Diploma thesis

dr Łukasz Banasiak

Tematyka badawcza

Moje zainteresowania dotyczą ewolucji i ekologii roślin kwiatowych, a w szczególności rzędu selerewców (Apiales). Od kilku lat prowadzę badania nad zmiennością morfologiczną i ewolucją pyłku w kontekście datowania filogenezy. W swojej pracy łączę zarówno tradycyjny warsztat morfologiczny jak i nowoczesne metody filogenetyczne. Podczas wykonywania prac dyplomowych pod moją opieką studenci mogą się nauczyć:

• klasycznej analizy pyłkowej (izolacja, utrwalanie i obserwacje mikroskopowe pyłku),
• szacownia relacji pokrewieństwa na podstawie zmienności markerów molekularnych,
• klasyfikacji organizmów w oparciu o relacje pokrewieństwa,
• rekonstrukcji stanów ancestralnych cech organizmów,
• modelowania i rekostrukcji niszy ekologicznej,
• datowania filogenezy z wykorzystaniem skamieniałości,
• analizy tempa dywersyfikacji.

Proponowane tematy prac

• Datowanie filogenezy rzędu selerowców (Apiales) w oparciu o skamieniałości pyłku.
• Automatyczna kontrola jakości danch molekularnych służących do szacowania relacji pokrewieństwa.

Przykładowe tematy zakończonych prac dyplomowych

• Jakub Baczyński (2017). Rekonstrukcja ewolucji morfologii pyłku roślin baldaszkowatych (Apiaceae). Praca magisterska na kierunku Biologia.
• Karolina Sobecka (2017). Wpływ klimatu na morfologię pyłku roślin baldaszkowatych (Apiaceae). Praca licencjacka na kierunku Biologia.
• Hanna Kranas (2016). MatPhylobi – narzędzie do automatycznej konstrukcji macierzy danych molekularnych do analiz filogenetycznych na podstawie rekordów GenBank. Praca licencjacka na kierunku Bioinformatyka i Biologia Systemów.

dr hab. Kenneth De Baets, prof. ucz.

Themes of theses

Our thesis and research topics are diverse but mostly focused on the evolution and paleobiology of invertebrates. Various themes are connected to our currently running IDUB-funded project PARADIVE which focuses on the impact of climate-warming and extinction on parasite-host associations but other re-occuring themes in my research are macroevolutionary patterns and biomineralization.

Some examples of potential topics:

• Paleoparasitology of coprolites and paleopathology
• Geometric morphometric analysis
• Geochemistry and sclerochronology of mineralized tissues of cephalopod mollusks
• Co-evolution and co-extinction of parasite-host associations

Depending on the topic, techniques can involve:

• Paleontological or stratigraphic paleobiological field work
• Museum collection and paleontological preparation work
• Digital microscope, microfacies analysis and computed tomography
• (Geometric) Morphometrics
• Experimental taphonomy and conservation paleobiology
• Data and literature mining
• Quantitative (paleo)biological analysis and modelling particularly statistical analyses in R
• Molecular divergence time or co-phylogenetic analyses

Themes of recently supervised theses

• Różnorodność, biomineralizacja i dynamika wzrostu rozmiarów ciała bezkręgowców morskich
• Holoceńskie trendy w występowaniu układów pasożyt-żywiciel uchwycone w koprolitach i patologiach szkieletowych
• Rekonstrukcja 3D i morfometria oraz eksperymentalna taponomia bezkręgowców i kręgowców

