Supervisors from Institute of Bioorganic Chemistry

 agnieszka.fiszer@ibch.poznan.pl

@ https://portal.ichb.pl/en/zaklad-biotechnologii-medycznej-en-2

Since 2019 Agnieszka Fiszer is leading the Department of Medical Biotechnology at IBCh. She received MSc at the Technical University of Lodz and in 2012 PhD at IBCh. Agnieszka Fiszer was a postdoc at IBCh, specializing in RNAi-based therapeutic approaches for polyglutamine diseases. In the meantime, she had research stays in the Institute of Myology (Paris, France) and the Institute of Genetics and Molecular and Cellular Biology (Illkirch, France). She has been a leader of 3 grants so far and has been the main investigator in several projects, including the EU grant. Agnieszka Fiszer received the Polish Prime Minister Award for PhD thesis, Ministry of Science and Higher Education scholarship for young scientists (2014-2018), and several awards for publications, for example, Prof. Szybalski Award for the best article in the field of biotechnology. She is a co-author of 19 papers, including published in Molecular Cell, Nucleic Acids Research, and RNA Biology (https://orcid.org/0000-0001-7829-1926)The main interest of the Department is the study of pathogenic pathways of polyglutamine diseases with the use of advanced cell culture models and with particular emphasis on RNA-oriented methods.  

Research interests:

Polyglutamine diseases, Huntington’s disease, triplet repeat tracts, RNA interference, RNA biology 

Major publications:

Ciesiolka et al. Cell Mol Life Sci (2021). 

Jazurek-Ciesiolka et al. J Mol Biol (2020). 

Witkos TM et al. RNA Biol (2018). 

Fiszer et al. Nucleic Acids Res (2014). 

Fiszer et al. Nucleic Acids Res (2013) 

Patent US9970004B2 (2018). 

jacek.kolanowski@ibch.poznan.pl

@ http://jacek.kolanowski.com

Jacek Kolanowski is head of the Department of Molecular Probes and Prodrugs (since 2017) and head of Poland’s first Centre for High-Throughput Screening Studies (since 2018) at the Institute of Bioorganic Chemistry, Polish Academy of Sciences (IBCh PAS). Since 2019 he is also a vice-chair of the Polish Young Academy. After graduating simultaneously in biotechnology and chemistry from AMU in Poznan, in 2010–2012 he held a PhD scholarship from Ligue Nationale contre le Cancer at ENS Lyon, where he completed his PhD in 2013. Then, he worked at the University of Sydney, first as postdoctoral fellow of the French Fondation ARC pour la Recherche sur le Cancer (2014-2015) and then as a postdoctoral research associate (2015-2017).

Currently, he is a principal investigator on three research projects from major Polish funding agencies and a local / work-package coordinator for the EU-OPENSCREEN-DRIVE international project (under the INFRADEV H2020 framework). He is an expert in chemical biology with research interests including, but not limited to, the design and development of small molecule tools to study biology (fluorescent and bioluminescent probes, protein labelling for studying local environments), high-throughput screening technologies and live cell imaging (including <2 nm fluorescent microscopy in MINFLUX technology).   Research interests:

Chemical biology, bioorganic chemistry, fluorescent probes, high-throughput screening, high-resolution fluorescent microscopy.

 

Major publications:

Kolanowski J.L., Liu F., New E.J. (2018).  “Fluorescent probes for the simultaneous detection of multiple analytes in biology”, Chemical Society Reviews, 47, 195-208.

Kolanowski J.L., Dawson LJ., Mitchell L., Lim Z., Graziotto M.E., Filipek W.K., Hambley TW., New E.J. (2018). “A fluorescent probe for investigating metabolic stability of active transplatin analogues”, Sensors and Actuators B: Chemical, 255 (3), 2721-2724.

Kolanowski J.L., Shen C., New E.J. (2017). “Fluorescent probes for the analysis of labile metals in brain cells”, in: Metals in the Brain, “Neuromethods” 124, 51-70.

