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QTB Team Details

Photo of Ovidiu Popa

PostDoc

Dr. Ovidiu Popa
Quantitative und Theoretische Biologie
Heinrich-Heine-Universität Düsseldorf
Universitätsstraße 1

Building: 22.07
Floor/Room: 00.030
Düsseldorf
+49 211 81-10175


Responsibilities

Project description

Bacterial Community Profile of Phaeodactylum tricornutum Cultures

Bacteria and diatoms have co-existed in unison for over 200 million years establishing a symbiotic relationship: bacteria are naturally suited to occupying ecological niches presented by any diatom culture [1]. The utilisation of resources is maximied in a species-rich community because every possible niche is occupied, avoiding competition and so productivity is maximised. Studying species-specific bacterial-diatom interactions may be important industrially, especially if we encourage favourable bacteria that will enhance the growth of the diatom through the provision of expensive nutrients such as vitamin B12 or iron, therefore keeping production costs down.
[1] Amin SA; Parker MS; Armbrust EV, 2012. Interactions between diatoms and bacteria. Microbiology and Molecular Biology Reviews 76: 667-684

Molecular Diversification and Adaptation in Arabidopsis thaliana Population

Adaptation to particular environments is the driving force for diversification and molecular evolution in all organisms. Plants are the most complex photoautotrophic organisms able to colonise a wide range of ecological niches for larger time periods. The adaption process to particular condition has left its mark into the genome. Studying the diversification process of closely related species enables to understand how exactly environmental conditions can change the genome on evolutionary level with consequences for further research approaches and industrial applications.

Phage genetic elements in prokaryotic cells

Bacteriophages or phages are viruses that infect and replicate within a prokaryotic cell by injection of their own genetic material into the bacterial cytoplasm. Phages are the most common and diverse entities on the planet. They outnumbered the bacteria cells by a factor of 10 to 1. Phages can multiply through a lysogenic cycle (prophages or temperate phages) by insertion of their genome into the bacterial chromosome and remains dormant until the lytic cycle is induced. In the lytic cycle phages are using the bacterial metabolism to replicate and escape from the cell. The extensive co-evolution of the phages with their host has resulted in a remarkable diversity of phage elements. Studying the variety of phage elements existing in bacterial cells enable us to understand the process of phage-host interaction and to discover key elements, which may be of importance for several research and engineering applications

Discovery of blood biomarkers predicting treatment response in schizophrenia patients

An accurate diagnosis of mental diseases is still a big challenge as well as the evaluating of particular treatments. This project focuses towards identification of blood biomarkers that helps to predict the accuracy of a specific therapy. Therefore, individual transcriptome data is subjected to advanced statistical analysis (e.g. Discriminant Function Analysis (DFA), regression analysis, weighted gene correlation network analysis (WGCNA) in order to identify effects of particular treatment to expression pattern). This type of analysis allows to identify within a network of gene expression, co-expression pattern that can be the result of co-regulation initiated by underlying conditions. Co-expressed genes summarized in expression cluster are the best candidates for discovering promising blood biomarkers.

