@article{MTMT:34856915,
	title = {Triggered cagedSTORM microscopy},
	url = {https://m2.mtmt.hu/api/publication/34856915},
	author = {Bíró, Péter and Novák, Tibor and Czvik, Elvira and Mihály, József and Szikora, Szilárd and van de Linde, Sebastian and Erdélyi, Miklós},
	doi = {10.1364/BOE.517480},
	journal-iso = {BIOMED OPT EXPRESS},
	journal = {BIOMEDICAL OPTICS EXPRESS},
	volume = {15},
	unique-id = {34856915},
	issn = {2156-7085},
	abstract = {In standard SMLM methods, the photoswitching of single fluorescent molecules and the data acquisition processes are independent, which leads to the detection of single molecule blinking events on several consecutive frames. This mismatch results in several data points with reduced localization precision, and it also increases the possibilities of overlapping. Here we discuss how the synchronization of the fluorophores’ ON state to the camera exposure time increases the average intensity of the captured point spread functions and hence improves the localization precision. Simulations and theoretical results show that such synchronization leads to fewer localizations with 15% higher sum signal on average, while reducing the probability of overlaps by 10%.},
	year = {2024},
	eissn = {2156-7085},
	pages = {3715-3726},
	orcid-numbers = {Novák, Tibor/0000-0003-0756-6851; Erdélyi, Miklós/0000-0002-9501-5752}
}

@article{MTMT:34506131,
	title = {Peripheral thickening of the sarcomeres and pointed end elongation of the thin filaments are both promoted by SALS and its formin interaction partners},
	url = {https://m2.mtmt.hu/api/publication/34506131},
	author = {Farkas, Dávid and Szikora, Szilárd and Jijumon, A S and Polgár, Tamás Ferenc and Patai, Roland and Szütsné Tóth, Mónika Ágnes and Bugyi, Beáta and Gajdos, Tamás and Bíró, Péter and Novák, Tibor and Erdélyi, Miklós and Mihály, József},
	doi = {10.1371/journal.pgen.1011117},
	journal-iso = {PLOS GENET},
	journal = {PLOS GENETICS},
	volume = {20},
	unique-id = {34506131},
	issn = {1553-7390},
	abstract = {During striated muscle development the first periodically repeated units appear in the premyofibrils, consisting of immature sarcomeres that must undergo a substantial growth both in length and width, to reach their final size. Here we report that, beyond its well established role in sarcomere elongation, the Sarcomere length short (SALS) protein is involved in Z-disc formation and peripheral growth of the sarcomeres. Our protein localization data and loss-of-function studies in the Drosophila indirect flight muscle strongly suggest that radial growth of the sarcomeres is initiated at the Z-disc. As to thin filament elongation, we used a powerful nanoscopy approach to reveal that SALS is subject to a major conformational change during sarcomere development, which might be critical to stop pointed end elongation in the adult muscles. In addition, we demonstrate that the roles of SALS in sarcomere elongation and radial growth are both dependent on formin type of actin assembly factors. Unexpectedly, when SALS is present in excess amounts, it promotes the formation of actin aggregates highly resembling the ones described in nemaline myopathy patients. Collectively, these findings helped to shed light on the complex mechanisms of SALS during the coordinated elongation and thickening of the sarcomeres, and resulted in the discovery of a potential nemaline myopathy model, suitable for the identification of genetic and small molecule inhibitors.},
	year = {2024},
	eissn = {1553-7404},
	orcid-numbers = {Gajdos, Tamás/0000-0002-5288-4659; Novák, Tibor/0000-0003-0756-6851; Erdélyi, Miklós/0000-0002-9501-5752}
}

@article{MTMT:34600475,
	title = {Detection of Actin in Nuclear Protein Fraction Isolated from Adult Drosophila Ovary},
	url = {https://m2.mtmt.hu/api/publication/34600475},
	author = {Kristó, Ildikó and Borkúti, Péter and Kovács, Zoltán and Szabó, Anikó and Szikora, Szilárd and Vilmos, Péter},
	doi = {10.1007/978-1-0716-2970-3_19},
	journal-iso = {METHODS MOL BIOL},
	journal = {METHODS IN MOLECULAR BIOLOGY},
	volume = {2626},
	unique-id = {34600475},
	issn = {1064-3745},
	year = {2023},
	eissn = {1940-6029},
	pages = {353-364}
}

