People
Dr Thomas Mock FRSB FHEA
Professor (Chair) in Marine Microbiology at the School of Environmental Sciences, UEA
Guest Professor (Honorary Chair) of Ocean University of China, Qingdao
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 (GEOMAR) and the PhD (2003) at Bremen University (AWI), 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 was appointed Guest Professor of the Ocean University of China (Qingdao) in 2019.
Research Interests
Environmental and functional genomics of marine microbial organisms; metagenomics of the upper ocean; physiological adaptation; diatom evolution and biology; photosynthesis; polar biology; biochemistry; biological oceanography.
Publications
For publications, please see the publications page.
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.
Thomas Birley
PhD Student (NRPDTP)
Email: t.birley@uea.ac.uk
Primary supervisor: Professor Cock van Oosterhout
Secondary supervisor: Professor Thomas Mock
Biography
I obtained an MSci from University College London in Genetics, Evolution and Environment, undertaking a research project on the evolution of Apicomplexa. I am currently employed at the Mock Lab researching a method of obtaining cell free DNA from aquatic environment using CRISPR-Cas9. In October 2019 I am due to start a PhD in phytoplankton genetics. The polar phytoplankton Fragilariopsis cylindrus has been shown to an unusual biallelic expression in response to the seasonal variation in environmental conditions. I will be researching the molecular mechanisms that that cause this, whether this is unique in F. cylindrus, and what is the significance for this on its evolution.
Longji Deng
PhD Student
Email: longji.deng@uea.ac.uk
Primary supervisor: Professor Thomas Mock
Secondary supervisor: Professor Cock van Oosterhout
Biography
I have completed my BSc and MSci degrees in the School of Environmental Sciences at the University of East Anglia. In my Master’s project, I explored the impact of ocean acidification and iron limitation in the diatom Thalassiosira pseudonana. In my Ph.D. project at UEA, I will apply a combination of reverse genetics, transcriptomics and metatranscriptomics to explore the biochemical function of proton-pumping Rhodopsin proteins in diatoms.
Shunan Fu
PhD Student (CSC Funded Scholar)
Email: Shunan.fu@uea.ac.uk
Primary supervisor: Professor Thomas Mock
Secondary supervisor: Professor Cock van Oosterhout
Biography
I have completed my BSc in Environmental Science at Hohai University and my MSc at Ocean University of China(OUC), also in Environmental Science. While studying at OUC, my research interest is the ecology of plankton in the Yellow Sea, especially the variation of the community structure of zooplankton. In addition, I joined the OUC-UEA joint training project and got my second MSc in Environmental Science at UEA. Currently, I am a PhD student and my PhD project is going to work on identifying the role of DNA methylation in the adaptive evolution of diatoms.
Reuben Gilbertson
Ph.D. Student (The Leverhulme Trust)
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.
Awards
2nd best Poster Award at the 7th European Phycological Congress in Zagreb 2019.
Research Interests
Diatoms, genome editing, polar science, adaptive evolution, genomics, molecular biology
Dr Amanda Hopes
(Currently on maternity leave)
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.
Awards
Outstanding Poster Award at the 'Molecular Life of Diatoms' conference 2021.
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.
Haoyu Jin
Visiting PhD Student (CSC Funded Scholar)
Email: H.Jin@uea.ac.uk
Primary Supervisor: Professor Thomas Mock
Secondary Supervisor: Professor Huiwang Gao (OUC)
Biography
I have completed my BSc at Xi’an University of Architecture and Technology (China) and then started biogeochemical research as a MSc and PhD student at the Ocean University of China (OUC). In my Ph.D. project at OUC, I mainly worked on the impact of atmospheric deposition on phytoplankton growth and utilization of dissolved organic phosphorus (DOP) in China Coastal Seas through on-board microcosm experiments. In my visiting Ph.D. project at UEA, I will apply bioinformatics tools and cell model analyses to study the impact of atmospheric deposition on DOP utilization and related gene expression in microbial communities of the global ocean.
