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 three different diatoms: Thalossiosira pseudonana, Fragilariopsis cylindrus, and Emiliania huxelyi.

Small RNA Analysis; Microalgae genomics; Molecular evolution.

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 am looking into how to build simple and fast, yet representative models of the genetic evolution of the prokaryotes. Currently I am focused on the problem of genome streamlining.
I used to be a member of The Earth System Modelling Group led by Professor Tim Lenton. Currently I work in Dr Thomas Mock group.

More on Piotr Bentkowski.

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.

1. 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)
2. 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)
3. 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 currently investigating the role of an unknown DNA binding protein in T. pseudonana potentially involved in growth. I utilise overexpression mutants of T. Pseudonana and analyse whole genome expression to identify gene networks associated to this unknown protein.

Biogeochemical cycling in the ocean, Algal genomics and proteomics, Gene networks, Developing molecular tools with diatoms

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..

1. 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.2011.05.00)
2. 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)
3. 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 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.

I obtained my degree in Biology with emphasis on Biological Oceanography at the Christian-Albrechts University in Kiel and the PhD at Bremen University (Alfred-Wegener Institute for Polar and Marine Research), Germany. Before joining the University of East Anglia, most of my PostDoc research was conducted with a fellowship from the German Academic Exchange Service (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. I am a member of several genome 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.

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.

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.