecosystem collapse was preceded by prolonged ecological degradation. A common response of fossil plant communities to global environmental perturbation includes increasing dominance, decreasing evenness, loss of biodiversity and likely reduced productivity. High resolution records of fossil leaves and pollen indicate that ecosystem diversity can be maintained in response to major climatic change via continental scale migration and recruitment of immigrant taxa, yet the functional consequences of these changes are difficult to evaluate. Return of global environmental conditions to pre-excursion norms usually results in a rebound in plant diversity but with drastically altered ecological composition and evidence for ecosystem instability for hundreds of thousands to millions of years. The presentation will focus on the ecological and evolutionary consequences of a global warming event at the Triassic-Jurassic boundary and the feedback effects of plant adaption on fire ecology and marine biodiversity.
Departmental Research Seminar
24 November 2011
‘From butterfly wings to plant sex chromosomes: ideas about recombination and why it is sometimes suppressed’
Professor Deborah Charlesworth
University of Edinburgh
The advantages of genetic recombination are well known, but some situations have led to its suppression. I will show how ideas about the evolution of mimicry in butterflies led to an understanding of how the evolution of complex adaptations, that are built up in several evolutionary steps, may select for suppressed recombination, and how this understanding illuminates the evolution of sex chromosomes. Although the theoretical work involved in understanding these situations was done many years ago, recent developments in molecular methods are allowing empirical studies to test the hypotheses involved, even though the best species for these tests are non-model animal and plant species. I will particularly focus on the value of plants for studying sex chromosome evolution, and the consequences of evolving non-recombining Y chromosomes.
Mary Snow Lecture 2011
17 November 2011
‘How purple photosynthetic bacteria harvest solar energy’
Professor Richard Cogdell
University of Glasgow
The light harvesting system of purple photosynthetic bacteria is now very well understood, both structurally and functionally (1). It consists of two types of light harvesting complexes, called LH1 and LH2, which are each made up of oligomers of alpha/beta apoprotein dimers. Each dimer non-covalently binds bacteriochlorophyll and carotenoid molecules. Light is usually absorbed by LH2 and then the excitation energy is transferred via LH1 to the reaction centre, where it is used to drive a trans-membrane charge separation reaction. Figure 1 shows a cartoon representation of how these components are organised relative to each other in the photosynthetic membrane. This presentation will describe in detail the structure and function of the LH1 and LH2 complexes. The pathways of energy transfer from LH2 to the reaction centre will be presented from fs out to longer times.
1. Cogdell, R. J., Gall, A., and Kohler, J. 2006, The architecture and function of the light-harvesting apparatus of purple bacteria: from single molecules to in vivo membranes Quarterly Reviews of Biophysics 39, 227-324
Figure 1. A diagrammatic representation of the organisation of the light harvesting system in purple bacterial membranes
Departmental Research Seminar
10 November 2011
‘Motor cooperation in secretion: lessons from a plant pathogen’
Professor Gero Steinberg
University of Exeter
Tip growth is essential for invasive growth and virulence of fungal plant pathogens. It requires the activity of molecular motors that deliver secretory vesicles, containing wall-synthesizing enzymes such as chitin synthases, to the growth region. Visualizing motors and their cargo in living fungal cells reveals unexpected cooperation between motors in delivery and secretion of chitin synthases: Class V chitin synthase, which has a class 17 myosin motor domain, moves bi-directionally, with myosin-5 and kinesin-1 cooperating in delivery to the growth region, and dynein taking it back to the cell centre. The myosin-17 motor domain competes with dynein by tethering the chitin synthase to the plasma membrane prior to exocytosis. This fungal specific secretion pathway is essential for fungal virulence and might offer novel targets for fungicide development.
Departmental Research Seminar
27 October 2011
‘Evolutionary responses of European oaks to climate change’
Dr Antoine Kremer
INRA University of Bordeaux
There are widespread concerns that long lived species as trees may not be able to cope with future environmental change. However, there is a growing body of evidence stemming from different sources of information that were recently documented (Quaternary evolutionary history; observations from population and species transfers; provenance experiments) that trees may have resources and mechanisms to respond to climate change. I will review the genetic and ecological mechanisms that have facilitated adaptation of trees during historical “natural” warming periods taking as an example European oaks. Assembling lessons from phylogeography, paleobotany and simulations, I will show how oaks have responded quite rapidly to environmental change, despite their low evolutionary rate at the gene level. I will further examine how these mechanisms may be stimulated during the ongoing climatic changes.
Departmental Research Seminar
20 October 2011
‘Plants communicating with pathogens: membranes in motion and cellular responses’
Dr Silke Robatzek
The Sainsbury Laboratory
Cell surface receptors of plant cells constitute recognition sites to detect invading pathogens and to active defenses. Arabidopsis FLS2 encodes the receptor kinase for bacterial flagellin (flg22) and is required for immunity against a broad-spectrum of potentially pathogenic bacteria. Upon flg22 perception FLS2 accumulates at plasma membrane microdomains and is internalized. Although receptor trafficking became a focus of research in the past years, there is largely nothing known about downstream molecules and regulatory components of receptor endocytosis. I will present quantitative high throughput confocal imaging in plants and will discuss results from our current research, which addresses the identity of the FLS2 endosome, molecular components regulating FLS2 endocytosis, and the interception of FLS2 endocytosis and flg22 signaling. These results provide good evidences for a role of late endosomes/multivesicular bodies in plant immunity. To further study cellular defenses we focus on stomatal closure as a first layer of plant immunity. I will describe approaches using high throughput confocal imaging for the genetic dissection of stomata response pathways, and present exciting data how pathogens inhibit stomatal closure by interference with hormonal signaling. Altogether, these studies allow us to better understand the molecular mechanisms underlying the subcellular changes in plant-pathogen interactions.
Departmental Research Seminar
13 October 2011
‘A model for all genomes: the role of RNA polymerases immobilized in specialized factories’
Professor Peter Cook
Dunn School of Pathology
A parsimonious model for all genomes involving one major architectural motif will be presented: DNA/chromatin loops are tethered to transcription factories through active RNA polymerases and/or transcription factors. The polymerases are immobile and produce their transcripts by reeling in the DNA; this contrasts with the conventional view where polymerases track like locomotives down the template. At least two theoretical mechanisms probably drive the required protein clustering and DNA looping – the dimerization of bound transcription factors and an (entropic) depletion attraction acting between engaged polymerizing complexes. We have also tested experimentally whether active polymerases are immobile using chromosome conformation capture and human genes switched on rapidly (i.e., within 10 min) and synchronously by tumor necrosis factor a. This potent cytokine signals through NFkB to stimulate and repress many genes. Two of the first to respond are SAMD4A (a 221-kbp gene that a polymerase takes >1 h to transcribe), and TNFAIP2 (a 10-kbp gene that is used as a reference and which is transcribed repeatedly). Ten minutes after stimulation, the reference gene develops new contacts with the SAMD4A promoter. Subsequently, these contacts are lost as new ones appear further downstream in SAMD4A; contacts are invariably between sequences being transcribed at that particular moment. Super-resolution microscopy confirms that nascent transcripts (detected by RNA fluorescence in situ hybridization) co-localize at relevant times. These results are consistent with active polymerases being immobilized. Moreover, many genes responding to TNFa often come together to be transcribed in specialized “NFkB” factories. In additional experiments, we have isolated complexes of >8 MDa that represent factory cores, and determined their proteomes by mass spectrometry.
Departmental Research Seminar
30 June 2011
‘Inform as well as amuse’: understanding plants before Darwin
Dr Stephen Harris
Department of Plant Sciences
9th Week Seminar
23 June 2011
Insights to Function and Evolution of the microtubule cytoskeleton: from trypanosomes to plants
Professor Keith Gull
Sir William Dunn School of Pathology
Plant microtubule cytoskeletons have been shown to have many attributes common to all microtubule systems but there has often been a celebration of differences – microtubules linked to the inner face of the plasma membrane, lack of centriole containing centrosomes, dispersed microtubule organising centres, etc. Consideration of function and evolution allow these structural differences to be placed in a continuum and there are interesting parallels with eukaryotic microbes. However, the diversity of plants and their evolution offer some excellent opportunities for comparative genomic approaches to understand the evolution of the cytoskeleton and its components. These studies of motor protein gene families such as dyneins and kinesins and organelles such as flagella and cilia reveal a complex microtubule cytoskeleton in the Last Common Eukaryotic Ancestor (LCEA) and a pattern of gene loss in plants. There are intriguing exceptions to this which are likely to be of specific interest to understanding the plant cytoskeleton.
Departmental Research Seminar
16 June 2011
Using the past to predict the future: disentangling the complexity of plant community responses to intervals of rapid environmental change
Professor Kathy Willis
Department of Zoology
Using the past to predict the future: disentangling the complexity of plant community responses to intervals of rapid environmental change ‘Thresholds’, ‘regime shifts’, ‘tipping points’, ‘species loss’, ‘resilience’, ‘persistence’ – these well-used terms are often embedded within any scientific debate on current and future biotic responses to intervals of climate change. Many of these terms have been used in conjunction with outputs from vegetation-climate models. However, a large amount of uncertainty is also acknowledged in these models due to both their coarse scale of resolution and also lack of understanding of complexity of abiotic/biotic mechanisms and their spatial distribution across landscapes. In order to reduce some of this uncertainty, baseline datasets are needed that record the actual rate and nature of ecosystem responses during intervals of rapid climate change; one method to do this is to look at past intervals of rapid environmental change and the corresponding ecosystem responses. Palaeoecological records contained in lake sedimentary sequences provide an important data source for doing this. These records, which include fossil pollen, plant macrofossils, charcoal, ɗ15N, geochemical elements and faunal dung spores, can provide a wealth of information on the biotic/abiotic responses at a landscape scale of an ecosystem to past intervals of rapid environmental change. Traditionally such records have only been used to broadly describe the patterns of change with little attention paid to disentangling the key biotic/abiotic processes responsible and the lags/leads in the system. In this talk results will be presented from recent work in NW Europe, Madagascar and Western Ghats where we have developed new long-term ecological datasets and modelling techniques to start to disentangle plant community responses to intervals of environmental change. The potential of this approach will then be discussed in terms of its use in mapping landscapes that are important for providing resilience to current and future environmental change.
Departmental Research Seminar
09 June 2011
Plant Computational Morphodynamics: Predictive Modelling of Plant Development
Professor Elliot M. Meyerowitz
California Institute of Technology
To develop a predictive theory of plant development, of how to get from genome to phenotype, my laboratory and others have been developing Computational Morphodynamics: the use of live imaging and computational models to capture and model the causal mechanisms of development at the cellular and tissue level. By live image analysis of shoot apical meristems, we have found that chemical and physical signals interact to lead to pattern. Chemical signals in the shoot meristem include secretion of signaling peptides such as CLAVATA3 that are ligands for receptor kinases like CLAVATA1, diffusion of cytokinins, and regulated transport of auxins. Physical signals are also involved in signaling. The cytoskeleton of meristem cells responds directionally to stress, and recent evidence indicates that stress may control auxin flow by regulating auxin transporter localization. It appears that both chemical and physical processes interact in producing the phyllotactic pattern, the spiral pattern of leaves and flowers around the stem, and may play key roles in other patterning processes as well, such as the patterns and planes of cell division. Computational models of phyllotaxis and primordial growth at the shoot apex show how local interactions of cells by chemical and physical means can lead to complex global patterns.
GE Blackman Lecture
26 May 2011
Temperature Sensing in Plants
Dr Philip Wigge
John Innes Centre
Our lab is interested in understanding how plants sense and respond to differences in ambient temperature. We have used a forward genetic screen to identify components of the temperature sensing pathway in Arabidopsis thaliana. In this screen, we discovered that thermosensory regulation of the transcriptome is mediated by the alternative nucleosome, H2A.Z. Interestingly, we find that nucleosome loss appears to occur as a function of temperature, suggesting that nucleosome dynamics may convey temperature information. H2A.Z-nucleosomes are highly conserved across all eukaryotes, suggesting this pathway may be present in other systems. We are further interested in understanding the underlying molecular basis of temperature perception and how temperature signals are integrated into developmental pathways in the plant.
Departmental Research Seminar
25 May 2011
Context-dependent invasion and management of invasive species
Dr Katriona Shea
PSU
Ecological context affects the success of invasive species, and hence optimal management strategies for their control. Furthermore, optimal control of local abundance and population growth may require different management strategies than optimal control of spatial spread. In this talk, I synthesize field data on an invasive plant species in different parts of its native and invaded range. I use recently developed theory to understand how different and changing ecological and environmental conditions may affect the success of invasive species, and hence the most appropriate management strategy for a biological invasion.
Additional Seminar
19 May 2011
Evolutionary genetics of flowering time in Arabidopsis thaliana
Dr Paula X Kover
University of Bath
A major goal of evolutionary genetics is to understand how genetic changes contribute to adaptive evolution. To achieve such an understanding it is necessary to combine knowledge of the genetic basis of traits under selection with knowledge of how selection acts on the genetic variation available to modify phenotype. The fact that most traits of ecological, evolutionary and economical importance are complex (i.e. determined by multiple loci and affected by the environment), has made it more difficult to study the evolutionary process at the genetic level empirically. In this seminar I will present results from mapping efforts to characterize the genetic basis of natural variation in flowering time, and results from genome-wide searches for loci that respond to selection for early flowering (using an experimental evolution approach). Comparison of these two approaches allows interesting conclusion about the predictability and repeatability of the adaptive process.
Departmental Research Seminar
13 May 2011
Return to gynodioecy: the curious case of Waterman Mountain Bursera microphylla
Professor D Lawrence Venable
University of Arizona
There are many documented cases of the evolution of dioecy from gynodioecy in the plant reproductive ecology literature, but none in the reverse direction. This is somewhat surprising since there doesn't seem to be an a priori reason that this breeding transition should not occur. We have documented (the first?) case of such a reversion in a population of Bursera microphylla in the Waterman Mountains near Tucson, Arizona, where a highly female-biased gynodioecious population exists. Bursera microphylla is a member of a large tropical genus of ~100 species that is predominantly dioecious and, outside of this one population, the rest of the species is apparently dioecious. I will describe the reproductive ecology of this population, comparing it to two "normal" populations. Then I will explore how this reversion may have occurred. A standard sex allocation ESS model suggests the population is far from breeding system equilibrium and should rapidly become hermaphroditic. By contrast, a model assuming chromosomal sex determination can generate the observed breeding structure. Possible avenues of further inquiry to determine what is driving the evolution of this curious system will be discussed.
Additional Seminar
12 May 2011
Ecological population and community dynamics: long-term data from desert annual plants
Professor D Lawrence Venable
University of Arizona
Desert annual plants are frequently used to illustrate the principles of adaptation to variable environments, the population dynamic functions of dispersal and dormancy, and how temporal variation may promote species coexistence. All of these topics involve ecological and evolutionary responses to environmental variability. High levels of environmental variation driven by rainfall is a signature characteristic of hot deserts. Desert annuals have provided useful conceptual models because they have very simple life cycles and respond on a rapid time scale to such environmental variation . “Good wildflower years,” when showy flowered annuals blanket the desert, often occur in association with abrupt desert annual population increases. Such years are correlated with greater than average germination-season rainfall and global climatic cycles, such as El Niño and Pacific Decadal Oscillations, in the case of US Southwestern deserts. Desert annuals spend most of their lives as seeds and may even go unnoticed during their normal flowering season in years of little germination or high mortality. Persistent seed banks play an important role in population and community dynamics and it is not uncommon for species to reappear following years of absence. While desert annuals are small and short-lived, they occur as members of mature, persistent communities. This means that it is relatively easy to monitor multiple generations during the course of a single long-term project. Thus, in addition to being good conceptual models, desert annuals make good empirical models for exploring ecological and evolutionary dynamics in variable environments. Here, I will present the results of our work combining the collection of long-term population dynamic data with several short-term focused approaches to understanding the ecology of Sonoran Desert winter annuals. I demonstrating how our data provide evidence for bet hedging and coexistence via the storage effect. Next, I describe a fundamental functional tradeoff that structures the dominant members of our community and determines the degree of inter-annual variation in fecundity. Finally, I explain long-term trends in response to climate change.
Departmental Research Seminar
05 May 2011
Defining Dynamic Transcription Units in Yeast – Does it make sense or antisense?
Professor E J C Mellor
Department of Biochemistry
Ana Serra Barros, Tania Nguyen, Struan Murray, Michael Youdell, Jon Ayling, David Brown, James Halstead and Jane Mellor. Department of Biochemistry, University of Oxford.
A well established paradigm indicates that sequences at the 5’ promoter region are critically important for transcription from eukaryotic genes. These include TATA-related promoter sequences which help to define the frequency of transcription initiation at defined start-sites. The 3’ regions of genes are generally considered to contain sequences that determine transcript cleavage, polyadenylation and subsequent transcription termination.
