http://helios.wbbib.uj.edu.pl/

Prof dr hab. Jerzy Dobrucki
room: C041 (2.01.32), phone: +48 12 664 63 82

Dr Mirosław Zarębski, room: B004 (3.01.32), phone: +48 12 664 63 81, e-mail: miroslaw.zarebski@uj.edu.pl

Dr Svitlana Levchenko, room: C002 (2.01.33a), phone: +48 12 664 62 19, e-mail: svitlana.levchenko@uj.edu.pl

Dr Agnieszka Hoang-Bujnowicz, room: C043 (2.01.30), phone: +48 12 664 61 30, e-mail: agnieszka.hoang@uj.edu.pl

Dr Julita Wesołowska, room: C043 (2.01.30), phone: +48 12 664 61 30, e-mail: julita.wesolowska@uj.edu.pl

Dr Marta Hoffmann, room: C002 (2.01.33a), phone: +48 12 664 62 44, e-mail: marta1990.hoffmann@uj.edu.pl

Ahmed Ismail Hassan Ahmed Mohamed Eatmann, room:  C002 (2.01.33), phone: +48 12 664 61 30
Izabela Harla, room: C043 (2.01.30), phone: +48 12 664 61 30
Beata Nosal, room: C002 (2.01.33), phone: +48 12 664 62 19

•  
• Mechanisms of induction and repair of DNA damage in human cells
• Functions played by HP1, XRCC1 and 53BP1 proteins in DNA repair,
• Mechanisms of induction of DNA damage by visible light,
• Internal architecture of DNA repair foci forming in the cell nucleus in response to various types of damage, including the damage induced by visible light, chemical cytotoxic agents (including antitumour drugs), and CRISPR/Cas9,
• Dynamics of repair factors recruited to DNA repair foci,
• DNA repair processes under conditions of hypoxia and anoxia,
• Phenomena associated with saturating cellular capacity to repair DNA damage,
• Methods of detecting and quantitative analysis of DNA damage: (1) STRIDE – SensiTive Recognition of Individual DNA Ends – a method of direct detection of individual single- and double-strand DNA breaks [Kordon M. et al., Nucleic Acids Res. 2020;48(3):e14.; US Patent US20200255884A1], (2) algorithm and software for quantitative cytometric analysis of DNA damage and spatial correlations between the damage and discrete localised nuclear phenomena (Dot-to-Dot software) [Berniak K. et al., Cytometry A. 2013;83(10):913-24].

• fluorescence confocal microscopy, 
• microscopy methods of investigating dynamics and interactios between proteins in situ, in live cells, such as FRAP, FRET, FCS, BiFc, and others, 
• the newest methods of super-resolution microscopy (dSTORM – direct stochastic optical reconstruction microscopy, SMLM – single molecule localisation microscopy, STED – stimulated emission depletion microscopy),

as well as

• methods of processing and analysis of digital images (reconstruction of three-dimensional images, noise removal, deconvolution, multidimensional quantitative analysis), 
• basic methods of molecular biology and biochemistry.

Instrumentation:

• confocal microscope Leica SP5 SMD (FLIM, FCS), 
• confocal microscope Leica SP5 (STED), 
• confocal microscope Bio-Rad MRC2014, 
• micromanipulator and microinjector (Eppendorf),
• super-resolution microscope based on detection of individual molecules (dSTROM – direct stochastic optical reconstruction microscopy; SMLM, single molecule localisation microscopy),
• graphics stations and software for processing and analysis of imaging data, including Huygens software (SVI),
• cell culture equipment.

1. Jerzy Dobrucki: Genome stability in mammalian oocytes and somatic cells. (2021–2025). OPUS LAP 20, National Science Centre (NCN).

