Functional Evolution of Biological Systems Team
Leader
Grzegorz Koczyk, Post-doctoral degree
Staff
Katarzyna Czyż, PhD
Michał Kawaliło, MSc (PhD student)
We research the emergence and evolution of genomic elements (genes and non-coding sequences), as a derivative of selection resulting from both functional constraints and the constraints imposed by laws of physics, chemistry and probability. We employ, develop and test algorithms and models merging molecular biology, structural bioinformatics, biophysics and game theory. Our goal is to seek simplified general relationships in a complex world using both molecular tools and in silico approaches, as well as create publicly available tools enabling easy analysis and visualisation of research data based on these principles. We research the emergence and evolution of genomic elements (genes and non-coding sequences), as a derivative of selection resulting from both functional constraints and the constraints imposed by laws of physics, chemistry and probability. We employ, develop and test algorithms and models merging molecular biology, structural bioinformatics, biophysics and game theory. Our goal is to seek simplified general relationships in a complex world using both molecular tools and in silico approaches, as well as create publicly available tools enabling easy analysis and visualisation of research data based on these principles
Research profile
- Phylogenomics of substrate specificity and enzyme activity in biosynthesis, modification and efflux of secondary metabolites in Eukaryotes (especially fungal toxins and crop plant metabolites).
- Regulation of metabolite production and growth in changing climate conditions (in model fungi).
- Inquiry into modes of evolution for both artificial and natural fungicide resistance strategies (efflux, accumulation, growth).
- Evolution of domain architecture and functional sites in proteins.
Methods:
- molecular diagnostic methods (PCR, qRT-PCR, direct sequencing and high-throughput sequencing of environmental samples),
- phylogenomics (approximate maximum likelihood methods, statistical analysis of patterns and trends in phylogeny vs. phenotype),
- homology modelling of proteins,
- unsupervised and supervised clustering of patterns in bibliographic and functional annotation,
- extraction and annotation of functional sites using profile methods, interactions and structural constraints in proteins.
Current research activities
- Assesment of biodiversity and toxigenic potential of fungi in anthropogenic environments.
- Molecular mechanisms of multidrug resistance in Fusarium species.
- Inquiry into modes of evolution for both artificial and natural fungicide resistance strategies.
Selected papers
- Popiel D., Dawidziuk A., Koczyk G., Mackowiak A., Marcinkowska K. (2017). Multiple facets of response to fungicides–the influence of azole treatment on expression of key mycotoxin biosynthetic genes and candidate resistance factors in the control of resistant Fusarium strains. European Journal of Plant Pathology 147(4): 773-785
- Fedorowicz-Strońska O., Koczyk G., Kaczmarek M., Krajewski P., Sadowski J. (2017). Genome-wide identification, characterisation and expression profiles of calcium-dependent protein kinase genes in barley (Hordeum vulgare L.) Journal of Applied Genetics 58(1):11-22.
- Nelson MN., Książkiewicz M., Rychel S., Besharat N., Taylor C., Wyrwa K., Jost R., Erskine W., Cowling W., Berger JD., Batley J., Weller J., Naganowska B., Wolko B. (2017). The loss of vernalization requirement in narrow-leafed lupin is associated with a deletion in the promoter and de-repressed expression of a Flowering Locus T (FT) homologue. New Phytologist 213(1): 220-232.
- Pniewski T., Czyż M., Wyrwa K., Bociąg P., Krajewski P., Kapusta J. (2017). Micropropagation of transgenic lettuce containing HBsAg as a method of mass-scale production of standardised plant material for biofarming purposes. Plant Cell Report 36:49–60
Grants
Project no: 2016/21/B/NZ9/01875
Project title:
Subtype: OPUS
Principal investigator: G. Koczyk
Duration: 7 March 2017 - 6 March 2020
Project no: 2016/21/D/NZ8/01300
Project title:
Subtype: SONATA
Principal investigator: K. Czyż
Duration: 7 March 2017 - 6 March 2020