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Article ; Online: The Doctor of Delayed Publications: The Remarkable Life of George Streisinger (1927-1984).

Varga, Máté

2018 Volume 15, Issue 3, Page(s) 314–319

Abstract: The history of science offers multiple examples of how the perseverance of a single visionary person could open the floodgates for a whole new area of research. Zebrafish research is one of these fields with an exciting founding story, as it was the ... ...

Abstract	The history of science offers multiple examples of how the perseverance of a single visionary person could open the floodgates for a whole new area of research. Zebrafish research is one of these fields with an exciting founding story, as it was the dogged persistence of one man, George Streisinger, that ultimately lifted this little fish out of the obscurity of pet shops into the pantheon of genetic model organisms. The Hungarian born Streisinger was one of the most gifted geneticists of his era and his network of mentors and friends really reads like a who-is-who of 20th century genetics. And it was not only science where he excelled: the way he took his civic duties seriously and outspokenly fought social injustice wherever he met it offers an important lesson on integrity for today's scientists as well.
MeSH term(s)	Animals ; Biomedical Research/history ; Disease Models, Animal ; History, 20th Century ; Hungary ; Publications ; United States ; Zebrafish
Language	English
Publishing date	2018
Publishing country	United States
Document type	Biography ; Historical Article ; Journal Article
ZDB-ID	2156020-1
ISSN	1557-8542 ; 1545-8547
ISSN (online)	1557-8542
ISSN	1545-8547
DOI	10.1089/zeb.2017.1531
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Article ; Online: The role of post-transcriptional modifications during development.

Hamar, Renáta / Varga, Máté

Biologia futura

2022 Volume 74, Issue 1-2, Page(s) 45–59

Abstract: While the existence of post-transcriptional modifications of RNA nucleotides has been known for decades, in most RNA species the exact positions of these modifications and their physiological function have been elusive until recently. Technological ... ...

Abstract	While the existence of post-transcriptional modifications of RNA nucleotides has been known for decades, in most RNA species the exact positions of these modifications and their physiological function have been elusive until recently. Technological advances, such as high-throughput next-generation sequencing (NGS) methods and nanopore-based mapping technologies, have made it possible to map the position of these modifications with single nucleotide accuracy, and genetic screens have uncovered the "writer", "reader" and "eraser" proteins that help to install, interpret and remove such modifications, respectively. These discoveries led to intensive research programmes with the aim of uncovering the roles of these modifications during diverse biological processes. In this review, we assess novel discoveries related to the role of post-transcriptional modifications during animal development, highlighting how these discoveries can affect multiple aspects of development from fertilization to differentiation in many species.
MeSH term(s)	Animals ; RNA Processing, Post-Transcriptional ; RNA/genetics ; RNA/metabolism ; Proteins ; High-Throughput Nucleotide Sequencing
Chemical Substances	RNA (63231-63-0) ; Proteins
Language	English
Publishing date	2022-12-08
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2987596-1
ISSN	2676-8607 ; 2676-8615
ISSN (online)	2676-8607
ISSN	2676-8615
DOI	10.1007/s42977-022-00142-3
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Article ; Online: Gene expression changes during the evolution of the tetrapod limb.

Varga, Zsombor / Varga, Máté

Biologia futura

2022

Abstract: Major changes in the vertebrate anatomy have preceded the conquest of land by the members of this taxon, and continuous changes in limb shape and use have occurred during the later radiation of tetrapods. While the main, conserved mechanisms of limb ... ...

Abstract	Major changes in the vertebrate anatomy have preceded the conquest of land by the members of this taxon, and continuous changes in limb shape and use have occurred during the later radiation of tetrapods. While the main, conserved mechanisms of limb development have been discerned over the past century using a combination of classical embryological and molecular methods, only recent advances made it possible to identify and study the regulatory changes that have contributed to the evolution of the tetrapod appendage. These advances include the expansion of the model repertoire from traditional genetic model species to non-conventional ones, a proliferation of predictive mathematical models that describe gene interactions, an explosion in genomic data and the development of high-throughput methodologies. These revolutionary innovations make it possible to identify specific mutations that are behind specific transitions in limb evolution. Also, as we continue to apply them to more and more extant species, we can expect to gain a fine-grained view of this evolutionary transition that has been so consequential for our species as well.
Language	English
Publishing date	2022-11-10
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2987596-1
ISSN	2676-8607 ; 2676-8615
ISSN (online)	2676-8607
ISSN	2676-8615
DOI	10.1007/s42977-022-00136-1
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Article ; Online: Trehalose-Bearing Carriers to Target Impaired Autophagy and Protein Aggregation Diseases.

