Department of Plant Biotechnology

Website

Head

professor Halina Gabryś, PhD, DSc
room: B223 (3.1.27), phone: +48 12 664 63 40, e-mail: halina.gabrys@uj.edu.pl

Staff

Agnieszka K. Banaś, PhD
room: B242 (3.1.33), phone: +48 12 664 64 10, e-mail: a_katarzyna.banas@uj.edu.pl

Wojciech Strzałka, PhD
room: B242 (3.1.33), phone: +48 12 664 64 10, e-mail: wojciech.strzalka@uj.edu.pl

Weronika Krzeszowiec-Jeleń, PhD
room: B242 (3.1.33), phone: +48 12 664 64 10, e-mail: weronika.krzeszowiec@uj.edu.pl

Ewa Biela, PhD
room: B105 (3.0.33), phone: +48 12 664 63 47, e-mail: ewa.biela@uj.edu.pl

Anna Hebda, PhD
room: B105 (3.0.33), phone: +48 12 664 63 47

Ewa Kowalska, PhD
room: B242 (3.1.33), phone: +48 12 664 64 10, e-mail: ewa.b.kowalska@uj.edu.pl

Justyna Łabuz, PhD
room: A220 (4.1.22), phone: +48 12 664 65 45, e-mail: justyna.sojka@uj.edu.pl

Aleksandra Giza, MSc
room: B232 (3.1.8), phone: +48 12 664 63 91, e-mail: aleksandra2.giza@uj.edu.pl

PhD students

Filip Bartnicki, room: B232 (3.1.8), phone: +48 12 664 63 91
Aleksandra Eckstein, room: B105 (3.0.33), phone: +48 12 664 63 47
Paweł Hermanowicz, room: B105(3.0.33), phone: +48 12 664 63 47
Dominika Jagiełło-Flasińska, room: A220 (4.1.22), phone: +48 12 664 65 45
Klaudia Muszyńska, room: B105 (3.0.33), phone: +48 12 664 63 47
Piotr Zgłobicki, room: B232 (3.1.8), phone: +48 12 664 63 91

Research topics

  • Photoreceptor control of gene expression
  • Phototropin gene expression and role of different phototropin splice variants
  • Signals regulating chloroplast movements, especially those originating from the organelles themselves
  • Second messengers of blue light signals in chloroplast reactions controlled by phototropins (phosphoinositides and Ca2+).
  • Proteins associated with the chloroplast envelope and their interactions
  • Functioning of the cytoskeleton in homozygous Arabidopsis thaliana mutants with insertions in myosin genes
  • Role of chloroplast and nucleus movements in the protection of DNA against UV-induced damage.
  • Role of Arabidopsis thaliana PCNA (proliferating cell nuclear antigen) protein in DNA replication, repair and recombination
  • Plant proteins interacting with PCNA
  • Functions of cyclin-dependent kinases interacting with PCNA
  • Functional differentiation of Arabidopsis PCNA proteins
  • Applications of DNA aptamers in molecular biology, biotechnology and medicine

Methods

  • Plant cell and tissue culture
  • Organelle movement analysis
  • Fluorescence and confocal microscopy
  • Bacteria and yeast transformation
  • Stable and transient transformation of plants using Agrobacterium and biolistic method (gene gun)
  • Protein analysis: ELISA, Western blotting, SDS page, chromatography
  • Protein interaction: yeast one/two-hybrid system, BIFC, pull-down, co-immunoprecipitation,
  • mRNA and DNA analyses: real-time PCR, Southern blotting

Current projects

  1. Halina Gabryś: The signaling role of basic metabolites in the phototropin-controlled chloroplast responses. (2017-2020). OPUS 12, National Science Centre (NCN).
  2. Agnieszka Banaś: Arabidopsis photolyases: the role of post-transcriptional and post-translational modifications, influence on DNA repair, chloroplast functioning and plant responses to abiotic stresses. (2017-2022). SONATA BIS 6, National Science Centre (NCN).
  3. Wojciech Strzałka: Characterizing the functions of plant PCNA1 and PCNA2 proteins using Arabidopsis thaliana as an experimental model. (2014-2019). SONATA-BIS, National Science Centre (NCN).
  4. Wojciech Strzałka: Opracowanie, charakterystyka i optymalizacja innowacyjnych aptamerów DNA przeznaczonych do oczyszczania białek rekombinowanych. (2015-2018). TANGO, National Centre for Research and Development (NCBiR)

