Projects funded by the NCN

Information on the principal investigator and host institution

Information of the project and the call

Keywords

Equipment

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Super-resolution optical imaging of higher order chromatin structures in nuclei of human cells, during DNA replication and repair

2013/11/B/NZ3/00189

Keywords:

chromatin structure DNA optical super-resolution microscopy nanoscopy DNA dyes Hoechst DAPI photoconversion

Descriptors:

  • NZ3_1: Cell biology
  • NZ3_2: Cell physiology

Panel:

NZ3 - Cellular and developmental biology: cell biology, developmental biology, ageing biology, neurobiology

Host institution :

Uniwersytet Jagielloński w Krakowie, Wydział Biochemii, Biofizyki i Biotechnologii

woj. małopolskie

Other projects carried out by the institution 

Principal investigator (from the host institution):

prof. Jerzy Dobrucki 

Number of co-investigators in the project: 5

Call: OPUS 6 - announced on 2013-09-16

Amount awarded: 909 400 PLN

Project start date (Y-m-d): 2014-07-16

Project end date (Y-m-d): 2018-07-15

Project duration:: 48 months (the same as in the proposal)

Project status: Project settled

Equipment purchased [PL]

  1. Elementy optyczne, mechaniczne, filtry do mikroskopu wysokorozdzielczego (12 861 PLN)
  2. Układ laserow diodowych z światłowodem (405, 445, 488, 532, 640nm), np. Topteca ICHROME MLE FFC wraz z IBEAM-SMART-PT-445, lub podobny układ laserowy (211 000 PLN)
  3. Laser diodowy 488nm (31 951 PLN)
  4. Obiektyw imersyjny do detekcji migotania pojedynczych molekul fotokonwertowanych znacznikow fluorescencyjnych związanych z DNA w jądrach komorek, np. Leica HCX PlanApo 100x NA 1.47 lub podobny (51 000 PLN)
  5. Piezoelektryczny silnik krokowy do obiektywu mikroskopowego (27 366 PLN)
  6. Podpory antywstrząsowe pod stół optyczny (14 530 PLN)
  7. Układ laserów diodowych (647 nm, 561 nm).