Antonia Otte
PhD Student (NRPDTP)
Email: A.Otte@uea.ac.uk
Biography
During my B.Sc. degree in biology at the University of Bremen, Germany, I studied Trypanosoma sp., the pathogen causing African sleeping sickness in livestock and humans. To look at the transmitting tsetse fly and bacteria present in its gut will help to understand how infections are established, and eventually to identify potential points of intervention. Seeing the importance and benefits that molecular life sciences can have on health and the environment, I decided to continue research at the interface of molecular and environmental biology in collaboration with the Alfred Wegener Institute in Bremerhaven during my M.Sc. in Biochemistry and Molecular Biology. In my master’s project, I analysed metatranscriptomic data from a harmful algal bloom (HAB) to identify cellular processes and enzymes involved in the formation of HABs and the associated toxicity. Following up on the use of molecular analyses to understand marine organisms, I started my PhD in October 2022 and will study the role of mitotic recombination in genome evolution of polar phytoplankton.
Monica Pichler
Ph.D. Student (NRPDTP)
Email: M.Pichler@uea.ac.uk
Primary Supervisor: Professor Thomas Mock
Secondary Supervisor: Dr Nicola Patron (The 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
Johanna Winder
PhD Student (NRPDTP)
Email: J.Winder@uea.ac.uk
Primary Supervisor: Professor Thomas Mock
Secondary Supervisor: Professor Cock van Oosterhout
I obtained my BA (Hons) in Natural Sciences from the University of Cambridge, graduating in 2020. During my undergraduate degree, I pursued a variety of interests, ranging from cell and developmental biology to ecology and evolution. This piqued my interest in environmental microbiology, and I furthered this by embarking on a research project in northwestern Canada, using shotgun metagenomics to explore how permafrost thaw affects microbes in thermokarst lake sediments. Following this, I became interested in applying microbiology to solve global challenges, and to this end undertook an MSc by research at the University of Exeter in the Exeter Microbial Biofuels Group. I then decided to turn to the intersection of biotechnology and microbial physiology, ecology and evolution, through a PhD at UEA supervised by Professor Mock. I began my studies in October 2021, and my research aims to understand at the function of ice-binding protein diversity in the polar diatom F. cylindrus.
Awards
Prize for the best poster at the Annual Meeting of the British Phycological Society in 2023 (Newcastle).
Biointerphases Presentation Award at the IBP Conference in 2022.
Research Interests
Polar microbiology, biotechnology, diatom ecophysiology, extremophiles
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.
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)
William Boulton
PhD Student (ARIES)
Email: W.Boulton@uea.ac.uk
Primary Supervisor: Professor Vincent Moulton (School of Computing)
Secondary Supervisors: Professor Thomas Mock
Dr Richard Leggett (The Earlham Institute)
Biography
I studied mathematics at the University of Cambridge and graduated in 2016 with an Math degree, before working in mathematical modelling and software engineering at a small engineering firm. I became interested in metagenomics during an internship at EMBL-EBI, where I worked on projects about SARS-CoV-2 evolution and variant tracking through wastewater metagenomes. This led to applying for a PhD place at the UEA, supervised by Vincent Moulton, Thomas Mock, and Richard Leggett, and funded by the ARIES DTP. I started my PhD in October 2021, and will be analysing the largest single collection of Arctic ocean metagenomes, collected by MOSAiC - which is the first survey of the Arctic ocean observing a full annual cycle, including the polar winter. My research aims to uncover the microbial diversity of a warming Arctic ocean, and understand the biotic and abiotic drivers of this diversity.
Awards
Student Travel Award for a talk at the 2nd MOSAiC Conference / University of Colorado Boulder (USA) in 2023.
Research interests: Bioinformatics, data science, metagenomics and metagenomic assembly, Arctic microbiology
Anthony Duncan
PhD Student (NERC)
Email: A.Duncan@uea.ac.uk
Primary Supervisor: Professor Vincent Moulton (School of Computing)
Secondary Supervisors: Professor Thomas Mock
Dr Richard Leggett (The Earlham Institute)
Biography
I am PhD student in the School of Computing Science researching and applying computational techniques to help understand complex metagenomics data, with a particular interest in genome-resolved metagenomics and polar microbe communities. My undergraduate studies were in American and English literature also at UEA completed in 2009. I later returned to study after about a decade, completing an MSc in Computer Science where my dissertation project involving methods of phylogenetic tree construction kindled and interest in computational biology. To date my research has included generating some of the first eukaryotic metagenomic-assembled genomes for ocean microbes, and investigating the application of unsupervised machine learning techniques to functional profiles of ocean microbe communities.
