People

T_Mock

Professor Thomas Mock FRSB FHEA

Chair in Marine Microbiology

Email: T.Mock@uea.ac.uk

Biography

I obtained my MSc (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 German Academic Exchange Service (DAAD) in the School of Oceanography, University of Washington (E.V. Armbrust lab) in joint cooperation with the Biotechnology Center, University of Wisconsin (M.R. Sussman lab), USA. Before I was promoted to Professor (Personal Chair) in 2014, I was Reader (2012-2014) and 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.

Research Interests

Environmental and functional genomics of marine microbial organisms; metagenomics of the upper ocean; physiological adaptation; diatom biology; photosynthesis; polar biology; biochemistry; biological oceanography.

Publications

For publications, please see the publications page.

Nigel Belshaw

Dr Nigel Belshaw

Laboratory Technician
Email: N.Belshaw@uea.ac.uk

Biography

After obtaining a degree in Biochemistry from the University of East Anglia (UEA) I studied for a PhD on the regulation of gene expression in filamentous fungi at the Institute of Food Research (IFR) in the Norwich Research Park. This project and my subsequent research were focussed on the role of chromatin structure and epigenetic modifications as regulators of gene expression. Until recently I led a team at IFR investigating the role of epigenetics in gut disease and the influence of lifestyle factors. In my current role I will be developing and utilising the CRISPR/Cas genome editing tool to understand gene function in the polar diatom Fragilariopsis cylindrus.

Simin Gao

Ph.D. student

Email: simin.gao@uea.ac.uk

Primary supervisor: Dr. Nikolai Pedentchouk

Secondary supervisor: Prof. Thomas Mock

Supervisor at SUSTech (China): Dr. Xinxin Li

Biography

I have received my MSc in Marine Biology at the Tongji University (China), where I studied membrane lipids of deep sea Archaea (glycerol dialkyl glycerol tetraether). In my masters project, I was applying organic geochemistry methods to identify the differential archaeal carbon molecules. In my Ph.D. project at UEA and SUSTech, I will study is sea-ice dynamics in the Holocene using algal biomarkers. This is a splite-site Ph.D. programme between University of East Anglia (UEA) and Southern University of Science and Technology (SUSTech). I am going to culture sea-ice algae under different conditions in the laboratory, extract specific organic molecules and determine their stable isotope characteristics of both natural and cultured sea-ice algal biomarkers.

 

 

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Reuben Gilbertson

Ph.D. Student

Email: r.gilbertson@uea.ac.uk

Primary Supervisor: Professor Thomas Mock

Secondary Supervisor: Professor Cock van Oosterhout

Team member: Dr. Amanda Hopes

Biography

I graduated from the University of North Carolina Wilmington (UNCW), in July 2017 with a degree in Marine Biology. During my undergraduate studies at UNCW, I served as a research intern at the Sea Turtle Protection Program, Bald Head Island, North Carolina, where I studied epibiotic communities on the carapaces of nesting sea turtles. As an undergraduate, I became increasingly fascinated in marine phytoplankton, specifically diatoms, and their ability to adapt to different environmental conditions. Following graduation I returned home to the UK, working first as Research Assistant within a team at the University of Cambridge studying gene expression and methylation patterns in neonatal and adult stem cells. I then moved to begin my graduate studies at UEA where I am currently in the first year studying for my PhD with Professor Mock. The focus of my research is the use of reverse gene editing methods to further understand the adaptive evolution of the model polar diatom Fragilariopsis cylindrus.

 Research Interests

Diatoms, genome editing, polar science, adaptive evolution, genomics, molecular biology

Amanda Hopes

Dr. Amanda Hopes

Post-Doctoral Researcher
Email: a.hopes@uea.ac.uk

Biography

I finished my PhD in Thomas Mock’s group in 2017, working on developing new molecular tools for diatoms and investigating the function of a gene potentially involved in regulating silica metabolism in the polar diatom Fragilariopsis cylindrus. During this time, I developed a transformation system for F. cylindrus, CRISPR-Cas using a Golden-Gate approach for gene-editing in the model diatom Thalassiosira pseudonana and started development of an Inverse yeast 1-hybrid system for F. cylindrus.

Prior to my PhD I worked for a biotechnology company for four and half years as a researcher, developing molecular clinical diagnostic tools.

Following my PhD I started a short- term NRP Post-Doc investing protein regulation in T. pseudonana through ribosome profiling and adapting codon usage using CRISPR-driven homologous recombination developed in the Mock lab.

I have just started my second Post-Doc with Thomas researching the molecular underpinnings of adaptive evolution in polar diatoms.