Selected publications

  1. Łabuz J, Samardakiewicz S, Hermanowicz P, Wyroba E, Pilarska M, Gabryś H. 2016. Blue light-dependent changes in loosely bound calcium in Arabidopsis mesophyll cells: an X-ray microanalysis study. Journal of Experimental Botany, doi:10.1093/jxb/erw089
  2. Eckstein A, Krzeszowiec W, Waligórski P, Gabryś H. 2015. Auxin and chloroplast movements. Physiologia Plantarum 105: 271-281.
  3. Bartnicki F, Kowalska E, Pels K, W. Strzalka W. 2015. Imidazole-free purification of His3-tagged recombinant proteins using ssDNA aptamer-based affinity chromatography. Journal of  Chromatography A 1418:130-9.
  4. Sztatelman O, Grzyb J, Gabryś H, Banaś AK. 2015. The effect of UV-B on Arabidopsis leaves depends on light conditions after treatment. BMC Plant Biology 15:281.
  5. Strzałka W, Aggarwal C, Krzeszowiec W, Jakubowska A, Sztatelman O,  Banaś AK. 2015. Arabidopsis PCNAs form complexes with selected D-type cyclins. Frontiers in Plant Science 6:516.
  6. Łabuz J, Hermanowicz P, Gabryś H. 2015. The impact of temperature on blue light induced chloroplast movements in Arabidopsis thaliana. Plant Science 239: 238-249
  7. Aggarwal Ch, Banaś AK, Kasprowicz-Maluśki A, Borghetti C, Łabuz J, Dobrucki J, Gabryś H. 2014. Blue-light-activated phototropin2 trafficking from the cytoplasm to Golgi/post-Golgi vesicles. Journal of Experimental Botany 66 (12): 3263–3276.
  8. Hermanowicz P, Sarna M, Burda K, Gabryś H. 2014. AtomicJ: an open source software for analysis of force curves. Rev Sci Instrum 85(6): 063703.
  9. Aggarwal Ch, Łabuz J, Gabryś H. 2013. Phosphoinositides play differential roles in regulating phototropin1- and phototropin2-mediated chloroplast movements in Arabidopsis. PlosOne 8(2): e55393.
  10. Strzałka W, Bartnicki F, Pels K, Jakubowska A, Tsurimoto T, Tanaka K. 2013. RAD5a ubiquitin ligase is involved in ubiquitination of Arabidopsis thaliana proliferating cell nuclear antygen. Journal of Experimental Botany 64(4): 859-869.

Batchelor/master thesis topics

Chloroplast movements and light signal transduction
Identification of transcription factors and promoter sequences involved in the regulation of gene expression by light. Chloroplast movements in A. thaliana mutants with impaired light signal transduction. The role of Ca2+  in signaling to organelle movements in plants. The mechanism of chloroplast movement – importance of cytoskeleton structure and its interactions with chloroplast envelope.

Plant PCNA and its role in DNA replication and repair
The role of PCNA in DNA replication, repair and recombination and its importance in plant cell genetic transformation. Identifying plant proteins interacting with PCNA. Biochemical and structural characterization of PCNA-interacting proteins and their complexes with PCNA. Analyzing and characterizing the interactions between transcription factors and DNA. Construction and characterization of plants with overexpression or silencing of PCNA genes. Characterizing A. thaliana mutants with impaired DNA repair and recombination. Functioning of proteins involved in repair of the UV-induced DNA damage (UVR3 photolyase).

Transgenic plants and plant genes expression
Cloning plant genes and construction of plant transformation vectors. Optimization of methods for plant transformation (Agrobacterium, gene gun). Optimization of system for efficient gene overexpression and silencing in A. thaliana, using constitutive and induced expression. Determining the role of  miRNA in transgene silencing. Analysis of plant gene expression at transcription (RT-PCR, real-time PCR) and translation level (Western blotting).

Requirements for students

Basic knowledge of biochemistry, microbiology, molecular genetics, cell biology and plant physiology/biotechnology