Selected publications co-authored by students

• De Baets, K., Nätscher*, P. S., Rita*, P., Fara, E., Neige, P., Bardin, J., Dera, G., Duarte, L.V., Hughes, Z., Laschinger*, P, García-Ramos, J. C., Piñuela, L., Übelacker*, C. & Weis, R. (2021). The impact of the Pliensbachian–Toarcian crisis on belemnite assemblages and size distribution. Swiss Journal of Palaeontology, 140(1), 1-14.
• Nätscher*, P. S., Dera, G., Reddin, C. J., Rita*, P., & De Baets, K. (2021). Morphological response accompanying size reduction of belemnites during an Early Jurassic hyperthermal event modulated by life history. Scientific Reports, 11(1), 1-11.
• Rita*, P., Weis, R., Duarte, L. V., & De Baets, K. (2021). Taxonomical diversity and palaeobiogeographical affinity of belemnites from the Pliensbachian–Toarcian GSSP (Lusitanian Basin, Portugal). Papers in Palaeontology, 7(3), 1321-1349.
• Rita*, P., Nätscher*, P., Duarte, L. V., Weis, R., & De Baets, K. (2019). Mechanisms and drivers of belemnite body-size dynamics across the Pliensbachian–Toarcian crisis. Royal Society Open Science, 6(12), 190494.
• Rita*, P., De Baets, K., & Schlott*, M. (2018). Rostrum size differences between Toarcian belemnite battlefields. Fossil Record, 21(1), 171-182.
• Clements*, T., Colleary, C., De Baets, K., & Vinther, J. (2017). Buoyancy mechanisms limit preservation of coleoid cephalopod soft tissues in Mesozoic Lagerstätten. Palaeontology, 60(1), 1-14.
• Stilkerich*, J., Smrecak, T. A., & De Baets, K. (2017). 3D-Analysis of a non-planispiral ammonoid from the Hunsrück Slate: natural or pathological variation? PeerJ, 5, e3526.
• Gügel*, B., De Baets, K., Jerjen, I., Schuetz, P., & Klug, C. (2017). A new subdisarticulated machaeridian from the Middle Devonian of China: Insights into taphonomy and taxonomy using X-ray microtomography and 3D-analysis. Acta Palaeontologica Polonica, 237-247.
• Übelacker, C., Jansen, U., & De Baets, K. (2016). First record of the Early Devonian ammonoid Teicherticeras from the Eifel (Germany): biogeographic and biostratigraphic importance. Neues Jahrbuch für Geologie und Paläontologie—Abhandlungen, 282, 201-208.

dr Stanisław Dunin-Horkawicz

The thesis topics are related to the development and application of computational methods for the analysis of protein sequences and structures.

Applied methods

Modeling of protein structures, molecular dynamics simulations, classification of protein sequences and structures, and machine learning.

Theses in progress

• Jędrzej Kubica, “Sequence analysis and structure modeling of bacterial receptor proteins of unknown function“, Master’s thesis, Department of Chemistry (supervised also by prof. Dominik Gront, Department of Chemistry)
• Kamil Pawlicki, “Application of different language model architectures to the task of protein sequence classification“, Master’s thesis, Faculty of Biology
• Bartosz Szymański, „Modelling and substrate spectra characteristics  of laccase from Trametes versicolor”, Bachelor’s thesis, IISMNS

Examples of completed theses

• Julia Gołębiowska, „Predicting absorption wavelengths of rhodopsins using machine learning-based methods”, Master’s thesis, Faculty of Mathematics, Informatics and Mechanics (supervised also by Anna Karnkowska, PhD, Faculty of Biology)
• Kamil Kamiński, „Re-engineering cofactor specificity of the Rossmann fold proteins using graph neural networks”, 2020, Master’s thesis, Faculty of Physics
• Adriana Bukała, „Ancestral state reconstruction approach in investigating Rossmann fold evolution”, 2020, Bachelor’s thesis, Faculty of Mathematics, Informatics and Mechanics
• Aleksander Wiński, „The use of deep learning methods to predict protein π helix secondary structure based on sequence and evolutionary information”, 2018, Bachelor’s thesis, Faculty of Physics

Examples of publications co-authored by students

• Kamiński, K., Ludwiczak, J., Jasiński, M., Bukala, A., Madaj, R., Szczepaniak, K., & Dunin-Horkawicz, S. (2022). Rossmann-toolbox: a deep learning-based protocol for the prediction and design of cofactor specificity in Rossmann fold proteins. Briefings in Bioinformatics, 23(1), bbab371.
• Ludwiczak, J., Winski, A., da Silva Neto, A. M., Szczepaniak, K., Alva, V., & Dunin-Horkawicz, S. (2019). PiPred – a deep-learning method for prediction of π-helices in protein sequences. Scientific Reports, 9(1), 6888.
• Szczepaniak, K., Bukala, A., da Silva Neto, A. M., Ludwiczak, J., & Dunin-Horkawicz, S. (2021). A library of coiled-coil domains: from regular bundles to peculiar twists. Bioinformatics, 36(22–23), 5368–5376.

dr hab. Anna Karnkowska, prof. ucz.

The proposed topics of diploma theses are linked with our research projects (Evolution and Genomics of Microbial Eukaryotes) and revolve around:

• Diversity and role of eukaryotic microorganisms in aquatic environments.
• Symbiotic relationships between protists and bacteria.
• Evolution of the eukaryotic cell and the origin of plastids.
• Diversity and evolution of microbial rhodopsins.
• Bioinformatics tools and pipelines for metagenomic data analysis.