More recently it has become clear that sequences at the 3’ ends of the genes also contribute to transcriptional regulation from the 5’ promoter, functioning either to repress or activate transcription from the promoter. These studies have implicated either direct physical interactions between the 5’ and 3’ region, structures known as gene loops, or antisense transcripts in this 3’ to 5’ communication.
In this seminar I will discuss the sequences and factors implicated in cross-talk between 3’ and 5’ ends of genes and how these lead to a new view of gene architecture and regulation.
Departmental Research Seminar
31 March 2011
Genetics and epigenetics of polyploidy and heterosis
Prof Z Jeffrey Chen
University of Texas at Austin
The long-term goal of the research in my laboratory is to elucidate at the mechanistic level of the advantages and disadvantages of being polyploids and hybrids and their impact on crop domestication and production. The understanding of these phenomena is among the grand challenges in plant biology and is vital to agriculture, food production, renewable energy, and the environment. Most crop plants including wheat and sugarcane are polyploids, and many others (e.g., maize) are ancient polyploids and/or are grown as hybrids. Although hybrid vigor has been widely applied in animal and plant breeding, the molecular bases remain elusive. Using Arabidopsis allopolyploids and hybrids as model systems, we have shown that nonadditive gene expression, small RNAs, and epigenetic regulation of circadian-mediated metabolic pathways, play central roles in growth vigor in hybrids and allopolyploids. Mechanistic understanding of polyploidy and hybrid vigor will facilitate the use and exploitation of the increased biomass and yield in hybrids and allopolyploids for food, feed, and fuels.
Annals of Botany Special Lecture
30 March 2011
Hybrid zones in Rhododendron
Dr Richard Milne
University of Edinburgh
17 March 2011
Ghost Forest: from Africa to Oxford
Angela Palmer
Artist-in-Residence, Dept of Plant Sciences
Ninth Week Seminar
10 March 2011
The Linnean shortfall and oceanic island biogeography
Dr Mark Carine
Natural History Museum
Isolated oceanic archipelagos have long been considered natural laboratories for the study of evolution, ideally suited to in-situ studies of speciation processes. The recent availability of checklist data for many archipelagos worldwide has stimulated research on the macroecology and evolution of island biota and this has led to the development of new models to explain the distribution of endemic diversity on islands. Whilst performing well for most archipelagos examined, such models fail to explain the patterns of diversity observed in the endemic angiosperm flora of the Azores. This is because the Azores flora is distinctive both in terms of the low number and extent of evolutionary radiations and in the widespread distribution of a high proportion of its endemic species. Hypotheses proposed to explain the distinctive features of the Azores endemic flora include the relatively young age of the archipelago, the limited ecological diversity of the islands, the dispersal ability and susceptibility of endemic lineages to extinction and the palaeoclimatic conditions across the region. A further possible explanation relates to the extent of taxonomic knowledge of the Azorean flora and specifically the possibility that our knowledge of the Azores flora may be inadequate - the so called 'Linnean shortfall' of Lomolino and Brown. This talk considers the extent to which the Linnean shortfall and other process-based hypotheses may explain the distinctive patterns observed in the endemic flora of the Azores.
03 March 2011
Field to wheel - Fuelling transport with plants
Dr Colin Bird
BP Biofuels, London
In recent years there has been considerable political momentum to increase the production and utilisation of liquid transport fuels from plant sources - so called biofuels. Drivers for the use of biofuels include: increasing energy security; reducing greenhouse gas emissions and providing rural jobs. Today's biofuels include bioethanol as a gasoline substitute made mainly from grain starch or sugarcane and biodiesel produced from plant oils. These biofuels have pioneered the small scale use of alternatives to petroleum based fuels. Further expansion of biofuels in a sustainable way requires new technology to enable biofuel production from cell wall sugars which will provide a much more abundant source of energy. Questions have been raised about the sustainability and net benefits of biofuels. Whilst producing fuel for transport will always have some environmental consequences, not all biofuel sources will have the same impact. This seminar will explore the technical advances from plant sciences to biological conversion that will enable the development of a sustainable biofuels industry and help to keep society on the move.
Departmental Research Seminar
24 February 2011
From Construct to Clinic: Production, Purification and Human Testing of Recombinant Human Insulin from Transgenic Safflower Seeds
Professor Maurice Moloney
Rothamsted Research
Recombinant human Insulin, including its analogues, is the largest volume protein pharmaceutical that is manufactured worldwide. It has a current market value in excess of $8 billion, with a demand that is growing due to increasing incidence of Type II diabetes worldwide and the improved detection of the condition in highly populated, but underserved countries. All commercial recombinant insulin is made in microorganisms, either in E. coli or yeast. Although the manufacturing process has been greatly streamlined over the past 20 years, the cost of goods (COGs) is still a significant factor in supplying the developing world with its necessary supply of Insulin. Furthermore, the capital cost of a conventional fermentation facility for Insulin is still a major disincentive for construction in undersupplied countries. Plants offer the possibility to meet these cost constraints in the production of Insulin and the construction of the necessary facilities. Plant-based production could decrease the COGs for Insulin by 40-50% and the capital cost of a facility by as much as 70%. We have used the oilseed plant Safflower as a platform for the expression of a recombinant proinsulin, which can be recovered inexpensively from the seeds using oilbody separation as a key step in the recovery and enrichment. This approach could allow inexpensive bulk production and purification under cGMP conditions. The plant-derived proinsulin is matured into Insulin chemically and is biochemically identical to commercially available Insulin. We have furthermore shown in human clinical trials that plant-made insulin is bioequivalent to Humulin-R, a predominant form of insulin prescribed in N. America.
Departmental Research Seminar
17 February 2011
Social evolution in bacteria
Professor Stuart West
Department of Zoology
I will discuss the evolution of signalling, cooperation and conflict in bacteria.
Departmental Research Seminar
10 February 2011
Population genetics from population-scale sequencing
Professor Gilean McVean
Department of Statistics
High throughput sequencing (HTS) technologies have made it possible to study genome-wide patterns of genetic variation across any species of interest. We have sequenced the genomes of 10 Western Chimpanzees (Pan troglodytes verus) to 10x coverage each in order to explore how recombination rates vary between closely related species. However, in assembling a map of genetic variation from the sequencing data, we have also discovered many challenges associated with the use of HTS in species with partially-assembled genomes. I will discuss these challenges, as well as what we have learned about the evolution of recombination hotspots between humans and our closest living relatives.
Departmental Research Seminar
04 February 2011
Muscle Systems Bioenergetics: linking organ-level observation to molecular-level information by means of computational modeling
Jeroen A.L. Jeneson
Utrecht / Eindhoven
Muscles convert the energy stored in chemical bonds in sugars and fat into mechanical energy to perform bodily functions such as locomotion. Knowledge of the underlying metabolic networks is extensive including detailed information at the molecular level. At the same time, contemporary experimental techniques such as nuclear magnetic resonance spectroscopy enable quantitative in vivo assay of energy conversion and ATP free energy homeostasis at the organ level. The challenge is to fully exploit and link all of the available information. Computational modeling may offer a means to integrate these microscopic and macroscopic information spaces. Specifically, it allows for precise formulation and testing of hypotheses regarding a particular cellular network of interest. Conversely, predictive tools may be gained to study the impact of molecular defects on performance of the cellular network if not the cell viz organ itself. Such tools are in high demand in modern medicine and drug industry.
Here, progress shall be presented of our efforts to develop computational models of energy metabolism in mammalian muscle including results of experimental and numerical studies as well as new hypotheses on metabolic control of glycolysis and mitochondrial energy transduction in this particular eukaryotic cell type.
Informal Seminar
03 February 2011
From rhizosphere to nodule senescence, the birth and death of the Rhizobium-legume symbiosis
Dr Philip Poole
John Innes Centre
The largest input of available nitrogen in the biosphere comes from biological reduction of atmospheric N2 to ammonium (1). Most of this comes from legume-Rhizobium symbioses, arising from infection of host plants and resulting in root structures called nodules (2). In the first phase symbioses are initiated by colonisation of the rhizosphere by rhizobia and their attachment to roots. A signalling dialogue is initiated where plants release flavonoids and related compounds which elicit synthesis of lipochitooligosaccharide Nod factors by rhizobia. In the second phase of symbiosis bacteria are trapped by curling root hairs that they enter via infection threads which initiates substantially metabolic changes in the bacteria. Infection threads grow into the root cortex into a zone of newly induced meristematic cells forming the origin of the nodule. In the third phase of symbiosis bacteria are released from infection threads by endocytosis and surrounded by a plant derived symbiosome membrane. Bacteria undergo dramatic increases in size, shape and DNA content (3), before they start to reduce N2. Plants provide differentiated bacteria (bacteroids) with dicarboxylic acids which energize N2 reduction to ammonium for secretion back to the plant (4). However, while a simple exchange of dicarboxylates and ammonium is the classical model of nutrient exchange in nodules amino acid transport by bacteroids has also been shown to be essential (5) This is because bacteroids become symbiotic auxotrophs where they exhibit organelle like dependence on the plant for biosynthetic intermediates (6-7). There is a massive reprogramming of bacteroid metabolism with biosynthesis largely shut down and catabolism channelled to fuelling N2 reduction (8).
1. Newton WE (2000) Nitrogen fixation in perspective. Nitrogen fixation: From molecules to crop productivity, eds Pedrosa FO, Hungria M, Yates MG, & Newton WE (Kluwer, Dordrecht), pp 3-8.
2. Oldroyd GED & Downie JA (2008) Coordinating nodule morphogenesis with Rhizobial infection in legumes. Ann. Rev. Plant. Biol. 59(1):519-546.
3. Mergaert P, et al. (2006) Eukaryotic control on bacterial cell cycle and differentiation in the Rhizobium-legume symbiosis. Proc. Natl. Acad. Sci. USA 103:5230-5235.
4. Prell J & Poole P (2006) Metabolic changes of rhizobia in legume nodules. Trends Microbiol. 14(4):161-168.
5. Lodwig EM, et al. (2003) Amino-acid cycling drives nitrogen fixation in the legume-Rhizobium symbiosis. Nature 422:722-726.
6. Prell J, et al. (2009) Legumes regulate Rhizobium bacteroid development and persistence by the supply of branched-chain amino acids. Proc. Natl. Acad. Sci. USA 106:12477-12482.
7. Prell J, et al. (2010) Role of symbiotic auxotrophy in the Rhizobium-legume symbioses. PLoS ONE 5(11):e13933.
8. Karunakaran R, et al. (2009) Transcriptomic analysis of Rhizobium leguminosarum b.v. viciae in symbiosis with host plants Pisum sativum and Vicia cracca. J. Bacteriol. 191(12):4002-4014.
27 January 2011
Cell-Cell Communication during Fertilization in Arabidopsis: a Surprising Link to Disease Resistance
Professor Ueli Grossniklaus
University of Zürich
Research in our laboratory focuses on the developmental genetics of plant reproduction. Our studies have shown that both genetic and epigenetic mechanisms play a key role in plant reproduction. In this seminar I will focus on cell-cell interactions during double fertilization. We have isolated a female gametophytic mutant, feronia, which disrupts double fertilization: in feronia mutant embryo sacs the pollen tubes, even if wild-type, are unable to release the sperm cells to effect fertilization (Huck et al., 2003, Development 130: 2149). This phenotype suggests that the female gametophyte plays a crucial role in pollen tube reception and, thus, controls the behaviour of the male gametophyte. The feronia mutant defines novel signalling processes between the male and female gametophytes in the process of double fertilization FERONIA was shown to encode a receptor-like kinase of a plant-specific subfamily (Escobar-Restrepo et al., 2007, Science 317: 656). Interestingly, some interspecific crosses result in phenotypes that are very similar to those observed in the feronia mutant. I will report on the molecular and biochemical characterization of FERONIA and on our search for additional components of this signal transduction process using genetic and biochemical approaches. Our recent attempts to identify novel components of the FERONIA signal transduction pathway have identified surprising links to disease resistance in plants. The evolutionary implications of these findings will be discussed.
S. Kessler1, J-M. Escobar-Restrepo1, N. Huck1, H. Asano1, N. F. Kienath2, R. Panstruga2, U. Grossniklaus1
1 Institute of Plant Biology & Zürich-Basel Plant Science Center, University of Zürich, Zollikerstrasse 107, 8008 Zürich, Switzerland
2 Max-Planck Institute for Plant Breeding Research, Carl-von-Linne-Weg 10, 50829 Köln, Germany
Departmental Research Seminar
20 January 2011
Auxin: establishing morphogen gradients and interlocking cell polarities
Dr Veronica Grieneisen
John Innes Centre
20 January 2011
How do monoterpenes determine the ecology of Scots pine?
Dr Glenn Iason
Macaulay Land Use Research Institute, Aberdeen
Coniferous trees within a population are very variable in their composition of monoterpene secondary metabolites. I will review evidence from research on Scots pine (Pinus sylvestris) on the many ecological roles of these compounds and ask how such variation in an ecosystem foundation plant species drives variation in the composition of associated assemblages of organisms and ecosystem processes. I specifically consider the variability among individual trees in the strongly heritable needle concentration of Δ3-carene, to investigate the effects of this polymorphism on the extended phenotype. This single compound mediates the trees’ interactions with ants and crown invertebrates, soil mites and their consequences for decomposition, and has defensive functions against the high impact herbivores, red deer and slugs. Although this points to a genetic basis for higher community and ecosystem level processes, it is predicted that confirmation of the feedbacks from the community to the fitness of the foundation species will remain elusive. The sign of the fitness consequences of these PSM-mediated interactions may not be consistently positive or negative, leading to weak selective effects and the net fitness gain varying spatially with local conditions. (Glenn Iason, Ben Moore Jack Lennon, Jenni Stockan, Julianne O’Reilly-Wapstra and Graham Osler)
Special seminar
09 December 2010
Save the male!
Professor John Pannell
Department of Plant Sciences
Ninth Week Seminar
02 December 2010
Reducing illegal logging in the tropics by timber tracking with DNA-fingerprints
Dr Bernd Degen
Institute of Forest Genetics, Germany
Illegal logging is one of the chief causes of worldwide deforestation that, by releasing green-house-relevant gasses, contributes to climate change. Moreover, trade with illegal timber and wood products creates market disadvantages for products from sustainable forestry. Although various measures have been established to counter illegal logging and the subsequent trade, we lack practicable mechanisms to identify the origin of timber and wood products. Using nuclear microsatellites (nSSRs) and single nucleotide polymorphism (SNPs) as DNA-fingerprints we have created a genetic reference database for determining the geographic origin of Mahogany timber (Swietenia macrophylla) in Latin America and Sapeli (Entandrophragma cylindricum) and Iroko (Milicia excelsa) in Cameroon. For Mahogany we have sampled leaves from 2000 trees from 30 stands from Mexico to Bolivia. We found more than 150 different genetic variants (alleles), a strong genetic differentiation and a clear correlation between genetic and spatial distances among stands. The DNA-timber tracking was tested in Cameroon on the area of forest concessions. Using a Bayesian approach it was possible to achieve statistical assignment of unidentified individuals (e.g. wood probes) to stands, regions or countries. Using anonymous wood samples from timber traders we demonstrate the power of the DNA-fingerprints to determine geographic origin. I will discuss the applicability and implementation into praxis of this technique to the tropical timber trade in general.
Departmental Research Seminar
25 November 2010
Old and new problems in the mechanics of plants
Professor Alain Goriely
OCCAM, Mathematical Institute
In the nineteenth century many biologists, such as Darwin, de Vries, and Sachs, were interested in the physics and mechanics of plants. In particular, they were fascinated by the growth of plants and how differential growth can induce plant movements and modify their mechanical properties. In this talk, I will revisit some old problems in plant physiology ranging from the dynamics of climbing plants to the hollowing of stems, and use them to motivate a general description of growth in continuum mechanics. Surprisingly, a proper study of growth and mechanics in plants requires the use of modern physical and mathematical theories, such as non-Euclidean geometry, nonlinear elasticity and anelasticity, dynamical systems theory, and bifurcation theory. In turn, the analysis of these different problems brings to light the complex interplay between growth, stresses, geometry, and material responses which give rise to fascinating shapes and movements in plants.
Departmental Research Seminar
18 November 2010
Paramutation: Transfer of Epigenetic Information Across Generations
Dr Vicki L Chandler
University of Arizona
Paramutation is the fascinating ability of specific homologous DNA sequences to communicate in trans to establish meiotically heritable expression states. Paramutation has been described in multiple species and can occur between alleles of a gene; a gene and a transgene; or two transgenes. In this talk paramutation at the b1 locus in maize, the best characterized example of paramutation will be described. Unique, transcribed non-coding tandem repeats are necessary and sufficient to communicate in trans to establish and maintain meiotically heritable chromatin states at b1. Several genes required for paramutation have been identified through genetic screens. These mediator of paramutation (mop) genes are required for paramutation at multiple loci, Mutator transposon silencing, reactivation of transcriptionally silent transgenes and several mutants exhibit pleiotropic developmental phenotypes. Characterization of three of these genes demonstrates that paramutation involves RNAi-mediated chromatin changes, yet many interesting questions remain.
