Section of Microbial Genetics

Head of the Department : dr hab. Paweł Stączek, prof. nadzw. UŁ

Address: 90-237 Łódź, ul. Banacha Street 12/16, building A

Phone: +48 42 635 44 66

Fax: +48 42 665 58 18

e-mail:

 

Staff:

Name and surname

Phone

e-mail

Building/room

Consultation hours

dr hab. Paweł Stączek, prof. nadzw. UŁ (Head of the Department)

+48 42 635 44 66

A / 388

Mn. 09:45-11:45

prof. dr hab. Adam Jaworski (professor emeritus)

+48 42 635 44 66

A / 388

 

dr hab. Anna Sajduda (univ. prof. )

+48 42 635 47 72

A / 386

Fr. 10:30-12:30

dr Anita Ciesielska (adjunct)

+48 42 635 47 72

A / 386

Tu. 08:15-10:15

dr Marek  Gadzalski (adjunct)

+48 42 635 47 72

A / 386

Th. 10:30-12:30

 

PhD students:

Name and surname

Phone

e-mail

mgr Alina Górna

+48 42 272 36 33

 

mgr Aleksandra Strzelczyk

+48 42 635 47 72

 

 

Research topics

Biological activity of new hydrazones as compounds of strong antimicrobial potential.

  • Evaluation of antimicrobial activity of newly synthesized compounds against reference strains and clinical isolates
  • Analysis of cytotoxicity, genotoxicity and mutagenicity of the selected, most potent antimicrobials
  • Estimation of the rate of drug resistance development in bacterial cells
  • Studies on the mechanism of antimicrobial activity of hydrazones as well as on the mechanisms of drug resistance against these compounds

 

Molecular diagnostics end epidemiology of mycobacteria.

  • Molecular differentiation of tubercle bacilli (Mycobacterium tuberculosis) based on the polymorphic DNA sequences (insertion elements, various types of repetitive DNA segments).
  • Identification of acid fast bacilli Mycobacterium sp. with the useof molecular methods (sequencing of 16S rDNA, rpoB; restriction analysis of hsp65).
  • Determination of molecular mechanisms of M. tuberculosis resistance to antituberculosis drugs (real-time PCR, sequencing of genomic DNA regions conferring drug resistance).
  • Identification and characterization of insertion sequences and other repetitive DNA elements in genus Mycobacterium

 

Molecular biology of dermatophytes

  • Identification and genotyping of clinical and environmental dermatophyte strains using molecular methods ((PCR, PCR- RFLP, RAPD, PCR-MP)
  • Search and analysis of genes involved in pathogenicity of dermatophytes. Two classes of genes were chosen: the ones encoding ABC transporters as well as the genes responsible for synthesis of proteins containing LysM domains. The project involves bioinformatic analysis of dermatophyte genomes, and identified genes as well as their products are subjects to phylogenetic and comparative studies, moreover the domain organization of these proteins is investigated. The results of this study will be useful in the planned analyses of the expression patterns of these chosen genes in response to environmental conditions related to the process of host infection

 

Other research interests:

  • Spatial organization of bacterial chromosome
  • The role of non-B-DNA structures in genetic variation

 

Research projects

  • 2011-2013.  NCN  (National Center of Science) grant  No  NN402 692640 -  Analysis of clonal structure of dermatophyte clinical strains isolated from patients of Łódź region in the years 2000-2010
  • 2010-2013. Grant from the Polish Ministry of Science and Higher Education No NN 304099039 – Analysis of species composition and diversity of intraspecies clonal structure of dermatophytes and other keratinolytic fungi transmitted in natural environments by selected bird species in Poland
  • 2010-2013.    NCN (National Center of Science)  grant No NN302 111338  -  Molecular epidemiology of mycobacteria: optimization and preliminary validation of high throughput genotyping methods
  • 2010-2012. Grant from the Polish Ministry of Science and Higher Education No  NN303 568938 – The studies of clonal structure of Microsporum canis and other dermatophyte species isolated from humans and animals in Poland

Cooperation

  • Department of Organic Chemistry, Faculty of Pharmacology, Medical University of Lublin
  • Institute of Medical Biology, Polish Academy of Sciences, Łódź, Poland
  • Chair of Environmental Microbiology, University of Life Sciences in Lublin, Poland
  • Clinic of Pediatric and Oncologic Dermatology, Medical University in Łódź, Poland
  • Department of Biochemistry and Molecular Biology, University of Alabama at Birmingham, USA
  • Institute of Tropical Medicine, Antwerpia, Belgium
  • Nationales Referenzzentrum für Mykobakterien, Forschungszentrum Borstel, Borstel, Germany
  • Institute of Medical Mycology, Tokyo University, Japan

Services/Expertise

  • Molecular diagnostics and epidemiology of pathogenic skin fungi (dermatophytes)
  • Molecular diagnostics and epidemiology of mycobacteria
  • Analysis of mutagenicity, genotoxicity and antimicrobial activity of drug precursors

 

 

Selected publications

Original papers

1. Jaworski A., Hsieh W.T., Larson J., Wells R.D., 1987. Left-handed DNA in vivo. Science, 238, 773-777.

2. Zacharias W., Jaworski A., Larson J., Wells.R.D., 1988. The B-Z DNA equilibrium in vivo is perturbed by biological processes. PNAS USA, 85, 7069-7073.