Depending on the topic, techniques can involve

• bioinformatics analysis, including genome and transcriptome assembly, gene prediction and annotation, in silico reconstruction of metabolic pathways, phylogenetic analyses,
• environmental sequencing data analyses (taxonomic – amplicon analysis and functional – metagenomic analyses)
• molecular biology techniques: DNA and RNA isolation, electrophoretic techniques, cDNA synthesis, PCR, RT-PCR, DNA cloning
• sequencing techniques: Sanger sequencing, NGS high-throughput sequencing, nanopore sequencing
• sampling, isolation and cultivation of eukaryotic microorganisms.
• light and transmission electron microscopy techniques and fluorescence in situ hybridization technique

Some examples of potential topics

• Identification and analysis of symbiotic interactions between protists and bacteria isolated from the water column and sediments of the Masurian lakes based on genomic and microscopic analysis of single cells

thesis will be part of the NCN OPUS grant, and the scholarship of PLN 1,500/month will be awarded in the open competition

• Analysis of the prokaryotic and eukaryotic diversity of Masurian lakes in the eutrophication gradient based on amplicon and metagenomic data
• Analysis of photosymbiotic interactions of ciliates and their symbionts based on single-cell genome and transcriptome analysis
• Early stages of plastid evolution in the kleptoplastidic euglenid Rapaza viridis based on in silico analysis of genomic and transcriptomic data and experiments using RNAi and CRISPR techniques

thesis supervised in English and co-supervised by a post-doc Dr Iván García-Cunchillos

• Diversity, evolution and function of microbial rhodopsins in freshwater protists based on metatranscriptomic data analysis and laboratory experiments.
• Diversity of freshwater protist viruses based on analysis of metagenomic and genomic data and culturing experiments

thesis supervised in English and co-supervised by a post-doc Dr Anhelina Kyrychenko in collaboration with  Dr Matthias Fisher

Examples of completed theses

• Stanisław Antonowicz, Ścieżka postępowania w rekonstrukcji sieci interakcji mikroorganizmów w oparciu o dane z sekwencjonowania wysokoprzepustowego, 2022, Master’s thesis at Bioinformatics and Systems Biology
• Małgorzata Chwalińska, Porównanie krótkich i długich amplikonów genu 18S rDNA w analizie różnorodności słodkowodnych protistów, 2022, Master’s thesis at Biology
• Julia Gołębiowska, Przewidywanie długości fali świetlnej absorbowanej przez rodopsyny z wykorzystaniem metod opartych na uczeniu maszynowym, 2022, Master’s thesis at Bioinformatics and Systems Biology, co-supervised with dr Stanisław Dunin-Horkawicz
• Metody Hollender, Identyfikacja i analiza metabolizmu symbiontów wybranych protistów na podstawie badań pojedynczych komórek, 2022, Bachelor’s thesis at Biotechnology
• Weronika Popławska, Analiza występowania i różnorodności Archaea w pelagialu wybranych jezior Pojezierza Mazurskiego na podstawie danych molekularnych, 2021, Bachelor’s thesis at Biotechnology
• Julia Gołębiowska, Analiza występowania i różnorodności rodopsyn mikrobialnych w Jeziorze Roś w oparciu o dane metatranskryptomowe i amplikony, 2021, Master’s thesis at Biotechnology

Examples of publications co-authored by students

1. Karlicki M, Antonowicz S*, Karnkowska A (2022) Tiara: deep learning-based classification system for eukaryotic sequences. Bioinformatics, 38: 344–50.

2. Łukomska-Kowalczyk M, Karnkowska A, Krupska M*, Milanowski R, Zakryś B (2016) DNA Barcoding In Autotrophic Euglenids: Evaluation of COI and 18S rDNA. J Phycol 52: 951-60

