TY - JOUR AU - Cinege, Gyöngyi Ilona AU - Fodor, K. AU - Magyar, Lilla Brigitta AU - Lipinszki, Zoltán AU - Hultmark, D. AU - Andó, István TI - Cellular Immunity of Drosophila willistoni Reveals Novel Complexity in Insect Anti-Parasitoid Defense JF - CELLS J2 - CELLS-BASEL VL - 13 PY - 2024 IS - 7 SN - 2073-4409 DO - 10.3390/cells13070593 UR - https://m2.mtmt.hu/api/publication/34804520 ID - 34804520 N1 - Innate Immunity Group, Institute of Genetics, HUN-REN Biological Research Centre, Szeged, 6726, Hungary Doctoral School of Biology, University of Szeged, Szeged, 6720, Hungary MTA SZBK Lendület Laboratory of Cell Cycle Regulation, Institute of Biochemistry, HUN-REN Biological Research Centre, Szeged, 6726, Hungary National Laboratory for Biotechnology, Institute of Genetics, HUN-REN Biological Research Centre, Szeged, 6726, Hungary Department of Molecular Biology, Umea University, Umea, 901 87, Sweden Export Date: 22 April 2024 Correspondence Address: Cinege, G.; Innate Immunity Group, Hungary; email: cinege.gyongyi@brc.hu LA - English DB - MTMT ER - TY - JOUR AU - Hudhud, Lina AU - Rozmer, Katalin AU - Kecskés, Angéla AU - Pohóczky, Krisztina AU - Bencze, Noémi AU - Buzás, Krisztina AU - Szőke, Éva AU - Helyes, Zsuzsanna TI - Transient Receptor Potential Ankyrin 1 Ion Channel Is Expressed in Osteosarcoma and Its Activation Reduces Viability JF - INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES J2 - INT J MOL SCI VL - 25 PY - 2024 IS - 7 PG - 13 SN - 1661-6596 DO - 10.3390/ijms25073760 UR - https://m2.mtmt.hu/api/publication/34797924 ID - 34797924 N1 - * Megosztott szerzőség AB - 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. LA - English DB - MTMT ER - TY - JOUR AU - Faragó, Anna AU - Zvara, Ágnes AU - Tiszlavicz, László AU - Hunyadi-Gulyás Éva, Csilla AU - Darula, Zsuzsanna AU - Hegedűs, Zoltán AU - Szabó, Enikő AU - Surguta, Sára Eszter AU - Tóvári, József AU - Puskás, László AU - Szebeni, Gábor TI - Lectin-Based Immunophenotyping and Whole Proteomic Profiling of CT-26 Colon Carcinoma Murine Model. JF - INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES J2 - INT J MOL SCI VL - 25 PY - 2024 IS - 7 PG - 21 SN - 1661-6596 DO - 10.3390/ijms25074022 UR - https://m2.mtmt.hu/api/publication/34790193 ID - 34790193 N1 - * Megosztott szerzőség AB - 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. LA - English DB - MTMT ER - TY - JOUR AU - Grexa, István AU - Iván, Zsanett Zsófia AU - Migh, Ede AU - Kovács, Ferenc AU - Bolck, Hella A AU - Zheng, Xiang AU - Mund, Andreas AU - Moshkov, Nikita AU - Csapóné Miczán, Vivien AU - Koós, Krisztián AU - Horváth, Péter TI - SuperCUT, an unsupervised multimodal image registration with deep learning for biomedical microscopy JF - BRIEFINGS IN BIOINFORMATICS J2 - BRIEF BIOINFORM VL - 25 PY - 2024 IS - 2 PG - 11 SN - 1467-5463 DO - 10.1093/bib/bbae029 UR - https://m2.mtmt.hu/api/publication/34786803 ID - 34786803 AB - 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. LA - English DB - MTMT ER - TY - JOUR AU - Helena-Bueno, Karla AU - Rybak, Mariia Yu. AU - Ekemezie, Chinenye L. AU - Sullivan, Rudi AU - Brown, Charlotte R. AU - Dingwall, Charlotte AU - Basle, Arnaud AU - Schneider, Claudia AU - Connolly, James P. R. AU - Blaza, James N. AU - Csörgő, Bálint AU - Moynihan, Patrick J. AU - Gagnon, Matthieu G. AU - Hill, Chris H. AU - Melnikov, Sergey V. TI - A new family of bacterial ribosome hibernation factors JF - NATURE J2 - NATURE VL - 626 PY - 2024 IS - 8001 SP - 1125 EP - 1132 PG - 26 SN - 0028-0836 DO - 10.1038/s41586-024-07041-8 UR - https://m2.mtmt.hu/api/publication/34782533 ID - 34782533 N1 - Funding Agency and Grant Number: Newcastle University NUORS 2021 Award; James W. McLaughlin Fellowship Fund; Medical Research Council [MR/N013840/1]; Biotechnology and Biological Sciences Research Council UK [BB/T008695/1]; UKRI Future Leader Fellowship [MR/T040742/1]; Lenduelet (Momentum) Program of the Hungarian Academy of Sciences [LP2022-4/2022a]; National Institutes of Health [R01GM136936]; Welch Foundation [H-2032-20230405]; Wellcome Trust & Royal Society Sir Henry Dale Fellowship [221818/Z/20/Z]; Royal