Shen C., Kolanowski J.L., Tran C.M.-N.,Kaur  A., Akerfeldt M.C., Rahme M.S., Hambley T.W.,New E.J. (2016). “A ratiometric fluorescent sensor for the mitochondrial copper pool”, Metallomics, 8, 915-919;

Hasserodt J., Kolanowski J.L., Touti F., (2014). “Magnetogenesis in Water Induced by a Chemical Analyte”, Angewandte Chemie International Edition in English, 53, 60-73.

 mfigiel@ibch.poznan.pl

ORCID iD https://orcid.org/0000-0003-3961-4635

Maciej Figiel earned his PhD from the Department of Anatomy and Cell Biology of the University of Ulm, Germany (2001) for the discovery of regulation of glial glutamate transporters, which control glutamatergic signaling. After returning to Poland, he joined the Institute of Bioorganic Chemistry, Polish Academy of Sciences (IBCh PAS) in Poznań where he managed to produce the first knock-in mouse model of SCA3/MJD. He obtained his DSc (habilitation) degree in 2015 at the Nencki Institute of Experimental Biology. Since 2017, he has led the Department of Molecular Neurobiology at IBCh PAS in Poznań. As an independent researcher, he has discovered early molecular phenotypes of Huntington's disease related to p53 protein, MAPK, and WNT pathways in induced pluripotent stem cells. He is currently working on identifying the mechanisms of neurodegeneration in HD and SCA3/MJD by discovering both the early pre-symptomatic and symptomatic mechanisms of neurodegenerative disease, new biomarkers, and drug targets. Recently obtained extended Ki150 SCA3/MJD mouse model. He also works to define the neurodevelopmental mechanisms of neurodegenerative disorders. He is an expert and reviewer at the National Center for Research and Development, Polish National Science Centre, and Israel Science Foundation. A reviewer and expert for several neurobiology journals, the Jackson Laboratory and CHDI Foundation. Member of the EHDN. Principal investigator on research projects: Therapeutic research in E-RARE projects (SCA-CYP and TreatPolyQ) in international consortia; Single-cell project on HD as a neurodevelopmental disease. One of the co-authors and designer of the Polish SARS-CoV-2 diagnostic tests.

 

Research interests:

Polyglutamine diseases, mouse models, in vivo studies, neurodegeneration and stem cells, organoids, neurodevelopment, iPSC, AAV gene delivery.

 

Major publications:

Wiatr K., Piasecki P., Marczak Ł., Wojciechowski P., Kurkowiak M., Płoski R., Rydzanicz M., Handschuh L., Jungverdorben J., Brüstle O., Figlerowicz M., Figiel M. (2019). “Altered Levels of Proteins and Phosphoproteins, in the Absence of Early Causative Transcriptional Changes, Shape the Molecular Pathogenesis in the Brain of Young Presymptomatic Ki91 SCA3/MJD Mouse”, Mol Neurobiol.  Dec;56(12):8168-8202.

Świtońska K., Szlachcic W.J., Handschuh L., Wojciechowski P., Marczak Ł., Stelmaszczuk M., Figlerowicz M., Figiel M. (2019). “Identification of Altered Developmental Pathways in Human Juvenile HD iPSC with 71Q and 109Q Using Transcriptome Profiling”, Front Cell Neurosci.; 12:528.

Wiatr K., Szlachcic W.J., Trzeciak M., Figlerowicz M., Figiel M. (2018). “Huntington Disease as a Neurodevelopmental Disorder and Early Signs of the Disease in Stem Cells”, Mol Neurobiol. ; 55(4):3351-337.

Szlachcic W.J., Wiatr K., Trzeciak M., Figlerowicz M., Figiel M. (2017). “The Generation of Mouse and Human Huntington Disease iPS Cells Suitable for In vitro Studies on Huntingtin Function”, Front Mol Neurosci.; 10:253.

Szlachcic W.J., Switonski P.M., Krzyzosiak W.J., Figlerowicz M., Figiel M. (2015). “Huntington disease iPSCs show early molecular changes in intracellular signaling, the expression of oxidative stress proteins and the p53 pathway”, Dis Model Mech. 8(9):1047-57.

Switonski P.M., Szlachcic W.J., Krzyzosiak W.J., Figiel M. (2015). “A new humanized ataxin-3 knock-in mouse model combines the genetic features, pathogenesis of neurons and glia and late disease onset of SCA3/MJD”, Neurobiol Dis. 73:174-88.

 marta.olejniczak@ibch.poznan.pl

Marta Olejniczak is a molecular biologist, an expert in the field of gene therapy and neurodegenerative diseases, for many years associated with the Institute of Bioorganic Chemistry of the Polish Academy of Sciences (IBCh PAS) in Poznań, where she heads the Department of Genome Engineering. She obtained her DSc (habilitation) degree in 2016 at the Faculty of Biology of Adam Mickiewicz University in Poznań. She has completed several research internships, including CRISPR-Lab, Protein Technologies Facility, Vienna; the Department of Cancer Immunotherapeutics and Tumor Immunology, Beckman Research Institute, the City of Hope National Medical Center, USA; Stanford University, Palo Alto, USA.

