|Primary Supervisor:||Professor Vincent Moulton (School of Computing)|
|Secondary Supervisors:||Dr Tamas Dalmay (School of Biological Sciences)|
|Dr Thomas Mock|
I have been interested in the field of Computational Biology since my degree in Applied Computer Science with Ecology, at the University of East Anglia. The degree included a third year project on simulating the evolution of a plant population. I followed this with a Masters in Computational Biology, which concluded with a project analysing the quality of automatic gene annotations. My PhD is focused on investigating the presense and evolutionary relationships of small RNAs within two different diatoms: Thalossiosira pseudonana & Fragilariopsis cylindrus, and a Coccolithophore, Emiliania huxelyi.
Small RNA Analysis; Microalgae genomics; Molecular evolution.
I obtained my undergraduate degree in Molecular Biology and Genetics at the University of East Anglia. During my degree, I became interested in molecular microbiology and did my PhD on the molecular genetic aspects of iron uptake in the nitrogen-fixing bacterium Rhizobium leguminosarum, in Professor Andrew (Andy) Johnston's group in the School of Biological Sciences at the University of East Anglia. Since completing my PhD, my post-doctoral research has been focussed on the molecular and biochemical analysis of the genes and proteins involved in the bacterial catabolism of dimethylsulphoniopropionate (DMSP) and production of dimethyl sulphide (DMS). DMS is an influential marine gas, with a key role in the marine sulphur cycle and potentially in climate control, through its effect on cloud formation. My current project, working in the groups of Dr Jonathan Todd and Dr Thomas Mock, is to investigate the pathway for DMSP synthesis in marine diatoms. This should allow us to identify the genes required for DMSP synthesis and the function of DMSP in this important group of marine phytoplankton, and possibly in other DMSP-producing organisms.
- Todd, J.D., Curson, A.R.J., Sullivan, M.J., Kirkwood, M., and Johnston, A.W.B. (2012) The Ruegeria pomeroyi acuI gene has a role in DMSP catabolism and resembles yhdH of E. coli and other bacteria in conferring resistance to acrylate. PLoS One. (DOI: 10.1371/journal.pone.0035947)
- Curson, A.R.J., Fowler, E.K., Dickens, S., Johnston, A.W.B., and Todd, J.D. (2012) Multiple DMSP lyases in the gamma-proteobacterium Oceanimonas doudoroffii. Biogeochemistry. (DOI: 10.1007/s10533-011-9663-2)
- Sun, L., Curson, A.R.J., Todd, J.D., and Johnston, A.W.B. (2012) Diversity of DMSP transport in marine bacteria, revealed by genetic analyses. Biogeochemistry. (DOI: 10.1007/s10533-011-9666-z)
- Curson, A.R.J., Todd, J.D., Sullivan, M.J., and Johnston, A.W.B. (2011) Catabolism of dimethylsulphoniopropionate: microorganisms, enzymes and genes. Nat Rev Microbiol. (DOI: 10.1038/nrmicro2653)
- Curson, A.R.J., Sullivan, M.J., Todd, J.D., and Johnston, A.W.B. (2011) DddY, a periplasmic dimethylsulfoniopropionate lyase found in taxonomically diverse species of Proteobacteria. Isme J. (DOI: 10.1038/ismej.2010.203)
- Todd, J.D., Curson, A.R.J., Kirkwood, M., Sullivan, M.J., Green, R.T., and Johnston, A.W.B. (2011) DddQ, a novel, cupin-containing, dimethylsulfoniopropionate lyase in marine roseobacters and in uncultured marine bacteria. Environ Microbiol. (DOI: 10.1111/j.1462-2920.2010.02348.x)
- Sullivan, M.J., Curson, A.R.J., Shearer, N., Todd, J.D., Green, R.T., and Johnston, A.W.B. (2011) Unusual regulation of a leaderless operon involved in the catabolism of dimethylsulfoniopropionate in Rhodobacter sphaeroides. PLoS One. (DOI: 10.1371/journal.pone.0015972)
- Todd, J.D., Curson, A.R.J., Nikolaidou-Katsaraidou, N., Brearley, C.A., Watmough, N.J., Chan, Y., Page, P.C., Sun, L., and Johnston, A.W.B. (2010) Molecular dissection of bacterial acrylate catabolism-unexpected links with dimethylsulfoniopropionate catabolism and dimethyl sulfide production. Environ Microbiol 12: 327-343.
- Curson, A.R.J., Sullivan, M.J., Todd, J.D., and Johnston, A.W.B. (2010) Identification of genes for dimethyl sulfide production in bacteria in the gut of Atlantic Herring (Clupea harengus). Isme J 4: 144-146.