Society [RGS/R2/202003]; Medical Research Council; Newcastle University Structural Biology Laboratory; Biotechnology and Biological Sciences Research Council; Wellcome Trust [206161/Z/17/Z]; Sealy and Smith Foundation; York Centre of Excellence in Mass Spectrometry; Engineering and Physical Sciences Research Council [EP/K039660/1, EP/M028127/1]; Yorkshire Forward; Northern Way Initiative; Wellcome Trust [BI28576]; Wellcome Trust [221818/Z/20/Z] Funding Source: Wellcome Trust Funding text: We thank B. Javid, Z. Lightowlers, B. van der Berg and H. Murray for comments on the manuscript; J. Turkenburg and S. Hart for work supporting the York cryo-EM facility; and A. Kereszt for providing the conjugative strain E. coli BW29427. This work was financed by the Newcastle University NUORS 2021 Award (to K.H.-B.), the James W. McLaughlin Fellowship Fund (to M.Yu.R.), the Medical Research Council (MR/N013840/1 to C.L.E.), the Biotechnology and Biological Sciences Research Council UK (BB/T008695/1 to C.R.B.), a UKRI Future Leader Fellowship (MR/T040742/1 to J.N.B.), the Lenduelet (Momentum) Program of the Hungarian Academy of Sciences (LP2022-4/2022a to B.C.), a National Institutes of Health grant (R01GM136936 to M.G.G.), a Welch Foundation grant (H-2032-20230405 to M.G.G.), a Wellcome Trust & Royal Society Sir Henry Dale Fellowship (221818/Z/20/Z to C.H.H.) and the Royal Society (RGS/R2/202003 to S.V.M.). This project was undertaken on the NSBL Cluster and the Viking Cluster, which are high-performance compute facilities provided by Newcastle University and the University of York, respectively. We are grateful for computational support from the University of York High Performance Computing service, Viking and the Research Computing team, and support from the Newcastle University Structural Biology Laboratory. We also acknowledge the York cryo-EM facility supported by the Wellcome Trust (206161/Z/17/Z) and the York Centre of Excellence in Mass Spectrometry that was created with a capital investment through Science City York and supported by the Engineering and Physical Sciences Research Council (EP/K039660/1; EP/M028127/1) and Yorkshire Forward with funds from the Northern Way Initiative. We also acknowledge Diamond UK for access to and support of the cryo-EM facilities at the UK national electron Bio-Imaging Centre, proposal BI28576, financed by the Wellcome Trust, the Medical Research Council and the Biotechnology and Biological Sciences Research Council. We are grateful to M. Sherman for advice and support; K.-Y. Wong and J. Perkyns for computational support; and to the Sealy and Smith Foundation for supporting the Sealy Center for Structural Biology at the University of Texas Medical Branch. For the purpose of open access, the authors have applied a CC BY public copyright license to any author accepted manuscript version arising from this submission. AB - 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. LA - English DB - MTMT ER - TY - JOUR AU - Moshkov, Nikita AU - Bornholdt, Michael AU - Benoit, Santiago AU - Smith, Matthew AU - Mcquin, Claire AU - Goodman, Allen AU - Senft, Rebecca A. AU - Han, Yu AU - Babadi, Mehrtash AU - Horváth, Péter AU - Cimini, Beth A. AU - Carpenter, Anne E. AU - Singh, Shantanu AU - Caicedo, Juan C. TI - Learning representations for image-based profiling of perturbations JF - NATURE COMMUNICATIONS J2 - NAT COMMUN VL - 15 PY - 2024 IS - 1 PG - 17 SN - 2041-1723 DO - 10.1038/s41467-024-45999-1 UR - https://m2.mtmt.hu/api/publication/34782532 ID - 34782532 N1 - Funding Agency and Grant Number: ECOST action [CA15124]; LENDULET-BIOMAG Grant [2018-342]; European Regional Development Funds [GINOP-2.2.1-15-2017-00072]; H2020; EU-Horizont (ERAPERMED-COMPASS, ERAPERMED-SYMMETRY, DiscovAIR, FAIR-CHARM, SWEEPICS); ELKH-Excellence grants; Cooperative Doctoral Programme (2020-2021) of the Ministry for Innovation and Technology; OTKA-SNN [P41 GM135019]; NIH [2018-192059]; Chan Zuckerberg Initiative DAF [2348683]; Silicon Valley Community Foundation; Schmidt Fellowship program of the Broad Institute; NSF DBI Award [R35 GM122547]; [TKP2021-EGA09]; [139455/ARRS]; [2020-225720] Funding