Project participants from QTB: Thomas Wenske, Ellen Oldenburg & Ovidiu Popa

 Short CV of Ovidiu Popa

Publications
  • Oldenburg, E., Kronberg, R. M., Niehoff, B., Ebenhöh, O., & Popa, O. DeepLOKI-A deep learning based approach to identify Zooplankton taxa on high-resolution images from the optical plankton recorder LOKI. Frontiers in Marine Science, 10, 1280510.
  • Thomas Mock, William Boulton, John-Paul Balmonte, Kevin Barry, Stefan Bertilsson, Jeff Bowman, Moritz Buck, Gunnar Bratbak, Emelia J. Chamberlain, Michael Cunliffe, Jessie Creamean, Oliver Ebenhöh, Sarah Lena Eggers, Allison A. Fong, Jessie Gardner, Rolf Gradinger, Mats A. Granskog, Charlotte Havermans, Thomas Hill, Clara J. M. Hoppe, Kerstin Korte, Aud Larsen, Oliver Müller, Anja Nicolaus, Ellen Oldenburg, Ovidiu Popa, Swantje Rogge, Hendrik Schäfer, Katyanne Shoemaker, Pauline Snoeijs-Leijonmalm, Anders Torstensson, Klaus Valentin, Anna Vader, Kerrie Barry, I.-M. A. Chen, Alicia Clum, Alex Copeland, Chris Daum, Emiley Eloe-Fadrosh, Brian Foster, Bryce Foster, Igor V. Grigoriev, Marcel Huntemann, Natalia Ivanova, Alan Kuo, Nikos C. Kyrpides, Supratim Mukherjee, Krishnaveni Palaniappan, T. B. K. Reddy, Asaf Salamov, Simon Roux, Neha Varghese, Tanja Woyke, Dongying Wu, Richard M. Leggett, Vincent Moulton, Katja Metfies: Multiomics in the central Arctic Ocean for benchmarking biodiversity change, PLoS Biology (2022), 17.10.2022
  • Estrada V, Oldenburg E, Popa O, Muller HW. Mapping the long rocky road to effective spinal cord injury therapy - A meta-review of pre-clinical and clinical research. J Neurotrauma. 2022 Feb 24. doi: 10.1089/neu.2021.0298. Epub ahead of print. PMID: 35196894.
  • Popa, O., Oldenburg, E., & Ebenhöh, O. (2020). From sequence to information. Philosophical Transactions of the Royal Society B, 375(1814), 20190448.
  • Trossbach, S. V. et al. Dysregulation of a specific immune-related network of genes biologically defines a subset of schizophrenia. Transl Psychiatry 9, 156 (2019)
  • Pfeifer, E., Hünnefeld, M., Popa, O. & Frunzke, J. Impact of Xenogeneic Silencing on Phage-Host Interactions. J. Mol. Biol. (2019). doi:10.1016/j.jmb.2019.02.011
  • Moejes, F., Succurro, A., Popa, O., Maguire, J. & Ebenhöh, O.  (2017): Dynamics of the Bacterial Community Associated with Phaeodactylum tricornutum Cultures. Processes 5, 77
  •  E. Pfeifer, M. Hünnefeld, O. Popa, T. Polen, D. Kohlheyer, M. Baumgart, and J. Frunzke (2016): “Silencing of cryptic prophages in Corynebacterium glutamicum.,” Nucleic Acids Research
  • Popa O, Landan G and Dagan T (2016): Phylogenomic networks reveal limited phylogenetic range of lateral gene transfer by transduction. The ISME Journal 11(2)
  • Eugen Pfeifer, Max Hunnefeld, O Popa, Tino Polen, Dietrich Kohlheyer, Meike Baumgart and Julia Frunzke (2016): Silencing of cryptic prophages in Corynebacterium glutamicum. Nucleic Acids Research 44(21):gkw692
  • Popa O, Landan G and Dagan T (2015): Phylogenomic transduction networks reveal genetic barriers to phage-mediated lateral gene transfer during microbial evolution. submitted
  • Dagan T, Popa O, Klösges T, Landan G. (2014). Phylogenomic networks of microbial genome evolution in Manual of Environmental Microbiology, 4th Ed. ASM Press, in press.
  • Gophna U, Kristensen DM, Wolf YI, Popa O, Drevet C, and Koonin EV (2014): No evidence of inhibition of horizontal gene transfer by CRISPR-Cas on evolutionary timescales. ISME J 9, 2021–2027 (2015).
  • Engelen A, Convey P, Popa O, Ott S. (2014): Lichen photobiont diversity and selectivity at an inland site of the south of the southern maritime Antarctic (Coal Nunatak, Alexander Island). submitted
  • Nelson-Sathi S, Popa O, List J-M, Geisler H, Martin WF, Dagan T (2013): Reconstructing the lateral component of language history and genome evolution using network approaches. In:Classification and Evolution in Biology, Linguistics and the History of Science. Concepts – Methods – Visualization, eds Fangerau H, Geisler H, Halling T, Martin W. (Steiner, Stuttgart) pp. 163–180, www.steiner-verlag.de/titel/59821.html
  • Popa O. and Dagan T. (2011). Trends and barriers to lateral gene transfer in prokaryotes. Current Opinion in Microbiology 1–9.
  • Popa O., Hazkani-Covo E., Landan G., Martin W., and Dagan T. (2011). Directed networks reveal genomic barriers and DNA repair bypasses to lateral gene transfer amongprokaryotes. Genome Research 21, 599–609.
  • Kloesges T., Popa O., Martin W., and Dagan T. (2011). Networks of gene sharing among 329 proteobacterial genomes reveal differences in lateral gene transfer frequency at different phylogenetic depths. Molecular Biology and Evolution 28, 1057–1074.
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