Conference presentations of students

1. Antonowicz S*, Karlicki M, Karnkowska A (2020) Machine learning-based approach for aminoacid sequence representation and classification, 4th EMBO Workshop on Computational and Structural Biology and Chemistry, Waplewo, Poland.
2. Chwalińska M*, Karlicki M., Karnkowska A. (2021) 18S rDNA amplicon-based analysis of the diversity of microbial eukaryotes’ communities in the salinity gradient of Świna river estuary; 9. Międzyuczelniane Sympozjum Biotechnologiczne „Symbioza”
3. Gołębiowska J*, Karlicki M., Karnkowska A. (2021) Pipeline for diversity assessment of eukaryotic rhodopsins in metatranscriptomic data; 9. Międzyuczelniane Sympozjum Biotechnologiczne „Symbioza”.
4. Hollender M*, Sałek M, Karlicki M, Karnkowska A. (2022) Workflow for genome recovery of protistan prokaryotic symbionts from single-cell data; Meeting of the EMBO Young Investigator Network on computational methods in ecology and evolutionary biology of microbes, Chęciny, Poland.
5. Gołębiowska J*, Kamiński K., Karnkowska A., Dunin-Horkawicz S. (2022) Predicting absorption wavelengths of rhodopsins using machine learning-based methods; Meeting of the EMBO Young Investigator Network on computational methods in ecology and evolutionary biology of microbes, Chęciny, Poland.
6. Hollender M*, Sałek M., Hess S., Karnkowska A. (2022) Metagenomic and fluorescence in situ hybridization analyses of Eutreptiella endosymbiont. 2nd Annual International Congress on Euglenoids, online.
7. Chwalińska M*, Karlicki M., Sałek M., Smacchia V., Hałakuc P., Maciszewski K., Karnkowska A. (2022) Freshwater protists diversity elucidated with the short Illumina vs long MinION amplicons of 18S rRNA gene. 51st Jírovec’s Protozoological Conference, Czechia.

dr Sergi López-Torres

My main research interests revolve around topics on mammalian evolution, in particular those focusing on the functional anatomy of fossil primates and closely related mammalian lineages.

Some examples of potential topics:

(all theses will be written and supervised in English)

• Dietary reconstruction in fossil mammals
• Dental anatomy and dental development in fossil mammals
• Mammalian brain evolution
• Ear anatomy and evolution of hearing in mammals
• Mammalian comparative cranial anatomy
• Functional anatomy of the postcranial skeleton in fossil mammals
• Phylogenetic relationships among primitive mammalian lineages

Methods used:

• Computed tomography
• Phylogenetic analysis
• Ancestral reconstruction analysis
• Dental topographic analysis
• Geometric morphometrics
• Museum data collection
• Paleontological fieldwork

Theses in progress

• Korneliusz Durał, “The cranial endocast of Allen’s galago (Sciurocheirus alleni, Galagidae, Primates)“, Bachelor’s thesis, Faculty of Biology, University of Warsaw

Examples of completed theses

• Adam Lis, “A virtual cranial endocast of the Miocene primate Mioeuoticus shipmani (Lorisidae, Strepsirrhini) from Kenya“, 2023, Master’s thesis, Faculty of Biology, University of Warsaw
• Giulia Lodi, “How big was the primate ancestor? A state reconstruction analysis using fossil primate data from Paleogene beds“, 2020, Bachelor’s thesis, Department of Chemical and Geological Sciences, University of Modena and Reggio Emilia (co-supervised with Annalisa Ferretti)

Selected publications that were coauthored with students:

• Silcox, M. T., Bertrand, O. C., Harrington, A. R., Lang*, M. M., San Martin-Flores*, G., López-Torres, S. (2023) Early evolution of the brain in Primates and their close kin (Ch. 12). In Dozo MT, Paulina-Carabajal A, Macrini TE, Walsh S (eds.) Paleoneurology of Amniotes: New Directions in the Study of Fossil Endocasts, Springer Cham, Switzerland; pp. 457-506.
• López-Torres, S., Bhagat*, R., Bertrand, O. C., Silcox, M. T., Fostowicz-Frelik, Ł. (2023) Locomotor behaviour and hearing sensitivity in an early lagomorph reconstructed from the bony labyrinth. Ecology and Evolution, 13: e9890.
• Kraatz, B., Belabbas, R., Fostowicz-Frelik, Ł., Ge, D., Kuznetsov, A., Lang*, M. M., López-Torres, S., Mohammadi, Z., Racicot, R. A., Ravosa, M. J., Sharp, A. C., Sherratt, E., Silcox, M. T., Słowiak, Winkler, A. J., Ruf. I. (2021) Lagomorpha as a model morphological System. Frontiers in Ecology and Evolution, 9, 636402.
• López-Torres, S., Bertrand, O. C., Lang*, M. M., Silcox, M. T., Fostowicz-Frelik, Ł. (2020) Cranial endocast of the stem lagomorph Megalagus and brain structure of basal Euarchontoglires. Proceedings of the Royal Society B, 287, 20200665.
• López-Torres, S., Selig, K. R., Prufrock, K. A., Lin*, D., Silcox, M. T. (2017) Dental topographic analysis of paromomyid (Plesiadapiformes, Primates) cheek teeth: Moret han 15 million years of changing surfaces and shifting ecologies. Historical Biology, 30, 76-88.

dr Maja Łukomska-Kowalczyk

The proposed topics of diploma theses are linked with our research, that is focused on the biodiversity of eukaryotic microorganisms in the environment with the use of high-throughput sequencing (NGS) and molecular identification. The research focuses largely on the impact of seasonal drying up of water bodies on the communities of microorganisms inhabiting them.

dr hab. Rafał Milanowski, prof. ucz.

