Dr Andrew Toseland
Senior Research Associate
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.
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. I am currently a PhD candidate investigating the physiological and molecular long-term thermal adaptation mechanisms of two model diatoms with relations to ocean warming and climate change.
In addition to work completed as part of my PhD project, I am also participating in an international metatranscriptome and –genome project investigating phytoplankton diversity and function in the Atlantic Ocean. For this, samples have been taken a long a temperature gradient onboard the Polarstern, a German research vessel. From these samples RNA and DNA has been isolated and is getting sequenced at the Joint Genome Insitute (USA). The gained metagenom and –transcriptom data will later be correlated to abiotic factors.
Experimental evolution; phytoplankton physiology and ecology; ocean warming; algal genomics; biological oceanography.
- Jahn, M.T., Schmidt, K. , and Mock, T. (2014) A novel cost effective and high-throughput isolation and identification method for marine microalgae. Plant Methods
- Passow, U., De La Rocha, C.L., Fairfield, C. and Schmidt, K. (2014) Aggregation as a function of and mineral particles. ASLO.
- Schmidt, K. De La Rocha, C.L., Gallinari, M., and Cortses, G. (2014) Not all calcite ballast is created equal: differing effects of foraminiferan and coccolith calcite on the formation and sinking of aggregates.Biogeosciences.
- Medlin, L. K., and Schmidt, K. (2010) Molecular probes improve the taxonomic resolution of Cryptophyte abundance in Arcachon Bay, France. Vie et Milieu [Life and Environment]
I received both my Bachelor's degree (2003) and Master's degree (2008) at the University of Oradea in Romania. n order to satisfy my innate curiosity for the surrounding world, I studied Biology and Chemistry at Bachelor's level and Ecology at Master's level preceded by studies in Mathematics-Information Technology at high-school level.
I am currently a third year PhD research student. My research project is focused on identifying the molecular underpinnings of bloom formation in marine diatoms. Diatoms often dominate phytoplankton communities by forming seasonal blooms in coastal upwelling zones. However, understanding of the molecular underpinning for diatoms ability to dominate these waters is less known.
My project's purpose is to investigate cell cycle regulatory components with emphasis on a DNA-binding protein which seems to induce faster growth in the diatom Thalossiosira pseudonana. In order to provide a better understanding of these cell cycle components, I examine transformants that either overexpress or knock-down the gene involved in expressing the protein of interest. I combine genomics, biochemical and bioinformatics approaches with the aim of elucidating the genomic binding sites of different transcription factors that are involved in faster growth in response to environmental stresses and epigenetics related connections in diatoms.
Algal genomics and proteomics, ecology, aquatic trophic chains, bioinformatics.
Dr Andrew Curson
Senior Research Associate
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 Professor 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.
- Curson, A.R.J., Burns, O.J. Voget, S., Daniel, R., Todd, J.D., McInnis, K., Wexler, M., and Johnston, A.W.B (2015) Screening of Metagenomic and Genomic Libraries Reveals Three Classes of Bacterial Enzymes That Overcome the Toxicity of Acrylate. PLoS One.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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
- 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.
- 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.
- 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.
- 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
Dr Amy Kirkham
Post Doctoral Researcher
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., and Scanlan D.J. (2013) A global perspective on marine photosynthetic picoeukaryote community structure. ISME J.
- 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
- Mock T., and Kirkham A. (2011). What can we learn from genomics approaches in marine ecology? From sequences to eco-systems biology! Marine Ecology
- 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.
- 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.
- 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.
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 Professor 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.
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 Professor 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.
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 Bachelors degree in Biological Sciences from the University of Heidelberg, Germany. During that time I did an exchange year to Canada, where I wrote my Bachelor thesis under supervision of Prof. Dr. Jonathan Newman (Canada) and Prof. Dr. Ursula Kummer (Germany). I created a mathematical model including the interactions between the fungus Neotyphodium coenophialum with the grass Schedonorus arundinaceus. With the help of the model, I worked on identifying costs and benefits of the fungus to know more about this mutualistic symbiosis.
I have always had a broad interest in system biology, biochemistry and also ecology, especially when it comes to interactions and feedbacks between the biotic and abiotic environment. In order to gain a more systematic and global viewpoint on interactions, I started my master degree in climate change at the University of East Anglia. This sparked my interest in studying the molecular biology of diatoms, which play a crucial role in the wider climate system. For my Masters thesis in the Mock-Lab, I will therefore try to make the method of ribosome profiling applicable to diatoms, in order to learn more about their adaptation to different environments by observing their gene regulation on a translational level.
Dr Jan Strauss
Senior Research Associate [Project Outline]
I obtained a German diploma degree in Biological Sciences (2008) from the University of Rostock, Germany, and a Ph.D. (2013) from the University of East Anglia (UEA), Norwich, UK, investigating the genome and transcriptome of the sea ice microalga Fragilariopsis cylindrus. During my studies I developed a high interest in the science at the interface of genetics and biological oceanography and my research interest is in the unique and diverse biology of globally important marine microalgae (phytoplankton). I am applying genomics-enabled tools (e.g. genome and transcriptome sequencing, RNA-seq, qRT-PCR, genetic transformation) in combination with biochemical approaches (e.g. Western blot, protein assays) to understand the biology of marine phytoplankton and elucidate the molecular underpinnings of their adaptation to marine environments. Since finishing my Ph.D., I have been working, as a research technician, on investigating the physiological role of the abundant sulfur compound dimethylsulfoniopropionate (DMSP) in marine phytoplankton. In my current research, as postdoctoral fellow at the School of Environmental Sciences at UEA Norwich, I am investigating the global significance of light-driven rhodopsin proton pumps in eukaryotic marine phytoplankton.