- Todd, J.D., Curson, A.R.J., Dupont, C.L., Nicholson, P., and Johnston, A.W.B. (2009) The dddP gene, encoding a novel enzyme that converts dimethylsulfoniopropionate into dimethyl sulfide, is widespread in ocean metagenomes and marine bacteria and also occurs in some Ascomycete fungi. Environ Microbiol 11: 1376-1385.
- Curson, A.R.J., Rogers, R., Todd, J.D., Brearley, C.A., and Johnston, A.W.B. (2008) Molecular genetic analysis of a dimethylsulfoniopropionate lyase that liberates the climate-changing gas dimethyl sulfide in several marine alpha-proteobacteria and Rhodobacter sphaeroides. Environ Microbiol 10: 757-767.
- Johnston, A.W.B., Todd, J.D., Sun, L., Nikolaidou-Katsaridou, M.N., Curson, A.R.J., and Rogers, R. (2008) Molecular diversity of bacterial production of the climate-changing gas, dimethyl sulphide, a molecule that impinges on local and global symbioses. J Exp Bot 59: 1059-1067.
- Johnston, A.W.B., Todd, J.D., Curson, A.R.J., Lei, S., Nikolaidou-Katsaridou, N., Gelfand, M.S., and Rodionov, D.A. (2007) Living without Fur: the subtlety and complexity of iron-responsive gene regulation in the symbiotic bacterium Rhizobium and other alpha-proteobacteria. Biometals 20: 501-511.
- Todd, J.D., Rogers, R., Li, Y.G., Wexler, M., Bond, P.L., Sun, L., Curson, A.R.J., Malin, G., Steinke, M., and Johnston, A.W.B. (2007) Structural and regulatory genes required to make the gas dimethyl sulfide in bacteria. Science 315: 666-669.
- Rodionov, D.A., Gelfand, M.S., Todd, J.D., Curson, A.R.J., and Johnston, A.W.B. (2006) Computational reconstruction of iron- and manganese-responsive transcriptional networks in alpha-proteobacteria. PLoS Comput Biol 2: e163.
- Young, J.P., Crossman, L.C., Johnston, A.W.B., Thomson, N.R., Ghazoui, Z.F., Hull, K.H., Wexler, M., Curson, A.R.J., Todd, J.D., Poole, P.S. et al. (2006) The genome of Rhizobium leguminosarum has recognizable core and accessory components. Genome Biol 7: R34.
- Yeoman, K.H., Curson, A.R.J., Todd, J.D., Sawers, G., and Johnston, A.W.B. (2004) Evidence that the Rhizobium regulatory protein RirA binds to cis-acting iron-responsive operators (IROs) at promoters of some Fe-regulated genes. Microbiology 150: 4065-4074.
I obtained my degree in Biological Sciences at the University of Exeter, and my Ph.D., investigating the distribution and diversity of eukaryotic picophytoplankton using molecular techniques, at the University of Warwick (Group of Prof. David Scanlan). I have since worked, as a post-doctoral researcher, on the application of molecular techniques to DNA preserved in sediments, in order to characterise historic lake communities. Following this work, I was eager to move into the field of functional genetics. Understanding the genetic basis of diatoms' unique silica shell construction has great potential for explaining the evolutionary success of this hugely abundant and diverse group. Furthermore, this understanding may have significant application in nanotechnology. Knock-down of genes involved in making silica cell walls is expected to result in recognisable phenotypic differences between transformed and wild-type cell lines. Starting with a short-term EMBO fellowship in the laboratory of Dr. Angela Falciatore (Université Pierre et Marie Curie, Paris) to establish RNA interference mediated gene knock-down in Thalassiosira pseudonana, my project aims to characterise a suite of silica responsive genes whose function is currently unknown. This approach will reveal how these unique and intricate shell structures are formed..
