@article{MTMT:34804520, title = {Cellular Immunity of Drosophila willistoni Reveals Novel Complexity in Insect Anti-Parasitoid Defense}, url = {https://m2.mtmt.hu/api/publication/34804520}, author = {Cinege, Gyöngyi Ilona and Fodor, K. and Magyar, Lilla Brigitta and Lipinszki, Zoltán and Hultmark, D. and Andó, István}, doi = {10.3390/cells13070593}, journal-iso = {CELLS-BASEL}, journal = {CELLS}, volume = {13}, unique-id = {34804520}, year = {2024}, eissn = {2073-4409}, orcid-numbers = {Lipinszki, Zoltán/0000-0002-2067-0832; Andó, István/0000-0002-4648-9396} } @article{MTMT:34797924, title = {Transient Receptor Potential Ankyrin 1 Ion Channel Is Expressed in Osteosarcoma and Its Activation Reduces Viability}, url = {https://m2.mtmt.hu/api/publication/34797924}, author = {Hudhud, Lina and Rozmer, Katalin and Kecskés, Angéla and Pohóczky, Krisztina and Bencze, Noémi and Buzás, Krisztina and Szőke, Éva and Helyes, Zsuzsanna}, doi = {10.3390/ijms25073760}, journal-iso = {INT J MOL SCI}, journal = {INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES}, volume = {25}, unique-id = {34797924}, issn = {1661-6596}, abstract = {Osteosarcoma is a highly malignant, painful cancer with poor treatment opportunities and a bad prognosis. Transient receptor potential ankyrin 1 (TRPA1) and vanilloid 1 (TRPV1) receptors are non-selective cation channels that have been of great interest in cancer, as their expression is increased in some malignancies. In our study we aim to characterize the expression and functionality of the TRPA1 and TRPV1 channels in human and mouse osteosarcoma tissues and in a mouse cell line. TRPA1/Trpa1 and TRPV1/Trpv1 mRNA expressions were demonstrated by PCR gel electrophoresis and RNAscope in situ hybridization. The function of these channels was confirmed by their radioactive 45Ca2+ uptake in response to the TRPA1 agonist, Allyl-isothiocyanate (AITC), and TRPV1 agonist, capsaicin, in K7M2 cells. An ATP-based K2M7 cell viability luminescence assay was used to determine cell viability after AITC or capsaicin treatments. Both TRPA1/Trpa1 and TRPV1/Trpv1 were expressed similarly in human and mouse osteosarcoma tissues, while Trpa1 transcripts were more abundantly present in K7M2 cells. TRPA1 activation with 200 µM AITC induced a significant 45Ca2+ influx into K7M2 cells, and the antagonist attenuated this effect. In accordance with the lower Trpv1 expression, capsaicin induced a moderate 45Ca2+ uptake, which did not reach the level of statistical significance. Both AITC and capsaicin significantly reduced K7M2 cell viability, demonstrating EC50 values of 22 µM and 74 µM. The viability-decreasing effect of AITC was significantly but only partially antagonized by HC-030031, but the action of capsaicin was not affected by the TRPV1 antagonist capsazepine. We provide here the first data on the functional expression of the TRPA1 and TRPV1 ion channels in osteosarcoma, suggesting novel diagnostic and/or therapeutic perspectives.}, keywords = {CAPSAICIN; TRPV1; Cell viability; mustard oil; TRPA1; Osteosarcoma; RNAscope in situ hybridization; radioactive 45Ca2+ uptake}, year = {2024}, eissn = {1422-0067}, orcid-numbers = {Pohóczky, Krisztina/0000-0003-0385-5162; Buzás, Krisztina/0000-0001-8933-2033} } @article{MTMT:34790193, title = {Lectin-Based Immunophenotyping and Whole Proteomic Profiling of CT-26 Colon Carcinoma Murine Model.}, url = {https://m2.mtmt.hu/api/publication/34790193}, author = {Faragó, Anna and Zvara, Ágnes and Tiszlavicz, László and Hunyadi-Gulyás Éva, Csilla and Darula, Zsuzsanna and Hegedűs, Zoltán and Szabó, Enikő and Surguta, Sára Eszter and Tóvári, József and Puskás, László and Szebeni, Gábor}, doi = {10.3390/ijms25074022}, journal-iso = {INT J MOL SCI}, journal = {INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES}, volume = {25}, unique-id = {34790193}, issn = {1661-6596}, abstract = {A murine colorectal carcinoma (CRC) model was established. CT26 colon carcinoma cells were injected into BALB/c mice's spleen to study the primary tumor and the mechanisms of cell spread of colon cancer to the liver. The CRC was verified by the immunohistochemistry of Pan Cytokeratin