Marine genomics; environmental and functional genomics; adaptation to low temperature and nutrients; polar biology; biological oceanography.
Developing a CRISPR-Cas system in diatoms for genetic engineering
As part of a larger team and in collaboration with Prof. Sophien Kamoun's team at The Sainsbury Laboratory, I will create a construct to allow development of a CRIPSR-Cas type II system for genetic engineering of the model diatom Thalassiosira pseudonana. CRISPR-Cas is a RNA-guided endonuclease system, which induces double strand breaks (DSB) in target DNA, allowing repair mechanisms that induce mutations (Non-homologous end joining) and gene exchange (HR) to be employed. It is a powerful system with applications across multiple fields.
Dr Barbara (Bobbie) Lyon
NSF Post-Doctoral Research Fellow
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.
Graduate Student Intern
Martin obtained his bachelor degree in Biological Sciences (majors: Microbiology, Ecology) at the University of Wuerzburg, Germany. In the context of my bachelor thesis I performed an immunological analysis of guttation fluid of Bacillus thuringiensis maize for the presence of Cry1Ab protein (Group of Prof. Steffan-Dewenter). During my masters I was involved in a NGS database project focusing on the transcriptional gene expression of the marine sponge associated candidate phylum Poribacteria (Group of Prof Hentschel Humeida). During my internship between September and December 2013 at the University of East Anglia (UEA) I worked with phytoplankton samples originating from a cruise to the Arctic Ocean. My aim was to isolate and identify different species out of these samples using methods for isolation like Single-Cell Isolation by Micropipette, Single Cell Sorting and Plating and methods for identification like 18srRNA sequencing, light microscopy and flow cytometry.
Currently Martin is at the University of Wurzburg, Germany; where he is writing his Masters theses.
Bioinformatics; Microbial Ecology; Plant-Microbe Interactions
Lian worked on establishing a protocol for chromatin immunoprecipitation (ChIP) in the marine diatom Thalassiosira pseudonana and other diatoms.
Professor Lian Ma, College of Life Science, Yangtze University, 88 Jingmi Road, Jingzhou, Hubei, P. R. China.
Before coming to UEA I studied and later worked as a research assistant in the Faculty of Biology at the University of Warsaw, Poland; where I looked at how the environment influences the behaviour and life history of fresh water zooplankton via, physiological pathways, using Daphnia as a model organism. During my undergraduate studies I became interested in hardcore theoretical ecology and later simultaneously studied biology and Computational Methods of Physics in the Faculty of Physics, UW, Polnad.
As a Ph.D. student in the School of Environmental Sciences, University of East Anglia; I looked into how to build simple and fast, yet representative models of the genetic evolution of the prokaryotes. Previously I was focused on the problem of genome streamlining.
I used to be a member of The Earth System Modelling Group led by Professor Tim Lenton; and work with Professor Thomas Mock.
Currently I work at the University of Warsaw, Poland.
Theoretical fundamentals of evolution; impact of the biosphere on earth systems; linking theoretical and experimental ecology; pray-predator interactions; mathematical models as way to discover the world.
- Bentkowski P., Markowska M., Pijanowska J. (2010). Role of melatonin in the control of depth distribution of Daphnia magna. Hydrobiologia (DOI: 10.1007/s10750-010-0134-x)
- Markowska M., Bentkowski P, Kloc–Stepkowska M., Pijanowska J. (2009). Presence of melatonin in Daphnia magna. Journal of Pineal Research (DOI: 10.1111/j.1600-079X.2008.00642.x)
- Bentkowski P., Markowska M. (2008). Evolution of Melatonin Functions among Invertebrates. (in Polish with English summary) Kosmos 56: 276–277.
I became interested in the application of genomics to investigate the marine environment during my undergraduate degree in Marine Biology with Oceanography at the National Oceanography Centre (NOC), University of Southampton. I went on to continue with my studies at the NOC carrying out a Masters of Research studying the functional role of Phosphoenolpyruvate carboxykinase in the coccolithophorid Emiliania huxleyi. Once completed I worked as a technician within the Plant Membrane Transporters lab of Lorraine Williams, University of Southampton supporting molecular work involved in the EU funded PHIME (Public health impact of long-term, low-level mixed element exposure in susceptible population strata) project. Using cloning methods I worked analysing the role of heavy metal transporters of Barley.
I am previously investigated the role of an unknown DNA binding protein in T. pseudonana potentially involved in growth. I utilised overexpression mutants of T. Pseudonana and analysed whole genome expression to identify gene networks associated to this unknown protein.
I am currently working at Qiagen, Fleming Way, Crawley, West Sussex, UK.
Biogeochemical cycling in the ocean; Algal genomics and proteomics; Gene networks; Developing molecular tools with diatoms
I am an undergraduate student at the University of East Anglia studying Environmental Sciences and am currently doing my dissertation under the supervision of Professor Thomas Mock. For this, I am looking at cadmium toxicity on different strains of the diatom Phaeodactylum Tricornutum. I am enjoying getting to know more about the species, as well as working and observing the research in the laboratory and learning more about such an important group like diatoms in general.
Clara Martinez Perez
I am an Erasmus student from the Universidad Autonoma de Madrid (UAM), Spain, studying my final year of Undergraduate in Biology at UEA. My experience in a summer program at the Microbial Ecology laboratory at the Centre of Advanced studies in Blanes (CEAB, CSIC), Spain, where I worked in microbial biodiversity in alpine lakes, encouraged me to do my final year project in marine microbiology. My project is a side project to Jan Strauss PhD thesis, in which I am studying the distribution of the bacteria-like rodopsin gene found in Fragilariopsis cylindrus in marine eukaryotic phytoplankton.