Research Interests

Functional genomics; molecular biology; diatoms/algae; silica metabolism; gene and protein regulation, evolution, polar biology.

Publications

Hopes, A., Nekrasov, V., Belshaw, N., Grouneva, I., Kamoun, S., Mock, T. 2017. Genome Editing in Diatoms Using CRISPR-Cas to Induce Precise Bi- allelic Deletions. Bio-protocol, 7(23).

Hopes, A., Thomas, D.N. and Mock, T., 2017. Polar Microalgae: Functional Genomics, Physiology, and the Environment. In Psychrophiles: From Biodiversity to Biotechnology (pp. 305-344). Springer International Publishing.

Hopes, A., Nekrasov, V., Kamoun, S. and Mock, T., 2016. Editing of the urease gene by CRISPR-Cas in the diatom Thalassiosira pseudonana. Plant methods, 12(1), p.49.

Hopes A., Mock, T. 2015. Evolution of Microalgae and Their Adaptations in Different Marine Ecosystems. eLS (DOI: 10.1002/9780470015902.a0023744).

Hopes A. & Mock T. (2014) Diatoms: Glass-dwelling dynamos. Microbiology Today :41(1), 20-23.

 

Monica  Pichler

Ph.D. Student

Email: M.Pichler@uea.ac.uk
Primary Supervisor: Professor Thomas Mock
Secondary Supervisor: Dr Nicola Patron (Earlham Institute)

Team members: Dr. Amanda Hopes

Biography

I have completed my Master in Geobiology and Paleobiology, with an emphasis on Geomicrobiology, at the University of Munich. Through my research projects I have gained experience in high-throughput sequencing and bioinformatics for bacterial and eukaryotic diversity studies. For my PhD project at UEA, I apply ribosome profiling to reveal how temperature, which is one of the most important growth factors, affects translation in diatoms. Furthermore, I use CRISPR/Cas9 in combination with ribosome profiling to provide insights how codon usage, tRNA abundance and tRNA- derived small non-coding RNAs impact protein synthesis in the model diatom Thalassiosira pseudonana under changing environmental conditions.

Publications

Pichler M et al., 2018.  A 16S rRNA gene sequencing and analysis protocol for the Illumina MiniSeq platform. Microbiology Open https://onlinelibrary.wiley.com/doi/abs/10.1002/mbo3.611

 

 

Dr. Krisztina Sarkozi

Post-Doctoral Researcher
Email: k.sarkozi@uea.ac.uk

Biography

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. 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.

Research Interests

Algal genomics and proteomics, ecology, aquatic trophic chains, bioinformatics.

Dr. Andrew Toseland

Post-Doctoral Researcher
Email: Andrew.Toseland@earlham.ac.uk

Biography

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.

Research Interests

Eukaryotic marine metatranscriptomics; genome assembly; high-throughput sequencing.

Selected publications:

Toseland A., Daines S. J., Clark J. R., Kirkham A., Strauss J., Uhlig C., Lenton T. M., Valentin K., Pearson G. A., Moulton V., Mock T. (2013) The impact of temperature on marine phytoplankton resource allocation and metabolism. Nature Climate Change
(DOI: 10.1038/nclimate1989)

Toseland A., Moxon S., Mock T., Moulton V. (2014) Metatranscriptomes from diverse microbial communities: assessment of data reduction techniques for rigorous annotation. BMC Genomics (DOI: 10.1186/1471-2164-15-901)

 

Kara Martin

Kara Martin

PhD Student
Email: K.Martin@uea.ac.uk
Primary Supervisor: Professor Vincent Moulton (School of Computing)
Secondary Supervisor: Professor Thomas Mock
Dr Richard Leggett (The Genome Analysis Centre)

Biography

Bioinformatics approaches for assessing the impact of temperature on eukaryotic phytoplankton

I graduated from the University College Dublin (UCD) with a degree in Science, majoring in Microbiology in 2011. My final year project was 'Investigating the role of sigma factor in physiology of Rhodococcus equi.' I then went to pursue a masters and graduated with a MSc. in Bioinformatics from University of Leicester in 2012. My final year project for my masters was 'In silico mining for microsatellites'. I gained research experience in bioinformatics at the National Institute for Cellular Biotechnology (NICB). The role involved statistical analysis of microarray data generated from colorectal cancer samples conducted within the R/Bioconductor software environment.

I am currently in my first year of my PhD. My project is "Bioinformatics approaches for assessing the impact of temperature on eukaryotic phytoplankton".