@article{MTMT:34409947,
	title = {FRL and DAAM are required for lateral adhesion of interommatidial cells and patterning of the retinal floor},
	url = {https://m2.mtmt.hu/api/publication/34409947},
	author = {Gazsó-Gerhát, Gabriella and Gombos, Rita I and Tóth, Krisztina and Kaltenecker, Péter and Szikora, Szilárd and Bíró, Judit and Csapó, Enikő and Asztalos, Zoltán Imre and Mihály, József},
	doi = {10.1242/dev.201713},
	journal-iso = {DEVELOPMENT},
	journal = {DEVELOPMENT},
	volume = {150},
	unique-id = {34409947},
	issn = {0950-1991},
	abstract = {Optical insulation of the unit eyes (ommatidia) is an important prerequisite of precise sight with compound eyes. Separation of the ommatidia is ensured by pigment cells that organize into a hexagonal lattice in the Drosophila eye, forming thin walls between the facets. Cell adhesion, mediated by apically and latero-basally located junctional complexes, is crucial for stable attachment of these cells to each other and the basal lamina. Whereas former studies have focused on the formation and remodelling of the cellular connections at the apical region, here, we report a specific alteration of the lateral adhesion of the lattice cells, leaving the apical junctions largely unaffected. We found that DAAM and FRL, two formin-type cytoskeleton regulatory proteins, play redundant roles in lateral adhesion of the interommatidial cells and patterning of the retinal floor. We show that formin-dependent cortical actin assembly is crucial for latero-basal sealing of the ommatidial lattice. We expect that the investigation of these previously unreported eye phenotypes will pave the way toward a better understanding of the three-dimensional aspects of compound eye development.},
	year = {2023},
	eissn = {1477-9129},
	orcid-numbers = {Csapó, Enikő/0009-0001-1980-4020}
}

@article{MTMT:34043007,
	title = {The oxoglutarate dehydrogenase complex is involved in myofibril growth and Z-disc assembly in Drosophila},
	url = {https://m2.mtmt.hu/api/publication/34043007},
	author = {González Morales, Nicanor and Marescal, Océane and Szikora, Szilárd and Katzemich, Anja and Correia-Mesquita, Tuana and Bíró, Péter and Erdélyi, Miklós and Mihály, József and Schöck, Frieder},
	doi = {10.1242/jcs.260717},
	journal-iso = {J CELL SCI},
	journal = {JOURNAL OF CELL SCIENCE},
	volume = {136},
	unique-id = {34043007},
	issn = {0021-9533},
	abstract = {Myofibrils are long intracellular cables specific to muscles, composed mainly of actin and myosin filaments. The actin and myosin filaments are organized into repeated units called sarcomeres, which form the myofibrils. Muscle contraction is achieved by the simultaneous shortening of sarcomeres, which requires all sarcomeres to be the same size. Muscles have a variety of ways to ensure sarcomere homogeneity. We have previously shown that the controlled oligomerization of Zasp proteins sets the diameter of the myofibril. Here, we looked for Zasp-binding proteins at the Z-disc to identify additional proteins coordinating myofibril growth and assembly. We found that the E1 subunit of the oxoglutarate dehydrogenase complex localizes to both the Z-disc and the mitochondria, and is recruited to the Z-disc by Zasp52. The three subunits of the oxoglutarate dehydrogenase complex are required for myofibril formation. Using super-resolution microscopy, we revealed the overall organization of the complex at the Z-disc. Metabolomics identified an amino acid imbalance affecting protein synthesis as a possible cause of myofibril defects, which is supported by OGDH-dependent localization of ribosomes at the Z-disc.},
	year = {2023},
	eissn = {1477-9137},
	orcid-numbers = {González Morales, Nicanor/0000-0003-1305-8992; Marescal, Océane/0000-0002-1417-1041; Szikora, Szilárd/0000-0003-4339-4946; Erdélyi, Miklós/0000-0002-9501-5752; Mihály, József/0000-0003-3399-2424; Schöck, Frieder/0000-0002-1351-0574}
}

@article{MTMT:33708203,
	title = {Machine learning framework to segment sarcomeric structures in SMLM data},
	url = {https://m2.mtmt.hu/api/publication/33708203},
	author = {Varga, Dániel and Szikora, Szilárd and Novák, Tibor and Pap, Gergely and Lékó, Gábor and Mihály, József and Erdélyi, Miklós},
	doi = {10.1038/s41598-023-28539-7},
	journal-iso = {SCI REP},
	journal = {SCIENTIFIC REPORTS},
	volume = {13},
	unique-id = {33708203},
	abstract = {Object detection is an image analysis task with a wide range of applications, which is difficult to accomplish with traditional programming. Recent breakthroughs in machine learning have made significant progress in this area. However, these algorithms are generally compatible with traditional pixelated images and cannot be directly applied for pointillist datasets generated by single molecule localization microscopy (SMLM) methods. Here, we have improved the averaging method developed for the analysis of SMLM images of sarcomere structures based on a machine learning object detection algorithm. The ordered structure of sarcomeres allows us to determine the location of the proteins more accurately by superimposing SMLM images of identically assembled proteins. However, the area segmentation process required for averaging can be extremely time-consuming and tedious. In this work, we have automated this process. The developed algorithm not only finds the regions of interest, but also classifies the localizations and identifies the true positive ones. For training, we used simulations to generate large amounts of labelled data. After tuning the neural network’s internal parameters, it could find the localizations associated with the structures we were looking for with high accuracy. We validated our results by comparing them with previous manual evaluations. It has also been proven that the simulations can generate data of sufficient quality for training. Our method is suitable for the identification of other types of structures in SMLM data.},
	year = {2023},
	eissn = {2045-2322},
	orcid-numbers = {Varga, Dániel/0000-0003-0391-5057; Novák, Tibor/0000-0003-0756-6851; Lékó, Gábor/0000-0001-8679-9156; Erdélyi, Miklós/0000-0002-9501-5752}
}