Maruf, Ali / Milewska, Małgorzata / Varga, Máté / Wandzik, Ilona

Journal of medicinal chemistry

2023 Volume 66, Issue 23, Page(s) 15613–15628

Abstract: In recent years, trehalose, a natural disaccharide, has attracted growing attention because of the discovery of its potential to induce autophagy. Trehalose has also been demonstrated to preserve the protein's structural integrity and to limit the ... ...

Abstract	In recent years, trehalose, a natural disaccharide, has attracted growing attention because of the discovery of its potential to induce autophagy. Trehalose has also been demonstrated to preserve the protein's structural integrity and to limit the aggregation of pathologically misfolded proteins. Both of these properties have made trehalose a promising therapeutic candidate to target autophagy-related disorders and protein aggregation diseases. Unfortunately, trehalose has poor bioavailability due to its hydrophilic nature and susceptibility to enzymatic degradation. Recently, trehalose-bearing carriers, in which trehalose is incorporated either by chemical conjugation or physical entrapment, have emerged as an alternative option to free trehalose to improve its efficacy, particularly for the treatment of neurodegenerative diseases, atherosclerosis, nonalcoholic fatty liver disease (NAFLD), and cancers. In the current Perspective, we discuss all existing literature in this emerging field and try to identify key challenges for researchers intending to develop trehalose-bearing carriers to stimulate autophagy or inhibit protein aggregation.
MeSH term(s)	Humans ; Trehalose/metabolism ; Protein Aggregates ; Disaccharides ; Autophagy ; Neurodegenerative Diseases/drug therapy
Chemical Substances	Trehalose (B8WCK70T7I) ; Protein Aggregates ; Disaccharides
Language	English
Publishing date	2023-11-29
Publishing country	United States
Document type	Journal Article ; Review ; Research Support, Non-U.S. Gov't
ZDB-ID	218133-2
ISSN	1520-4804 ; 0022-2623
ISSN (online)	1520-4804
ISSN	0022-2623
DOI	10.1021/acs.jmedchem.3c01442
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Article ; Online: Geometry-Dependent Efficiency of Dean-Flow Affected Lateral Particle Focusing and Separation in Periodically Inhomogeneous Microfluidic Channels.

Bányai, Anita / Tóth, Eszter Leelőssyné / Varga, Máté / Fürjes, Péter

Sensors (Basel, Switzerland)

2022 Volume 22, Issue 9

Abstract: In this study, inertial focusing phenomenon was investigated, which can be used as a passive method for sample preparation and target manipulation in case of particulate suspensions. Asymmetric channel geometry was designed to apply additional inertial ... ...

Abstract	In this study, inertial focusing phenomenon was investigated, which can be used as a passive method for sample preparation and target manipulation in case of particulate suspensions. Asymmetric channel geometry was designed to apply additional inertial forces besides lift forces to promote laterally ordered particles to achieve sheathless focusing or size-dependent sorting. The evolving hydrodynamic forces were tailored with altered channel parameters (width and height), and different flow rates, to get a better understanding of smaller beads' lateral migration. Fluorescent beads (with the diameter of 4.8 µm and 15.8 µm) were used to distinguish the focusing position in continuous flow, and experimental results were compared to in silico models for particle movement prediction, made in COMSOL Multiphysics. The focusing behaviour of the applied microfluidic system was mainly characterised for particle size in the range close to blood cells and bacteria.
MeSH term(s)	Hydrodynamics ; Microfluidic Analytical Techniques/methods ; Microfluidics/methods ; Particle Size
Language	English
Publishing date	2022-05-03
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2052857-7
ISSN	1424-8220 ; 1424-8220
ISSN (online)	1424-8220
ISSN	1424-8220
DOI	10.3390/s22093474
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Article ; Online: Dean-Flow Affected Lateral Focusing and Separation of Particles and Cells in Periodically Inhomogeneous Microfluidic Channels.

Bányai, Anita / Farkas, Enikő / Jankovics, Hajnalka / Székács, Inna / Tóth, Eszter Leelőssyné / Vonderviszt, Ferenc / Horváth, Róbert / Varga, Máté / Fürjes, Péter

Sensors (Basel, Switzerland)

2023 Volume 23, Issue 2

Abstract: The purpose of the recent work is to give a better explanation of how Dean vortices affect lateral focusing, and to understand how cell morphology can alter the focusing position compared to spherical particles. The position and extent of the focused ... ...