- Kirkham A.R., Lepère C., Jardillier L.E. Not F., Bouman H., Mead A., Scanlan D.J. (2013). A global perspective on marine photosynthetic picoeukaryote community structure. ISME J. (DOI: 10.1038/ismej.2012.166)
- Domaizon I., Lepère C., Debroas D., Bouvy M, Ghiglione J.F., Jacquet S., Bettarel Y., Bouvier C., Torréton J.P., Vidussi F., Mostajir B., Kirkham A., LeFloc'h A., Fouilland E., Montanié H. and Bouvier T. (2012). Short-term responses of unicellular planktonic eukaryotes to increases in temperature and UVB radiation. BMC Microbiology (DOI: 10.1186/1471-2180-12-202)
- Mock T., and Kirkham A. (2011). What can we learn from genomics approaches in marine ecology? From sequences to eco-systems biology! Marine Ecology (DOI: 10.1111/j.1439-0485.2011.00479.x)
- Kirkham A.R., Jardillier L.E., Holland R., Zubkov M.V., Scanlan D.J. (2011). Analysis of photosynthetic picoeukaryote community structure along an extended Ellett Line transect in the northern North Atlantic reveals a dominance of novel prymnesiophyte and prasinophyte phylotypes. Deep-Sea Res Pt I. (DOI: 10.1016/j.dsr.2011.05.004)
- Kirkham A.R., Jardillier L.E., Tiganescu A., Pearman J., Zubkov M.V., Scanlan D.J. (2011). Basin-scale distribution patterns of photosynthetic picoeukaryote along an Atlantic Meridional Transect. Environ Microbiol. (DOI: 10.1111/j.1462-2920.2010.02403.x)
- Guillou L., Viprey M., Chambouvet A., Welsh R.M., Kirkham A.R., Massana R., Scanlan D.J., Worden A.Z. (2008). Widespread occurrence and genetic diversity of marine parasitoids belonging to Syndiniales (Alveolata). Environ Microbiol. (DOI: 10.1111/j.1462-2920.2008.01731.x)
I obtained my Bachelor of Sciences degree at Arizona State University and afterwards worked for the U.S. National Ocean Services in Charleston, South Carolina, on a highly collaborative marine mammal health assessment project where I helped examine antibiotic resistance in bottlenose dolphin populations. When I returned to school to obtain my PhD in molecular and cellular biology in the Marine Biomedicine & Environmental Sciences program at the Medical University in South Carolina I began my studies on eukaryotic phytoplankton physiology. I obtained my degree in the labs of Drs. Jack DiTullio and Micheal Janech studying the sea-ice diatom Fragilariopsis cylindrus. Sea-ice algae thrive under extreme conditions, overcoming freezing temperatures that form internal ice crystals, shut-down metabolic activity, and create cell-wide oxidative stress in most organisms; but they also synthesize a sulfur compound, DMSP, that is believed to help mitigate cellular damage through its proposed antioxidant, antifreeze, and salt buffering properties. Other marine algae and salt tolerant plants also produce large amounts of this potentially important anti-stress compound which has more than 10 proposed physiologically functions. To date, the specific enzymes controlling DMSP synthesis remain unknown which prevents studies to determine the exact function(s) of DMSP production. To overcome this critical gap in knowledge protein changes associated with DMSP increases were examined in sea-ice algae and advanced protein identification techniques were used to identify candidate DMSP synthesis genes. Molecular genetic techniques are now being applied to confirm their role in DMSP synthesis and finally provide unequivocal evidence for the physiological functions of DMSP. Furthermore, algal DMSP production has global impacts on climate and biogeochemical cycles so understanding biological production is fundamental to understanding and predicting climate and biogeochemical cycles.
Fellow of Higher Education Academy
I obtained my diploma degree (1998) in Biology with emphasis on Biological Oceanography at the Christian-Albrechts University in Kiel and the PhD (2003) at Bremen University (Alfred-Wegener Institute for Polar and Marine Research), Germany. Before joining the University of East Anglia (UEA) in 2007, most of my PostDoc research was conducted with a fellowship from the (DAAD) in the School of Oceanography, University of Washington (EV Armbrust lab) in joint cooperation with the Biotechnology Center, University of Wisconsin (MR Sussman lab), USA. Before I was promoted to Reader in 2012, I had a Research Councils UK (RCUK) Academic Fellowship (2007-2012). I am a member of several genome and metagenome projects with marine microalgae (e.g. diatoms) and bacteria and conducted transcriptome analysis with diatoms using microarrays and expressed sequence tags (ESTs) in order to find the molecular basis of adaptation to environmental conditions. A crucial part of this research is the identification of metabolic pathways (e.g carbon fixation, silicon bioprocesses in diatoms) and their key regulatory components (e.g. DNA-binding proteins) to find mechanisms on how these organisms sense changes in environmental conditions. This fundamental knowledge about microbes from the upper ocean will help to interpret future responses to global change.
Environmental and functional genomics of marine microbial organisms; metagenomics of the upper ocean; physiological adaptation; diatom biology; photosynthesis; polar biology; biochemistry; biological oceanography.
|Primary Supervisor:||Dr Jonathan Todd (School of Biological Sciences)|
|Secondary Supervisor:||Dr Thomas Mock|
I obtained a first class degree in Analytical Sciences from the University of Coventry. During these studies I concentrated on environmental and industrial chemistry. I am currently a second year PhD student at the University of East Anglia under the supervision of Dr Jonathan Todd and Dr Thomas Mock. My PhD project is focused on the application of molecular genetics and biochemistry to study enzymes known generically as "DMSP lyases" that exist within marine bacteria and the coccolithophore Emiliania huxleyi. These DMSP lyases function to cleave the abundant algal sulfonium osmolyte dimethylsulfoniopropionate (DMSP) generating the volitile dimethysulfide (DMS). The gaseous product of this reaction has important roles in the global sulfur cycle, chemoattraction in organisms ranging from bacteria to penguins and potentially in regulating both the local and global climate.