The proposed topics of diploma theses are linked with our research (Molecular Biology of Euglenids).

Proposed titles of theses

• Conventional and nonconventional splicing efficiency.
• Alternative splicing and complex introns in nuclear genes of euglenids.
• Transposons and transposon-related elements in genomes of euglenids.
• Spliced leader trans-splicing in protists.

Techniques

Methods of molecular biology and bioinformatics.

Former diploma theses (review)

• Diana Nikalayenka (2024). Introns in nuclear genes of euglenids: spliceosome inhibition, change of intron type, form of excision.
• Adam Milewski (2023). Evolution of 5′ ends of euglenids transcripts.
• Weronika Mikina (2023). Analysis of evolutionary events shaping the structure of nuclear genomes of euglenids based on manual annotation of selected genes.
• Maria Jagielska (2022). Analysis of mitochondrial genomes of selected euglenid species.
• Anna Semik (2021). Analysis of nonconventional introns in nuclear genes of euglenids.
• Michalina Komorowska (2020). Analysis of physical form of nonconventional introns found in gapC and tubB genes in E. gracilis.
• Antonina Ignatenko (2019). Mechanisms of loss and gain of spliceosomal introns in nuclear genes of Eukarya.
• Paweł Hałakuc (2018). Tracing evolutionary changes in rRNA genes of Euglenozoa.
• Agata Gondek (2015). Studying the effect of human spliceosome inhibitors on Euglena gracilis spliceosome..

Publications co-authored by students (review)

• Jagielska M.*, Płechca M., Hałakuc P., Milanowski R. (2023). Mitochondrial genomes – unity and diversity. Postępy Biochcemii 69(2): 113-121 (pdf)
• Ignatenko A.*, Gumińska N., Milanowski R. (2019). Mechanisms of spliceosomal introns loss and gain. Postępy Biochemii 65(4): 289-298 (pdf).
• Gumińska N., Płecha M., Walkiewicz H., Hałakuc P.*, Zakryś B., Milanowski R. (2018). Culture purification and DNA extraction procedures suitable for next-generation sequencing of euglenids. J Appl Phycol 30: 3541–3549 (pdf).
• Kulczycka A.*, Łukomska-Kowalczyk M., Zakryś M., Milanowski R. (2018). PCR identification of toxic euglenid species Euglena sanguinea. J Appl Phycol 30: 1759-1763 (pdf).
• Zganiacz D.*, Milanowski R. (2017). Characteristics of circular ribonucleic acid molecules (circRNA). Postępy Biochemii 63(3): 221-232 (pdf).
• Milanowski R., Gumińska N.*, Karnkowska A., Ishikawa T., Zakryś B. (2016). Intermediate introns in nuclear genes of euglenids – are they a distinct type? BMC Evol Biol 16:49 (pdf).

Conference presentations co-authored by students (review)

• Hałakuc P., Semik A.*, Jagielska M., Karnkowska A. Milanowski R. (2023). Automatic annotation of nonconventional introns as a necessary step in the analysis of Euglena genomes. 3rd Annual International Congress on Euglenoids 2023, 17-18 July, Prague, Czech Republic.
• Jagielska M., Hałakuc P., Semik A.*, Milanowski R. (2023). Nulcear genomes of euglenids: discoveries and challenges. 40th International Conference of Polish Phycological Society. 23-36 May, Bydgoszcz, Poland.
• Semik A.*, Hałakuc P., Mikina W.*, Milanowski R. (2022). Statistical machine learning aiding the recognition of noncanonical introns in three Euglena genomes. 41th Jirovec’s Protozoological Days by Czech Society for Parasitology, 21-24 June, Svratka, Czech Republic.
• Hałakuc P., Jagielska M.*, Płecha M., Maciszewski K., Zakryś B., Milanowski R., Karnkowska A. (2022). Structure and evolution of mitochondrial genomes in phototrophic Euglenids. 41th Jirovec’s Protozoological Days by Czech Society for Parasitology, 21-24 June, Svratka, Czech Republic.
• Mikina W.*, Hałakuc P. Milanowski R. (2021). Manual annotation as a key reference for automatic prediction of nonconventional introns. 1st Annual International Congress on Euglenoids. 8-11 November, Online.
• Hałakuc P., Semik A.*, Mikina W.*, Różycka J.*, Płecha M., Gumińska N., Karnkowska A., Milanowski R. (2021). Canonical and nonconventional introns in three new Euglena genomes. 1st Annual International Congress on Euglenoids. 8-11 November, Online.
• Płecha M., Hałakuc P., Jagielska M.*, Karnkowska A., Milanowski R. (2021). Mitochondrial genomes of Euglena gracilis , E. hiemalis and E. longa obtained from the whole genome assemblies (WGA). EMBO Young Scientists Forum. 21-22 October, Warsaw, Poland.