Abstract	The purpose of the recent work is to give a better explanation of how Dean vortices affect lateral focusing, and to understand how cell morphology can alter the focusing position compared to spherical particles. The position and extent of the focused region were investigated using polystyrene fluorescent beads with different bead diameters (Ø = 0.5, 1.1, 1.97, 2.9, 4.8, 5.4, 6.08, 10.2, 15.8, 16.5 µm) at different flow rates (0.5, 1, 2 µL/s). Size-dependent focusing generated a precise map of the equilibrium positions of the spherical beads at the end of the periodically altering channels, which gave a good benchmark for focusing multi-dimensional particles and cells. The biological samples used for experiments were rod-shaped
MeSH term(s)	Humans ; Microfluidics/methods ; Escherichia coli ; Erythrocytes ; Saccharomyces cerevisiae ; HeLa Cells ; Microfluidic Analytical Techniques/methods
Language	English
Publishing date	2023-01-10
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2052857-7
ISSN	1424-8220 ; 1424-8220
ISSN (online)	1424-8220
ISSN	1424-8220
DOI	10.3390/s23020800
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Article ; Online: Using Selective Enzymes to Measure Noncanonical DNA Building Blocks: dUTP, 5-Methyl-dCTP, and 5-Hydroxymethyl-dCTP.

Surányi, Éva Viola / Perey-Simon, Viktória / Hirmondó, Rita / Trombitás, Tamás / Kazzazy, Latifa / Varga, Máté / Vértessy, Beáta G / Tóth, Judit

Biomolecules

2023 Volume 13, Issue 12

Abstract: Cells maintain a fine-tuned balance of deoxyribonucleoside 5'-triphosphates (dNTPs), a crucial factor in preserving genomic integrity. Any alterations in the nucleotide pool's composition or chemical modifications to nucleotides before their ... ...

Abstract	Cells maintain a fine-tuned balance of deoxyribonucleoside 5'-triphosphates (dNTPs), a crucial factor in preserving genomic integrity. Any alterations in the nucleotide pool's composition or chemical modifications to nucleotides before their incorporation into DNA can lead to increased mutation frequency and DNA damage. In addition to the chemical modification of canonical dNTPs, the cellular de novo dNTP metabolism pathways also produce noncanonical dNTPs. To keep their levels low and prevent them from incorporating into the DNA, these noncanonical dNTPs are removed from the dNTP pool by sanitizing enzymes. In this study, we introduce innovative protocols for the high-throughput fluorescence-based quantification of dUTP, 5-methyl-dCTP, and 5-hydroxymethyl-dCTP. To distinguish between noncanonical dNTPs and their canonical counterparts, specific enzymes capable of hydrolyzing either the canonical or noncanonical dNTP analogs are employed. This approach provides a more precise understanding of the composition and noncanonical constituents of dNTP pools, facilitating a deeper comprehension of DNA metabolism and repair. It is also crucial for accurately interpreting mutational patterns generated through the next-generation sequencing of biological samples.
MeSH term(s)	Deoxyribonucleotides/metabolism ; Deoxycytosine Nucleotides ; DNA
Chemical Substances	2'-deoxycytidine 5'-triphosphate (2056-98-6) ; 5-methyldeoxycytidine triphosphate (22003-12-9) ; Deoxyribonucleotides ; Deoxycytosine Nucleotides ; DNA (9007-49-2)
Language	English
Publishing date	2023-12-15
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2701262-1
ISSN	2218-273X ; 2218-273X
ISSN (online)	2218-273X
ISSN	2218-273X
DOI	10.3390/biom13121801
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Article ; Online: The paradise fish, an advanced animal model for behavioral genetics and evolutionary developmental biology.

Szabó, Nóra / Fodor, Erika / Varga, Zoltán / Tarján-Rácz, Anita / Szabó, Kata / Miklósi, Ádám / Varga, Máté

Journal of experimental zoology. Part B, Molecular and developmental evolution

2023 Volume 342, Issue 3, Page(s) 189–199

Abstract: Paradise fish (Macropodus opercularis) is an air-breathing freshwater fish species with a signature labyrinth organ capable of extracting oxygen from the air that helps these fish to survive in hypoxic environments. The appearance of this evolutionary ... ...