|Primary Supervisor:||Dr Thomas Mock|
|Secondary Supervisors:||Dr Cock van Oosterhout (School of Environmental Sciences)|
|Professor Vincent Moulton (School of Computing)|
I studied at Oradea University in Romania where I also received my Bachelor's (2003) and Master's degree (2008). Until now, I have been involved in monitoring heron colonies (Fam. Ardeidae) in Arad and Bihor county, Romania, my thesis aimed at filling a gap existing in the field of herons' research since the seventies. The purpose of my Master's Degree thesis was to analyze the trophic spectrum of a Triturus cristatus population from a severely affected habitat by human activity. I have an analytical mind and enjoy logical challenges since I graduated a Mathematics and Computer studies. In my opinion constant improvement is part of life. I was raised to walk with open eyes and an open mind and I would like to pass on the same approach. My PhD thesis is focused on identifying the molecular underpinnings of bloom formation in marine diatoms, particularly in Thalossiosira pseudonana.
Algal genomics and proteomics, ecology, studying variations that can occur in aquatic trophic chains.
|Primary Supervisor:||Dr Thomas Mock|
|Secondary Supervisor:||Professor Vincent Moulton (School of Computing)|
I obtained a degree in marine biology from the University of Groningen where I was working on different projects ranging from marine viruses, organic matter fluxes and anti-freeze proteins in polar diatoms. During my undergraduate and graduate studies I develop a high interest in marine phytoplankton with focus on diatoms. Therefore I chose a PhD project that reflects my research interest. My project is called Sea of Change and will focus on eukaryotic phytoplankton, mainly diatoms and their diversity and activity in the polar ocean. For this, samples have been taken a long a temperature gradient onboard the Polarstern, a German research vessel. From these samples we will isolate and sequence the RNA as well as DNA. The gained metagenom and –transcriptom data will later be correlated to abiotic factors.
- Medlin, L. K., Schmidt, K. (2010). Molecular probes improve the taxonomic resolution of Cryptophyte abundance in Arcachon Bay, France. Vie et Milieu [Life and Environment]
|Primary Supervisor:||Dr Thomas Mock|
|Secondary Supervisor:||Dr Gill Malin (School of Environmental Sciences)|
I did my degree in biology majoring in Biological Oceanography at the University of Rostock, Germany. During my studies I developed a high interest in the science at the interface of genomics and marine ecology. Before coming to the University of East Anglia (UEA) I did my MSc thesis research at the Alfred-Wegener Institute for Polar and Marine Research in Bremerhaven, Germany (AWI). For my thesis research I worked on the development of a genetic transformation system for the marine microalga Emiliania huxleyi gaining experience with reverse genetic tools. I will use my previous experience in my ongoing PhD project, focusing on the polar diatom Fragilariopsis cylindrus to study its genome and transcriptome.
Algal genomics; environmental and functional genomics; microalgae virus interactions; physiological adaptation to low temperature and nutrients; polar biology; sea ice ecology; biological oceanography.
|Primary Supervisor:||Professor Vincent Moulton (School of Computing)|
|Secondary Supervisor:||Dr Thomas Mock|
My degree in Software Engineering at UWE Bristol focused on Object Oriented design and programming in Java. My main interests lay in Computer Science topics, particularly machine learning, which was the focus of my final year project. My PhD is focused on a computational analysis of marine eukaryote metatranscriptome data using Perl and published bioinformatics tools to develop an analysis pipeline. I am also involved in the assembly of Emiliania huxleyi RCC1217 genome underway at The BBSRC Genome Analysis Centre (TGAC) in Norwich.
Eukaryotic marine metatranscriptomics; genome assembly; high-throughput sequencing.
Before my PhD I obtained a BSc in Biochemistry and MRes in Systems & Synthetic Biology at Imperial College London, which sparked my interest in using a systematic rational approach to biological engineering in order to carry out projects with "real-world" applications. My PhD research, carried out at Rothamsted Research in collaboration with UEA under the supervision of Professor Johnathan Napier, Dr. Olga Sayanova (Rothamsted Research) and Dr Thomas Mock, is based on using such an approach combined with metabolic engineering to enhance the production of omega-3 polyunsaturated fatty acids in marine microbes, which are the primary producers of omega-3 fatty acids (FAs). Omega-3 FAs are vital to human health, and the project aims to find a sustainable way to produce a high level of these, along the way learning more about the molecular biology of diatoms and developing tools in which to work with them.