1. June 2022

The event was opened by professor Michaela Wimmerová. She emphasized that PhD conference is an excellent tool to follow up on students’ progress, where everyone has the opportunity to see what his/her colleagues are working on and last but not least it is a good chance for the 12 participating 4th year students to practice to present their results in a rather informal environment. Despite all technological advances, person-to-person interactions are still irreplaceable and everyone welcomed that this year, the PhD conference took place again in person. Each student delivered 15 minutes-long presentation introducing the research topic, methodology and results that were achieved so far. The presentations were followed by a Q and A discussion. Additional 28 students delivered their poster presentations in the CEITEC Atrium. The jury nominated four winners in each category – Presentation and Posters – and each winner in the Presentation category received a financial reward of 6 000 CZK and each winner in the Poster category received 3 000 CZK.

The winners in the category Presentations were: (in alphabetical order)

The winners in the category Posters were:

Věra Dosedělová from the Institute of Analytical Chemistry of the Czech Academy of Sciences introduced her study of application of modern microcolumn separation techniques coupled to mass spectrometry for analysis of non-invasive biological samples. Non-invasive biological samples such as saliva and exhaled breath condensate (EBC) are gaining attractivity in clinical research and disease diagnostics due to their simple collection and the rich analyte composition. Levels of bile acids in saliva or EBC could serve as possible biomarkers for the alternative non-invasive diagnostics. In her work, Věra Dosedělová and her colleagues focused on method development for sample collection, sample preparation, and analysis of bile acids by liquid chromatography-mass spectrometry. Věra proposes that analysis of salivary bile acids including taurine conjugates could be applicable in diagnostics of gastroesophageal disease Barret´s esophagus (BE), following a larger clinical study.

Shekoufeh Ebrahimi Naghani from Hélène Robert Boisivon Research Group introduced her study of the genetic pathways controlling high-temperature stress during embryogenesis in Arabidopsis Thaliana. Shekoufeh is trying to answer how is plant reproduction affected by high temperature and how plant sense temperature and how are seeds produced while exposed to heat stress. Her research has a high importance for the entire society since global temperatures are rising and climate change negatively impacts plant growth. Without plants there will be no food, without food there will be no life. Shekoufeh´s research will shed some light on the development response to growth stressor.

Juan Francisco Sánchez López from Hélène Robert Boisivon Research Group is studying long-term adaptation to high temperatures in model plant Arabidopsis Thaliana. He is investigating the process from the flowering up to the seed development. The average global temperature and frequency of extreme temperatures increased year after year. The yield production of temperate crops has decreased due to high temperatures and drought and is expected to reduce even more in the upcoming years. Most of the available data focus on heat shock and pollen development, while information regarding long-term adaptation is scarce, especially related to ovule and embryo development. Juan Francisco is trying to fill this gap. His results provide new insight into long-term adaptation to high temperatures during the reproductive phase of plants. He and his colleagues observed that pollen, but especially ovule development, are negatively affected by high temperatures. Embryo development is accelerated by high temperatures, resulting in morphological abnormalities similar to defects in various auxin-related mutants. The reduction of fertility is translated to smaller seed production and a worsened quality of those seeds.

Alesia Melnikava from Jan Hejatko Research Group introduced her research focused on cytokinin-induced dirigent gene AtDIR13 as potential player in plant stress response. Alesia found AtDIR13 to be root-specific, upregulated by cytokinins and active since early stage of postembryonic growth. AtDIR13-mCherry fusion protein is localised in the root endodermis of the differentiation zone with a strong expression in the overlying endodermal cells of developing lateral roots. Alesia and her colleagues also tested different stresses on 35S::AtDIR13 lines. Thus, in the presence of NaCl salt, 35S::AtDIR13 lines showed better germination rate and primary root growth in comparison to Col-0. Under drought stress conditions 35S::AtDIR13 lines exhibited higher wilting resistance and better recovery after plant rewatering. The preliminary results indicate that 35S::AtDIR13 leaves are hypersensitive to flg22-triggered ROS production in the apoplast. These findings suggest a potential role of AtDIR13 in abiotic and biotic plant stress responses.

