logoUW

Communities:

FacebookTwitter

Erasmus (archival record) Print option in slimbox / lytebox? (info)
Wednesday, 04 May 2011 12:16

Our ERASMUS coordinator:
prof. Anna M. Rychter

General information

The vast majority of regular lectures and courses at the Faculty of Biology are offered in Polish only. If your command of the language is satisfactory, please go to the Polish version of our www page to learn more about our offer.

For those of you not reading Polish we offer a choice of individual one-semester (3-5 months) laboratory projects in English at the departments listed below. To learn more do not hesitate to contact persons indicated (heads of the respective departments). Please note that the list is likely to be expanded soon, so if you do not find anything of particular interest now, do visit the site again in a week or two.

Białowieża Geobotanical Station
(Institute of Botany)

Head: dr. Bogdan Jaroszewicz, This e-mail address is being protected from spambots. You need JavaScript enabled to view it

Scientific activity of the Station focuses on ecology of natural forests, plant ecology, plant invasions and plant-animal interactions. The research is based on long-term studies, with the oldest ones started in 1960s.

Your laboratory training will focus on field and lab experiments related to seed dispersal and survival. Field experiments will be carried out in the Białowieża Forest and at Biebrza Marshes (North-East Poland).

Techniques and skills. Students will be trained in investigation of ecological phenomena related to plant dispersal: sampling of soil for seed bank studies, conduction of greenhouse experiments, design of field experiments focused on plant dispersal, especially by zoochory, determination of plant species on the basis of seed and seedling morphology.

Recent publications:

  • Jaroszewicz B., Pirożnikow E., Sagehorn R. 2008: European bison as seed dispersers: an effect on species composition of a disturbed pine forest community. Canadian Journal of Botany, 86: 475-484.
  • Jaroszewicz B., Pirożnikow E., Sagehorn R. 2009: Endozoochory by European bison (Bison bonasus) in Białowieża Primeval Forest across a management gradient. Forest Ecology and Management, in print.

Department of Plant Bioenergetics
(Institute of Experimental Plant Biology)

Head: prof. Anna M. Rychter

Scientific activity: Energy economy of the plant cell; influence of environment and role of mitochondria in maintaining cell redox homeostasis; cyanide-resistant respiration and alternative oxidase (regulation and activity); influence of environmental factors on formation of reactive species and oxidative defense systems.

Projects offered for visiting students: ATP and NADH changes as affected by differences in supply of sulphur or nitrogen; alternative oxidase and cyanide-resistant respiration during stress; plant defense against reactive species formation; structure and capacity of plant respiratory chain examined by Blue Native electrophoresis(BN PAGE).

You will receive training in (some of) the following techniques: spectrophotometry, oxygraphy, luminometry, HPLC, immunodetection, gel electrophoresis, electron and fluorescence microscopy.

Recent publications:

  • Szal B, Dąbrowska Z, Malmberg G, Gardestrom P, Rychter AM 2008 Changes in energy status of leaf cells as a consequence of mitochondrial genome rearrangement Planta 227:697-706
  • Juszczuk IM, Rychter AM 2009 BN-PAGE analysis of the respiratory chain complexes in mitochondria of cucumber MSC16 mutant Plant Physiol. Biochem. 47: 397-406
  • Skutnik M, Rychter AM 2009 Differential response of antioxidant systems in leaves and roots of barley subjected to anoxia and post-anoxia J. Plant Physiol.doi:10.1016/j.jplph.2008.11.010

Department of Metabolic Regulation
(Institute of Biochemistry)

Head: dr. Maciej Garstka, This e-mail address is being protected from spambots. You need JavaScript enabled to view it

Scientific activity. Metabolism of glucose and amino acids under normal and pathological conditions; proteome and lipidome of thylakoid membranes, changes in chloroplast structure under chilling stress.

Projects offered for visiting students: analysis of lipid and protein composition of thylakoids of higher plants; investigation of chloroplast structure in situ by confocal laser scanning microscopy; glucocorticoid effects on regulation of gluconeogenesis with the use of renal tubules grown in primary cultures; regulation of AMPK signaling pathways; diabetes-induced changes in mitochondrial morphology and function; effect of PPAR agonists on metabolic and proteomic profiles in kidney of diabetic animals; role of antioxidant status in energy metabolism of renal tubules

Methods used: electrophoretic techniques (native-PAGE, SDS-PAGE; immunodetection (Western));liquid chromatography and mass spectrometry of metabolites, lipids, pigments and proteins (HPLC- UV/VIS/Flu, HPLC-ESI/MS), ion chromatography; confocal laser scanning microscopy; absorption and emission spectrophotometry; determination and analysis of enzyme activity; isolation of renal tubules, hepatocytes and mitochondria, primary cultures and cell cultures; isolation of chloroplasts, thylakoids and chlorophyll-protein-complexes; gene silencing, transcript analysis.