and Vimentin expression. Immunophenotyping of leukocytes isolated from CRC-bearing BALB/c mice or healthy controls, such as CD19+ B cells, CD11+ myeloid cells, and CD3+ T cells, was carried out using fluorochrome-labeled lectins. The binding of six lectins to white blood cells, such as galectin-1 (Gal1), siglec-1 (Sig1), Sambucus nigra lectin (SNA), Aleuria aurantia lectin (AAL), Phytolacca americana lectin (PWM), and galectin-3 (Gal3), was assayed. Flow cytometric analysis of the splenocytes revealed the increased binding of SNA, and AAL to CD3 + T cells and CD11b myeloid cells; and increased siglec-1 and AAL binding to CD19 B cells of the tumor-bearing mice. The whole proteomic analysis of the established CRC-bearing liver and spleen versus healthy tissues identified differentially expressed proteins, characteristic of the primary or secondary CRC tissues. KEGG Gene Ontology bioinformatic analysis delineated the established murine CRC characteristic protein interaction networks, biological pathways, and cellular processes involved in CRC. Galectin-1 and S100A4 were identified as upregulated proteins in the primary and secondary CT26 tumor tissues, and these were previously reported to contribute to the poor prognosis of CRC patients. Modelling the development of liver colonization of CRC by the injection of CT26 cells into the spleen may facilitate the understanding of carcinogenesis in human CRC and contribute to the development of novel therapeutic strategies.}, keywords = {colorectal carcinoma; lectin binding sugar code; proteomic analysis of murine CRC}, year = {2024}, eissn = {1422-0067}, orcid-numbers = {Tóvári, József/0000-0002-5543-3204; Szebeni, Gábor/0000-0002-6998-5632} } @article{MTMT:34786803, title = {SuperCUT, an unsupervised multimodal image registration with deep learning for biomedical microscopy}, url = {https://m2.mtmt.hu/api/publication/34786803}, author = {Grexa, István and Iván, Zsanett Zsófia and Migh, Ede and Kovács, Ferenc and Bolck, Hella A and Zheng, Xiang and Mund, Andreas and Moshkov, Nikita and Csapóné Miczán, Vivien and Koós, Krisztián and Horváth, Péter}, doi = {10.1093/bib/bbae029}, journal-iso = {BRIEF BIOINFORM}, journal = {BRIEFINGS IN BIOINFORMATICS}, volume = {25}, unique-id = {34786803}, issn = {1467-5463}, abstract = {Numerous imaging techniques are available for observing and interrogating biological samples, and several of them can be used consecutively to enable correlative analysis of different image modalities with varying resolutions and the inclusion of structural or molecular information. Achieving accurate registration of multimodal images is essential for the correlative analysis process, but it remains a challenging computer vision task with no widely accepted solution. Moreover, supervised registration methods require annotated data produced by experts, which is limited. To address this challenge, we propose a general unsupervised pipeline for multimodal image registration using deep learning. We provide a comprehensive evaluation of the proposed pipeline versus the current state-of-the-art image registration and style transfer methods on four types of biological problems utilizing different microscopy modalities. We found that style transfer of modality domains paired with fully unsupervised training leads to comparable image registration accuracy to supervised methods and, most importantly, does not require human intervention.}, year = {2024}, eissn = {1477-4054}, orcid-numbers = {Mund, Andreas/0000-0002-7843-5341} } @article{MTMT:34782533, title = {A new family of bacterial ribosome hibernation factors}, url = {https://m2.mtmt.hu/api/publication/34782533}, author = {Helena-Bueno, Karla and Rybak, Mariia Yu. and Ekemezie, Chinenye L. and Sullivan, Rudi and Brown, Charlotte R. and Dingwall, Charlotte and Basle, Arnaud and Schneider, Claudia and Connolly, James P. R. and Blaza, James N. and Csörgő, Bálint and Moynihan, Patrick J. and Gagnon, Matthieu G. and Hill, Chris H. and Melnikov, Sergey V.