Pedro Faria Zeni from Marek Mráz Research Group spoke about the role of long non-coding RNAs in BCR-mediated CLL Activation. The B cell receptor (BCR) provides a critical signal for the maturation and survival of B lymphocytes and its dysregulation is a fundamental feature observed in multiple B cell malignancies, particularly in chronic lymphocytic leukaemia (CLL). Notably, CLL patients also show a universal clinical response to BCR inhibitor therapy and no recurrent mutations are found in the BCR-related genes of untreated patient. Short non-coding RNAs namely microRNAs can (dys)regulate the BCR signalling propensity but it is still unclear if long non-coding RNAs (lncRNAs) play a role in BCR activation. Pedro and his colleagues hypothesized that lncRNAs could be involved in BCR-mediated CLL activation and they identified 12 lncRNAs related to the BCR pathway inhibition/activity. The research team focused on a lncRNA that belongs to a class of lncRNA called long intergenic non-coding RNA (lincRNAs) which often play a role in trans-activating signalling pathways. To understand these observations mechanistically, Pedro and his colleagues transcriptionally repressed the lncRNA using dCAS9-KRAB system in MEC1 cell line and made some surprising conclusions. In summary, the studied lncRNA is directly regulated by the BCR activation and potentially acts in a negative feedback loop to limit BCR-mediated CLL activation.

Petr Tauš introduced his research focusing on interrogating the molecular heterogeneity of Chronic Lymphocytic Leukaemia (CLL) through computational approaches. CLL is an incurable lymphoproliferative disease of mature CD5+ B cells with very heterogeneous biological and clinical behaviour. Understanding the molecular heterogeneity of CLL and linking it with the clinical outcome of patients requires evidence from multiple biological layers, which can be obtained using genomics and transcriptomics methods. Firstly, Peter Tauš and his colleagues attempted to identify prognostic subtypes of CLL based on exome somatic mutation profiles and secondly, he aimed to explore the cellular origin of CLL. Altogether, Petr and his colleagues established and tested computational pipelines for mining insights from exome mutation and scRNA-seq datasets and for enriching in-house analyses with published findings. They created a solid ground for exploring CLL using integrative approaches, which is necessary for a deep understanding of CLL biology. The results enrich the use of available treatment options and their development, leading towards personalized medicine.

Adriana Ladungová from Michal Šmída Research Group spoke about prediction of novel treatment options for CLL and AML cells based on drug repurposing. Acute myeloid leukaemia (AML) and chronic lymphocytic leukaemia (CLL) are the most frequently occurring leukaemia types in adulthood. A significant barrier to their effective treatment is based on their molecular heterogeneity reflecting the variable clinical behaviour of the diseases. The presence of specific subclonal mutations often requires different therapeutic regimens on a patient-specific basis and thus, calls for the personalized medicine approach. This kind of personalized approach can be obtained through drug repurposing. This method is time-saving and cost-efficient and can vastly accelerate the lengthy approval process. Overall, Adriana and her colleagues performed and analysed the drug screening on 29 primary CLL samples representing the four major genetic subtypes and several AML samples. She identified several drugs that were recurrently found among the most efficient for the majority of samples and detected some specific drugs unique for individual patients. However, it does not seem that there would be any shared sensitivities specific to concrete CLL genetic subtypes. This research project points out the importance of a personalized treatment approach based on the application of approved-drug screening.

Sheng Zuo from Martin Lysák Research Group introduced genome diploidization and its association with cladogenesis, trait disparity and plastid gene evolution in a crucifer tribe. Angiosperm genome evolution was marked by many clade-specific whole genome duplication (WGD) events. The Microlepidieae is one of the monophyletic clades in the mustard family (Brassicaceae) formed after an ancient allotetraploidization. As post-polyploid genome diploidization is a trial-and-error process under natural selection, it may proceed with different intensity and be associated with speciation events. To gain a deeper understanding of postpolyploid genome evolution in Microlepidieae, Sheng and his colleagues analysed phylogenetic relationships in this tribe using complete chloroplast sequences, entire 35S rDNA units, and abundant repetitive sequences. He showed that faster genome diploidization is positively correlated with mean morphological disparity and evolution of chloroplast genes (plastid-nuclear genome coevolution). Higher speciation rates in perennials than in annual species were observed. Altogether, the newly acquired results confirm the potential of Microlepidieae as a promising subject for the analysis of post-polyploid genome diploidization in Brassicaceae.

