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Department of Cell Biophysics

WWW

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

Head

Prof Jerzy Dobrucki, PhD, DSc
room: C041 (2.01.32), phone: +48 12 664 63 82

Staff

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

Agnieszka Waligórska, PhD
room: B004 (3.01.32), phone: +48 12 664 62 81, e-mail: agnieszka.waligorska@uj.edu.pl

Magdalena Kordon, PhD
room: C002 (2.01.33), phone: +48 12 664 62 19, e-mail: magdalena.kordon@uj.edu.pl 

Kamil Solarczyk, PhD
room: C002 (2.01.33), phone: +48 12 664 62 19, e-mail: kj.solarczyk@uj.edu.pl

Krzysztof Berniak, MSc
pokój: C043 (2.01.30), phone: +48 12 664 61 30, e-mail: krzysztof.berniak@uj.edu.pl

Marta Hoffmann, MSc
room: C002 (2.01.33), phone: +48 12 664 62 19, mail: marta1990.hoffmann@uj.edu.pl

PhD students

Agnieszka Hoang-Bujnowicz, room: C043 (2.01.30), phone: +48 12 664 61 30
Oskar Szelest, room: C002 (2.01.33), phone: +48 12 664 62 19
Julita Wesołowska, room: C043 (2.01.30), phone: +48 12 664 61 30
Michał Mroziński, room:  C002 (2.01.33), phone: +48 12 664 62 19
Ahmed Ismail Hassan Ahmed Mohamed Eatmannroom:  C002 (2.01.33), phone: +48 12 664 61 30

Research topics

  • 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 mtitumour drugs), and CRISPR/Cas9,
  • Dynamics of repair factors recruited to DNA repair foci,
  • DNA repair processes under the conditions of hypoxia and anoxia,
  • Phenomena associated with saturating cellular capacity to repair DNA damage,
  • Methods of detecting and quntitative 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, (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).
 

Methods and specialistic equipment

Advanced optical microscopy techniques, including:
  • fluorescence confocal microscopy, 
  • microscopy methods of investigating dynamics and interactios between proteins in situ, in live cells, such as FRAP, FRET, FCS, BiFc, PLA 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,
  • cell culture equipment.

 

Current projects

  1. Krzysztof Berniak: Heterochromatin protein 1 (HP1) as a structure-stabilising factor in repair of DNA double-strand breaks. (2016-2019). PRELUDIUM 10, National Science Centre (NCN).
  2. Jerzy Dobrucki: Super-resolution optical imaging of higher order chromatin structures in nuclei of human cells, during DNA replication and repair. (2014-2018). OPUS 6, National Scince Centre (NCN).
  3. Oskar Szelest: ZintegrUJ – Kompleksowy Program Rozwoju Uniwersytetu Jagiellońskiego”, nr POWR.03.05.00-00-Z309/17-00. (2018-2020).

Selected publications

  1. 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 J2019 Feb;33(2):2301-2313. doi: 10.1096/fj.201801379R. Epub 2018 Sep 27. PubMed PMID: 30260704.
  2. 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. PubMed PMID: 28082388; PubMed Central PMCID: PMC5416826.
  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. PubMed PMID: 30228281; PubMed Central PMCID: PMC6143540.
  4. 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 Cycle2016;15(8):1156-67. doi: 10.1080/15384101.2016.1158377. PubMed PMID: 27097376; PubMed Central PMCID: PMC4889244.
  5. 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. Epub 2015 Nov 2. PubMed PMID: 26630398.
  6. 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. Epub 2015 Sep 1. PubMed PMID: 26341267.
  7. 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 A2013 Oct;83(10):913-24. doi: 10.1002/cyto.a.22327. Epub 2013 Jul 11. PubMed PMID: 23846844; PubMed Central PMCID: PMC3888650.
  8. 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. Epub 2013 Feb 15. PubMed PMID: 23418106.
  9. 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. Epub 2012 Oct 22. PubMed PMID: 23089313.
  10. Luijsterburg MS, Dinant C, Lans H, Stap J, Wiernasz E, Lagerwerf S, Warmerdam DO, Lindh M, Brink MC, Dobrucki JW, Aten JA, Fousteri MI, Jansen G, Dantuma NP, Vermeulen W, Mullenders LH, Houtsmuller AB, Verschure PJ, van Driel R. Heterochromatin protein 1 is recruited to various types of DNA damage. J Cell Biol2009 May 18;185(4):577-86. doi: 10.1083/jcb.200810035. PubMed PMID: 19451271; PubMed Central PMCID: PMC2711568.

Batchelor/master thesis topics

  • 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.

Requirements for candidates

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