The author of over 25 scientific publications published in international scientific journals (e.g. Nucleic Acids Research, Mol Ther Nucl Acids, RNA, BBA, Human Mutation) and co-inventor of 2 US patents on the use of RNA interference technology in the treatment of polyQ diseases.

 

Research interests:

Genome editing, RNA interference, gene therapy, polyglutamine disorders.

 

Major publications:

Kotowska-Zimmer A., Ostrovska Y., Olejniczak M. (2020). “Universal RNAi triggers for the specific inhibition of mutant huntingtin, atrophin-1, ataxin-3 and ataxin-7 expression”, Mol Ther Nucl Acids.

Dabrowska M., Olejniczak M. (2020). “Gene therapy for Huntington's disease using targeted endonucleases”, Methods Mol Biol.

Dabrowska M., Czubak K., Juzwa W., Krzyzosiak W.J., Olejniczak M., Kozlowski P. (2018).  “qEva-CRISPR: a method for quantitative evaluation of CRISPR/Cas-mediated genome editing in target and off-target sites”, Nucleic Acids Res.

Dabrowska M., Juzwa W., Krzyzosiak W.J., Olejniczak M. (2018). “Precise excision of the CAG tract from the Huntingtin Gene by Cas9 Nickases”, Front Neurosci.

Olejniczak M., Kotowska-Zimmer A., Krzyzosiak W.J. (2018). “Stress-induced changes in miRNA biogenesis and functioning”, Cell Mol Life Sci.

Olejniczak M., Galka P., Krzyzosiak W.J., (2010). “Sequence-non-specific effects of RNA interference triggers and microRNA regulators”, Nucleic Acids Res.

 msob@ibch.poznan.pl

@ https://publons.com/researcher/450165/michal-sobkowski/

Michał Sobkowski leads the Department of Chemistry of Nucleic Acids Components at the Institute of Bioorganic Chemistry, Polish Academy of Sciences (IBCh PAS), as well as the Institute’s Deputy Director for Scientific Affairs. He graduated from the Faculty of Chemistry of the Adam Mickiewicz University in Poznań and earned his PhD in organic chemistry in IBCh PAS in 1997, under the supervision of Prof. A. Kraszewski. After a post-doctoral stay (1998–2000) in Prof. H. Seliger’s lab at Universität Ulm (Germany), he returned to IBCh PAS where he became an assistant professor. His research activities are focused on the organophosphorus chemistry of natural products.

 

Research interests:

Bioorganic chemistry, organophosphorus chemistry, stereochemistry, reaction mechanism, H-phosphonate esters, nucleotide analogues, pronucleotides, oligonucleotides, protecting groups, antiviral drugs, anticancer drugs.

 

Major publications:

Romanowska J., Kolodziej K., Sobkowski M., Rachwalak M., Jakubowski T., Golebiewska J., Kraszewski A., Boryski J., Dabrowska A., Stawinski J. (2019). “Aryl H-phosphonates. 19. New anti-HIV pronucleotide phosphoramidate diesters containing amino- and hydroxypyridine auxiliaries”, Eur.J.Med.Chem. 164:47-58. http://dx.doi.org/10.1016/j.ejmech.2018.12.038.

Materna M., Stawinski J., Kiliszek A., Rypniewski W., Sobkowski M. (2016). “Oxyonium phosphobetaines - unusually stable nucleophilic catalyst-phosphate complexes formed from H-phosphonates and N-oxides”, RSC Adv. 6 (18):14448-14451. http://dx.doi.org/10.1039/C5RA27465F.

Kolodziej K., Romanowska J., Stawinski J., Kraszewski A., Sobkowski M. (2015). “The case of triethylammonium cation loss during purification of certain nucleotide analogues. A cautionary note”, Anal.Bioanal.Chem. 407 (6):1775-1780. http://dx.doi.org/10.1007/s00216-014-8397-0.

Kolodziej K., Romanowska J., Stawinski J., Boryski J., Dabrowska A., Lipniacki A., Piasek A., Kraszewski A.,  Sobkowski M. (2015). “Aryl H-Phosphonates 18. Synthesis, properties, and biological activity of 2',3'-dideoxynucleoside (N-heteroaryl)phosphoramidates of increased lipophilicity”, Eur.J.Med.Chem. 100:77-88. http://dx.doi.org/10.1016/j.ejmech.2015.06.004.