@article{MTMT:33260144,
	title = {Quantitative dSTORM superresolution microscopy},
	url = {https://m2.mtmt.hu/api/publication/33260144},
	author = {Novák, Tibor and Varga, Dániel and Bíró, Péter and H. Kovács, Bálint Barna and Majoros, Hajnalka and Pankotai, Tibor and Szikora, Szilárd and Mihály, József and Erdélyi, Miklós},
	doi = {10.1556/2051.2022.00093},
	journal-iso = {RESOL DISCOVERY},
	journal = {RESOLUTION AND DISCOVERY},
	volume = {6},
	unique-id = {33260144},
	abstract = {Localization based superresolution technique provides the highest spatial resolution in optical microscopy. The final image is formed by the precise localization of individual fluorescent dyes, therefore the quantification of the collected data requires special protocols, algorithms and validation processes. The effects of labelling density and structured background on the final image quality were studied theoretically using the TestSTORM simulator. It was shown that system parameters affect the morphology of the final reconstructed image in different ways and the accuracy of the imaging can be determined. Although theoretical studies help in the optimization procedure, the quantification of experimental data raises additional issues, since the ground truth data is unknown. Localization precision, linker length, sample drift and labelling density are the major factors that make quantitative data analysis difficult. Two examples (geometrical evaluation of sarcomere structures and counting the γH2AX molecules in DNA damage induced repair foci) have been presented to demonstrate the efficiency of quantitative evaluation experimentally.},
	year = {2022},
	eissn = {2498-8707},
	pages = {25-31},
	orcid-numbers = {Novák, Tibor/0000-0003-0756-6851; Varga, Dániel/0000-0003-0391-5057; Bíró, Péter/0000-0001-8103-6248; Majoros, Hajnalka/0000-0003-2020-971X; Pankotai, Tibor/0000-0001-9810-5465; Erdélyi, Miklós/0000-0002-9501-5752}
}

@article{MTMT:32840276,
	title = {The mechanisms of thin filament assembly and length regulation in muscles},
	url = {https://m2.mtmt.hu/api/publication/32840276},
	author = {Szikora, Szilárd and Görög, Péter and Mihály, József},
	doi = {10.3390/ijms23105306},
	journal-iso = {INT J MOL SCI},
	journal = {INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES},
	volume = {23},
	unique-id = {32840276},
	issn = {1661-6596},
	year = {2022},
	eissn = {1422-0067}
}

@article{MTMT:32153073,
	title = {Drosophila models rediscovered with super-resolution microscopy},
	url = {https://m2.mtmt.hu/api/publication/32153073},
	author = {Szikora, Szilárd and Görög, Péter and Kozma, Csaba and Mihály, József},
	doi = {10.3390/cells10081924},
	journal-iso = {CELLS-BASEL},
	journal = {CELLS},
	volume = {10},
	unique-id = {32153073},
	year = {2021},
	eissn = {2073-4409}
}

@article{MTMT:31661623,
	title = {Superresolution Microscopy of Drosophila Indirect Flight Muscle Sarcomeres},
	url = {https://m2.mtmt.hu/api/publication/31661623},
	author = {Szikora, Szilárd and Novák, Tibor and Gajdos, Tamás and Erdélyi, Miklós and Mihály, József},
	doi = {10.21769/BioProtoc.3654},
	journal-iso = {BIO-PROTOCOL},
	journal = {BIO-PROTOCOL},
	volume = {10},
	unique-id = {31661623},
	issn = {2331-8325},
	abstract = {Sarcomeres are extremely highly ordered macromolecular assemblies where proper structural organization is an absolute prerequisite to the functionality of these contractile units. Despite the wealth of information collected, the exact spatial arrangement of many of the H-zone and Z-disk proteins remained unknown. Recently, we developed a powerful nanoscopic approach to localize the sarcomeric protein components with a resolution well below the diffraction limit. The ease of sample preparation and the near crystalline structure of the Drosophila flight muscle sarcomeres make them ideally suitable for single molecule localization microscopy and structure averaging. Our approach allowed us to determine the position of dozens of H-zone and Z-disk proteins with a quasi-molecular, similar to 5-10 nm localization precision. The protocol described below provides an easy and reproducible method to prepare individual myofibrils for dSTORM imaging. In addition, it includes an in-depth description of a custom made and freely available software toolbox to process and quantitatively analyze the raw localization data.},
	year = {2020},
	eissn = {2331-8325},
	orcid-numbers = {Novák, Tibor/0000-0003-0756-6851; Gajdos, Tamás/0000-0002-5288-4659; Erdélyi, Miklós/0000-0002-9501-5752}
}