Abstract	Paradise fish (Macropodus opercularis) is an air-breathing freshwater fish species with a signature labyrinth organ capable of extracting oxygen from the air that helps these fish to survive in hypoxic environments. The appearance of this evolutionary innovation in anabantoids resulted in a rewired circulatory system, but also in the emergence of species-specific behaviors, such as territorial display, courtship and parental care in the case of the paradise fish. Early zoologists were intrigued by the structure and function of the labyrinth apparatus and a series of detailed descriptive histological studies at the beginning of the 20th century revealed the ontogenesis and function of this specialized system. A few decades later, these fish became the subject of numerous ethological studies, and detailed ethograms of their behavior were constructed. These latter studies also demonstrated a strong genetic component underlying their behavior, but due to lack of adequate molecular tools, the fine genetic dissection of the behavior was not possible at the time. The technological breakthroughs that transformed developmental biology and behavioral genetics in the past decades, however, give us now a unique opportunity to revisit these old questions. Building on the classic descriptive studies, the new methodologies will allow us to follow the development of the labyrinth apparatus at a cellular resolution, reveal the genes involved in this process and also the genetic architecture behind the complex behaviors that we can observe in this species.
MeSH term(s)	Animals ; Biological Evolution ; Developmental Biology ; Behavior, Animal/physiology ; Genetics, Behavioral ; Models, Animal
Language	English
Publishing date	2023-10-11
Publishing country	United States
Document type	Journal Article ; Review ; Research Support, Non-U.S. Gov't
ZDB-ID	2103823-5
ISSN	1552-5015 ; 0022-104X ; 1552-5007
ISSN (online)	1552-5015
ISSN	0022-104X ; 1552-5007
DOI	10.1002/jez.b.23223
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Article: Housing, Husbandry and Welfare of a “Classic” Fish Model, the Paradise Fish (Macropodus opercularis)

Rácz, Anita / Adorján, Gábor / Fodor, Erika / Sellyei, Boglárka / Tolba, Mohammed / Miklósi, Ádám / Varga, Máté

Animals. 2021 Mar. 11, v. 11, no. 3

2021

Abstract: Thanks to its small size, external fertilization and fecundity, over the past four decades, zebrafish (Danio rerio) has become the dominant fish model species in biological and biomedical research. Multiple lines of evidence, however, suggest that the ... ...

Abstract	Thanks to its small size, external fertilization and fecundity, over the past four decades, zebrafish (Danio rerio) has become the dominant fish model species in biological and biomedical research. Multiple lines of evidence, however, suggest that the reliance on only a handful of genetic model organisms is problematic, as their unique evolutionary histories makes them less than ideal to study biological questions unrelated to their historically contingent adaptations. Therefore, a need has emerged to develop novel model species, better suited for studying particular problems. The paradise fish (Macropodus opercularis) has a much more complex behavioral repertoire than zebrafish and has been a favored model animal in ethological research during the last decades of the previous century. We believe that with currently available, easily adaptable genetic toolkits, this species could be easily developed into a popular model of behavioral genetics. Despite its earlier popularity, however, the description of a detailed housing and husbandry protocol for this species is still missing from scientific literature. We present here a detailed description of how to raise and breed paradise fish successfully under laboratory conditions, and also discuss some of the challenges we faced while creating a stable breeding population for this species in our facility.
Keywords	Danio rerio ; Macropodus opercularis ; biomedical research ; fecundity ; fish ; genetic models ; genetics
Language	English
Dates of publication	2021-0311
Publishing place	Multidisciplinary Digital Publishing Institute
Document type	Article
Note	NAL-light
ISSN	2076-2615
DOI	10.3390/ani11030786
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Subcellular Dissection of a Simple Neural Circuit: Functional Domains of the Mauthner-Cell During Habituation.

Bátora, Dániel / Zsigmond, Áron / Lőrincz, István Z / Szegvári, Gábor / Varga, Máté / Málnási-Csizmadia, András

Frontiers in neural circuits

2021 Volume 15, Page(s) 648487

Abstract: Sensorimotor integration is a pivotal feature of the nervous system for ensuring a coordinated motor response to external stimuli. In essence, such neural circuits can optimize behavioral performance based on the saliency of environmental cues. In ... ...

Abstract	Sensorimotor integration is a pivotal feature of the nervous system for ensuring a coordinated motor response to external stimuli. In essence, such neural circuits can optimize behavioral performance based on the saliency of environmental cues. In zebrafish, habituation of the acoustic startle response (ASR) is a simple behavior integrated into the startle command neurons, called the Mauthner cells. Whereas the essential neuronal components that regulate the startle response have been identified, the principles of how this regulation is integrated at the subcellular regions of the Mauthner cell, which in turn modulate the performance of the behavior, is still not well understood. Here, we reveal mechanistically distinct dynamics of excitatory inputs converging onto the lateral dendrite (LD) and axon initial segment (AIS) of the Mauthner cell by
MeSH term(s)	Acoustic Stimulation ; Animals ; Dissection ; Habituation, Psychophysiologic ; Neurons ; Reflex, Startle ; Zebrafish
Language	English
Publishing date	2021-03-22
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2452968-0
ISSN	1662-5110 ; 1662-5110
ISSN (online)	1662-5110
ISSN	1662-5110
DOI	10.3389/fncir.2021.648487
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