Ana Bermejo Martinez

Ana Bermejo Martínez

PhD Student
Email: A.Bermejo-Martinez@uea.ac.uk
Primary Supervisor: Dr Jonathan Todd (School of Biological Sciences)
Secondary Supervisors: Dr Janneke Balk (School of Biological Sciences)
Dr Cristobal Uauy (School of Biological Sciences)
Professor Thomas Mock

Biography

I studied Biology at the University of Santiago de Compostela, where I majored in Molecular Biology and Biotechnology. My interest in the application of Biotechnology in the environment drove me to study for an MSc in Biotechnology for a Sustainable Future at the University of East Anglia (UEA). My Master's research project in the group of Dr Jonathan Todd focused on how Thalossiosira pseudonana, a model marine diatom, synthesises glycine betaine, the most abundant osmolyte in nature.

After my masters, I became a Senior Research Technician in the research groups of Dr Jonathan Todd and Professor Thomas Mock. My project involved dimethylsulphoniopropionate (DMSP) synthesis in phytoplankton, as well as continuing the work on glycine betaine synthesis from my Master's project.

In my current PhD project, I am taking a step further in the glycine betaine synthesis research in diatoms, as well as using these new findings for the improvement of key agricultural crops.‬‬

Emma Langan

PhD Student
Email: emma.langan@uea.ac.uk
Primary Supervisor: Professor Thomas Mock
Secondary Supervisors: Dr Richard Leggett (Earlham Institute)
Professor Vincent Moulton (School of Computing)
Dr Clara Manno (British Antarctic Survey)

Biography

I studied Infectious Diseases with a focus on microbiology at the University of Edinburgh and graduated in 2015.  My honours project was genetic identification of zoonotic trypanosomiasis strains in cattle, which sparked my interest in genomics and bioinformatics.  I completed an MSc in Bioinformatics, also at the University of Edinburgh, in 2017.  My MSc research project mainly involved genome assembly and analysis, I also created a genomic database and browser and performed DNA sequencing using the Nanopore MinION portable real-time long read sequencer.  In October 2017 I moved to Norwich to begin a PhD at the UEA.  My project is focussed on using the Nanopore MinION for real-time metagenomic sequencing of polar ocean samples to monitor polar microbe populations.

Shiri Graff van Creveld

Visiting PhD Student (EMBO Short-term fellowship) from Weizmann Institute of Science, Vardi Group, Israel

Email:  shiri.graff@weizmann.ac.il

Biography

After graduating in molecular biochemistry in the Technion (Israel Institute of Technology) my love to the sea drove me to peruse an MSc, and then a PhD studying marine diatoms in the lab of Assaf Vardi’s at the Weizmann Institute of Science (Israel).

I am interesting in diatom’s response to stress, how they perceive and response to the ever-changing marine environment. In particular, I am studying the role of redox in cell fate regulation in marine diatom’s response to environmental stresses. I received a short-term-EMBO fellowship to come to the lab Professor Thomas Mock at the University of East Anglia, in order to adapt the CRISPR/Cas9 tool for gene editing in the model diatom Phaeodactylum.

Research Interests

Programmed cell death, stress response, redox signaling, functional genetics; marine microbiology; diatoms; protein structure-function.

Publications

Graff van Creveld, S., Rosenwasser, S., Schatz, D., Koren, I., and Vardi, A. (2015). Early perturbation in mitochondria redox homeostasis in response to environmental stress predicts cell fate in diatoms. ISME J. 9, 385–395.

Graff van Creveld, S., Rosenwasser, S., Levin, Y., and Vardi, A. (2016). Chronic iron limitation confers transient resistance to oxidative stress in marine diatoms. Plant Physiol. 172, 968–979.

Rosenwasser, S., Graff van Creveld, S., Schatz, D., Malitsky, S., Tzfadia, O., Aharoni, A., Levin, Y., Gabashvili, A., Feldmesser, E., and Vardi, A. (2014). Mapping the diatom redox-sensitive proteome provides insight into response to nitrogen stress in the marine environment. Proc. Natl. Acad. Sci. U. S. A. 111, 2740–2745.

Rosenwasser, S., Ziv, C., Graff van Creveld, S., and Vardi, A. (2016). Virocell Metabolism: Metabolic Innovations During Host–Virus Interactions in the Ocean. Trends Microbiol. 24, 821–832.

Volpert, A., Graff van Creveld, S., Rosenwasser, S., and Vardi, A. (2018). Diurnal fluctuations in chloroplast GSH redox state regulate susceptibility to oxidative stress and cell fate in a bloom-forming diatom. J. Phycol. 0–2. (DOI: 10.1111/jpy.12638).