Mary Snow Lecture
To be followed by drinks reception in Plant Sciences Common Room, 17:00-18:00.
15 November 2010
Agriculture at a Crossroads: are we ready for the paradigm shift?
Dr Hans Herren
Co-Chair IAASTD, President Millennium Institute
The International Assessment of Agricultural Knowledge, Science and Technology for Development (IAASTD) is a unique and comprehensive assessment of Agricultural Knowledge, Science and Technology. It was initiated at the request of the private sector and NGOs to look at new ways for agriculture and food systems to assure sufficient and quality food, fiber and feed production for the long term under the challenges of increased and changing demand, shrinking natural resources and climate change, while also dealing with the more immediate perennial hunger and poverty nexus. The process was launched by the UN at the Johannesburg World Summit on Sustainable Development in 2002, and subsequently officially endorsed by the OECD and developing countries at a Plenary meeting in Nairobi in 2004. A Bureau made up of representatives from government, multilateral agencies and civil society groups, including the private sector, guided all the steps of the assessment and endorsed over 400 authors, from developed and developing nations covering agricultural and related disciplines. Key questions for the authors were how the AKSTs of the past 50 years influenced where we are today in terms of agricultural production and food systems and how to reshape these for reducing hunger and poverty; improving rural livelihoods; improving nutrition and human health; and facilitating environmentally, socially, equitable and economically sustainable development. “Agriculture at a Crossroads” emphasizes the need for a new paradigm in AKST that will lead to food systems, that are in harmony with the environment, i.e., sustainable, ecological, organic agriculture, that mitigates rather than contribute to climate change, that targets the small and family farms and one that assures food security and sovereignty at national level. It also emphasized the multifunctionality of agriculture, and in particular its social, environmental and economic aspects, which are all linked and key in moving to a socially, environmentally and economically sustainable and productive agriculture in the medium and long term.
Please note you will be required to show a valid University card on entry to the building. Seating capacity is limited.
11 November 2010
How does cohesin hold sister DNAs together for several decades in oocytes?
Professor Kim Nasmyth
Department of Biochemistry
The Segregation of sister DNA molecules at mitosis involves their traction to opposite poles by microtubules attached to kinetochores. By creating the tension required to stabilize kinetochore microtubules, sister chromatid cohesion has a key role in ensuring that sister kinetochores attach to microtubules with opposing polarity, a process known as bi-orientation. Cohesion is mediated by a cohesin complex whose Smc1, Smc3, and kleisin subunits form a tripartite ring thought to hold sister DNAs together by entrapping them (the ring model). Sister chromatid disjunction at the onset of anaphase is triggered by a thiol protease called separase whose activation only when all chromosomes have bi-oriented opens the cohesin ring by cleaving its kleisin subunit. Separase is inhibited by the binding of an inhibitory chaperone called securin whose destruction together with that of mitotic cyclins at the hands of a ubiquitin protein ligase called the anaphase-promoting complex/cyclosome (APC/C) is essential for kleisin cleavage and sister chromatid disjunction. Micro-injection experiments in Drosophila embryos demonstrate that cohesin cleavage and Cdk1 down regulation are sufficient to drive formation of daughter nuclei in cells arrested in metaphase due to inactivation of the APC/C. Similar experiments in mouse oocytes prove that a meiotic variant of cohesin containing a Rec8 kleisin subunit holds bivalent and dyad chromosomes together during meiosis I and II respectively. How sister DNAs enter the cohesin ring and are retained inside for long periods of time after the completion of DNA replication remains poorly understood. Recent evidence suggests that acetylation and de-acetylation of cohesin’s Smc3 subunit has a crucial role. Lastly, I will describe experiments addressing whether the cohesion holding bivalents together, which must last for several decades in females, can be regenerated after its initial creation during meiotic DNA replication prior to birth.
Departmental Research Seminar
04 November 2010
Herbaria are the major frontier for species discovery
Dr Robert Scotland
Department of Plant Sciences
Knowledge of species underpins current estimates of global biodiversity, rates of extinction, and the size of the task facing conservation. However, despite its importance, the processes of species discovery, including collecting, recognising and describing new species are poorly understood. The talk will present data for flowering plants, that measures quantitatively the lag between the date a specimen of a new species was collected for the first time and when it was subsequently described and published, which show that only 16% of new species between 1970 and 2010 were described within five years of being collected; description of the remaining 84% involved older specimens, with nearly one quarter of new species descriptions involving specimens more than 50 years old. Extrapolation of these results suggest that, of the estimated 70,000 species still to be described, more than half of these have already been collected and are currently stored in herbaria. Study of all collections is therefore crucial for completing the inventory of flowering plants as the description of taxa based on all collections and their inclusion in diagnostic keys makes the recognition of new species from more recent collections much more efficient. Effort should, therefore, be directed as much to examining extant herbarium material as collecting new material in the field.
Departmental Research Seminar
28 October 2010
Photosynthesis, feedbacks and fluctuations in climate
Dr Rosalind Rickaby
Department of Earth Sciences
The living ecosystem and CO2 and O2 levels in the atmosphere are inexorably linked though tight feedback mechanisms. The advent and radiation of photosynthetic life, dramatically changed CO2 and O2 levels, and transformed the anaerobic earth in two major steps to an earth with an O2 rich atmosphere, 2.5 Ba, and oxygenated deep ocean, 0.8-0.6 Ba, in addition to accelerating draw-down of atmospheric CO2 and providing an additional reservoir for carbon storage. Biological innovation certainly exerts an influence on the atmosphere, but atmospheric composition also drives genetic adaptation. Here, we explore each side of this feedback system. First to probe alternative genetic methods for reconstructing the ancient geological environment. We investigate whether it is possible to decipher the influence of atmospheric change on the genetic makeup of photosynthetic pathways of extant marine algae. Second, we aim to understand, in part, the driver and regulator of climate fluctuations. We shall investigate the role that photosynthetic life may play in regulating climate and atmospheric composition, through reconstructing the chemistry of the ocean, over recent relatively short (10s kyr) timescales.
Departmental Research Seminar
21 October 2010
Old landscapes reveal new perspectives on biological evolution, ecology and conservation
Professor Stephen D Hopper
Director, Royal Botanic Gardens, Kew
Recently, I have drawn together varying threads of research synthesized into a new perspective termed OCBIL theory – how biodiversity has evolved and might be conserved on the world’s oldest climatically-buffered infertile landscapes. OCBILs persist in relatively few places on Earth, but are common in southwest Australia, the Greater Cape region of South Africa, and the flat-topped tepui landscape of the Venezuelan/Guyanan highlands. Given that most people (including biologists) live on landscapes that are neither old nor climatically-buffered from extremes by prolonged oceanic moderation nor infertile, it is not surprising that knowledge of OCBIL biodiversity and conservation is embryonic. Of necessity, much of what we do in conservation programs such as protected area management borrows heavily from theory and practice developed elsewhere. Is this appropriate? There may well be significant pitfalls in uncritically applying ideas from afar without rigorous local experimentation. OCBIL theory predicts significant discrepancies in biological attributes of organisms and how they might best be conserved on old climatically-buffered infertile landscapes compared with those on young often-disturbed fertile landscapes (YODFLs). I will discuss these predictions and review evidence in this talk, highlighting the fresh insights and new opportunities for research presented by OCBIL theory. The world needs new generations of conservation biologists, enthusiastic about biodiversity and passionate about conservation science, rigorously testing ideas such as OCBIL theory, if we are to retain an irreplaceable global heritage.
Departmental Research Seminar
14 October 2010
How do sugars regulate plant growth?
Dr Matthew Paul
Rothamsted Research, UK
Plants are the only organisms in which the pathways for the synthesis of the non reducing disaccharides sucrose and trehalose coexist. Sucrose is synthesised in photosynthesis and its breakdown supplies a pool of “core metabolites” of hexose phosphates and UDP-glucose which provides the carbon source necessary for the growth of plants through synthesis of structural cell wall and other important constituents including protein, lipid and starch. Whilst this function of sucrose is clear, mechanisms that regulate sucrose utilisation are less well described. Yet, variation in the utilisation of sucrose - i.e. what plants do with their carbon - contributes to much of the variation in the growth and yield of plants and crops and underpins food, feed, fibre and biofuel production. Trehalose is synthesised in trace amounts from the core metabolite pool and does not function as a carbon source in plants as it does in other organisms. It has become clear nevertheless that the trehalose pathway is essential in plants, but with a hitherto unknown function. The talk will highlight the versatility of sugar function and present a model for how trehalose 6-phosphate, as a sugar signal molecule, regulates plant growth processes.
Departmental Research Seminar
13 July 2010
Climate and Agricultural Risk Management in the Asia-Pacific Region
Associate Professor Samsul Huda
University of Western Sydney, Australia
Farming is about managing risk. There is a large gap between potential crop yield and average on-farm yields, especially in developing countries in the Asia-Pacific region. Agricultural production can be increased through well-judged use of improved agronomic management. However, decisions occur in an uncertain environment created by weather, climate and market variations. Weather and climate uncertainty applies both to natural variability and systematic climate change. Results from our completed project “Climate Risk Management in Rural Communities in Developing Countries of the Asia-Pacific Region” will be shared. Ongoing activities from our recently funded research project “Food security and climate change in the Asia-Pacific region: evaluating mismatch between crop development and water availability” will be highlighted. Challenges will be explored in the context of integrating market and weather/climate uncertainty with improved decision-making with respect to soil fertility and pest management.
Special Seminar
24 June 2010
Biochemical noise from the top floor
R.G. Ratcliffe
Department of Plant Sciences
17 June 2010
Genetic signatures of local adaptation in Mediterranean conifer trees with contrasting demography
Professor Santiago C. González-Martínez
INIA Madrid
The Mediterranean basin is widely recognized as a biodiversity hotspot, with over 11,000 plant endemic species. This outstanding diversity is suggested to result from high environmental heterogeneity and complex geological history of the Mediterranean Basin. Conifer trees are a regular component of the Mediterranean landscape providing multiple ecosystem services and hosting a wide range of organisms that depend on the forest cover to survive. Conifers are good model system to study genetic signatures of local adaptation in the Mediterranean as they grow in contrasting environments and have shown notable levels of local adaptation in common garden experiments despite large capability for seed and pollen gene flow. In this seminar, I will present molecular evidence for local adaptation in candidate genes related to drought and secondary compounds for two widespread and partially sympatric conifer species, the maritime (Pinus pinaster Ait.) and Aleppo (P. halepensis Mill.) pines. These two pines show remarkable differences in population structure and demographical history, while maritime pine is a paleo-endemic in the western Mediterranean, Aleppo pine western populations are the outcome of relatively recent long-range colonization from ancient eastern populations in Greece and Turkey. Our approach combine extensive coalescent simulation and new generation neutrality tests with environmental correlations that take into account demographical processes and population structure, as these factors can mimic selection on patterns of polymorphism at candidate genes. Finally, some examples on the application of second generation high-throughput SNP genotyping to detect association between environmental clines (landscape genomic approaches) and phenotypic variation in quantitative traits (association genetic approaches) with SNP allelic variation will be developed based on our recent collaborative research on loblolly pine (P. taeda L.), a New World pine and emerging model for genomic research in conifer trees.
Departmental Research Seminar
10 June 2010
Genomic signature of strong balancing selection in the self-incompatibility (S-locus) region in the genus Arabidopsis
Prof Xavier Vekemans
University of Lille
Understanding the causes of the wide variation occurring in patterns of genetic structure across genomes is one of the great challenges of the population genomics era. High peaks of among population differentiation suggest the occurrence of strong diversifying selection. In contrast, low genetic structure may reveal the action of some form of balancing selection. We are investigating the effect of strong negative frequency-dependent selection, a form of balancing selection occurring at plant self-incompatibility loci, on expected patterns of genetic structure at two different levels: (1) among populations within species; (2) among closely related species. At each level, we identify statistical tools that enable to discriminate regions under balancing selection from the genomic background. We then analyze empirical allelic and nucleotide data from the self-incompatibility locus in Arabidopsis halleri, as well as from its genomic neighborhood, to assess the magnitude and genomic extent of reduction in genetic structure resulting from balancing selection. We also investigate genetic differentiation between A. halleri, A. lyrata and A. thaliana at the S-locus and test for evidence of adaptive introgression. Nucleotide sequence data from a sample of 29 unlinked genes and allelic data from microsatellite loci was used to assess genetic structure in the genomic background. The results indicate a strong signature of selection on patterns of genetic structure at the self-incompatibility locus, but which is strikingly narrowly distributed in the surrounding genomic region.
Departmental Research Seminar
03 June 2010
Mathematical modelling of cancer growth
Prof Philip Maini
University of Oxford
Mathematical and computational modelling is becoming increasingly important in the Life Sciences as we recognise that processes interact across a range of spatial and temporal scales. This requires us not only to be able to understand processes acting at a particular scale, but also to integrate them across scales in a computationally tractable manner. We also need to deal with mixed systems of discrete and continuous variables. Aspects of these challenges will be explored in the context of modelling cancerous growth and progression and will include ordinary/partial differential equation models, hybrid cellular automaton, with application to the acid-mediated invasion hypothesis, somatic evolution and vascular tumour growth.
Departmental Research Seminar
27 May 2010
Genetic dissection of plant RNA degradation pathways: lessons from silent trangenes
Prof Hervé Vaucheret
INRA, Versailles
MicroRNAs (miRNAs) and short interfering RNAs (siRNAs) are involved in a variety of phenomena that are essential for genome stability, development and adaptive responses to biotic and abiotic stresses. Their mode of action also is diverse. They guide DNA elimination during the formation of the macronucleus in protists and heterochromatin assembly in fungi and plants. They target endogenous mRNAs for cleavage and translational repression in plants and animals, and protect both plant and animal cells against virus infection through an RNA-based immune system. They also control the movement of transposable elements at the transcriptional and posttranscriptional level in plants and animals. Small RNA pathways coexist with RNA quality control (RQC) pathways that target endogenous aberrant RNA for degradation. Here I will present specificities, redundancies and antagonisms among the various plant small RNA pathways and the crosstalk between RQC and RNA silencing pathways.
Departmental Research Seminar
20 May 2010
Models for biological pattern formation and their application to plant development
Professor Hans Meinhardt
Max Planck Institute for Developmental Biology
Professor Hans Meinhardt
Studied physics in Cologne 1958-1966; 1966 PhD in physics. Fellow at the European High Energy Research Centre (CERN) in Geneva 1966-1968. Since 1969 at the Max-Planck Institute for Developmental Biology. Over the years has developed molecular-realistic models for several essential steps in development. 1980 EMBO member; 1982 Habilitation in Developmental Biology at Tübingen University
The first paper on pattern formation appeared in 1972 together with Alfred Gierer, showing that pattern formation from initially homogeneous situations is possible if and only if a local-acting self-enhancing process is coupled with an antagonistic reaction of longer range. In a book "Models of Biological Pattern Formation" (1982; Academic Press, London) he published models for pattern formation, gene activation, segmentation, somite formation, initiation of legs and wings and the formation of net-like structures. Since the book – now on his webpage – was published before the molecular-genetic approach became feasible, all these models were clear predictions. They found subsequent strong support from corresponding observations. In 1995 he published a book Algorithmic Beauty of Sea Shells in which the intricate pigment patterns of molluscs was used to get a deeper understanding of systems in which several space- and time-dependent pattern-forming reactions are linked to each other (the fourth edition appeared in 2009). The corresponding experience tuned out to be crucial for the development of realistic models for very different steps in development, such as the determination of the division plane in bacteria, the orientation of chemotactic cells and growth cones, phyllotaxis and barb formation in avian feathers. More recently his work has focussed on axes formation in vertebrates and on pattern formation within individual cells.
GE Blackman Lecture 2010. Contact the Department of Plant Sciences for details.
20 May 2010
The fastest flights (and rotations) in nature: Fungal spore discharge at one million frames per second
NP Money
Department of Botany, Miami University
Fungi are the evolutionary champions of fast movement and use a variety of microscopic devices to launch themselves into the air. These include pressurized asci that discharge streams of spores at maximum speeds in excess of 100 kilometers per hour, the explosive membrane that ejects the spore-filled gleba of the artillery fungus over a distance of 6 meters, and a catapult powered by fluid movement that propels 31,000 spores per second from the gills of a single mushroom. Recent technological advances in high-speed video microscopy have allowed unprecedented insights into the operation of these astonishingly beautiful mechanisms. This presentation will showcase these experiments, screen some wondrous videos, and explain their wider significance.
Informal seminar
06 May 2010
Genetic interactions in the shoot apex: diversity in mechanisms regulating meristem function and leaf patterning
Dr Mary Byrne
John Innes Centre
Plant shoots are characterized by reiterative production of organs from an indeterminate shoot apical meristem. Early in development lateral organs, such as leaves, establish dorsoventral polarity. Outgrowth of the leaf lamina depends on signaling from the meristem to the initiating leaf, as well as concerted interactions between adaxial (dorsal) and abaxial (ventral) domains of the leaf. Control of meristem function and leaf patterning is via a network of interactions between several families of transcription factors, a number of which are regulated by small RNAs. This network is therefore defined by transcription and post-transcriptional mechanisms. We have identified new players in the network as ribosomal proteins, and suggest the ribosome and translation play a role in regulating growth and patterning in plant development.