Karolina Trachtová from the Ondřej Slabý Research Group presented about her bioinformatic pipeline for comprehensive analysis of small RNA-seq data. Next-generation sequencing (NGS) is a revolutionary method that allows massive parallel sequencing of millions of DNA or RNA fragments. Although NGS is considered a state-of-the-art method, there is still a need for more comprehensive bioinformatical approaches for NGS data evaluation, especially in the research of small RNAs. In sequencing of small non-coding RNAs, the critical problem is accurate identification and quantification of a full spectrum of small RNA pool. Most of the available pipelines are however targeted on microRNA only and ignore other RNA types such as snoRNA, snRNA, piRNA, or isomiRs. Karolína proposed a bioinformatic pipeline for accurate quantification of various small RNA classes. The pipeline is divided into stand-alone modules, each focusing on one part of the sequencing data analysis. The most crucial is the RNA quantification module. Each module ends with a PDF/HTML report summarizing results, including tables, plots and their explanation which guides user in further exploration of various small RNA expression levels. Her tool also offers an interactive application implemented in Shiny for a real-time visualization of differential expression results.

Krishnendu Bera from Jozef Hritz lab studies the impact of phosphorylation for Tau210-240 peptide and interaction of small molecules and 14-3-3ζ protein studies using computational methods. The conformational dynamics of intrinsically disordered proteins (IDPs) regulated by post-translational modifications such as phosphorylation is challenging to elucidate. A well-known IDP Tau is found hyper-phosphorylated in Alzheimer’s disease (AD) in humans. Designing small molecules aiming to modulate the strength of interactions of binding partners with 14-3-3ζ proteins and proper understanding of the conformational and dynamics changes upon phosphorylation of Tau can extend the therapeutic options for Alzheimer disease. The computational predictions will be validated experimentally by NMR, ITC and fluorescence titration experiments. Krishnendu have also tested and explored relevant methods (molecular docking and MD simulation) for his planned studies by using different protein targets of our experimental partners (Dr Harekrushna Sahoo and Dr Monalisa Mishra) from India, which resulted in five publications and two manuscripts currently under peer-review.

Subhash Narasimhan from Lukáš Žídek Research Group spoke about mycobacterium protein moaB2 which inhibits sigma A against proteolytic cleavage. Bacteria need to modulate their gene expression to adapt to changing external conditions for survival. Transcription initiation is the crucial focal point of gene expression in prokaryotes. The key players in this process, sigma factors (σs) associate with the catalytic core RNA polymerase to guide them through the essential steps of initiation. Subhash and his colleagues hypothesize that the increased level of expression of the gene may suggest a role of moaB2 in conferring protection to σA against proteolytic cleavage. To better understand structural role of moaB2- σA interaction, Subhash solved the crystal structure of moaB2 from M. smegmatis to a resolution of 2.6 AO by molecular replacement. The data collection was performed at the DESY Beamlinein Hamburg and the co-crystal structural characterization of σA - moaB2 are under optimization trials. The significance of moaB2 may pave the path for a better understanding of the bacterial transcription pathway.

Filip Melicher from Michaela Wimmerová Research Group introduced structural characterization of lectins from photorhabdus species. Lectins are proteins and glycoproteins able to reversibly bind saccharide moieties of glycoconjugates with high specificity. Lectins are involved in many physiological processes and play crucial roles in cell-cell communication or recognition of the host by a pathogen. The research is focused on the lectins produced by Gram-negative bacteria Photorhabdus laumondii and Photorhabdus asymbiotica. Bacteria of Photorhabdus genus live in symbiosis with Heterorhabditis nematodes. This symbiotic complex can be found in soil, where it searches for insect prey. Unusual dual behaviour makes Photorhabdus bacterium a compelling organism for further study of its biomolecules. Protein crystallography was used to obtain the 3D structure of lectins and to identify the key residues involved in the protein-saccharide interaction. It was revealed that P. laumondii produce five lectins with the seven-bladed β-propeller fold. Determined structures differ in the oligomerization and number of binding sites despite high sequential similarities. Lectin complexes with saccharides revealed two different binding sites per monomeric unit for the same ligand. Obtained results may reveal the importance of the lectins in the bacterial pathogenic or symbiotic stage of life. 

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