Sobkowski M., Kraszewski A., Stawinski J. (2015). “Recent Advances in H-Phosphonate Chemistry. Part 1 & 2”, Topics in Current Chemistry 361, 2015. http://dx.doi.org/10.1007/128_2014_562 & http://dx.doi.org/10.1007/128_2014_563.

Sobkowski M. (2010). “Chemistry and stereochemistry of internucleotide bond formation by the H-phosphonate method”, New.J.Chem. 34 (4):854-869. http://dx.doi.org/10.1039/b9nj00679f.

 monika.piwecka@ibch.poznan.pl

Twitter: @monika_piwecka

@ www.researchgate.net/profile/Monika_Piwecka

Monika Piwecka holds a Junior Group Leader position and heads the Department of Non-coding RNAs at the Institute of Bioorganic Chemistry, Polish Academy of Sciences (IBCh PAS). In 2006-2009 she held the PAS President’s Scholarship for outstanding scientific achievements conducted as a PhD candidate within institutes of the Polish Academy of Sciences. She earned her PhD from IBCh PAS in 2012, then next spent a 5-year postdoctoral fellowship at Max Delbrück Center for Molecular Medicine in Berlin, during which she published a very influential paper in the prestigious journal Science on the functional aspects of non-coding RNAs called circRNAs. Currently, she is developing her team at the IBCh PAS with the aim of advancing research beyond the state-of-the-art in the interface of RNA biology, systems biology and neuroscience. Dr. Piwecka has presented her research at international conferences and collaborates with both Polish and international research institutes. She is co-author of 2 international patents and 18 publications, including 13 listed in PubMed.

 

Research interests:

Non-coding RNAs, regulation of gene expression, transcriptomics, single-cell RNA sequencing, neuroscience.

 

Major publications: 

Piwecka M., Glažar P., Hernandez-Miranda L.R., Memczak S., Wolf S.A., Rybak-Wolf A., Filipchyk A.,

Klironomos F., Cerda Jara C.A., Fenske P., Trimbuch T., Zywitza V., Plass M., Schreyer L., Ayoub S., Kocks C., Kühn R., Rosenmund C., Birchmeier C., Rajewsky N. (2017). “Loss of a mammalian circular RNA locus causes miRNA deregulation and affects brain function”, Science, Sep 22;357(6357).

Piwecka M., Rolle K., Belter A., Barciszewska A.M., Żywicki M., Michalak M., Nowak S., Naskręt-Barciszewska M.Z., Barciszewski J. (2015). “Comprehensive analysis of microRNA expression profile in malignant glioma tissues”, Mol Oncol.,Aug; 9(7):1324-40.

Belter A., Rolle K., Piwecka M., Fedoruk-Wyszomirska A., Naskręt-Barciszewska M.Z., Barciszewski J. (2016).  “Inhibition of miR-21 in glioma cells using catalytic nucleic acids”, Sci Rep.,  Apr 15, 6:24516.

Piwecka M., Rolle K., Wyszko E., Żukiel R., Nowak S., Barciszewska M.Z., Barciszewski J. (2011). “Nucleic acid-based technologies in therapy of malignant gliomas”, Curr Pharm Biotechnol., Nov; 12(11):1805-22.

zwarkocki@ibch.poznan.pl 

Zbigniew Warkocki performed his PhD project at the lab of Prof. Reinhard Luhrmann at the Max-Planck Institute for Biophysical Chemistry in Gottingen, Germany. There he studied dynamics of the spliceosome, an exciting multicomponent complex comprising 5 snRNA, pre-mRNA and over 80 constitutive proteins that assembles de novo onto pre-mRNA to catalyze splicing. His studies facilitated the understanding of the processes preceding step 1 of splicing. After graduating in 2012, he moved to the lab of Prof. Andrzej Dziembowski at the Institute of Biochemistry and Biophysics, Polish Academy of Sciences in Warsaw, Poland, where he changed gears to investigate the role of 3’ RNA uridylation in posttranscriptional RNA metabolism in humans and discovered regulatory potential of uridylation over LINE-1 retrotransposons.

Since late 2018, he has been an independent group leader at the Institute of Bioorganic Chemistry, Polish Academy of Sciences (IBCh PAS) Poznan, Poland where together with his team he continues to study uridylation, 3’ end variability of cellular RNAs and retrotransposons using human model cell lines. He uses cell culture, flow cytometry, molecular biological and biochemical methods and computational approaches to decipher how different cytoplasmic enzymes shape posttranscriptional RNA landscape in humans.