Departmental Research Seminar
29 April 2010
Ancient plant DNA: Tales of local evolution in the lower latitudes
Dr Robin Allaby
University of Warwick
Archaeogenetic evidence shows that barley in ancient Nubia appeared to become locally adapted, and gives further insight into DNA diagenesis at low latitudes where humidity is low, but temperature is high. Archaeogenomic studies using cotton from various low latitude dry sites around the world show that next generation technologies can be applied to such material with extraordinary success. Such evidence shows that genome evolution has been punctuated in recent history in cotton and gives intriguing insights into the origin of modern cotton. We are now tracking the genomic evolution of barley through time in ancient Nubia using archaeogenomic techniques to see directly how local adaptation occurred.
Departmental Research Seminar
18 March 2010
More than a yolk: The short life and exciting times of the maize endosperm
Professor Hugh Dickinson
Department of Plant Sciences
In addition to provisioning the earliest stages of seedling development, the endosperm of cereals is a major component of the human diet. Early development of the maize endosperm is regulated by imprinted genes and a fuller understanding of this process is vital if we are to maximise returns from our cereal crops. I wrote my first imprinting proposal in 1985 and in this talk shall follow the progress of this research over the subsequent 25 years, describing the key findings, charting the highs (a few) and lows (many), explaining how it IS possible to survive in the face of better-funded competition, and highlighting the absolute necessity of having good colleagues and setting up productive collaborations. The talk will conclude with a reflection on what has really been achieved over this time, the nature of ‘impact’ and – hopefully – an accurate assessment of whether the public has got value for money from the work.
Ninth Week Seminar
11 March 2010
Flagellar synchronization, eukaryotic random walks, and multicellular phototaxis
Professor Raymond E Goldstein
Department of Applied Mathematics and Theoretical Physics, University of Cambridge
One of the most fundamental issues in evolutionary biology is the nature of transitions from single cell organisms to multicellular ones, with accompanying cellular differentiation. Not surprisingly for microscopic life in a fluid environment, many of the processes relevant to this transition are physical ones such as diffusion, mixing, locomotion, and sensing. We have been studying these issues in the context of the Volvocine green algae, a lineage that spans from the unicellular Chlamydomonas to germ-soma differentiated Volvox. A key issue for these species is the nature of flagella-driven locomotion and fluid flows. This talk will focus on experimental and theoretical studies of the nature of flagellar synchronization, swimming, and phototaxis. A combination of micromanipulation, high-speed imaging, and three-dimensional tracking is used to uncover the interrelationship between these three processes, and to develop and then test appropriate mathematical models.
Departmental Research Seminar
04 March 2010
Photosynthesis requires cytoplasmic inheritance. Chloroplast Sensor Kinase is the redox messenger
Professor John Allen
University of London
Why are there genes in chloroplasts and mitochondria? The CoRR hypothesis states that these genes and their gene products must be Co-located in the cell in order to permit Redox Regulation. CoRR predicts (i) an irreducible core of cytoplasmic genes, retained by chloroplasts and mitochondria from their bacterial ancestors, and (ii) chloroplast and mitochondrial redox signalling by means of components that have operated continuously throughout the transition from prokaryote to subcellular organelle. Chloroplast Sensor Kinase (CSK) is a novel chloroplast protein encoded by the nuclear gene At1g67840 of Arabidopsis thaliana. CSK T-DNA insertion lines are impaired in plastoquinone redox control of transcription of genes for reaction centre apoproteins of photosystem I and photosystem I. CSK is an ancient homologue of bacterial histidine sensor kinases and yet universal in photosynthetic eukaryotes. I propose that CSK provides a regulatory coupling of electron transport with transcription. This coupling repays the huge cost of maintaining the small, quasi-autonomous genetic system that underlies cytoplasmic inheritance.
Departmental Research Seminar
25 February 2010
Food production versus biodiversity: How can science help us feed the world whilst minimising the environmental footprint of agriculture?
Professor Guy Poppy
University of Southampton
Man faces many challenges during the 21st century which are exacerbated by climate change. The Government’s Chief Scientist describes how shortages of food, energy and water will cause the “perfect storm” by 2030. Although plant scientists may suggest that technology can increase productivity from the land and thus solve these increasing problems, we also wish to live in an environment which is biodiverse and recreationally acceptable. In fact, two of the United Nations Millenium Development Goals could be set for collision; addressing hunger and poverty as well as achieving environmental sustainability and no further reduction in biodiversity is a big ask for agriculture. My research has focussed on both sides of this equation. I will describe how an understanding of plant genetics, chemistry and ecology can allow the development of new technologies for controlling insect pests and thus increasing productivity. The other area of my research focuses on environmental risk assessment. I will describe how risk assessments can be used to help advance technology, and not restrict it as too frequently thought by those developing “new” plants. The use of risk management and mitigation can allow optimised production with minimal impact, and I will outline how such an approach can allow food and environmental security.
Departmental Research Seminar
18 February 2010
Plant community genetics: diversity, traits and responses to climate change
Dr Raj Whitlock
University of Sheffield
The component populations of plant communities can harbour a fantastic range of genetically-controlled phenotypic diversity. Here I consider the significance of this intraspecific diversity for the structure and diversity of species-rich grasslands, and examine its impact in mediating the resistance of these communities to anthropogenic climate change.
Whitlock, R., Burke, T., Fridley, J. D., Ravenscroft, C., Askew, A. P. & Grime, J. P.
Departmental Research Seminar
11 February 2010
The dynamic plant chondriome: mitochondrial fusion, fission and positioning underpin cell health
Dr David Logan
University of Saskatchewen
Mitochondria are involved in many fundamental processes underpinning plant growth, development and death. Due to their multiple roles: as the sites of the TCA cycle and oxidative phosphorylation, as harbourers of their own genomes, and as sensors of cell redox status, amongst others, mitochondria are in a unique position to act as sentinels of cell physiology. The plant chondriome is typically organised as a population of physically discrete organelles, but visualisation of mitochondria in living tissues has shown that the mitochondrial population is highly interactive. Mitochondria are highly motile and movement on the cytoskeleton ensures that the physically discrete organelles come into contact with one another, which allows transient fusion, followed by division of the mitochondrial membranes. I will review our current knowledge of mitochondrial fusion and division and link this to recent discoveries regarding a putative mitochondrial “health-check” and repair process whereby non-repairable dysfunctional mitochondria can be removed from the chondriome. It is proposed that the unequal distribution of the multipartite plant mitochondrial genome between discrete organelles provides the driver for transient mitochondrial fusion that in turn is dependent on mitochondrial motility, and that both fusion and motility are necessary to maintain a healthy functional chondriome.
Departmental Research Seminar
04 February 2010
Patterning Arabidopsis primordium development
Dr Marcus Heisler
EMBL, Heidelberg
Primordium formation is a fundamental developmental process in plants and animals. It involves a positioning mechanism that defines where the tissue or organ will arise as well as changes to growth and differentiation that result in morphogenesis and the correct patterning of cell types. By confocal imaging of multiple GFP-labeled proteins coupled with cell tracking and mathematical modeling we have begun to gain an overall picture of how these interrelated processes are coordinated. The picture that emerges is one of cross regulation at multiple levels. For instance our imaging reveals a dual role for the plant hormone auxin in both regulating organ position as well as promoting adaxial cell type identity within developing organs. Primordial morphogenesis on the other hand depends both on auxin transport and the microtubule cytoskeleton. These two factors also appear linked since we find that the polarity of the auxin efflux carrier PIN1 correlates with microtubule interphase array orientations. Presently we are investigating the cell-cell communication pathways that determine PIN1 polarity and microtubule orientations and I will present evidence suggesting the involvement of biomechanical signals.
Departmental Research Seminar
28 January 2010
Engineering phenylpropanoid production for healthy foods
Professor Cathie Martin
John Innes Centre, Norwich, UK and Faculty of Life Science, Copenhagen University, Denmark
The past 20 years has seen an enormous rise in publicity about super foods that promote health and reduce the risk of cardiovascular disease, cancer and age-related degenerative diseases, related specifically to the metabolic syndrome. These claims are supported by robust evidence from cell studies, animal feeding trials, human intervention studies and epidemiological studies. However, despite all the positive messages about the value of eating fruit and vegetables (the 5-a-day program has been running for 25 years) the numbers of people meeting these dietary recommendations in the US remains below 25 per cent of the population, numbers are falling, and chronic diseases, especially those associated with obesity and the metabolic syndrome, are reaching epidemic proportions in Western societies. There is a need to engineer high levels of protective bioactives in the foods that people actually do consume, to help combat this rise in chronic diseases. Most attempts at engineering the levels of bioactives have focused on increasing the activity of key, rate-limiting steps, but such strategies usually result in only modest improvements in flux to bioactive end-products. Use of transcription factors to up-regulate entire pathways of plant secondary metabolism is a far more effective strategy and results in food material with very significantly elevated levels of health-promoting bioactives. While such improvements may, in part, be achievable for some crops through selective breeding, genetic modification offers bigger improvements because it can overcome limits in the natural variation available in transcription factor specificity and activity. Use of genetically improved foods in animal feeding studies with models of tumorigenesis have revealed that protection is afforded by diets enriched in high bioactive foods. Such health-promoting foods will offer consumers tangible improvements in the products available to them, and have the potential for public approval of genetically improved plant varieties and foods derived from them, in Europe.
Departmental Research Seminar
21 January 2010
Copenhagen – Kisangani and Kaimana – the realities of REDD and the role of the biological sciences
Professor Jeffrey Sayer
IUCN - International Union for Conservation of Nature
The Copenhagen agreements will provide unprecedented levels of funding for the conservation of tropical biodiversity. Based upon experience in the Congo Basin and in Indonesian Papua I will discuss some of the issues that will have to be confronted if this money is going to be used well. I will suggest an increased role for science in achieving practical conservation outcomes on the ground. This science will need to be conducted in new ways and to be integrated into knowledge and innovation systems where scientists work alongside local resource managers and populations to jointly experiment and learn how to reconcile environmental values with the legitimate developmental aspirations of the people on the ground.
Departmental Research Seminar
10 December 2009
Where to next for the Global Strategy for Plant Conservation?
Timothy Walker
University of Oxford
Ninth Week Seminar
03 December 2009
Systems analysis of lateral root development: an emerging story…
Prof Malcolm J Bennett
Centre for Plant Integrative Biology, University of Nottingham
Food security represents a major global issue. Significant improvements in crop yields are urgently required to meet the 50 per cent increase in world population by 2050. The degree of root branching determines the efficiency of water uptake and acquisition of nutrients in crops. Understanding the regulation of root branching is therefore of vital agronomic importance. Lateral root branching can be divided into two distinct, yet inter-connected, developmental processes; primordium initiation and emergence. To date, research has focused largely on lateral root (LR) initiation. However, recent evidence suggests that LR emergence is an important checkpoint for root branching which is regulated by nutrients such as nitrate and phosphate and hormone signals such as auxin. Lateral root primordia (LRP) originate exclusively from pericycle cells located deep within the parental root, necessitating that new primordia emerge through several overlaying tissues. In a recent article published in Nature Cell Biology (Swarup et al [2008] 10:625-628) we described how LRP emergence is a highly regulated process involving the active participation of cells in both new lateral root primordia and the parental root. The hormone auxin originating from the developing lateral root appears to act as a local inductive signal which reprograms adjacent cells. Auxin induces the expression of a previously uncharacterized auxin influx carrier LAX3 in cortical and epidermal cells directly overlaying new primordia. Increased LAX3 activity reinforces the auxin-dependent induction of a selection of cell wall remodelling enzymes, promoting cell separation in advance of developing lateral root primordia. I will describe how we are employing a systems approach to study the gene regulatory networks and biomechanics associated with lateral root emergence. Our systems approach involves creating increasingly sophisticated multi-cellular models of the lateral root emergence network, populating them with experimental data, and then testing the in-silico models predictive ability.
Departmental Research Seminar
26 November 2009
Acid, Metal and Punk Bacteria: Understanding the ability of Pseudomonas syringae to grow inside plants
Dr Gail Preston
University of Oxford
The bacterial plant pathogen Pseudomonas syringae colonises plant surfaces and the intercellular spaces between plant cells, and grows by assimilating metabolites present in leaf exudates and in apoplastic fluid. The ability of P. syringae to colonise plant leaves depends on the activity of a type III protein secretion system, which injects proteins into plant cells, and on low molecular weight toxins and phytohormones. However, relatively little is known regarding the physiological and metabolic adaptations that allow P. syringae to grow in plant tissues. In this talk I will describe how experimental and bioinformatic analyses of stress tolerance and nutrient assimilation in Pseudomonas can be integrated with metabolomic analyses of apoplast composition to show how P. syringae is adapted for growth in the plant apoplast, and to understand why some plants, such as the metal hyperaccumulator Thlaspi caerulescens, are highly resistant to P. syringae infection.
Departmental Research Seminar
19 November 2009
The evolution of eukaryotes: mechanistic insights from the Archaea
Prof Stephen Bell
Sir William Dunn School of Pathology, University of Oxford
It is generally believed that chloroplasts and mitochondria arose as a consequence of endosymbioses involving bacterial organisms early in the evolution of eukaryotes. Our studies of the information processing and cell division machineries of archaea have yielded insight into the contributions that this other prokaryotic domain of life has made to the evolution of eukaryotes. In the talk I will describe our studies of Sulfolobus, a hyperthermophilic crenarchaeal genus. In common with other archaea, they have transcription and replication machineries that resemble an ancestral form of the eukaryotic apparatus. The relative simplicity of the archaeal replication machinery has facilitated the biochemical analyses of replication proteins. Further, Sulfolobus has three replication origins per chromosome and these fire in all cells. The firing of all three origins occurs within a narrow temporal window in the archaeal cell cycle, closely following cell division. We have recently identified archaeal orthologs of the eukaryotic ESCRT apparatus as key components of the cell division apparatus, shedding light on the ancestral role of this conserved membrane manipulation system.
Departmental Research Seminar
12 November 2009
Signalling modules controlling the stem cell niche in Arabidopsis
Prof Dr Rüdiger Simon
Institute for Genetics, University of Dusseldorf
Stem cell fate in shoot and root meristems is controlled by the interaction with the stem cell niche. Several genes (encoding transcription factors or signaling molecules) have been identified in recent years that are essential to promote or restrict stem cell fate. I will discuss some of the mechanisms regulating stem cell fate, and present recent data addressing commonalities and differences between root and shoot meristems.
Departmental Research Seminar
05 November 2009
Reversible phosphorylation of thylakoid proteins: mechanisms, enzymes and physiological relevance
Prof Dario Leister
University of Munich
Photosynthesis is regulated at multiple levels, including the reversible phosphorylation of thylakoid proteins. This includes core proteins of photosystem II, as well as of the mobile antenna complex of photosystem II, which can migrate between the photosystems depending on its phosphorylation state (state transitions). In addition to state transitions, which represent a short-term acclimatory response, also the long-term acclimatory response seems to depend on reversible phosphorylation events. Some of the underlying regulatory mechanisms and their interdependencies are becoming unveiled. Recent developments in the field of the reversible phosphorylation of thylakoid proteins, particularly concerning its physiological relevance and the enzymes involved, will be presented and discussed.
Departmental Research Seminar
29 October 2009
Inheritance patterns of DNA methylation in Arabidopsis: molecular mechanisms and phenotypic consequences
Prof Vincent Colot
CNRS, Paris
From a classical perspective, the heritable basis of complex traits rests solely on the transmission from parents to offspring of multiple DNA sequence variants that are stable and causative. Accumulating evidence suggests that this view may be too restrictive, insofar as chromatin variation (such as differential DNA methylation) can also be propagated across generations with phenotypic consequences, independent of DNA sequence changes. However, attempts to assess the extent of epigenetic variation in natural or experimental populations and to quantify its impact on complex traits have been hampered by the confounding effects of DNA sequence polymorphisms. To overcome this problem as much as possible, we established a panel of so-called epigenetic Recombinant Inbred Lines (epiRILs) in the reference plant Arabidopsis thaliana. The epiRILs were derived by crossing a hypomethylation mutant with its wild type relative, backcrossing the F1 to the wild type, and selecting the homozygous wild type offspring for further propagation. Robust and progressive remethylation was observed for approximately half of the parental DNA hypomethylation variants (epialleles), mediated by the RNAi machinery. Nonetheless, stable inheritance of DNA hypomethylation was observed over at least eight generations at numerous loci. Moreover, the epiRILs exhibited significant heritable variation for flowering time and plant height (~30%). These findings provide a first rationale to identify epiallelic variants that contribute to heritable variation in complex traits using linkage or association studies. More generally, the demonstration that numerous epialleles across the genome can be stable over many generations in the absence of selection or extensive DNA sequence variation highlights the need to integrate epigenetic information into population genetics studies.