Recent publications:

  • Gruszecki WI, Gospodarek M, Grudziński W, Mazur R, Gieczewska K, Garstka M (2009) Light-induced change of configuration of the LHCII-bound xanthophyll (tentatively assigned to violaxanthin): A resonance Raman study. J. Phys. Chem. B 113: 2506-2512
  • Kiersztan A, Baranska A, Hapka M, Lebiedzińska M, Winiarska K, Dudziak M, Bryla J (2009) Differential action of methylselenocysteine in control and alloxan diabetic rabbits. Chem.-Biol. Interac.; J. Mol. Cell. Biochem. Toxicol. 177: 161-171
  • Winiarska K, Szymański K, Górniak P, Dudziak M, Bryla J (2009) Hypoglycaemic, antioxidative and nephroprotective effects of taurine in alloxan-diabetic rabbits. Biochimie, 91: 261-270
  • Derlacz RA, Hyc K, Usarek M, Jagielski AK, Drożak J, Jarzyna R (2008) PPAR-γ-independent inhibitory effect in primary cultured rabbit kidney-cortex tubules. Biochem. Cell Biol. 86: 396-404
  • Garstka M, Venema JH, Rumak I, Gieczewska K, Rosiak M, Kozioł-Lipińska J, Kierdaszuk B, Vredenberg WJ, Mostowska A. (2007) Contrasting effect of dark-chilling on chloroplast structure and arrangement of chlorophyll-protein complexes in pea and tomato: plants with a different susceptibility to non-freezing temperature. Planta 226:1165-1181

Department of Molecular Biology
(Institute of Biochemistry)

Head: prof. Krzysztof Staroń, This e-mail address is being protected from spambots. You need JavaScript enabled to view it  

Scientific activity. Investigation of selected nuclear proteins: topoisomerase I (topo I), enhancer of rudimentary homolog (ERH) and protein kinase CK2 (CK2). Studies are aimed at finding protein partners of topo I, ERH and CKII and understanding the structural basis of the interactions as well as their role in subnuclear localization of the proteins. Two of these proteins are also targets of anti-cancer drugs.

Projects offered for visiting students: protein kinase activity of topo I; interactions between ERH and its protein partners; apoptotic proteins phosphorylated by CKII.

Techniques used: bacterial transformation, heterologous protein expression; DNA isolation and purification, PCR, DNA recombination in vitro, DNA electrophoresis, protein isolation and affinity purification, Blue Native- and SDS-PAGE, western-blotting, protein interaction assays, siRNA, eukaryotic cell cultures, confocal and fluorescence microscopy of tagged proteins.

Recent publications:

  • Malanga M, Czubaty A, Girstun A, Staron K, Althaus FR. (2008) Poly(ADP-ribose) binds to the splicing factor ASF/SF2 and regulates its phosphorylation by DNA topoisomerase I. J Biol Chem. 283,19991-19998.
  • Lukasik A, Uniewicz KA, Kulis M, Kozlowski P. (2008) Ciz1, a p21Cip1/Waf1-interacting zinc finger protein and DNA replication factor, is a novel molecular partner for human enhancer of rudimentary homolog. FEBS J. 275, 332-340.

Department of Applied Microbiology
(Institute of Microbiology)

Head: prof. Jacek Bielecki, This e-mail address is being protected from spambots. You need JavaScript enabled to view it

Scientific activity. Mechanisms of microbial pathogenesis and production of vaccines, use of live vectors (Listeria monocytogenes) in biotechnology of new-generation vaccines (induction of intracellular immunity, use of molecular mechanisms of toxin activity and different determinants of pathogenesis in vaccine design), anti-cancer vaccines.

Projects offered for visiting students: investigation of molecular mechanisms of bacterial toxin activity and different determinants of pathogenesis for use in vaccine design; construction of bacterial strains expressing toxins as potential anti-cancer vaccines.