1. Kordon M, Zarębski M, Solarczyk K, Ma H, Pederson T, Dobrucki J. STRIDE - a fluorescence method for direct, specific in situ detection of individual single- or double-strand DNA breaks in fixed cells. Nucleic Acid Research. 2020 Feb;48(3):e14. doi: 10.1093/nar/gkz1118. 
2. Kordon MM, Szczurek A, Berniak K, Szelest O, Solarczyk K, Tworzydło M, Wachsmann-Hogiu S, Vaahtokari A, Cremer C, Pederson T, Dobrucki JW. PML-like subnuclear bodies, containing XRCC1, juxtaposed to DNA replication-based single-strand breaks. FASEB J. 2019 Feb;33(2):2301-2313. doi: 10.1096/fj.201801379R. 
3. Szczurek A, Contu F, Hoang A, Dobrucki J, Mai S. Aqueous mounting media increasing tissue translucence improve image quality in Structured Illumination Microscopy of thick biological specimen. Sci Rep. 2018 Sep 18;8(1):13971. doi: 10.1038/s41598-018-32191-x. 
4. Szczurek A, Klewes L, Xing J, Gourram A, Birk U, Knecht H, Dobrucki JW, Mai S, Cremer C. Imaging chromatin nanostructure with binding-activated localization microscopy based on DNA structure fluctuations. Nucleic Acids Res. 2017 May 5;45(8):e56. doi: 10.1093/nar/gkw1301.
5. Pierzyńska-Mach A, Szczurek A, Cella Zanacchi F, Pennacchietti F, Drukała J, Diaspro A, Cremer C, Darzynkiewicz Z, Dobrucki JW. Subnuclear localization, rates and effectiveness of UVC-induced unscheduled DNA synthesis visualized by fluorescence widefield, confocal and super-resolution microscopy. Cell Cycle. 2016;15(8):1156-67. doi: 10.1080/15384101.2016.1158377. 
6. Solarczyk KJ, Kordon M, Berniak K, Dobrucki JW. Two stages of XRCC1 recruitment and two classes of XRCC1 foci formed in response to low level DNA damage induced by visible light, or stress triggered by heat shock. DNA Repair (Amst). 2016 Jan;37:12-21. doi: 10.1016/j.dnarep.2015.10.006. 
7. Żurek-Biesiada D, Szczurek AT, Prakash K, Mohana GK, Lee HK, Roignant JY, Birk UJ, Dobrucki JW, Cremer C. Localization microscopy of DNA in situ using Vybrant(®) DyeCycle™ Violet fluorescent probe: A new approach to study nuclear nanostructure at single molecule resolution. Exp Cell Res. 2016 May 1;343(2):97-106. doi: 10.1016/j.yexcr.2015.08.020. 
8. Berniak K, Rybak P, Bernas T, Zarębski M, Biela E, Zhao H, Darzynkiewicz Z, Dobrucki JW. Relationship between DNA damage response, initiated by camptothecin or oxidative stress, and DNA replication, analyzed by quantitative 3D image analysis. Cytometry A. 2013 Oct;83(10):913-24. doi: 10.1002/cyto.a.22327. 
9. Zurek-Biesiada D, Kędracka-Krok S, Dobrucki JW. UV-activated conversion of Hoechst 33258, DAPI, and Vybrant DyeCycle fluorescent dyes into blue-excited, green-emitting protonated forms. Cytometry A. 2013 May;83(5):441-51. doi: 10.1002/cyto.a.22260. 
10. Solarczyk KJ, Zarębski M, Dobrucki JW. Inducing local DNA damage by visible light to study chromatin repair. DNA Repair (Amst). 2012 Dec 1;11(12):996-1002. doi: 10.1016/j.dnarep.2012.09.008. 

• Mechanisms of interaction of antitumour drugs with DNA (anthracycline antibiotics, agents inducing crosslinks, methylating agents),
• Interaction of visible light with DNA – mechanism of induction of DNA damage,
• Structure of DNA and chromatin in situ; structural changes induced by antitumour drugs and cytotoxic agents,
• Structure of the cell nucleus – influence of drugs on interations between DNA and histones,
• Dynamics of subnuclear structures (PML bodies) and nuclear proteins (histones,  heterochromatin protein 1, XRCC1, Rad51, 53BP1),
• Interactions between heterochromatin protein 1 and DNA in nuclei of live cells,
• Role of heterochromatin protein 1 in DNA repair,
• Molecular architecture of DNA repair foci.

We welcome students who are interested in biology of DNA and like experimental laboratory work.