Departmental Research Seminar
22 October 2009
Some natural history observations from the mitochondrial genomes of plants, animals, and fungi
Dr Douglas Taylor
University of Virginia
The evolutionary processes affecting mitochondrial genomes are relevant to understanding the evolution of sex and recombination, mutation accumulation, genetic conflict, not to mention the dynamics of human mitochondrial disease within the soma. Conventional wisdom suggests the haploid, maternally-inherited, asexual, and relatively conserved structure of the mitochondrial genome is relatively easy to understand. The reality is that mitochondrial genomes vary widely in genome structure and inheritance, and that this variation has important consequences for their evolution. I will outline our ongoing research into levels of selection, mutation accumulation, and patterns of sequence evolution in the mitochondrial genomes of plants, animals and fungi. Our findings illustrate the various evolutionary forces that drive the molecular evolution of nuclear and mitochondrial genomes.
Departmental Research Seminar
13 October 2009
Genomics-guided discovery of novel traits in plant-associated bacteria.
Dr Joyce Loper
USDA, Horticultural Crops Research Unit, Corvallis, Oregon
Pseudomonas fluorescens is a diverse bacterial species known for its ubiquity in natural habitats and tremendous metabolic capacity. Certain strains, such as P. fluorescens Pf-5 live in close association with plant roots and function as biological control agents, protecting roots from infection by plant pathogenic fungi and Oomycetes. Pf-5 is known to produce a number of secondary metabolites toxic to plant pathogens, and many orphan gene clusters, which encode for the biosynthesis of unknown natural products, have been identified the Pf-5 genome. Through combined bioinformatic and chemical analyses, the products of orphan gene clusters have been identified and new aspects of the biology of Pf-5 revealed.
Departmental Research Seminar
18 June 2009
Shaping the plant endomembrane system
Professor Christopher Hawes,
Oxford Brookes
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Departmental Research Seminar
11 June 2009
The secrets of a plant killer: evolution and function of the effector secretome of phytophthora infestans
Dr Sophien Kamoun
The Sainsbury Laboratory, Norwich
Eukaryotic plant pathogens, such as oomycetes and fungi, cause highly destructive diseases that negatively impact commercial and subsistence agriculture worldwide. These pathogens secrete an arsenal of effector proteins to modulate plant innate immunity and enable parasitic infection. Deciphering the biochemical activities of effectors to understand how pathogens successfully colonize and reproduce on their host plants became a driving paradigm in the field. This presentation will focus on effectors of oomycetes, such as the Irish potato famine pathogen Phytophthora infestans. Tremendous progress has been made recently in understanding the biology of oomycete effectors. Two classes of effectors target distinct sites in the host plant: apoplastic effectors are secreted into the plant extracellular space, while cytoplasmic effectors are translocated inside the plant cell, where they target different subcellular compartments. Of particular interest are the RXLR and Crinkler host-translocated (cytoplasmic) effectors that are characterized by conserved motifs following the signal peptide. The RXLR domain is functionally interchangeable with a malaria host targeting domain and functions in delivery into host cells. The recent completion of six oomycete genome sequences enabled genome-wide cataloguing of the effector secretome revealing hundreds of candidate effectors. Effectors are frequently organized in clusters of paralogous genes, many of which exhibit hallmarks of positive selection probably as a result of a coevolutionary arms race with host factors. We also utilized the discovered RXLR effectors in high-throughput in planta expression assays to screen for avirulence and virulence activities. The perturbations caused by these effectors is helping to elucidate the mechanisms of pathogenicity as well as further illuminate mechanisms of plant defense and innate immunity.
Departmental Research Seminar
04 June 2009
Forest Research - objectives and outputs
Dr Peter Freer-Smith
Forestry Commission Alice Holt
operations occur in steps (e.g. road construction, ground preparation, planting, felling) interspersed with long periods of gradual change and management objectives are not always obvious. However, in the policy objectives and associated forest practices have changed substantially over the last 90 years.
The current overarching objective is sustainable forestry which seeks to balance present and future needs and to cater for a range of societal and individual needs.
Charged with providing the evidence base and technical advice for forestry, Forest Research (FR) has to be forward looking and flexible in its science programme.
I will describe FR’s current objectives and illustrate our delivery by describing ongoing work in three areas: sustainable forest management, climate change and the role of urban greenspace in improving air quality.
Departmental Research seminar
28 May 2009
Modeling plant shoot development
Dr Henrik Jonsson
Lund University
The plant shoot involves highly regulated patterns of gene expressions, hormone gradients, mechanical stresses, and of cellgrowth and proliferation. These patterns control as well as result from the mechanisms of plant shoot development. An understanding of their origin is thereby essential for understanding the development ofthe aerial part of the plant. The complex interactions appearing in the shoot need to be accountedfor in computational models describing shoot development. In this talk I will discuss several models of plant shoot development including different mechanistic aspects with focus on stem cell regulation and early primordia development. Molecular as well as mechanical models will be discussed.
References:
Developmental patterning by mechanical signals in Arabidopsis O. Hamant, M. Heisler, H. Jönsson, P. Krupinski, M. Uyttewaal, P. Bokov, F. Corson, P. Sahlin, A. Boudaoud, E. M. Meyerowitz, Y. Couder, and J. Traas Science 322, 1650-1655 (2008)
An auxin-driven polarized transport model for phyllotaxis H. Jönsson, M. Heisler, B.E. Shapiro, E.M. Meyerowitz, and E. Mjolsness Proceedings of the National 103, 1633-1638 (2006)
Departmental Research Seminar
21 May 2009
Light and temperature signal crosstalk in plant environmental adaptation
Dr Kerry Franklin
University of Leicester
Light and temperature are two of the most important environmental signals regulating plant development. Our work has shown complex crosstalk between light and temperature signalling pathways in the regulation of shade avoidance strategy and freezing tolerance in Arabidopsis thaliana. We have additionally identified a key molecular mechanism through which plants integrate light and temperature signals following the discovery that the light-regulated bHLH transcription factor PHYTOCHROME INTERACTING FACTOR 4 (PIF4) functions as a master regulator of high temperature-mediated elongation growth.
Departmental Research Seminar
14 May 2009
First steps in manipulating plant cell wall synthesis: functional and industrial implications
Dr Paul Dupree
University of Cambridge
Plant cell wall polysaccharides have important roles in growth, development, and resistance to pathogens. They are also of enormous importance in industry and agriculture, being substantial components of human and animal food, and determine the yield and properties of timber, paper and pulp. Recently, there has been great interest in using the polysaccharides as a source of renewable bioenergy, for example by degrading them to monosaccharides and fermenting to ethanol. In addition to cellulose, which may constitute 40% of the cell wall, hemicellulosic sugars from xylan and mannan are also an important bioenergy target, and may constitute a further 30% of the mass. To utilise them effectively, we need to understand how they are made, so that their structure and quantity can be optimised. With this knowledge, strategies can be devised to improve the release of sugars from the cell wall for fermentation. Most plant cell wall polysaccharides are synthesized in the Golgi apparatus by a largely unknown set of enzymes. We do not understand either the role of the different wall components or how they might be altered to improve their properties for the various applications. To discover proteins involved in the synthesis of these glycans and in their sorting to the plasma membrane, we have been analyzing the protein composition of the Golgi apparatus by developing new proteomics tools. We have identified putative glycosyltransferases, sugar transporters and other novel proteins in the Golgi apparatus in Arabidopsis. We prioritise the study of candidates by integrating transcriptomic and proteomic datasets to predict function. We are studying the corresponding mutant plants using our enzymatic polysaccharide profiling technique PACE, which reveals structure and quantity of oligosaccharides released by cell wall digestion. Plants with altered cell wall polysaccharides have recently been identified, and show unexpected phenotypes.
Departmental Research seminar
07 May 2009
Using plant phylogenies to understand the historical assembly of tropical forests
Dr Toby Pennington
Royal Botanic Garden Edinburgh
Molecular phylogenies calibrated with a time dimension play a central role in understanding tropical biotic history. They indicate whether species diversity is ancient or recent, whether in-situ speciation or dispersal has dominated assembly of continental and local floras, and whether 'ecological' speciation between habitats has been a key evolutionary force.
Departmental Research Seminar
30 April 2009
Plants and insufficient oxygen - from cellular response to submergence tolerance
Professor Julia Bailey-Serres
University of California
Oxygen is vital for aerobic respiration in plants. Cells faced with insufficient oxygen must conserve energy to survive. This lecture will present a perspective on the response to low oxygen stress from the cellular to the whole plant level. Recent exploration of the responses of individual cell types of the seedling root and shoot of Arabidopsis thaliana to low oxygen stress has revealed an unified response that reconfigures metabolism to enhance substrate-level ATP production. The response is fine-tuned at the cellular level, providing distinctions in response of individual cell types and organs. A decline in cellular oxygen content is a component of the stress invoked upon waterlogging of a root system or complete submergence of a plant. The characterization of the submergence response governed by the multi-gene Sub1 locus of rice (Oryza sativa) has uncovered the molecular basis of distinct strategies in energy utilization during submergence that engender survival under different flooding regimes. These acclimation responses involve a cascade of regulation mediated by the phytohormones ethylene, abscisic acid and gibberellins. The Sub1A ethylene responsive transcription factor orchestrates a robust submergence tolerance phenotype that has the potential to dramatically improve the yield of rice from submergence prone fields in .
Departmental Research Seminar
16 April 2009
Reducing forest degradation in the tropics: can REDD promote green forest management?
Dr Mary Menton
University of Oxford
REDD (reduced greenhouse gas emissions from deforestation and forest degradation) is currently being promoted as a means to mitigate climate change whilst protecting tropical forests. Much of the debates surrounding REDD have focused on avoided deforestation with less attention brought to the potential to support carbon retention via reductions in forest degradation. I will present the case for the potential to include reduced degradation as part of REDD schemes, drawing on data on carbon loss via forest fires and poor logging practices.
02 April 2009
Metabolic Systems Biology: Assembling the Clockwork to Reveal its Properties
Dr Igor Libourel
Metabolic Systems Biology is a discipline that involves the definition, population, and functional behavior of metabolic networks. Both experimental and theoretical aspects of Metabolic Systems Biology will be presented in this seminar. First, work will be shown that demonstrates the use of pathway-wide analysis of anoxic metabolism. With insight gained through computational analysis, in-vivo 31P-NMR was used to experimentally validate and redefine the role of nitrate in anoxic pH regulation in maize and tobacco roots. This work on anoxic metabolism demonstrates the value of integrating computational and experimental methods. Secondly, two new predictive methods for metabolic modeling will be presented. The first method involves the transformation of 13C-based steady-state flux maps into fractional bidirectional mass action models. Through the integration of Gibbs free energy of formation, these models become suitable for comparative flux analysis and can be used to pinpoint specific enzymes with altered activities. This capability of comparative flux analysis can therefore be used to quantify metabolic regulation. The second predictive method incorporates thermodynamic constraints in the commonly used “minimization of metabolic adjustment” method, and identifies the interesting special metabolic case of maximum metabolic regulation. The theory development has made predictive and comparative flux analysis possible from previously just descriptive flux models, and opens doors to novel insights into the regulation of metabolic networks.
26 March 2009
Germlines, gametophytes and parallel small RNA worlds
Dr Robert Grant -Downton
University of Oxford
At a first glance, sexual reproduction in animals and flowering plants appears to be quite dissimilar. Whilst almost all animals segregate and sequester a germline early in development, flowering plants do not and are instead sexual opportunists that can easily switch their aerial vegetative meristems to reproductive developmental programmes. Whereas animals form their gametes directly from the products of meiosis, the meiotic products of flowering plants undergo further mitotic divisions to form a gametophyte generation that contains the gametes. Nevertheless, germlines and gametophytes have some interesting parallels. A particularly striking parallel involves the substantial reorganisation of epigenetic systems in both germline and gametophyte cells. In the male gametophyte (pollen), the first mitotic division generates two cells with highly divergent fates and epigenetic states – the vegetative cell and the generative cell. Only the generative cell divides again to form two sperm cells. Unfortunately, the epigenetic systems of the male gametophyte have remained poorly understood. Until recently, it was assumed that small RNA systems played little part as they were allegedly down-regulated during pollen development. This is in contrast to animals where small RNA systems are of profound importance to germlines. I will demonstrate that small RNAs such as microRNAs and tasiRNAs are diverse in pollen and likely make a hitherto unappreciated contribution to this critical stage of development. As in animal systems, I show that small RNAs may behave rather differently during reproductive development.
"out of term" seminar
19 March 2009
Fungal sex: a conserved pathway adapted to life style
Professor Lorna Casselton
University of Oxford
Attracting a mating partner is a universal problem. We are used to the wonderful antics and displays that the male of the species has to give in order to attract a female and the powerful scents and colours used by flowers to ensure that the male pollen alights on a compatible female recipient. But what of fungi? Their mating cells are indistinguishable to us but, never the less, they can recognise each other. Some fungi signal to each other by means of secreted sex pheromones, others just try it and see if it works. However, the steps in the mating pathway are highly conserved in the fungi I shall talk about, but different life styles have modified the way key components are regulated. With so much information available from genome sequences it is now interesting to see how evolution has led to changes in the genes that are found at the so-called sex loci.
Ninth week seminar
12 March 2009
The history of rice domestication; genetic isolation punctuated by genetic exchange
Professor Susan McCouch
Cornell University
Knowledge about the structure and evolutionary history of naturally occurring variation in crops and their wild relatives provides a road map for understanding domestication and new opportunities for utilizing novel alleles in crop improvement. Domesticated Asian rice (Oryza sativa L.) is comprised of five, well-differentiated subpopulations that evolved from a common, out-crossing wild ancestor, O. rufipogon that is found distributed throughout tropical . The evolutionary forces that gave rise to the current population structure of O. sativa are unclear at this time. Using recently isolated domestication genes, we trace the evolutionary history of alleles that both define and transcend the deep population structure of domesticated rice. Documented patterns of allele dispersal suggest a complex pattern of gene flow and genetic exchange coupled with an increase in genetic isolation reinforced by inbreeding. Understanding the biological, social and cultural dynamics of these opposing processes challenges existing models of crop domestication and provides a framework for conserving, characterizing and utilizing wild and exotic germplasm in crop improvement.
MARY SNOW LECTURE
Drinks reception in the Common Room afterwards
05 March 2009
Why bother with a chloroplast genome? Hints from dinoflagellate algae
Professor Christopher Howe
University of Cambridge
Chloroplast DNA is remarkably similar in its organization and gene content across a wide range of plants and algae. However, dinoflagellate algae - an ecologically important group of organisms that break most of the rules in cell biology textbooks - have a chloroplast genome unlike any other. Most of the genes usually found in chloroplasts have been forfeited to the nucleus, and the few remaining are distributed over a collection of small plasmids, most of which carry a single gene (and some of which do not appear to carry any genes at all). Dinoflagellate mitochondrial genomes are equally unusual. The anomalous chloroplast genome organization of these algae prompts the question of why plant and algal cells retain a chloroplast genome, and hints at possible answers.
Departmental Research Seminar
26 February 2009
The Citrus Story
Professor David Mabberley
Royal Botanic Garden Kew
Citrus, the world's most important subtropical fruit and crop is under threat, yet the taxonomy and analysis of the group is little understood.
The systematic relationships of the group are revealed by molecular systematics and the history of the principal crop taxa are explained.
Departmental seminar
19 February 2009
Auxin transport - developmental output of subcellular dynamics
Dr Jiri Friml
University of Gent
Auxin is a prominent intercellular signal in plants. Directional, active, cell-to-cell auxin transport mediates local auxin gradients, which are required for various patterning processes including apical-basal axis formation, organogenesis and tropisms. The chemiosmotic hypothesis postulates that auxin transport is accomplished by the action of auxin influx and efflux carriers, which are localized at the plasma membrane of transporting cells. Genetic approaches in Arabidopsis thaliana identified candidate genes coding for regulators of auxin efflux including plant-specific plasma membrane PIN proteins. PIN proteins show dynamic polar subcellular localisation, which correlates with and determines direction of auxin flow. In turn, auxin distribution itself is regulating PIN occurrence at the plasma membrane and PIN polarity. In addition, other internal as well as external signals can modulate endocytic recycling-based PIN localization and thus directional auxin signalling.
We will provide new insights into the mechanism of auxin transport, PIN polar targeting, endocytosis-dependent cell polarity and auxin-dependent regulation of plant development.
Departmental Research Seminar
12 February 2009
Insect food webs: patterns, processes and applications
Dr Owen Lewis
University of Oxford
Food webs describe networks of feeding interactions among species within ecological communities. I will describe empirical studies of food webs (involving plants, insect herbivores and their parasitoids) that are fully quantified in terms of the abundance of interacting species and the frequency of each interaction. I will present evidence that these 'quantitative food webs' can inform us about (1) the dynamic processes structuring and organising biological diversity; (2) the consequences of extinction or invasion of individual species; and (3) the effects of humans on ecosystem organisation, integrity and functioning.