}, doi = {10.1038/s41586-024-07041-8}, journal-iso = {NATURE}, journal = {NATURE}, volume = {626}, unique-id = {34782533}, issn = {0028-0836}, abstract = {To conserve energy during starvation and stress, many organisms use hibernation factor proteins to inhibit protein synthesis and protect their ribosomes from damage1,2. In bacteria, two families of hibernation factors have been described, but the low conservation of these proteins and the huge diversity of species, habitats and environmental stressors have confounded their discovery3-6. Here, by combining cryogenic electron microscopy, genetics and biochemistry, we identify Balon, a new hibernation factor in the cold-adapted bacterium Psychrobacter urativorans. We show that Balon is a distant homologue of the archaeo-eukaryotic translation factor aeRF1 and is found in 20% of representative bacteria. During cold shock or stationary phase, Balon occupies the ribosomal A site in both vacant and actively translating ribosomes in complex with EF-Tu, highlighting an unexpected role for EF-Tu in the cellular stress response. Unlike typical A-site substrates, Balon binds to ribosomes in an mRNA-independent manner, initiating a new mode of ribosome hibernation that can commence while ribosomes are still engaged in protein synthesis. Our work suggests that Balon-EF-Tu-regulated ribosome hibernation is a ubiquitous bacterial stress-response mechanism, and we demonstrate that putative Balon homologues in Mycobacteria bind to ribosomes in a similar fashion. This finding calls for a revision of the current model of ribosome hibernation inferred from common model organisms and holds numerous implications for how we understand and study ribosome hibernation. A study identifies a new bacterial ribosome hibernation factor, Balon, and describes its association with EF-Tu and its initiation of mRNA-independent hibernation during protein synthesis.}, keywords = {MECHANISM; PROTEIN; ESCHERICHIA-COLI; STRUCTURAL BASIS; CRYSTAL-STRUCTURE; ELONGATION; TERMINATION; EF1-alpha; PEPTIDE-BOND FORMATION}, year = {2024}, eissn = {1476-4687}, pages = {1125-1132}, orcid-numbers = {Rybak, Mariia Yu./0000-0002-0478-0222; Blaza, James N./0000-0001-5420-2116; Csörgő, Bálint/0000-0003-0397-6845; Moynihan, Patrick J./0000-0003-4182-6223} } @article{MTMT:34782532, title = {Learning representations for image-based profiling of perturbations}, url = {https://m2.mtmt.hu/api/publication/34782532}, author = {Moshkov, Nikita and Bornholdt, Michael and Benoit, Santiago and Smith, Matthew and Mcquin, Claire and Goodman, Allen and Senft, Rebecca A. and Han, Yu and Babadi, Mehrtash and Horváth, Péter and Cimini, Beth A. and Carpenter, Anne E. and Singh, Shantanu and Caicedo, Juan C.}, doi = {10.1038/s41467-024-45999-1}, journal-iso = {NAT COMMUN}, journal = {NATURE COMMUNICATIONS}, volume = {15}, unique-id = {34782532}, issn = {2041-1723}, abstract = {Measuring the phenotypic effect of treatments on cells through imaging assays is an efficient and powerful way of studying cell biology, and requires computational methods for transforming images into quantitative data. Here, we present an improved strategy for learning representations of treatment effects from high-throughput imaging, following a causal interpretation. We use weakly supervised learning for modeling associations between images and treatments, and show that it encodes both confounding factors and phenotypic features in the learned representation. To facilitate their separation, we constructed a large training dataset with images from five different studies to maximize experimental diversity, following insights from our causal analysis. Training a model with this dataset successfully improves downstream performance, and produces a reusable convolutional network for image-based profiling, which we call Cell Painting CNN. We evaluated our strategy on three publicly available Cell Painting datasets, and observed that the Cell Painting CNN improves performance in downstream analysis up to 30% with respect to classical features, while also being more computationally efficient. Assessing cell phenotypes in image-based assays requires solid computational methods for transforming images into quantitative data. Here, the authors present a strategy for learning representations of treatment effects from high-throughput imaging, following a causal interpretation.