dr hab. Julia Pawłowska

The proposed topics of diploma theses are linked with our research (Mycology), i.e.:

• Bacterial-fungal interactions
• Evolution and ecology of Mucoromycota
• Fungal diversity on contaminated soils
• Characterization of enzymatic activity of Mucoromycota

Students can learn basic microbiological techniques, molecular biology (including DNA and RNA isolation, electrophoretic techniques, PCR, DNA cloning, Sanger sequencing, NGS high-throughput sequencing, FISH), spectrophotometric methods (GC-MS, Biolog system) and bioinformatics.

Proposed titles of thesis

• Influence of endohyphal bacteria on enzymatic activity of Mucoromycota.
• Taxonomy and phylogeny of Mortierellaceae.
• Monitoring and mapping fungal diversity for nature conservation.
• DNA barcoding of selected fungal taxa relevant for nature conservation.

Examples of completed theses

• Justyna Borowiecka (2023). Revision of the genus Umbelopsis based on multigene phylogenetic analysis.
• Blanka Sokołowska (2022). Lipid metabolism of Mucoromycota representatives.
• Grzegorz Ostrowski (2021). The diversity of the Mucoraceae colonizing dry-aged beef.
• Aleksandra Gęsiorska (2020). Prevalence of endosymbiotic bacteria in Umbelopsis representatives.

Selected publications co-authored by students

1. Sokołowska, B., Orłowska, M., Okrasińska, A., Piłsyk, S., Pawłowska, J., Muszewska, A. (2023) What can be lost? Genomic perspective on the lipid metabolism of Mucoromycota. IMA Fungus 14(22): https://doi.org/10.1186/s43008-023-00127-4
2. Okrasińska, A., Decewicz, P., Majchrowska, M., Dziewit, L., Muszewska, A., Dolatabadi, S., Kruszewski, Ł., Błocka, Z., Pawłowska, J. (2022) Marginal lands and fungi – linking the type of soil contamination with fungal community composition. Environmental Microbiology. https://doi.org/10.1111/1462-2920.16007.
3. Okrasińska, A., Bokus, A., Duk, K., Gęsiorska, A., Sokołowska, B., Miłobędzka, A., Wrzosek, M., Pawłowska, J. (2021) New Endohyphal Relationships between Mucoromycota and Burkholderiaceae Representatives. Applied and Environmental Microbiology, 87 (7): e02707-20. https://aem.asm.org/content/87/7/e02707-20

Selected students’ conference presentations

1. Beniamin Abramczyk. XIX Congress of European Mycologists Perugia (Italy), 4-8.09.2023. oral presentation: Mucoromycota-bacterial interactions in postindustrial soil.
2. Zuzanna Błocka, Julia Pawłowska. CYEBB.  Cracow (Poland), 3-5.9.2021. Analysis of Diesel Oil Degradation by Fungi and Endohyphal Bacteria.
3. Alicja Okrasińska, Katarzyna Duk, Aleksandra Bokus, Julia Pawłowska. 6^th Young Natural History scientists Meeting. Paris (France), 12-16.3.2019. New lineages of endohyphal bacteria detected in land colonizing fungi.

prof. dr hab. Krzysztof Spalik

Tematy prac licencjackich

• filogenetyka molekularna
• biogeografia i taksonomia roślin

Tematy prac magisterskich

• filogenetyka molekularna
• biogeografia i taksonomia roślin

Przykładowe tematy zakończonych prac dyplomowych

• Michał Gierek (2018). Analiza filogenetyczna kladu Athamanta-Conopodium z wykorzystaniem znaczników chloroplastowych i jądrowych. Praca licencjacka na kierunku Biologia.