Departmental Research Seminar
05 February 2009
Cell fate determination by hormonal patterning in fruits
Dr Lars Ostergaard
John Innes Centre, Norwich
The fruit of flowering plants provides an excellent system to study cell differentiation and tissue specification, since it is divided into discrete sections with juxtaposed cell types that are dramatically different from each other. Patterning the Arabidopsis fruit involves formation of polarity along the proximo-distal and medio-lateral axes. Getting it right is crucial for proper development and much of the information has been laid down well before fertilisation. At maturity, the Arabidopsis fruit disperse their seeds through a process known as fruit dehiscence or pod shatter. This process requires a timely cell separation event in a highly specialised tissue called the valve margin.
Within the past decade, several of the key regulators involved in Arabidopsis fruit development have been identified and their genetic interactions established. Our work on how distribution of the plant hormone, auxin, is controlled by this genetic network to ensure proper cell specification, will be presented.
Departmental Research Seminar
29 January 2009
Changing landscapes: the evolutionary origins of a plant diversity hotspot
Dr Timothy Barraclough
Imperial College, London
The Cape region of has attracted considerable attention as a global hotspot for flowering plant diversity. Over ten thousand species are packed into a small, temperate region, many of them the result of endemic radiation. Recent systematic work has shown that the timing of diversification varies widely among different taxa: some have accumulated species at their leisure over long timescales whereas others have radiated rapidly, perhaps in response to climate change during the last few million years. However, the causes of diversification in the , and their importance for generating diversity patterns, remain unclear. Analyses of the genus Protea, one of the most charismatic clades, are used to explore the evolutionary mechanisms behind diversity patterns in the region. The results are discussed in terms of the role of equilibrium versus non-equilibrium processes in generating diversity pattern.
Departmental Research Seminar
19 January 2009
Exploring the links between climate change, plant biology and public health
Dr Lewis Ziska
USDA, Beltsville, Maryland
The epidemiological implications with respect to climate change and public health (e.g. shifts in disease vectors) are beginning to be acknowledged. Less recognized however, are the potential links between climate, plant biology and public health. In addition to being affected by climate (e.g. temperature determines plant range), carbon dioxide (CO2) represents the raw material needed for photosynthesis and its rapid increase in the atmosphere is expected to stimulate plant growth. There are a number of means by which plant biology intersects with human health including aero-biology (allergens, asthma), contact dermatitis (rashes), toxicology (poison ingestion), pharmacology (plant based analgesics) that are likely to be affected by the ongoing changes in CO2/climate. In this over-view I will discuss current research efforts by USDA-ARS to address these issues, current progress and future directions
Departmental Lecture Series
04 December 2008
Investigating the Biology of Plant Infection by the Rice Blast Fungus Magnaporthe oryzae
Professor Nicholas Talbot
School of Biosciences, University of Exeter
Rice blast disease is the most serious disease of cultivated rice and is responsible for serious harvest losses every year. The seminar will recent advances in our understanding of the early events in plant infection by the rice blast fungus Magnaporthe oryzae. The fungus elaborates a special infection structure called an appressorium. The developmental process leading to its formation is cell cycle regulated and involves autophagic programmed cel death. The cell then generates enormous turgor, which is translated into mechanical force in order to rupture the rice leaf cuticle. This process and its genetic control will be described in addition to a discussion of how the deployment of genomic analysis is revolutionizing the study of this plant-fungus interaction.
Departmental Research Seminar
27 November 2008
Friends and enemies within - genetic incompatibility in Arabidopsis thaliana
Dr Kirsten Bomblies
University of Tuebingen, Germany
Understanding the causes and consequences of genetic divergence among lineages within species can help inform our understanding of complex processes such as adaptation and speciation. Arabidopsis thaliana is a primarily self-fertilizing plant species; thus it is made up of many essentially independently diverging lineages with little gene flow among them, providing a good model system for investigating early events in genetic divergence. To survey how compatible diverging A. thaliana genomes actually are, we intercrossed 311 wild A. thaliana accessions in 1487 combinations. Most hybrids were normal, as expected for crosses within species, but 21 first-generation hybrids showed strongly deleterious phenotypes including dwarfism, severe tissue necrosis and sterility. Very similar “hybrid necrosis” phenotypes have been observed in many plant hybrids, often in interspecies crosses, suggesting that 1) A. thaliana is a useful model for understanding a common phenomenon in plants, and 2) necrosis may be an important factor in plant evolution and perhaps speciation. We found that hybrid necrosis in several independent cases in A. thaliana is due to hyperactivation of the plant immune system (effectively, plant autoimmunity). We have found that at least two independent cases are caused by different known or suspected pathogen resistance (R) genes. Because R genes in plants - like MHC genes in animals - are numerous and especially diverse, and because coordination among R proteins and other gene products regulates a strong cell death response, it is perhaps not surprising that these genes might be among the earliest causes of incompatibility among diverging plant lineages. Thus, similarly to what has been proposed for rapidly evolving animal "incompatibility genes," plant incompatibility due to necrosis is likely a by-product of the normal rapid evolution of resistance genes. I will also briefly discuss our investigations of actual outcrossing and population structure in wild A. thaliana populations from southwestern .
Departmental seminar series
20 November 2008
Genetic warfare between plants and their pathogens leads to weapons proliferation
Professor Jim Beynon
University of Warwick
The interaction between Arabidopsis thaliana and the downy mildew parasite Hyaloperonospora arabidopsidis has played a major role in the identification of key genes involved in plant disease resistance. Recent advances have allowed us to identify the pathogen genes that are the weapons used to suprress host immune systems. The cloning of these genes has allowed the definition of the RXLR motif that allows targetting of these pathogenicity efectors to the host plant cytoplasm. The H. arabidopsidis genome sequence is being assembled in a collaboration between and The Sanger Centre in the and Virginia Tech and Wash U in the . The genome reveals that it is adapted to an obligate biotrophic lifestyle, containing a vast repetoire of potential pathogenicity effector proteins. These genes imply an exquisite and complex relationship with their host plant and represent new tools with which to elucidate the host immune system.
13 November 2008
Genomics based analysis of cell wall signaling processes
Professor Thorsten Hamann
Imperial College, University of London
Development, abiotic and biotic stress impact on the physical architecture and chemical composition of the plant cell wall, making "cell wall stress" (CWS) an integral element of many plant processes. The ability of the plant to respond to CWS is an essential requirement for the maintenance of cell integrity. Over the last years evidence has been mounting that plants have developed a specialised mechanism to perceive CWS and adjust composition and structure of the cell wall in order to ensure cell survival and meet the changing functional requirements during cell differentiation. Understanding the mode of action of this mechanism has obvious possible applications when it comes to improvement of cell wall composition for improved bioenergy production or for increased biotic stress resistance.
Departmental Research Seminar
06 November 2008
Ethylene-induced shoot elongation: regulation of an escape strategy
Professor Rens Voesenek
Institute of Environmental Biology, University of Utrecht
The semi-aquatic dicot Rumex palustris responds to complete submergence by upward movement of leaves (hyponastic growth) and elongation of young petioles. These two responses together can bring leaves above the water surface, thus restoring gas exchange with the atmosphere and increasing survival in flood-prone environments. So far our work suggests that these two responses are regulated via an ethylene-driven signaling network in which apoplastic acidification, expansin action and the activity of the hormones abscisic acid (), gibberellin (GA) and auxin (IAA) are important.
Hyponastic growth and petiole elongation can also be induced in Arabidopsis thaliana by ethylene and canopy shade. We aim to use Arabidopsis as a tool to unravel signal transduction routes involved in hyponastic growth and petiole elongation. To this end we performed pharmacological experiments, full genome micro-array studies, QTL analyses and a mutant screen. Some results of these approaches will be presented and discussed.
Departmental Research Seminar
04 November 2008
Peptide drugs and drug scaffolds from sunflower seeds
Dr Joshua Mylne
University of Queensland
Water-soluble albumins and salt-soluble globulins are the major storage proteins found in seeds. I have cloned a sunflower gene encoding 151-residue preproalbumin PawS1 that includes sequence for a 14-residue cyclic peptide SFTI-1; a trypsin inhibitor with drug-like potency (sub-nanomolar Ki). By homology I also cloned PawS2 which contains 12-residue cyclic peptide SFTL-2. SFTI-1 and SFTL-2 reside in a proalbumin region removed during albumin maturation by asparaginyl-endo-peptidase - a protease also implicated in peptide cyclization. These findings suggest PawS1 and PawS2 have developed an additional role to that of storage and represent an alternative biosynthetic route to those of known cyclic peptides from plants, bacteria and mammals.
Extra research lecture
30 October 2008
Glutathione metabolism and cellular redox homeostasis in plants
Dr Andreas Meyer
Heidelberg Institute of Plant Sciences, University of Heidelberg
The tripeptide glutathione is a key component of the cellular defence system against xenobiotics and reactive oxygen species. In non-stressed cells, glutathione is maintained in almost completely reduced form by glutathione reductases at the expense of NADPH. Based on the use of novel in vivo probes for the glutathione redox potential there is now mounting evidence that stress conditions can elicit a transient oxidation of glutathione, which may affect downstream signal transduction pathways. In this seminar, I will describe recent advances in our understanding of glutathione biosynthesis and the role of glutathione for cellular redox control and signalling.
Departmental Research Seminar
23 October 2008
Quantitative trait analysis of Arabidopsis Thaliana using heterogeneous recombinant inbred lines
Professor Richard Mott
Wellcome Trust Centre for Human Genetics, University of Oxford
Departmental Research Seminar
16 October 2008
Imprinted expression of small silencing in RNA plants
Professor David Baulcombe
Department of Plant Sciences,University of Cambridge
Small silencing RNA in plants are the specificity determinants of mechanisms that silence gene expression at both the transcriptional and posttranscriptional levels. I will describe the evidence that some of these RNAs may have roles in control of growth and development but that others may influence genome defense and interactions between maternal and paternal genomes in hybrid plants
Departmental Research Seminar
14 October 2008
All roads lead to auxin: regulation of axillary meristem initiation in maize
Dr Paula McSteen
Pennsylvania State University, USA
Auxin plays a fundamental role in plant development. During vegetative development, auxin is required for the initiation of leaves and axillary meristems while during inflorescence development, auxin is required for the initiation of floral meristems and floral organs. The maize inflorescence is highly branched due to the production of multiple types of axillary meristem. We have shown that auxin is required for the initiation of all axillary meristems in the maize inflorescence. To dissect the role of auxin in inflorescence development, we have screened for mutants that fail to initiate axillary meristems. This approach has led to the identification of genes required for auxin biosynthesis, auxin transport and auxin response. I will discuss the roles of sparse inflorescence1, a flavin mono-oxygenase which functions in localized auxin biosynthesis, barren inflorescence2 which encodes a serine threonine protein kinase functioning in auxin transport and barren stalk1, a bHLH transcription factor required for axillary meristem initiation. The genetic, molecular and biochemical interaction of these components demonstrate that auxin biosynthesis and auxin transport function together to control plant development. Our research shows that although some aspects of the control of auxin biosynthesis and transport are conserved between monocots and eudicots, important differences have also evolved.
02 July 2008
Molecular Evolutionary Genomics of Plant Adaptations - Lessons from Arabidopsis
Professor Michael Purugganan
University of New York, USA
12 June 2008
Seasonal control of flowering in annual and perennial plants
Professor George Coupland
Max Planck, Koln
We are comparing the mechanisms by which the life cycles of annual and perennial plants are synchronised to the changing seasons. Arabidopsis thaliana is a model annual plant and we have shown how circadian-clock regulation of transcription of specific regulatory genes and photoreceptor signaling can combine to promote flowering of this species in response to long summer days. As a perennial species, we have used Arabis alpina, which diverged from Arabidopsis around 30 million years ago. We have studied the effects of vernalization (exposure to low winter temperatures) on the life cycle of Arabis alpina and propose that correlated selection of the vernalization response occurs as species evolve from perennial to annual. The talk will expand on these comparative approaches to study flowering-time control.
Departmental Research Talk
05 June 2008
Early fossils and the origins of plant roots, shoots and life cycles
Dr Paul Kenrick
Natural History Museum, London
Plants inherited their biochemistry from the green algae, but most of their morphology evolved on land. Developing an understanding of the origins of fundamental organs and tissue systems – a key aim of research in molecular developmental biology – entails a focus on groups such as bryophytes (liverworts, mosses, hornworts), basal vascular plants (clubmosses, horsetails, ferns) and their close relatives in the charophycean algae. Model organisms are invaluable, but at these deep phylogenetic levels extinction has taken a heavy toll. Because of this it becomes difficult using modern groups alone to relate aspects of morphology among major clades and to trace the course of life cycle evolution. The fossil record of plants during the early phases of their diversification on land (Devonian Period 417-354 Million Years) provides an effective means of addressing these issues. It also reveals an astonishing diversity of forms and life cycle variants completely unknown in the modern world. Phylogenetic analysis indicates that this record is skewed towards the vascular plants, providing a static but detailed record of their origins and the early development of their roots, stems, leaves, internal tissue systems and life cycles. Recent advances in molecular developmental biology bring a fresh new perspective to testing hypotheses on the early evolution of plant form, and they raise new questions to put to the fossil record.
Departmental Research Talk
29 May 2008
Ocean Circulation and Climate
Dr Helen Johnson
Earth Sciences, Oxford
The ocean circulation plays a key role in the climate system, and therefore global-warming induced changes in the ocean have the potential to significantly feed back on climate. However, our understanding of and ability to model important processes in the ocean is limited, and poses a serious problem for future predictions of climate change.
This talk will present an overview of the ways in which ocean circulation influences climate, and the changes we might expect as a result of greenhouse gas emissions. Some of the most pressing questions about the ocean's response to change will be discussed, together with work being conducted by Oxford's new Physical Oceanography group to address these issues.
Departmental Research Talk
22 May 2008
G-proteins and all that JAZ
Dr Haruko Okamoto
University of Oxford
Heterotrimeric G-proteins, comprising a, b, and γ subunits, are common signalling molecules in multicellular organisms across the phyla. The primary function of G-proteins is to relay extra cellular signals to downstream partners that initiate the cellular responses that enable organisms to adapt to their environment. In animals, each G-protein subunit is encoded by a large gene family. This allows each subunit to form a heterotrimer complex in a number of different combinations and thus serve in a wide range of distinct signalling pathways. In plants, G-proteins have also been implicated in having a role in a number of signalling pathways including, ABA, GA, auxin, brassinolide, sugar and light, as well as in pathogen defence responses. The Arabidopsis genome encodes a single copy each of Ga and Gb and two Gγ subunits leaving the plant with just 2 heterotrimeric combinations to potentially serve in these seemingly multiple pathways. Analysis of loss of function Ga and Gb mutants has allowed us to identify yet another hormone signalling pathway, jasmonate, in which G-proteins have a function. The role of G-proteins in jasmonate signalling and why jasmonate may help us understand broader aspects of G-protein signalling in plants will be discussed.
Departmental Research Talk
08 May 2008
Understanding and predicting plant population dynamics at a range of scales
Professor Robert Freckleton
University of Sheffield
Departmental Research Talk
01 May 2008
The control of plant development by gibberellic acid signaling
Dr Claus Schwechheimer
University of Tuebingen
We are interested in understanding the role of protein degradation-dependent growth processes in plant development. The gibberellic acid (GA) and proteasome-dependent degradation of the DELLA proteins via the E3 ligase SCF(SLY1) is essential for germination, elongation growth, and flowering in plants. We (and others) have characterized the three genes that encode GA receptor (GID1) function in Arabidopsis. We could show that these receptors require the DELLA domain for their interaction with the DELLA proteins and that this interaction is essential for DELLA protein degradation. Using transcriptomics, we identified GA-regulated genes that are downstream of the DELLA protein degradation, and the characterization of mutants of individual GA-regulated genes has allowed us to attribute specific physiological functions to at least some of these target genes. Finally, we are studying a protein kinase that is required for efficient auxin transport and data will be presented suggesting a cross-talk between this kinase and the GA signaling pathway.
Departmental Research Talk
24 April 2008
Auxin response networks in early plant embryogenesis
Dr Dolf Weijers
Wageningen University
The main focus of our lab is the initiation of the meristems in the plant embryo. We have previously established that specification of the root meristem founder cell is controlled by a pair of transcription factors that mediate responses to the plant hormone auxin. Recently, we found that auxin-dependent transcription factors (ARFs) control early plant embryogenesis at many other levels. I will present the results from our efforts to systematically dissect the mechanisms of auxin-dependent transcription in early plant embryogenesis.
Departmental Research Talk
13 March 2008
Mushrooms to run UK rail network?