}, year = {2024}, eissn = {2041-1723} } @article{MTMT:34749009, title = {Isolation and identification of fungal biodeteriogens from the wall of a cultural heritage church and potential applicability of antifungal proteins in protection}, url = {https://m2.mtmt.hu/api/publication/34749009}, author = {Dán, Kinga and Kocsubé, Sándor and Tóth, Liliána and Farkas, Attila and Rákhely, Gábor and Galgóczi, László Norbert}, doi = {10.1016/j.culher.2024.03.002}, journal-iso = {J CULT HERIT}, journal = {JOURNAL OF CULTURAL HERITAGE}, volume = {67}, unique-id = {34749009}, issn = {1296-2074}, year = {2024}, eissn = {1778-3674}, pages = {194-202}, orcid-numbers = {Tóth, Liliána/0000-0003-1400-6174; Galgóczi, László Norbert/0000-0002-6976-8910} } @article{MTMT:34743202, title = {A bipartite NLS motif mediates the nuclear import of Drosophila moesin}, url = {https://m2.mtmt.hu/api/publication/34743202}, author = {Kovács, Zoltán and Bajusz, Csaba and Szabó, Anikó and Borkúti, Péter and Vedelek, Balázs and Benke, Reka and Lipinszki, Zoltán and Kristó, Ildikó and Vilmos, Péter}, doi = {10.3389/fcell.2024.1206067}, journal-iso = {FRONT CELL DEV BIOL}, journal = {FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY}, volume = {12}, unique-id = {34743202}, issn = {2296-634X}, abstract = {The ERM protein family, which consists of three closely related proteins in vertebrates, ezrin, radixin, and moesin (ERM), is an ancient and important group of cytoplasmic actin-binding and organizing proteins. With their FERM domain, ERMs bind various transmembrane proteins and anchor them to the actin cortex through their C-terminal F-actin binding domain, thus they are major regulators of actin dynamics in the cell. ERMs participate in many fundamental cellular processes, such as phagocytosis, microvilli formation, T-cell activation and tumor metastasis. We have previously shown that, besides its cytoplasmic activities, the single ERM protein of Drosophila melanogaster, moesin, is also present in the cell nucleus, where it participates in gene expression and mRNA export. Here we study the mechanism by which moesin enters the nucleus. We show that the nuclear import of moesin is an NLS-mediated, active process. The nuclear localization sequence of the moesin protein is an evolutionarily highly conserved, conventional bipartite motif located on the surface of the FERM domain. Our experiments also reveal that the nuclear import of moesin does not require PIP2 binding or protein activation, and occurs in monomeric form. We propose, that the balance between the phosphorylated and non-phosphorylated protein pools determines the degree of nuclear import of moesin.}, keywords = {PHOSPHORYLATION; BINDING; LOCALIZATION; IDENTIFICATION; NUCLEUS; STRUCTURAL BASIS; DROSOPHILA; CELL BIOLOGY; ERM PROTEINS; ezrin; moesin; CYTOPLASMIC TAIL; ERM; PIP2; importin; MERLIN; LINKS ACTIN}, year = {2024}, eissn = {2296-634X}, orcid-numbers = {Vedelek, Balázs/0000-0001-6981-0026; Lipinszki, Zoltán/0000-0002-2067-0832} } @{MTMT:34723493, title = {Mikovírusok azonosítása Rhizopus fajokban}, url = {https://m2.mtmt.hu/api/publication/34723493}, author = {Sávai, Gergő and Kartali, Tünde and Benci, Dániel Attila and Patai, Roland and Lipinszki, Zoltán and Vágvölgyi, Csaba and Papp, Tamás}, booktitle = {Biotechnológiai Szakmai Nap Absztraktfüzet}, unique-id = {34723493}, year = {2024}, orcid-numbers = {Lipinszki, Zoltán/0000-0002-2067-0832; Vágvölgyi, Csaba/0000-0003-0009-7773; Papp, Tamás/0000-0001-8211-5431} } @article{MTMT:34721641, title = {Mutation in Arabidopsis mitochondrial Pentatricopeptide repeat 40 gene affects tolerance to water deficit}, url = {https://m2.mtmt.hu/api/publication/34721641}, author = {Kant, Kamal and Rigó, Gábor and Faragó, Dóra and Benyó, Dániel and Tengölics, Roland and Szabados, László and Zsigmond, Laura}, doi = {10.1007/s00425-024-04354-w}, journal-iso = {PLANTA}, journal = {PLANTA}, volume = {259}, unique-id = {34721641}, issn = {0032-0935}, year = {2024}, eissn = {1432-2048}, orcid-numbers = {Benyó, Dániel/0000-0002-4537-2866; Zsigmond, Laura/0000-0002-1388-1762} }