Research interests:

RNA; uridylation; retrotransposons; posttranscriptional RNA metabolism.

Major publications:

Warkocki Z., Liudkovska V., Gewartowska O., Mroczek S., Dziembowski A., (2018). “Terminal nucleotidyl transferases (TENTs) in mammalian RNA metabolism”, Philos Trans R Soc Lond B Biol Sci., Nov 5;373(1762). https://doi.org/10.1098/rstb.2018.0162 PMID:30397099.

Warkocki Z., Krawczyk P., Adamska D., Bijata K., Garcia-Perez J., Dziembowski A. (2018). “Uridylation by TUT4/7 restricts retrotransposition of human LINE-1s”, Cell, Sep 6;174(6):1537-1548.e29. https://doi.org/10.1016/j.cell.2018.07.022.

Warkocki Z., Odenwälder P., Schmitzová J., Platzmann F., Stark H., Urlaub H., Ficner R., Fabrizio

P., Lührmann R. (2009). “Reconstitution of both steps of Saccharomyces cerevisiae splicing with purified spliceosomal components”, Nat Struct Mol Biol., Dec;16(12):1237-43. doi: 10.1038/nsmb.1729.

 akisiel@ibch.poznan.pl

Agnieszka Żmieńko earned her master's degree in biotechnology in 2000 and PhD in biochemistry in 2006. She works at the Laboratory of Genomics at IBCH PAS, where she manages its plant research division. In 2014-2020 she also worked as an assistant professor at the Institute of Computational Biology at Poznan University of Technology. During her career, Agnieszka was involved as a leader or collaborator in multiple research projects in plant genomics field, involving Arabidopsis, Brassica, Nicotiana, barley and maize species. Her current research interests focus on Arabidopsis intraspecies genomic variation and its influence on transcriptomic variation, especially in the context of plant response to biotic and abiotic stresses, as well as the links between noncoding RNA metabolism and genome stability. In her projects she uses cutting-edge genomics technologies (including second- and third generation sequencing) and she combines molecular and bioinformatics approaches. Agnieszka supervised numerous students at undergraduate and doctoral level, who succesfully published the results of their theses as coauthors in recognizable scientific journals.

 

Research interests:

Copy number variation, plant resistance, abiotic stress, nonocoding RNA, linear gene clusters, repeats, genome stability

 

Major publications:

Zmienko A., Marszalek-Zenczak M., Wojciechowski P., Samelak-Czajka A., Luczak M., Kozlowski P., Karlowski W.M., Figlerowicz M. (2020) „AthCNV - a map of DNA copy number variations in the Arabidopsis thaliana genome”. The Plant Cell, 32:1-23.

Macioszek V.K., Gapińska M., Zmienko A., Sobczak M., Skoczowski A., Oliwa J., Kononowicz A.K. (2020) „Complexity of Brassica oleracea–Alternaria brassicicola Susceptible Interaction Reveals Downregulation of Photosynthesis at Ultrastructural, Transcriptional, and Physiological Levels”. Cells, 9:2329

Obrepalska-Steplowska A., Zmienko A., Wrzesinska B., Goralski M., Figlerowicz M., Zyprych-Walczak, J., Siatkowski I., Pospieszny H. (2018) „The Defense Response of Nicotiana benthamiana to Peanut Stunt Virus Infection in the Presence of Symptom Exacerbating Satellite RNA” . Viruses-Basel, 10, 449.

Samelak-Czajka A., Marszalek-Zenczak M., Marcinkowska-Swojak M., Kozlowski P., Figlerowicz M., Zmienko A. (2017) „MLPA-based Analysis of Copy Number Variation in Plant Populations”. Front. Plant Sci., 8:222.

Zmienko A., Samelak-Czajka A., Kozlowski P., Szymanska M., Figlerowicz M. (2016) „Arabidopsis thaliana population analysis reveals high plasticity of the genomic region spanning MSH2, AT3G18530 and AT3G18535 genes and provides evidence for NAHR-driven recurrent CNV events occurring in this location”. BMC Genomics, 17:893.

Sobieszczuk-Nowicka E.*,Kubala S., Zmienko A., Małecka A., Legocka J. (2016) “From accumulation to degradation: reprogramming polyamine metabolism facilitates dark-induced senescence in barley leaf cells”. Front. Plant Sci., 6:1198.


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