Dr Mark Fricker
Plant Sciences
Excerpt from The Independent, Thursday, 3 January 2008
“A new year has dawned and, with it, the realisation that our rail system is hopelessly inadequate. Liverpool Street Station in London was still closed last night after holiday maintenance works overran. The West Coast main line was also severely disrupted because works in the Rugby area had not been completed on time. Tens of thousands of commuters returning to work after the Christmas break were affected. The Rail Regulator has launched an inquiry into the failure of Network Rail to complete the maintenance, partly in response to loud complaints from Virgin Trains... Whatever the truth, this is an appalling way to run a railway.”
Conversely, foraging woodland fungi form extensive transport networks that are both efficient at transporting resources around the colony to where they are needed and also resilient to attack by mycophagous insects – all despite the absence of a centralized control system. This provides an ideal opportunity to abstract the critical features that enable self-organisation of a network with decentralised control, and may act as a future paradigm for robust network design. Inherent in this approach is the assumption that solutions adopted by biological networks will exemplify useful generic theoretical principles, such as persistence, robustness, error-handling or appropriate redundancy, as they have been honed by many cycles of evolutionary selection. This talk will describe our attempts to characterise the properties of such biological networks and explore the possibility that biological principles may illuminate rational network design in an emerging field termed biologistics.
Ninth week seminar
13 March 2008
Producing biodiesel from algae: is green the new black
Dr. Oliver Jones
Cambridge
10 March 2008
Regulatory phosphorylation of novel phosphoenolpyruvate carboxylase isoforms in developing castor oil seeds
Professor Bill Plaxton
Queen’s University, Kingston, Canada
06 March 2008
The role of DELLA proteins in the integration of GA and ABA control of dormancy
Professor Ian Graham
University of York
Seed dormancy is a key adaptive trait in plants responsible for the soil seed bank. Germination terminates dispersal and therefore regulates the time and place of plant growth. The long established hormone balance theory describes the antagonistic roles of the dormancy promoting plant hormone abscisic acid (ABA), and the germination promoting hormone gibberellin (GA) in dormancy control, yet little is known about how these signals are integrated in the seed. Furthermore, although many genetic loci mediate the hormonal regulation of seed dormancy, the way in which these genes influence germination potential has remained elusive. Following on from our demonstration that the control of Arabidopsis seed dormancy by cold and light is mediated through the SPT and PIL5 bHLH transcription factors, at least in part through regulation of GA biosynthesis (Penfield et al., 2005 Current Biology 15:1998-200), we have found that the DELLA protein regulators of the GA response are required for seed dormancy control. DELLA proteins RGL2, RGA and GAI are required for dormancy and the ABA inhibition of seed germination (Penfield et al., 2006 Current Biology 16:2366-70). This is the first demonstration that DELLA proteins integrate ABA and GA signals during seed dormancy and germination. We have also found that cotyledon expansion precedes radicle emergence during Arabidopsis seed germination, and that seedling cotyledon size correlates strongly with dormancy in the DELLA mutants. GA, ABA and mutants affected in hormonal regulation of seed dormancy also control cotyledon size in a manner consistent with their effect on germination potential. We propose that light, temperature and hormonally responsive cotyledon expansion prior to radicle emergence overcomes dormancy imposed by the seed coat and underlies seed dormancy control in Arabidopsis.
28 February 2008
It’s not size but coordination that matters
Professor Graham Moore
John Innes Centre, Norwich
The foundation of western civilisation owes much to the high fertility of bread wheat which results from the stabilisation of its polyploid genome. Hexaploid wheat possessing multiple related genomes, but behaves as a diploid at meiosis. Correct pairing of homologous chromosomes is controlled by the Ph1 locus which has been defined to a cluster of genes related to Cdk2 in humans and mice, into which a segment of heterochromatin inserted. Overexpression of Cdk2 in mice results in non-homologous synapsis of chromosomes. Deletion of the Ph1 locus in wheat results in overexpression of the Cdk2-like loci from the other genomes and pairing between related chromosomes. Chromosomes need to remodel their chromatin in order to pair at meiosis. The chromatin remodelling occurs before the chromosomes are in intimate contact. In the presence of Ph1, both homologues need to be near identical in order to remodel their chromatin. Without Ph1, chromosomes remodel irrespective of homology.
14 February 2008
The pathways and contol of starch breakdown in Arabidopsis thaliana
Professor Samuel Zeeman
ETH Zurich
Starch is the major form in which plants store their carbohydrate and is an essential resource for our society. It is composed of branched glucans which form insoluble, semi-crystalline granules. In Arabidopsis, starch is stored transiently in leaves where its metabolism in intimately linked with other primary metabolic pathways. We study the pathway of starch breakdown and the way in which liberated carbon is exported from the chloroplast. Glucan phosphorylation is the first step, which may serve to de-crystallise the granule surface, allowing degradative enzymes access. Recent results suggest that glucan dephosphorylation is also required for complete degradation. Surprisingly, we have found that some of the degradative enzymes previously associated with starch breakdown are not required. Others, which we know are required, are present as multiple isoforms, and some appear to have regulatory functions. In my seminar I will outline our current understanding of the pathway and highlight outstanding questions.
07 February 2008
Physcomitrella patens: a plant system to elucidate the mechanism of polar growth and desiccation tolerance
Professor Ralph Quatrano
University of Washington at St Louis, USA
31 January 2008
How repeatable is evolution? The genetics of parallel architectural evolution in Brassicaceae
Professor David Baum
University of Wisconsin, Madison, USA
How commonly do independent evolutionary origins of the same morphological trait result from changes to the same genetic and developmental systems? To explore this question we have been evaluating the role of the floral meristem identity gene, LEAFY (LFY), in three lineages of Brassicaceae (Idahoa, Leavenworthia and Ionopsidium) that have transitioned from an ancestral inflorescence-flowering architecture to a derived rosette flowering architecture. In Ionopsidium LFY shows a distinct expression pattern in rosette flowering versus inflorescence flowering species, and transgenic experiments suggest that this is due to upstream trans-acting regulators. In Idahoa the two LFY genes show anomalous patterns of molecular evolution and alter plant architecture when introduced into an inflorescence flowering species, supporting the hypothesis that changes at the LFY loci contributed to the evolution of rosette flowering. In Leavenworthia the single LFY gene shows anomalous patterns of molecular evolution and has apparently coevolved with the TERMINAL FLOWER 1 gene to influence plant architecture. Overall these data, suggest that even among close relatives there may be several molecular paths to the same evolutionary outcome, but that these paths may all impinge on the same small number of developmental regulators.
24 January 2008
Mechanisms driving epidermal polarity in the Arabidopsis root
Dr Markus Grebe
University of Umeå, Sweden
The co-ordinated polarity of cells within the plane of a single tissue layer (planar polarity) is intensively studied in animal epithelia but has only recently been systematically analysed in plant epidermal cells. The polar positioning of hairs in the root epidermis of Arabidopsis thaliana provides a system for the functional dissection of a plant-specific planar polarity1. We recently reported that a concentration gradient of the plant hormone auxin in the root tip provides vectorial information that coordinates polar hair positioning2. Action of the auxin gradient on planar hair polarity takes place prior to the polar positioning of Rho-of-Plant (ROP) GTPases at the hair initiation site and relies on the combinatorial activity of the AUX1 auxin influx carrier, GNOM and EIN2 genes2,3. Here, I additionally discuss our recent findings including a novel mutation that affects a repressor of auxin gradient and planar polarity formation.
1. Fischer U, Ikeda Y & Grebe M 2007. Biochem. Soc. Trans. 35, 149-151.
2. Fischer U et al. 2006. Curr. Biol. 16, 2143-2149.
3. Grebe M et al. 2002. Curr. Biol. 12, 329–334.
17 January 2008
Prochlorococcus under the macroscope
Dr Heather Bouman
University of Oxford
Discovered nearly two decades ago, the marine cyanobacterium Prochlorococcus is believed to be the most abundant photosynthetic organism on Earth.
Covering altitudinal band from 40oN to 40oS, Prochlorococcus frequently dominates, both in terms of abundance and biomass, the vast expanses of blue waters lying in the subtropical gyres. Here, Prochlorococcus cells can be found throughout the photic zone, which covers a range of environmental conditions from the nutrient-depleted, well-lit waters at the sea surface to the nutrient-rich, light-limiting waters at depth. The ability of this single genus to thrive under a wide variety of environmental conditions has been has been explained by the occurrence of genetically and physiologically distinct populations called ecotypes. The seminar will explore the macroecological patterns of the distribution Prochlorococcus and its associated ecotypes and how they are related to the physical and chemical properties of the ocean.
06 December 2007
A prudent man with a beautiful mistress: Sibthorp, Bauer and the Flora Graeca
Dr Stephen A Harris
University of Oxford
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Special Lecture with drinks reception afterwards
29 November 2007
Trusted scientist or idiot savant?
Professor Christopher Leaver
University of Oxford
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21 November 2007
Understanding the other Big Bang: how TEs amplify throughout Genomes
Professor Susan Wessler
Department of Plant Biology, University of Georgia, Athens, Georgia, USA
The results of genome sequencing projects have revealed that the genes and genomes of higher plants and animals are littered with transposable elements (TEs). However, virtually nothing is known about how some TEs in some genomes overcome host repression and scatter like buckshot throughout the chromosomes of a population. While the impact of TEs on mammalian genome evolution has begun to receive considerable attention, TE analysis has been central to plant genetics and genomics. Most characterized plant genomes have rich collections of TEs including many active elements. In particular, members of the grass clade, including maize and rice, are in an epoch of TE-mediated genome diversification and, as such, are ideal for analyzing the earliest stages of TE amplification.
My laboratory has employed computational methods to determine the TE content of plant genomes and to identify potentially active elements. These studies led to the discovery of MITEs, short, nonautonomus DNA transposons that are the prevalent TE in and near plant genes. In this talk I will focus on the ability of MITEs to rapidly increase their copy number from one or a few elements to thousands of insertions in genic regions. For one rice MITE family, mPing, we have caught the element in the act of bursting from 1 to over 1000 elements and have documented the impact of insertion at these early stages. For another rice MITE family called Stowaway, successful transposition in yeast has facilitated the isolation of a hyperactive MITE and the identification of features necessary for its efficient transposition. I will also discuss how knowledge of the TE landscape of the relatively stable rice genome is informing our studies into the extremely dynamic genome of maize.
MARY SNOW LECTURE nb starts @ 4.15 p m followed by drinks at 5.30 p m in the Common Room
15 November 2007
Conflicting gene phylogenies and their possible explanations - examples from flowering plants
Professor Bengt Oxelman
University of Gôteborg and University of Uppsala, Sweden
Even though it was early recognized that gene trees are not equivalent to species trees, many systematic studies have made this assumption, at least implicitly. However, gene trees from a set of organisms often show conflicts. I review some possible explanations for gene tree incongruencies, and give some examples from Sileneae (campions and their relatives) where polyploid and homoploid hybridization, as well as raised substitution rates due to positive selection, likely have been important.
08 November 2007
Assembling a green metronome: defining the Arabidopsis circadian clock
Dr Seth Davis
Max Planck Institute for Plant Breeding Research, Cologne, Germany
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01 November 2007
How did that get there? From bacterial chemotaxis to cellular organisation
Professor Judith Armitage
Director, Oxford Centre for Integrative Systems Biology, Department of Biochemistry, University of Oxford
All organisms sense and respond to changes in their environment, bacteria
are no exception. Bacteria can have several hundred sensory systems
regulating everything from gene expression, local enzyme activity to
swimming behaviour. Chemotaxis has been the best studied system and E.coli
chemotaxis has become a paradigm for these sensory systems. However, using
different bacterial species it has become apparent that things can be much
more complex. Using the photosynthetic bacterium, Rhodobacter sphaeroides
we have shown that many species have multiple chemosensory pathways
operating simultaneously to control flagellar motor rotation. We have
combined molecular genetic, biochemistry and in vivo imaging to start to
characterise complex interaction networks. The talk will outline (with
videos!) the research that has lead to the current state of knowledge,
identification a novel protein localisation system and cautionary tales
about extrapolating from in vitro to in vivo.
25 October 2007
Challenges faced by environmental businesses and knowledge transfer from universities
Dr Simon Jackman
Director, The Integrated Pollution Management Network (IPM-Net), Oxford University Begbroke Science Park
This talk will describe the work of the Integrated Pollution Management
Network (IPM-Net) as a Knowledge Transfer Network in helping to identify
the challenges faced by industry in the field of environmental remediation
and clean-up of contaminated land and water. IPM-Net is part of the
University's new Institute of Advanced Technology at the Begbroke Science
Park and aims to provide innovation, networking and business opportunities
for environmental professionals, regulators and academics. Specifically,
the talk will describe opportunities for biological sciences in the waste
industry and energy sectors, and the ways in which these fields might
develop in the next 10 to 15 years.
18 October 2007
Solar Power: the ecological significance of C4 photosynthesis
Dr Colin Osborne
University of Sheffield
Plants with the C4 photosynthetic pathway dominate ecosystems in the world’s warm climate regions, from Death Valley to the Amazon wetlands, and account for 25% of terrestrial carbon fixation. Recent molecular phylogenies show more than 30 independent origins for this pathway – a remarkable example of convergent evolution thought to be driven by past global change. This talk explores the selective advantage of C4 photosynthesis using experimental evidence from a unique modern grass species with C3 and C4 subspecies. Unexpected experimental findings challenge current thinking about the advantages and costs of the C4 pathway.
11 October 2007
Regulation of plant development by signalling mechanisms
Dr Iain Searle
Sainsbury Laboratory, John Innes Centre, Norwich
Plants are multi-cellular organisms and cell-to-cell and
long-distance signalling are important for determining organ shape and
body plan. Understanding the molecular mechanisms that govern these
processes is a major challenge. My research interests are to determine
the molecular mechanisms involved in cell-to-cell signalling mediated by
mobile small RNAs during plant growth and development. I have developed
a novel RNA silencing based screen to understand this process.
RNA silencing in plants is associated with a signal that spreads from
cell-to-cell. To identify components required for spread of the RNA
silencing signal, Arabidopsis thaliana lines were generated in which an
inverted repeat transgene was expressed under the control of a
phloem-specific promoter. The silencing phenotype in these lines was
manifested as photobleaching in regions around the veins indicating that
a silencing signal had spread out of the phloem. After mutagenesis,
plants were identified that have decreased photobleaching, and
interestingly, some of these mutants have clear defects in organ shape
and body plan. These mutants may represent components required for
cell-to-cell signalling, that mediate mobile RNAs.
02 October 2007
Functional genomics of salinity tolerance in cereals
Professor Mark Tester
Australian Centre for Plant Functional Genetics, University of Adelaide
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14 June 2007
Plant glyoxalases: metal-dependent enzymes involved in stress responses
Renee Lee
University of Oxford
Glyoxalases form a two-step reaction pathway involved in the detoxification of methylglyoxal, a by-product of primary metabolism that can cause covalent modification of DNA, RNA and proteins. Analysis of genomic data suggests that plants contain three genes encoding the metalloenzyme glyoxalase I, whereas most organisms possess only a single gene for this enzyme. Using a combination of molecular techniques, I have investigated the localization, enzymatic properties and regulation of the three isoforms of glyoxalase I found in Arabidopsis thaliana to investigate their evolutionary origins and biochemical functions.
LOCAL HEROES SEMINAR
14 June 2007
Patterns of cell division in the Selaginella meristem
Dr Jill Harrison
University of Oxford
The transition of plants from water to land necessitated major morphological innovations that were accompanied by the development of three-dimensional apical growth. In different land plant lineages, meristems function in different ways to produce distinct plant morphologies, yet our understanding of the developmental basis of meristem function is limited to angiosperms. To redress this balance, we have examined meristem function in the lycophyte Selaginella kraussiana using a cell lineage analysis. I will present the results obtained and discuss aspects of interest.
LOCAL HEROES SEMINAR
07 June 2007
The genetic architecture of introgression and reproductive isolation in Louisiana irises
Professor Mike Arnold
University of Georgia, Athens, USA
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31 May 2007
Cell fate specification in the root epidermis of Arabidopsis
Dr Silvia Costa
WellcomeTrust Biocentre, University of Dundee
In the root epidermis of Arabidopsis cells differentiate in alternating
files of hair and non-hair cells in response to positional information.
I will illustrate how root epidermal patterning is established during
embryogenesis and propagated in the seedling where higher order
chromatin organization is required to control position-dependent cell
fate specification.
24 May 2007
How will plants respond to global atmospheric change? From genes to fields
Professor Stephen P Long
University of Illinois at Urbana-Champaign, USA
none
27th BLACKMAN LECTURE
17 May 2007
Plants in a Chemical World
Professor Rob Edwards
University of Durham
As part of their secondary metabolism, plants are able to biotransform a diverse range of synthetic compounds (xenobiotics) which they encounter in the form of pollutants and agrochemicals. We have termed this detoxification system the ‘Xenome’ and are interested in its regulation and component enzymes and their roles in both xenobiotic and endogenous metabolism. Using a combination of work in model systems (Arabidopsis), crops and weeds we have identified and functionally characterised enzymes involved in both the bioactivation and inactivation of pesticides and recent progress in these studies and their potential significance will be presented.