3. Kang S., Jaworski A., Ohshima K., Wells R.D., 1995. Expansion and deletion of CTG triple repeats from human diseases genes are determined by the direction of replication. Nature Genetics, 10. pp. 213-218.

4. aworski A., Rosche W.A., Gellibolian R., Kang S., Shimizu M., Bowater R.P., Sinden R.R., Wells R.D., 1995. Mismatch repair in E. coli  enhances instability of (CTG)n triplet repeats from human hereditary diseases. PNAS USA, 92, 11019-11023.

5. Bowater R.P., Jaworski A., Rosche W.A., Kang S., Sinden R.R., Wells R.D., 1996. Relationship between E. coli growth and deletions of CTG/GAC triplet repeats in plasmids. J. Biol. Chem., 264, 82-96.

6. Stączek P., N.P. Higgins. 1998. Gyrase and Topo IV modulate chromosome domain size in vivo.  Mol. Microbiol., 29, 6, 1435-1448.

7. Bacolla A., Jaworski A., Connors T.D., Wells R.D. 2001.  PKD1 unusual DNA conformations are recognized by nucleotide excision repair. J. Biol. Chem., 276, 21, 18597-18604.

8. Bacolla A.,  Jaworski A., Larson J. E., Jakupciak J. P., Chuzanova N., Abeysinghe S. S., O’Connell C.D., Cooper D. N., and Wells R. D. 2004. Breakpoints of Long Deletions Coincide With non-B DNA Conformation. Proc. Natl. Acad. Sci. USA, 101, 39, 14162-14167.

9. Sajduda A., Brzostek A., Popławska M., Augustynowicz-Kopeć E., Zwolska Z., Niemann S., Dziadek J. and Hillemann D. 2004. Molecular characterization of rifampin and isonazid-resistant Mycobacterium tuberculosis strains isolated in Poland. J. Clin. Microbiol. 42, 2425-2431.

10. Majchrzak M. , Bowater R.P., Stączek P., Parniewski P. 2006. SOS Repair and DNA Supercoiling Influence the Genetic Stability of DNA Triplet Repeats in Escherichia coli.  J. Mol. Biol. 364, 612–624.

11. Sajduda A., Dziadek J., Kotłowski R. and Portaels F. 2006. Evaluation of multiple genetic markers for typing drug-resistant Mycobacterium tuberculosis strains from Poland. Diagn. Microbiol. Infect. Dis. 55, 59-64.

12. Brudey K., Driscoll J.R., Rigouts L., Prodinger W.M., Gori A., Al-Hajoj S.A., Allix C., Aristimuno L., Arora J., Baumanis V., Binder L., Cafrune P., Cataldi A., Cheong S., Diel R., Ellermeier C., Evans J.T., Fauville-Dufaux M., Ferdinand S., Garcia de Viedma D., Garzelli C., Gazzola L., Gomes H.M., Gutierrez M.C., Hawkey P.M., van Helden P.D., Kadival G.V., Kreiswirth B.N., Kremer K., Kubin M., Kulkarni S.P., Liens B., Lillebaek T., Ly H.M., Martin C., Martin C., Mokrousov I., Narvskaia O., Ngeow Y.F., Naumann L., Niemann S., Parwati I., Rahim M.Z., Rasolofo-Razanamparany V., Rasolonavalona T., Rossetti M.L., Rusch-Gerdes S., Sajduda A., Samper S., Shemyakin I., Singh U.B., Somoskovi A., Skuce R., van Soolingen D., Streicher E.M., Suffys P.N., Tortoli E., Tracevska T., Vincent V., Victor T.C., Warren R., Yap S.F., Zaman K., Portaels F., Rastogi N. and Sola C. (2006): Mycobacterium tuberculosis complex genetic diversity: mining the fourth international spoligotyping database (SpolDB4) for classification, population genetics and epidemiology. BMC Microbiol. 6, 23.

13. Szwarocka S.T.,  Stączek P.,  Parniewski P. 2007. Chromosomal model for analysis of a long CTG/CAG tract stability in wild-type Escherichia coli and its nucleotide excision repair mutants. Can. J. Microbiol.53, 860-868.