text: We thank Salil Bhate for the valuable discussions and feedback provided to improve the clarity of this manuscript. NM acknowledges the short-term scientific mission grants provided by eCOST action CA15124 (NEUBIAS) in 2019 and 2020. NM and PH acknowledge support from the LENDULET-BIOMAG Grant (2018-342), from the European Regional Development Funds (GINOP-2.2.1-15-2017-00072), from the H2020 and EU-Horizont (ERAPERMED-COMPASS, ERAPERMED-SYMMETRY, DiscovAIR, FAIR-CHARM, SWEEPICS), from TKP2021-EGA09, from the ELKH-Excellence grants and from the Cooperative Doctoral Programme (2020-2021) of the Ministry for Innovation and Technology, from OTKA-SNN no.139455/ARRS. Researchers in the Carpenter-Singh lab were supported by NIH R35 GM122547 to AEC. Researchers in the Cimini lab were supported by NIH P41 GM135019. AG was supported by grant number 2018-192059 and BAC was additionally supported by grant number 2020-225720 from the Chan Zuckerberg Initiative DAF, an advised fund of the Silicon Valley Community Foundation. JCC was supported by the Schmidt Fellowship program of the Broad Institute and by the NSF DBI Award 2348683. AB - 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. LA - English DB - MTMT ER - TY - JOUR AU - Dán, Kinga AU - Kocsubé, Sándor AU - Tóth, Liliána AU - Farkas, Attila AU - Rákhely, Gábor AU - Galgóczi, László Norbert TI - Isolation and identification of fungal biodeteriogens from the wall of a cultural heritage church and potential applicability of antifungal proteins in protection JF - JOURNAL OF CULTURAL HERITAGE J2 - J CULT HERIT VL - 67 PY - 2024 SP - 194 EP - 202 PG - 9 SN - 1296-2074 DO - 10.1016/j.culher.2024.03.002 UR - https://m2.mtmt.hu/api/publication/34749009 ID - 34749009 N1 - Export Date: 16 April 2024 Correspondence Address: Galgóczy, L.; Department of Biotechnology, Közép fasor 52, Hungary; email: galgoczi@bio.u-szeged.hu LA - English DB - MTMT ER - TY - JOUR AU - Kovács, Zoltán AU - Bajusz, Csaba AU - Szabó, Anikó AU - Borkúti, Péter AU - Vedelek, Balázs AU - Benke, Reka AU - Lipinszki, Zoltán AU - Kristó, Ildikó AU - Vilmos, Péter TI - A bipartite NLS motif mediates the nuclear import of Drosophila moesin JF - FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY J2 - FRONT CELL DEV BIOL VL - 12 PY - 2024 PG - 14 SN - 2296-634X DO - 10.3389/fcell.2024.1206067 UR - https://m2.mtmt.hu/api/publication/34743202 ID - 34743202 N1 - Funding Agency and Grant Number: NKFIH (Hungarian National Research, Development and Innovation Office) through the National Laboratory for Biotechnology program [PD127968, LP2017-7/2017]; Hungarian Academy of Sciences Lendulet Grant; [2022-2.1.1-NL-2022-00008] Funding text: This work was supported by NKFIH (Hungarian National Research, Development and Innovation Office) through the National Laboratory for Biotechnology program, grant 2022-2.1.1-NL-2022-00008 (PV), and PD127968 (IK), and the Hungarian Academy of Sciences Lendulet Grant LP2017-7/2017 (ZL). AB - 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. LA - English DB - MTMT ER - TY - CHAP AU - Sávai, Gergő AU - Kartali, Tünde AU - Benci, Dániel Attila AU - Patai, Roland AU - Lipinszki, Zoltán AU - Vágvölgyi, Csaba AU - Papp, Tamás TI - Mikovírusok azonosítása Rhizopus fajokban T2 - Biotechnológiai Szakmai Nap Absztraktfüzet PB - Doktoranduszok Országos Szövetsége (DOSZ) CY - Budapest SN - 9786156457448 PY - 2024 UR - https://m2.mtmt.hu/api/publication/34723493 ID - 34723493 LA - Hungarian DB - MTMT ER - TY - JOUR AU - Kant, Kamal AU - Rigó, Gábor AU - Faragó, Dóra AU - Benyó, Dániel AU - Tengölics, Roland AU - Szabados, László AU - Zsigmond, Laura TI - Mutation in Arabidopsis mitochondrial Pentatricopeptide repeat 40 gene affects tolerance to water deficit JF - PLANTA J2 - PLANTA VL - 259 PY - 2024 IS - 4 SN - 0032-0935 DO - 10.1007/s00425-024-04354-w UR - https://m2.mtmt.hu/api/publication/34721641 ID - 34721641 N1 - Funding Agency and Grant Number: HUN-REN Biological Research Centre, Szeged Funding text: Open access funding provided by HUN-REN Biological Research Centre, Szeged. LA - English DB - MTMT ER -