Publikacje, których współautorami byli studenci

1. Spalik K., A. Wojewódzka, T. Constantinidis, S.R. Downie, M. Gierek & Ł. Banasiak. 2019. Laserocarpum, a new genus of Apiaceae endemic to Greece. Acta Societatis Botanicorum Poloniae, 88: 1–9.
2. Wojewódzka A., J. Baczyński, Ł. Banasiak, S.R. Downie, A. Czarnocka-Cieciura, M. Gierek, K. Frankiewicz & K. Spalik. 2019. Evolutionary shifts in fruit dispersal syndromes in Apiaceae tribe Scandiceae. Plant Systematics and Evolution 305(5): 401–414.
3. Banasiak Ł., A. Wojewódzka, J. Baczyński, J.-P. Reduron, M. Piwczyński, R. Kurzyna-Młynik, R. Gutaker, A. Czarnocka-Cieciura, S. Kosmala-Grzechnik & K. Spalik. 2016. Phylogeny of Apiaceae subtribe Daucinae and the taxonomic delineation of its genera. Taxon, 65: 563–585.

Wystąpienia konferencyjne, których współautorami byli studenci

1. Hanna Kranas, Krzysztof Spalik i Łukasz Banasiak. 2018. MatPhylobi – constructing and updating taxonomic and phylogenetic datasets from GenBank databases. Polish Evolutionary Conference, Warszawa 26-28.09.2018.
2. Michał Gierek, Łukasz Banasiak, Jakub Baczyński, Krzysztof Spalik. 2018.  Phylogenetic relationships within the Athamanta-Conopodium clade (tribe Scandiceae, family Apiaceae).  Polish Evolutionary Conference, Warszawa 26-28.09.2018.

prof. dr hab. Marta Szulkin

Our research focuses on the study of the ecology & evolution of living organisms in the Anthropocene – a human-dominated period generating a considerable global impact on Earth’s ecosystems. In particular, we look for patterns and processes associated with the natural variation of wild organisms living in a gradient of environments – from primary and secondary forests to suburban and urban areas.

Find out more about our team and research here

Methods used

• Field ecology
• Statistical analysis, mixed models (R)
• Laboratory work (microbiome, genotyping)
• Video image analysis (analysis of diet brought to the nest)

Proposed work topics

• Thermal profiles of anthropogenic nesting cavities in urban areas: the aim of the work would be to investigate the thermal properties of the numerous gaps in urban structures (lampposts, cracks under roofs, etc.) and their potential as breeding sites in the face of climate change and the heat island effect generated in cities such as Warsaw.

Current theses

• Lena Fus (MSc thesis): The Microbial Metropolis: Exploring the Impact of Urbanisation on the Gut Microbiota of Blue Tits

Examples of completed thesis topics

• Katarzyna Gęsicka (BA thesis, Anthropozoology, 2022): Is blue tit and great tit hissing behaviour associated with urbanisation?
• Ignacy Stadnicki (Bachelor thesis, Anthropozoology, 2021): Application of crime theory in urban eco-evo research: factors influencing the disappearance of scientific equipment
• Marta Celej (Master’s thesis, Department of Biology, 2018): Influence of the urbanisation gradient on phenotypic traits in the great tit (Parus major) and the praying mantis (Cyanistes caeruleus)

Examples of publications co-authored by students

• Corsini M, Jagiełło Z, Walesiak M, Redlisiak M, Stadnicki I*, Mierzejewska E & Szulkin M. 2022. Breeding in the pandemic: short-term lockdown restrictions do not alter reproductive decisions and avian life-history traits in a European capital city. Urban Ecosystems 1-11.
• Chatelain M, Da Silva A, Celej M*, Kurek E, Corsini M & Szulkin M. 2021. Replicated, Urban-Driven Exposure to Metal Pollutants in Two Passerines. Scientific Reports. 11:19662.

Selected conference presentations co-authored by students

• Fus, L.*, Maraci O, Szulkin M. 2023 (upcoming) The Microbial Metropolis: Exploring the Impact of Urbanisation on the Gut Microbiota of Blue Tits. Behaviour 2023 Conference, Bielefeld, Germany.
• Stadnicki I.*, Corsini M., Szulkin M. Application of crime theory in urban ecology and evolution: factors influencing the disappearance of scientific equipment. (1) ASAB Winter Conference, The Association for the Study of Animal Behaviour, 2021 (remote); (2) Seminar, Cornell Lab of Ornithology, The United States of America, 2022 (remote, video); (3) IX International Hole-Nesting Birds Conference, University of Oxford, United Kingdom, 2022.

dr Mateusz Tałanda

I study the early evolution of lizards and sphenodontians, their phylogeny and biogeography. I am also interested in the Triassic ecosystems with particular emphasis on various groups of vertebrates.