Methods used: determination of cytotoxicity of chosen bacterial pathogenic factors in eukaryotic cells, cloning and expression of genes encoding bacterial toxins. Modern molecular biology, microbiology (cloning, PCR, Southern (DNA) blotting, Northern (RNA) blotting, Western blotting, DNA sequencing, oligo-directed mutagenesis, protein expression) , advanced microscopy and optical imaging techniques. Some experience in tissue culture methods is desirable.

Recent publications:

  • Krawczyk-Balska A., Bielecki J. (2005). Listeria monocytogenes listeriolysin O and phosphatidylinositol-specific phospholipase C affect adherence to epithelial cells. Can. J. Microbiol., 51, 745-751
  • Wiśniewski J., Krawczyk-Balska A. and Bielecki J. (2006). Associated roles of hemolysin and p60 protein for the intracellular growth of Bacillus subtilis. FEMS Immunol. & Med. Microbiol., 46, 330 - 339.

Department of Bacterial Genetics
(Institute of Microbiology)

Head: prof. Dariusz Bartosik, This e-mail address is being protected from spambots. You need JavaScript enabled to view it

Research group of prof. Katarzyna Jagusztyn-Krynicka

Scientific activity. Investigations of pathogenic bacteria: functional analysis of Campylobacter and Helicobacter unique genes whose products are potentially involved in pathogenesis, construction of avirulent Salmonella expressing Campylobacter antigens and evaluation of the efficacy of vaccine prototype (animal model – chickens).

Projects offered for visiting students: mechanisms of Campylobacter spp. and H. pylori Dsb (disulphide bond) pathway functioning. Dsb family of redox proteins facilitate formation of disulfide bridges in periplasmic proteins of Gram-negative pathogens. Understanding of the process crucial in the pathogenicity of these microorganisms might also facilitate identification of new candidate proteins for vaccine construction.

Techniques used: classical bacterial genetics and molecular microbiology. Laboratory is equipped for conducting work on gene cloning, evaluation of gene expression, protein purification and studying interaction between pathogen and eukaryotic cells.

Recent publications:

  • Raczko A., J. M. Bujnicki, M. Pawłowski, R. Godlewska, M. Lewandowska and E. K. Jagusztyn-Krynicka. 2005. Characterisation of new DsbB-like thiol-oxidoreductases of Campylobacter jejuni and Helicobacter pylori and classification of the DsbB family based on phylogenomic, structural, and functional criteria. Microbiology. 51: 219-231
  • Jagusztyn-Krynicka E. K., P. Łaniewski, A. Wyszyńska. 2009. An update on Campylobacter jejuni vaccine development for bacterial gastroenteritis treatment. Expert Review of Vaccine 8:625-645

Research group of prof. Dariusz Bartosik

Scientific activity. Biology of mobile genetic elements (MGE) - transposable elements, integrons, plasmids and bacteriophages, as well as genomic islands and islets acquired by lateral transfer events. We analyze MGEs in strains of Proteobacteria isolated form various environments. The analyzed elements are a source of genetic modules used for construction of specific cassettes useful in genetic engineering and biotechnology.

Projects offered for visiting students: identification and characterization of novel bacterial plasmids and transposable elements; cloning of basal plasmid replicons (by construction of shuttle plasmids), characterization of the thus obtained mini-derivatives (e.g. determination of host range etc.); DNA sequencing and bioinformatic sequence analyses. Transposable elements will be identified using entrapment vectors which enable capture of functional TEs.

Techniques used: isolation of plasmid and megaplasmid DNA, DNA cloning, introduction of foreign DNA into bacterial cells, PCR amplification, DNA sequencing, DNA hybridization, bioinformatic sequence analyses.

Recent publications:

  • Dziewit, L., M. Jazurek, L, Drewniak, J. Baj, and D. Bartosik. 2007. SXT conjugative element and linear prophage N15 encode novel type of toxin-antitoxin stabilizing systems homologous to tad-ata locus of plasmid pAMI2 of Paracoccus aminophilus. J. Bacteriol. 189: 1983-1997.
  • Bartosik, D., M. Putyrski, L. Dziewit, E. Malewska, M. Szymanik, E. Jagiello, J. Lukasik and J. Baj. 2008. Transposable modules generated by a single copy of insertion sequence ISPme1 and their influence on structure and evolution of natural plasmids of Paracoccus methylutens DM12. J. Bacteriol. 190: 3306-3313.