14. Dobrowolska A, Stączek P. 2009. Development of transformation system for  Trichophyton rubrum by electropotration of germinated conidia.Curr. Genet., 55, 537-542.

15.Leibner-Ciszak J., Dobrowolska A., Krawczyk B. Kaszuba A., and Stączek P. 2010. Evaluation of a PCR melting profile method for intraspecies differentiation of Trichophyton rubrum and Trichophyton interdigitale.   J. Med. Microbiol. 59, 185-192.

16. Siwek A.,  Stączek P., Wujec M., Stefańska J., Kosikowska U., Malm A., Bielawska A., Bielawski K., Jankowki S., Paneth P. 2010. Biological and docking studies of topoisomerase IV inhibition by thiosemicarbazides. Journal of Molecular Modeling 17: 2297-2303

17. Siwek A, Stączek P, Stefańska J. 2011. Synthesis and structure-activity relationship studies of 4-arylthiosemicarbazides as topoisomerase IV inhibitors with Gram-positive antibacterial activity. Search for molecular basis of antibacterial activity of thiosemicarbazides. Eur J Med Chem., 46, 5717-5126.

18. Siwek A.,  Stączek P., Kosikowska U., Malm A., Paneth P., Jankowki S. 2012. Does dehydrocyclization of 4-benzoylthiosemicarbazides in acetic acid lead to s-triazoles or thiadiazoles? Structural Chemistry, 23, 1441–1448.

19. Pieczonka A.M., Strzelczyk A., Sadowska B., Mlostoń G. Stączek P., 2013. Synthesis and evaluation of antimicrobial activity of 3-oxido-1H-imidazole-4-carbohydrazides hydrazones.  Eur. J. Med. Chem. 64, 389-395.

20. Siwek A., Plech T., Stefańska J., Stączek P, Strzelczyk A., 2013.Molecular Properties Prediction, Docking Studies, and Antimicrobial Screening of 1,3,4-Thiadiazole and S-Triazole Derivatives. Current Computer-Aided Drug Design, Oct. 19, E-Pub ahead of Print, ISSN: 1573-4099.

21. Siwek A., Stączek P., Paneth P., Stefańska J. Nowa pochodna 1,4-dipodstawionego  tiosemikarbazydu oraz sposób jej wytwarzania. Zgłoszenie Patentowe P-390774. Biuletyn Urzędu Patentowego Nr 20(985), s. 16, 2011. (2012, Patent RP Nr 212639)

22. Sajduda A., Martin A., Portaels F., and Palomino J. C. 2012. hsp65 PCR-restriction analysis (PRA) with capillary electrophoresis for species identification and differentiation of Mycobacterium kansasii and M. chelonae-M. abscessus group. Int. J. Infect. Dis. 16 3, e193-e197

23. Sajduda A., Martin A., Portaels F. and Palomino J. C. 2012. hsp65 PCR-restriction analysis (PRA) with capillary electrophoresis in comparison to three other methods for identification of Mycobacterium species. J. Microbiol. Methods 80, 190-197.

 

Monographs

Parniewski P., Stączek P., 2002. Molecular  mechanisms of TRS instability. (w):    “Triplet Repeats Diseases of the NervousSystem”. Ed. L.Timchenko, Landes  Biosciences (Eurekah.com), USA,  s. 1-21, ISBN 1-58706-055-8 

Różalski A. Stączek P. 2010. Proteus. (w) Molecular detection of human pathogens. Ed. D. Liu, Taylor and Francis Group, LLC, p.981-996., ISBN 

 

Dissertation topics

Examples of dissertations for bachelor degree

  • Application of bacteriophages in molecular biology, medicine and genetic engineering
  • Quorum sensing in bacteria
  • Bacterial plasmids as vectors for foreign DNA transfer
  • New anti-mycobacterial drugs
  • Integrons and superintegrons

Examples of dissertations for master degree

  • The search for factors responsible for supercoil diffusion barriers in Salmonella Typhimurium chromosome
  • Analysis of antibacterial activity of tiosemicarbazide derivatives - potential inhibitors of type II topoisomerases
  • Genotyping of mycobacteria strains collection
  • Transformation of the selected dermatophyte species using ATMT method
  • Genotyping of environmental keratinolytic fungi of Chryzosporium genus

Best students may be enrolled into the exchange program which allows to conduct M.Sc project in the University of Virginia and the University of Chicago, USA

  • The role of fascin and myosin X in filopodial function
  • Biochemistry of bacterial cellulose synthesis
  •  An investigation of an evolutionarily conserved pathway for tail-anchored protein insertion

 

Materials for students

Useful links

Photo gallery