Research interests: Bioinformatics, data science, metagenomics and metagenomic assembly (e.g. MAGs), marine microbiology
Publications
(2020) Metagenome-assembled genomes of phytoplankton communities across the Arctic Circle. Microbiome (https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-022-01254-7)
Emma Langan
PhD Student (NERC)
Email: emma.langan@uea.ac.uk
Primary Supervisor: Professor Thomas Mock
Secondary Supervisors: Dr Richard Leggett (The 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.
Yixuan Li
PhD Student (CSC Funded Scholar)
Email: Yixuan.li@uea.ac.uk
Primary Supervisor: Professor Thomas Mock
Secondary Supervisors: Professor Cock van Oosterhout; Dr. Yunyun Zhuang (Ocean University of China)
Biography
I have received my MSc degree in College of Environmental Science and Technology at the Ocean University of China. In my Master’s project, I studied community structure of zooplankton and functional diversity of crustacean zooplankton in the Southern Yellow Sea, China. In my PhD project at UEA, I will apply molecular methods (RNAseq, RT-qPCR, CRISPR/Cas mediated genome editing, etc) to identify the gene encoding cyanate transporter in marine eukaryotic phytoplankton and reconstruct the pathways responsible for cyanate assimilation. And then, I will investigate the diversity, biogeographic distribution, evolution and expression of the target gene by screening the existing omics datasets.
Research Interests
Cyanate transporter, cyanate assimilation, diatoms, nitrogen, genome editing
Publications
Li, Y., Ge, R., Chen, H., Zhuang, Y., Liu, G., Zheng, Z., 2022. Functional diversity and groups of crustacean zooplankton in the southern Yellow Sea. Ecol. Indic. 136, 108699.
Ge, R†., Li, Y†., Chen, H., Lei, F., Zhuang, Y., Liu, G., 2022. Diel Vertical Distribution of Mesozooplankton Functional Groups in the North Pacific Subtropical Gyre: A Case Study. Front. Mar. Sci. 9, 854642.
Lulu Wang
Visiting PhD Student (CSC Funded Scholar)
Email: kgc22ssu@uea.ac.uk
Primary Supervisor: Professor Thomas Mock
Biography
I started my Postgraduate and Doctoral Program at Ocean University of China (OUC) in 2016, majoring in hydrobiology. During this time, I have conducted research on the hemostatic ability of diatom frustules (Thalassiosira weissflogii, Thalassiosira sp., Cyclotella cryptica, Cocconeiopsis orthoneoides, Navicula avium, Navicula sp., and Pleurosigma indicum) which can be utilized as a natural bio-silica material. I found that the unique physical properties of frustule (specific surface area, size, pore diameter) would influence its ability to concentrate coagulation components and activate the coagulation cascade pathway, and therefore play an important role in determining its hemostatic properties. Thus, I tried to manipulate morphology of C. cryptica frustule through regulating CcSAP3 expression (gene over expression and RNA antisense).
Following this, I became interested in the synthesis of diatom cell wall. I began my studies in Mock lab in June 2022, and my research aims to find new genes/proteins regulating T. pseudonana cell size through RNA-seq and verify their function using CRISPR-CAS.
Research interests
Diatoms, diatom cell wall (frustule), biomineralization, silica metabolism
Publications
Wang L, Pan K, Li J, Li Y, Zhu B, Wang Y, Feng C, Han J. Influence of the physicochemical characteristics of diatom frustules on hemorrhage control. Biomater Sci. 2019 Apr 23;7(5):1833-1841. doi: 10.1039/c9bm00099b.
Wang L, Pan K, Zhang L, Zhou C, Li Y, Zhu B, Han J. Tentative identification of key factors determining the hemostatic efficiency of diatom frustule. Biomater Sci. 2021 Jan 26. doi: 10.1039/d0bm02002h.