Some examples of potential topics

• Cretaceous roots of lizards
• Marine reptiles from the Triassic of Bliżyn
• Evolution of legs and locomotion in scorpions and horseshoe crabs
• Intraspecific variation and sexual dimorphism among lizards Slavoia darevskii
• Selected freshwater fishes at the dawn of dinosaur age
• Large Triassic amphibians – their anatomy and evolution

Methods used

3D visualization of anatomy (computed tomography, photogrammetry, surface scanning, 3D graphics), phylogenetic analyses, comparative anatomy, scanning electron microscope, morphometrics and principal component analysis, chemical and physical preparation of fossils.

Examples of completed theses

Emilia Olender. 2023. Biogeography of plesiosaur ancestors at the dawn of the dinosaur era. Bachelor’s Thesis.

Marceli Witasik. 2023. Histology and osteology of the sauropod femur from Baynshire Formation. Master’s Thesis.

Bartosz Bałdowski. 2021. The fossil record of chilopod myriapods. Bachelor’s Thesis.

Adam Rytel. 2021. Modularity of the neck in Tanystropheidae revealed by geometric morphometrics. Master’s Thesis.

prof. dr hab. Bożena Zakryś

Tematy prac licencjackich

• Wyizolowanie rzadkiego lub ciekawego gatunku eugleniny z naturalnych populacji z terenu Polski celem przeprowadzenia weryfikacji taksonomicznych, zdeponowania w światowych kolekcjach kultur glonowych czy wykorzystania w celach biotechnologicznych; stosujemy różne metody izolacji pojedynczych komórek (m.in. mikromanipulacja), zakładamy i prowadzimy hodowle jednogatunkowe.
• Badania morfologiczne wybranych gatunków (grup gatunków) euglenin; w tym celu wykorzystujemy mikroskopię świetlną, automatyczną biometrię (system analizy obrazu NIS Elements Br 3.1) i fotografię mikroskopową.
• Różnorodność euglenin wybranego zbiornika wodnego (m.in. silnie zanieczyszczonego ściekami przemysłowymi, komunalnymi); stosujemy mikroskopię świetlną, fotografię mikroskopową.

Tematy prac magisterskich

• Molekularna identyfikacja euglenin w próbach środowiskowych (metabarkoding) w celu poznania ich bioróżnorodności i ekologii; izolacja DNA, PCR, sekwencjonowanie nowej generacji (NGS), analiza bioinformatyczna.
• Badania molekularne i filogenetyczne wybranych grup gatunków euglenin w celu przeprowadzenia weryfikacji taksonomicznych; izolacja DNA, PCR, sekwencjonowanie metodą Sangera, analizy filogenetyczne.

Przykładowe tematy zakończonych prac dyplomowych

• Michał Woźniak (2020). Oczyszczanie wody zanieczyszczonej arsenem przez wybrane organizmy autotroficzne. Praca licencjacka na kierunku Ochrona Środowiska.
• Katarzyna Chaber (2019). Analiza morfologiczna i molekularna gatunków z kompleksu Lepocinclis ovum-Lepocinclis globulus (Euglenida). Praca magisterska na kierunku Biologia.
• Alicja Fells (2019). Badanie pokrewieństw w rodzaju Phacus Dujardin na podstawie danych molekularnych i morfologicznych. Praca magisterska na kierunku Biologia.
• Alicja Fells (2017). Ultrastruktura chloroplastu Cryptoglena skujae (Skuja) Marin i Melkonian. Praca licencjacka na kierunku Biologia.
• Michał Woźniak (2017). Bioróżnorodność autotroficznych euglenin w zbiornikach wodnych w okolicy Pruszkowa i Grodziska Mazowieckiego. Praca licencjacka na kierunku Ochrona Środowiska.

Publikacje, których współautorami byli studenci

1. Łukomska-Kowalczyk M, Chaber K, Fells A, Milanowski R, Zakryś B. 2020. Taxon-rich phylogeny and taxonomy of the genus Phacus (Euglenida) based on morphological and molecular data. Journal of Phycology (przyjęta do druku)
2. Łukomska-Kowalczyk M, Chaber K, Fells A, Milanowski R, Zakryś B. 2020. Molecular and morphological delimitation of species in the group of Lepocinclis ovum-like taxa. Journal of Phycology 56: 283-299; doi:10.1111/jpy.12949
3. Kulczycka A, Łukomska-Kowalczyk M, Zakryś B, Milanowski R. 2018. PCR identification of toxic euglenid species Euglena sanguinea. Journal of Applied Phycology, DOI: 10.1007/s10811-017-1376-z
4. Łukomska-Kowalczyk M., Karnkowska A, Milanowski R., Łach Ł., Zakryś B. 2015. Delimiting species boundaries within the Phacus longicauda complex (Euglenida) through morphological and molecular analyses. J Phycol. 51: 1147-1157.