10 May 2007
The secret life of mitochondria
Dr Nick Lane
Royal Free & University College Medical School, London
Mitochondria are often seen as little more than the 'powerhouses' of complex
eukaryotic cells - fascinating, certainly, but offering few insights into
the broader themes of life and evolution. Yet mitochondria are implicated in
the origin of the eukaryotic cell, in the evolution of two sexes, in
apoptosis, and in ageing and disease. The key to all these disparate fields
is the continued existance of mitochondrial genes, long considered merely a
frozen accident. But what if a core of mitochondrial genes is needed to
retain control of cellular respiration? I shall argue that the need for two
genomes to coadapt to each other in every cell is behind some of the biggest
themes in biology.
26 April 2007
The evolution of life-history decisions in the real world
Professor Mark Rees
University of Sheffield
Models for the evolution of life history decisions often assume all individuals are the same, the environment does not vary in either time or space, there is no limit to population size and that maximising simple measures of population growth allow the best life history strategy to be determined. In this seminar I will discuss how these unrealistic assumptions can be relaxed, and illustrate the ideas using several long term field studies of monocarpic plants.
08 March 2007
Sexual system evolution in Acer: the big picture
Professor Susanne Renner
Ludwig Maximilians University, Munich, Germany
to follow
01 March 2007
Tales of sex and spite, mainly amongst plants
Dr John Pannell
University of Oxford
Evolutionary transitions between combined (hermaphrodites) versus separate sexes (males or females) have occurred numerous times in both plants and animals. In this seminar, I will review what we know about these transitions, drawing particular attention to pathways in which males occur with hermaphrodites. Theory predicts that males and hermaphrodites should be difficult to maintain together, but the polymorphism is found in several species of plants and animals. I will describe recent studies of these species that highlight the importance of density-dependent mating, extinction-colonisation dynamics, sex-chromosome evolution, differences in gender between fathers and grandfathers, and the possible evolution of spiteful behaviour during mating.
22 February 2007
Making reproductive organs: the past and present of floral homeotic genes
Professor Brendan Davies
University of Leeds
Male and female reproductive organs form at the centre of flowers. The genes that dictate which organ forms where in the flower have been identified in a wide range of species and been found to mainly encode a specific type of transcription factor called MADS-box factors. Plants have many MADS-box factors, encoded by a large family of genes. The proliferation of MADS-box genes in plants, by gene duplication and subsequent modification, has allowed plants to use MADS-box genes to control many different aspects of their development. We compared the genes that surround the MADS-box genes that control reproductive organ development in two different plant species, as a sequence-independent way to trace their evolutionary history through gene duplication. Surprisingly, the genes that end up primarily dictating organ identity in plants today are not necessarily direct descendants of the same duplicated gene. We can use the differences that have accumulated since duplication to pinpoint the precise regions of these homeotic proteins that direct the formation of male reproductive organs or female reproductive organs.
15 February 2007
Sympatric speciation in Plants
Dr Vincent Savolainen
Royal Botanic Gardens, Kew
The origin of species diversity has challenged biologists for over two
centuries. Allopatric speciation, the divergence of species resulting
from geographical isolation, is well documented. However, sympatric
speciation, divergence without geographical isolation, is highly
controversial. Claims of sympatric speciation must demonstrate species
sympatry, sister relationships, reproductive isolation, and that an
earlier allopatric phase is highly unlikely. Here we provide clear
support for sympatric speciation in a case study of two species of palm
(Arecaceae) on an oceanic island. This case study of sympatric
speciation in plants provides an opportunity for refining theoretical
models on the origin of species, and new impetus for exploring putative
plant and animal examples on oceanic islands.
08 February 2007
Infection and symbiotic nodulation of legumes by Beta-rhizobia
Dr Euan K. James
University of Dundee
It is now well established that many species and strains in the large genus Burkholderia (formerly Pseudomonas) in the Beta-proteobacteria have the ability to fix nitrogen in free-living culture, particularly those that are associated with (mainly tropical) gramineous plants. Many Burkholderia strains have also been found within nodules of tropical legumes, particularly in those on Mimosa spp. These Burkholderia strains possess nod genes similar to those in Alpha-rhizobia (ie. Rhizobium and related genera in the Alpha-Proteobacteria) and, along with strains of a newly-described species of Ralstonia, R. taiwanensis (now renamed Cupriavidus taiwanensis), are collectively termed “Beta-rhizobia”. Recent studies with strains from South America and Taiwan have confirmed that both C. taiwanensis and Burkholderia Beta-rhizobia are effective symbionts of Mimosa, but so far there has been little evidence of effective nodulation in other plant genera. We present evidence for symbiotic nodulation of Mimosa and other Mimosoid genera (Acacia, Calliandra, Leucaena, Piptadenia, Pithecellobium) by Burkholderia phymatum STM815, and for effective nodulation of the South African Papilionoid genus Cyclopia by B. tuberum STM678. In addition, evidence is presented for nodulation of Mimosa spp. by “conventional” Alpha-rhizobia (mainly Rhizobium strains), but also that Burkholderia strains will out-compete both Alpha-rhizobia and Cupriavidus strains for nodulation of invasive Mimosa spp.
25 January 2007
Using C3 species to provide insight into the evolution of C4 photosynthesis
Dr Julian Hibberd
University of Cambridge
Between 12 and 6 million years ago C4 photosynthesis evolved at least forty-four times independently within the angiosperms. Despite its polyphyletic evolution, alterations to cell biology, leaf development and biochemistry are needed for the pathway to operate. The high growth rates of C4 compared to C3 species means that understanding the C4 pathway is likely to be of importance for future BioEnergy and food needs. I will discuss recent advances in the regulation of genes important for the C4 pathway.
25 January 2007
Using C3 species to provide insight into the evolution of C4 photosynthesis
Dr Julian Hibberd
University of Cambridge
Between 12 and 6 million years ago C4 photosynthesis evolved at least forty-four times independently within the angiosperms. Despite its polyphyletic evolution, alterations to cell biology, leaf development and biochemistry are needed for the pathway to operate. The high growth rates of C4 compared to C3 species means that understanding the C4 pathway is likely to be of importance for future BioEnergy and food needs. I will discuss recent advances in the regulation of genes important for the C4 pathway.
30 November 2006
Structure and function of phototropin receptor kinases
Dr John Christie
University of Glasgow
Phototropins are blue-light receptors controlling a range of responses that serve to optimize the photosynthetic efficiency of plants. These include phototropism, light-induced stomatal opening and chloroplast movements in response to changes in light intensity. Since the isolation of the Arabidopsis PHOT1 gene in 1997, phototropins have been identified in ferns and mosses where their physiological functions appear to be conserved. Arabidopsis contains two phototropins, phot1 and phot2 that exhibit overlapping functions in addition to having unique physiological roles. Phototropins are light-activated serine/threonine protein kinases. Light sensing by the phototropins is mediated by a repeated motif at the N-terminal region of the protein known as the LOV domain. Photoexcitation of the LOV domain results in receptor autophosphorylation and an initiation of phototropin signaling. Here we summarize the photochemical and biochemical events underlying phototropin activation in addition to the current knowledge of the molecular mechanisms associated with photoreceptor signaling.
30 November 2006
Structure and function of phototropin receptor kinases
Dr John Christie
University of Glasgow
Phototropins are blue-light receptors controlling a range of responses that serve to optimize the photosynthetic efficiency of plants. These include phototropism, light-induced stomatal opening and chloroplast movements in response to changes in light intensity. Since the isolation of the Arabidopsis PHOT1 gene in 1997, phototropins have been identified in ferns and mosses where their physiological functions appear to be conserved. Arabidopsis contains two phototropins, phot1 and phot2 that exhibit overlapping functions in addition to having unique physiological roles. Phototropins are light-activated serine/threonine protein kinases. Light sensing by the phototropins is mediated by a repeated motif at the N-terminal region of the protein known as the LOV domain. Photoexcitation of the LOV domain results in receptor autophosphorylation and an initiation of phototropin signaling. Here we summarize the photochemical and biochemical events underlying phototropin activation in addition to the current knowledge of the molecular mechanisms associated with photoreceptor signaling.
23 November 2006
The invasion of the land: challenges for plants and people
Professor Dianne Edwards
University of Cardiff
The challenges faced by pioneering land plants centred on survival in water
stressed environments and exploitation of a range of new habitats. They were
overcome by changes in morphology/anatomy, chemistry, physiology, reproductive
biology and life history. These adaptations will be briefly surveyed, but with
an emphasis on the pre-tracheophyte era, when major challenges for people are to
interpret a very sparse fossil record based on spores in terms of the nature and
affinities of the producers. This theme of interrogation of the record in terms
of its completeness and biases will be further explored by reference to the
inferred ecophysiology of the Rhynie Chert plants and yet further speculation on
the habitats and 'habits' of the postulated giant fungus, Prototaxites.
23 November 2006
The invasion of the land: challenges for plants and people
Professor Dianne Edwards
University of Cardiff
The challenges faced by pioneering land plants centred on survival in water
stressed environments and exploitation of a range of new habitats. They were
overcome by changes in morphology/anatomy, chemistry, physiology, reproductive
biology and life history. These adaptations will be briefly surveyed, but with
an emphasis on the pre-tracheophyte era, when major challenges for people are to
interpret a very sparse fossil record based on spores in terms of the nature and
affinities of the producers. This theme of interrogation of the record in terms
of its completeness and biases will be further explored by reference to the
inferred ecophysiology of the Rhynie Chert plants and yet further speculation on
the habitats and 'habits' of the postulated giant fungus, Prototaxites.
16 November 2006
Berries, bees and weevils: studies of gender and sexual dimorphism in a wild strawberry
Dr Tia-Lynne Ashman
University of Pittsburgh
While researchers agree that the abiotic environmental context can be instrumental in plant sexual system evolution, few have considered the enemy dimension of the environment (e.g., herbivores, pathogens). This is in spite of the fact that antagonists can alter plant-pollinator interactions and plant-antagonist) interactions and can be profoundly male-biased in gender dimorphic species. In this talk I will explore whether interactions with enemies hold the key to why traditional explanations for breeding system variation sometimes fall short. I will describe recent work on the impact of a flower clipping herbivore (Anthonomous sigtnatus) on the evolution of dioecy and sexual dimorphism in a gynodioecious wild strawberry (Fragaria virginiana). In particular, I will describe how florivory alters mating system, sex allocation, pollen limitation, and selection through male and female fertility. Ultimately, I aim to expand our understanding of the environmental context for the evolution of dioecy and sexual dimorphism beyond abiotic attributes and mutualists to include enemies.
09 November 2006
The evolution of sexual dimorphism in flowering plants
Mark Harris
University of Oxford
The South African Leucadendron genus includes some of the most sexually dimorphic species in the world, with males being more highly branched and possessing smaller leaves than females. Two hypotheses have been proposed to explain the evolution of such dimorphism. First, competition between males for pollinators may select for increased branching, as this allows the plants to support a greater number of inflorescences for pollinator attraction. Second, the production and maintenance of seeds in cones may select for reduced branching in females, as branching reduces stem width and thus the capacity to transplant water effectively. We conducted comparative and physiological analyses to test these two hypotheses. Species in which females maintained seeds in cones for several years were more dimorphic than those that did not maintain cones, supporting the water-limitation hypothesis, whereas there was only limited support for the pollination-limitation hypothesis. The water-limitation hypothesis is also supported by physiological data that show greater water stress in highly branched plants and phenotypic plasticity whereby individuals adjust the degree of branching in response to water availability.
Local Heroes Seminar
09 November 2006
Epigenetic asymmetry in plant gametes
Dr Jose Gutierrez-Marcos
University of Oxford
Plants differ from animals in their continuous development, flexible and reversible differentiation, the absence of a germline, and the alternation of haploid and diploid generations. Despite these differences, both plants and animals have evolved complex mechanisms that act to ensure successful reproduction and, after fertilization, cause parent of origin and chromosome dosage effects for specific genes. However, only the endosperm component of the seed in plants is regulated in such a manner, while the embryo can escape such surveillance. In this talk I will describe how epigenetic information present in plant gametes are responsible for parent of origin effects during endosperm development and might provide the basis for the distinct developmental pathways followed by the embryo and endosperm within the plant seed.
Local Heroes Seminar
02 November 2006
Signalling in symbiosis
Dr Giles Oldroyd
John Innes Centre, Norwich
The legume/rhizobial symbiosis that results in the induction of nodule development requires the bacterial signalling molecule Nod factor. Repetitive oscillations in cytosolic calcium in root hair cells are one of the earliest plant responses to Nod factor. Mutations in DMI3 block all Nod factor responses except calcium spiking, indicating that this protein functions in the perception of calcium spiking and in support of this we have shown that DMI3 encodes a chimeric calcium/calmodulin dependent protein kinase. Gain of function mutations in DMI3 activate the expression of nodulation nodulation without the need for Nod factor or rhizobial elicitation. This gain of function requires the activity of NSP1 and NSP2, both of which encode putative transcriptional regulators in the GRAS family. Proteins in the GRAS family are proposed to function in transcriptional regulation, however, their mechanism of action is unknown. It seems clear that GRAS family proteins do not have DNA binding activity. However, when we fuse NSP1 or NSP2 to the Gal4 DNA binding domain we see constitutive activation of the Gal4 system in yeast. Mutations that abolish NSP2 activity in planta also abolish this induction of gene expression in yeast indicating a relevance for these observations in the native activity of the protein. This work indicates that when brought to promoters NSP1 and NSP2 can activate RNA polymerase. This indicates the necessity for a DNA binding protein in the Nod factor signalling pathway. We have recently identified a transcription factor with a conserved DNA binding domain that is essential for Nod factor signalling. This protein is a good candidate for interacting with the GRAS proteins to allow induction of transcription at the nodulin promoters. We propose that calcium oscillations that occur in both the cytosol and the nucleus regulate the DMI3 kinase through a combination of calcium and calmodulin binding. DMI3 activates downstream components, including the transcriptional regulators NSP1 and NSP2 that coordinate Nod factor induced gene expression through this new transcription factor.
26 October 2006
Control of plant development by Polycomb-group genes
Dr Justin Goodrich
University of Edinburgh
In plants, genetic studies have shown that Polycomb-group genes (Pc-G) control key developmental transitions including seed formation, vernalization response and floral patterning. In animals, the Pc-G mediate cell fate determination by switching homeotic selector genes off in a stable, epigenetic fashion. However, cell fate is relatively labile in plants, suggesting either that Pc-G genes regulate relatively few targets, or that epigenetic changes in gene activity are more easily reversed. To address this, we have been using chromatin immunoprecipitation (ChIP) to determine the target genes for the Pc-G in plants and to characterise the changes that occur when targets are silenced. I will present our preliminary results from using whole genome approaches, and also results to indicate novel roles for Pc-G in controlling flowering.
19 October 2006
Agribiotics Inc: an example of modern microbiology - taking research through patents to commercialization
Alison McIver
Agribiotics Inc, Cambridge, Ontario
Alison McIver read Biochemistry in Oxford. In 1997, she and her sister founded Agribiotics, an agribiotech company, in the basement of their family home in Ontario, Canada. Initially the company focused on manufacturing high quality rhizobia bacterial cultures to increase crop yields for legume farmers. Over the nine years of the company's existence, however, the sisters made a strategic decision to plough much of the profits back into increasing the research focus of the business to support their vision of becoming the leading researcher, developer, manufacturer and marketer of microbial and microbial-based products to enhance the yields of global agricultural and horticultural crops. In March 2006, this dedication to research, and the exciting product pipeline that it had produced caused Merck KGgA to purchase the company, in their effort to gain an advantage in the rapidly expanding agribiotech market.
In this presentation, Alison will provide an overview of the patented areas of research that the company was involved in and some of the opportunities that she sees for future development in this dynamic business sector. She will also provide some insight into the trials and tribulations of running a rapidly growing organization, trying to balance a long-term strategic research focus with day-to-day operational needs.
12 October 2006
Vitamin B12 in algae: acquisition, role and regulation of gene expression
Dr Alison G Smith
University of Cambridge
Vitamin B12 in algae: acquisition, role and regulation of gene expression"
Higher plants do not contain vitamin B12 (cobalamin), so strict vegetarians must ensure that they get an adequate supply in their diet. Seaweed is often recommended as a good dietary source of the vitamin, suggesting that these macroalgae can synthesise cobalamin. However, we have found that the cobalamin biosynthetic pathway is absent from the algal kingdom, and that instead that more than half of all algal species require it for growth, so in this respect they are like animals. We have used genome sequence information to establish the reason for this auxotrophy, which is as a cofactor for methionine synthase. The source of cobalamin is bacteria, which appear to live in symbiosis with the algae, gaining fixed carbon in return for the vitamin. We are now beginning to dissect this interaction at the molecular level.
Croft et al (2005) "Algae acquire vitamin B12 a through symbiotic relationship with bacteria" Nature 438: 90-93