Information in the final report

  • Publication in academic press/journals (16)
  1. Imaging chromatin nanostructure with binding-activated localization microscopy based on DNA structure fluctuations
    Authors:
    Szczurek A, Klewes L, Xing J, Gourram A, Birk U, Knecht H, Dobrucki JW, Mai S, Cremer C.
    Academic press:
    Nucleic Acids Research (rok: 2017, tom: 45(8), strony: e56), Wydawca: Oxford University Press
    Status:
    Published
    DOI:
    10.1093/nar/gkw1301 - link to the publication
  2. Localization microscopy of DNA in situ using Vybrant® DyeCycle™ Violet fluorescent probe: A new approach to study nuclear nanostructure at single molecule resolution
    Authors:
    Żurek-Biesiada D, Szczurek AT, Prakash K, Mohana GK, Lee HK, Roignant JY, Birk U, Dobrucki JW, Cremer C.
    Academic press:
    Experimental Cell Research (rok: 2015, tom: 343, strony: 97-106), Wydawca: Elsevier
    Status:
    Published
    DOI:
    10.1016/j.yexcr.2015.08.020 - link to the publication
  3. Super-resolution binding activated localization microscopy through reversible change of DNA conformation
    Authors:
    Szczurek A, Birk U, Knecht H, Dobrucki J, Mai S, Cremer C
    Academic press:
    Nucleus (rok: 2018, tom: 9 (1), strony: 182-189), Wydawca: Taylor and Francis
    Status:
    Published
    DOI:
    10.1080/19491034.2017.1419846 - link to the publication
  4. Aqueous mounting media increasing tissue translucence improve image quality in Structured Illumination Microscopy of thick biological specimen
    Authors:
    Szczurek A, Contu F, Hoang A, Dobrucki J, Mai S.
    Academic press:
    Scientific Reports (rok: 2018, tom: 8, strony: 13971), Wydawca: Springer Nature Publishing
    Status:
    Published
    DOI:
    10.1038/s41598-018-32191-x - link to the publication
  5. Changes in lipid membrane mechanics induced by di- and tri-phenyltins.
    Authors:
    Przybyło M, Drabik D, Szostak K, Borowik T, Klösgen B, Dobrucki J, Sikorski AF, Langner M.
    Academic press:
    Biochimica Biophysica Acta - Biomembranes (rok: 2017, tom: 1859(8), strony: 1301-1309), Wydawca: Elsevier Science
    Status:
    Published
    DOI:
    10.1016/j.bbamem.2017.04.025 - link to the publication
  6. Molecular determinants of Drosophila immunophilin FKBP39 nuclear localization
    Authors:
    Orłowski M, Popławska K, Pieprzyk J, Szczygieł-Sommer A, Więch A, Zarębski M, Tarczewska A, Dobrucki J, Ożyhar A
    Academic press:
    Biological Chemistry (rok: 2018, tom: 399(5), strony: 467-484), Wydawca: De Gruyter
    Status:
    Published
    DOI:
    10.1515/hsz-2017-0251 - link to the publication
  7. Subnuclear localization, rates and effectiveness of UVC-induced unscheduled DNA synthesis visualized by fluorescence widefield, confocal and super-resolution microscopy
    Authors:
    Pierzyńska-Mach A, Szczurek A, Cella Zanacchi F, Pennacchietti F, Drukała J, Diaspro A, Cremer C, Darzynkiewicz Z, Dobrucki JW
    Academic press:
    Cell Cycle (rok: 2016, tom: 15(8), strony: 1156-67), Wydawca: Taylor and Francis
    Status:
    Published
    DOI:
    10.1080/15384101.2016.1158377 - link to the publication
  8. UV-induced spectral shift and protonation of DNA fluorescent dye Hoechst 3325
    Authors:
    Żurek-Biesiada D, Waligórski P, Dobrucki JW.
    Academic press:
    Journal of Fluorescence (rok: 2014, tom: 24(6), strony: 1791-1801), Wydawca: Spinger
    Status:
    Published
    DOI:
    10.1007/s10895-014-1468-y - link to the publication
  9. Activation of new replication foci under conditions of replication stress
    Authors:
    Rybak P, Waligórska A, Bujnowicz Ł, Hoang A, Dobrucki JW.
    Academic press:
    Cell Cycle (rok: 2015, tom: 14(16), strony: 2634-47), Wydawca: Landes Bioscience / Taylor & Francis
    Status:
    Published
    DOI:
    10.1080/15384101 - link to the publication
  10. Low level phosphorylation of histone H2AX on serine 139 (γH2AX) is not associated with DNA double-strand breaks
    Authors:
    Rybak P, Hoang A, Bujnowicz L, Bernas T, Berniak K, Zarębski M, Darzynkiewicz Z, Dobrucki J
    Academic press:
    Oncotarget (rok: 2016, tom: 7(31), strony: 49574-49587), Wydawca: Impact Journals
    Status:
    Published
    DOI:
    10.18632/oncotarget.10411 - link to the publication
  11. Human SUV3 helicase regulates growth rate of the HeLa cells and can localize in the nucleoli.
    Authors:
    Szewczyk M, Fedoryszak-Kuśka N, Tkaczuk K, Dobrucki J, Waligórska A, Stępień PP.
    Academic press:
    Acta Biochimica Polonica (rok: 2017, tom: 64(1), strony: 177-181), Wydawca: Acta Biochimica Polonica
    Status:
    Published
    DOI:
    10.18388/abp.2016_1419 - link to the publication
  12. PML-like subnuclear bodies, containing XRCC1, juxtaposed to DNA replication-based single-strand breaks
    Authors:
    Magdalena M. Kordon, Aleksander Szczurek, Krzysztof Berniak, Oskar Szelest, Kamil Solarczyk, Magdalena Tworzydło, Sebastian Wachsmann-Hogiu, Anne Vaahtokari, Christoph Cremer, Thoru Pederson, Jurek W. Dobrucki
    Academic press:
    FASEB Journal (rok: 2019, tom: 33(2), strony: 2301-2313), Wydawca: Federation of American Societies For Experimental Biology
    Status:
    Published
    DOI:
    10.1096/fj.201801379R - link to the publication
  13. The 4D nucleome in Kraków - Prospects for an emerging field
    Authors:
    Dobrucki J, Saitoh N
    Academic press:
    Nucleus (rok: 2017, tom: 8(5), strony: 447-448), Wydawca: Taylor and Francis
    Status:
    Published
    DOI:
    10.1080/19491034 - link to the publication
  14. Quantitative super-resolution localization microscopy of DNA in situ using Vybrant® DyeCycle™ Violet fluorescent probe
    Authors:
    Żurek-Biesiada D, Szczurek AT, Prakash K, Best G, Mohana GK, Lee HK, Roignant JY, Dobrucki JW, Cremer C, Birk U.
    Academic press:
    Data in Brief (rok: 2016, tom: 7, strony: 157-71), Wydawca: Elsevier
    Status:
    Published
    DOI:
    10.1016/j.dib.2016.01.041 - link to the publication
  15. Toll-Like Receptor 4, but Not Neutrophil Extracellular Traps, Promote IFN Type I Expression to Enhance Th2 Responses to Nippostrongylus brasiliensis
    Authors:
    Pellefigues C, Tang SC, Schmidt A, White RF, Lamiable O, Connor LM, Ruedl C, Dobrucki J, Le Gros G, Ronchese F
    Academic press:
    Frontiers in Immunology (rok: 2017, tom: 8, strony: 1575), Wydawca: Frontiers Media S.A.
    Status:
    Published
    DOI:
    10.3389/fimmu.2017.01575 - link to the publication
  16. 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
    Authors:
    Solarczyk KJ, Kordon M, Berniak K, Dobrucki JW.
    Academic press:
    DNA Repair (rok: 2016, tom: 37, strony: 45647), Wydawca: Elsevier
    Status:
    Published
    DOI:
    10.006 - link to the publication

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