Department of Hydrobiology
(Institute of Zoology)

Head: prof. Z. Maciej. Gliwicz, This e-mail address is being protected from spambots. You need JavaScript enabled to view it

Scientific activity. Evolutionary and population ecology of plankton and fish. Phytoplankton-zooplankton and zooplankton-fish interface. Molecular, behavioral, life-history and morphological adaptations to predation and food limitations. Role of Heat Shock Proteins (HSP) in individual reaction to stress from biotic and abiotic factors in Daphnia as a model.

Projects offered for visiting students: two patterns of prey selection by a planktivorous fish (roach as a predator harvester, and a predator hunter) and prey (Daphnia) demographic, life-history and behavioral responses to the risk of predation; variations in life history, morphology and depth selection behavior of Daphnia mediated by the presence of filamentous cyanobacteria.

Techniques used: standard methods in growing planktonic algae, cyanobacteria, zooplankton (flow-through cultures) and fish in lab cultures; video techniques in fish behavioural studies; “plankton organ” as a tool for studying depth selection patterns in Daphnia.

Recent publications:

  • Bednarska A. & Dawidowicz P. 2007. Change in filter-screen morphology and depth selection: uncoupled responses of Daphnia to the presence of filamentous cyanobacteria. Limnol. Oceanogr. 52: 2358-2363.
  • Gliwicz, Z.M. and Wrzosek, D. 2008. Predation-mediated coexistence of large- and small-bodied Daphnia at different food levels. Am. Nat. 172: 358-374.
  • Slusarczyk M. & Pietrzak B. 2008. To sink or float: the fate of dormant offspring is determined by maternal behaviour in Daphnia. Freshwater Biol. 53: 569-576.

Institute of Genetics and Biotechnology

Scientific activity: The main avenues of research concentrate on the regulation of gene expression in filamentous fungi (prof. Piotr Weglenski, Dr Agnieszka Dzikowska), RNA turnover and mitochondrial gene expression in yeast (prof. Pawel Golik), mitochondrial gene expression in vertebrates (prof. Piotr Stepien), mitochondrial mutations in human disease (prof. Ewa Bartnik, Dr Katarzyna Tonska), small nuclear RNA expression in yeast and plants (prof. Joanna Kufel) and applications of molecular genetics to population and conservation biology and archaeology (prof. Piotr Weglenski, Dr Ana Stanković), proteomics and mechanisms of nuclear RNA turnover (prof. Michal Dadlez, Dr Andrzej Dziembowski), mutagenesis and DNA repair (prof. Barbara Tudek). More details can be fount at the website: http://www.igib.uw.edu.pl/index.php?id=80

Example projects available for MS students (contact the respective Principal Investigators for curent possibilities, contact information to be found on the Institute’s website): 

  • nucleo-mitochondrial interactions in yeasts - functional analysis of the Irc3p putative RNA helicase (prof. Pawel Golik)
  • RNA maturation and surveillance in yeasts and plants (prof. Joanna Kufel)

Techniques: basic culture and phenotype analysis of bacteria, yeasts, filamentous fungi, vertebrate cells and Arabidopsis, bacterial and yeast transformation, heterologous protein overexpression; DNA isolation and purification, PCR, DNA recombination in vitro, DNA electrophoresis, protein isolation and affinity purification, SDS-PAGE, western-blotting, protein interaction assays, siRNA, microscopic observation of fluorescently tagged proteins, isolation of mitochondria from yeast and vertebrate cells, protein-RNA interactions.

Selected publications:

  • Malecki M, Jedrzejczak R, Stepien PP, Golik P. In vitro reconstitution and characterization of the yeast mitochondrial degradosome complex unravels tight functional interdependence. J Mol Biol. 2007 372(1):23-36.
  • Grzechnik P, Kufel J. Polyadenylation linked to transcription termination directs the processing of snoRNA precursors in yeast. Mol Cell. 2008 32(2):247-58.
  • Szczesny RJ, Borowski LS, Brzezniak LK, Dmochowska A, Gewartowski K, Bartnik E, Stepien PP. Human mitochondrial RNA turnover caught in flagranti: involvement of hSuv3p helicase in RNA surveillance. Nucleic Acids Res. 2009 Oct 28. [Epub ahead of print]
  • Lebreton A, Tomecki R, Dziembowski A, Séraphin B. Endonucleolytic RNA cleavage by a eukaryotic exosome. Nature. 2008 456(7224):993-6