Functional Evoluction of Biological Systems Team

Leader

Staff

Katarzyna Czyż, PhD

Piotr Zaręba, MSc (volunteer)

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.