@article{MTMT:34547379,
	title = {The zinc finger protein 3 of Arabidopsis thaliana regulates vegetative growth and root hair development},
	url = {https://m2.mtmt.hu/api/publication/34547379},
	author = {Benyó, Dániel and Bato, Emese and Faragó, Dóra and Rigó, Gábor and Racskóné Domonkos, Ildikó and Labhane, Nitin and Zsigmond, Laura and Prasad, Melvin and Nagy, István and Szabados, László},
	doi = {10.3389/fpls.2023.1221519},
	journal-iso = {FRONT PLANT SCI},
	journal = {FRONTIERS IN PLANT SCIENCE},
	volume = {14},
	unique-id = {34547379},
	issn = {1664-462X},
	abstract = {Introduction Zinc finger protein 3 (ZFP3) and closely related C2H2 zinc finger proteins have been identified as regulators of abscisic acid signals and photomorphogenic responses during germination. Whether ZFP3 and related ZFP factors regulate plant development is, however, not known.Results ZFP3 overexpression reduced plant growth, limited cell expansion in leaves, and compromised root hair development. The T-DNA insertion zfp3 mutant and transgenic lines with silenced ZFP1, ZFP3, ZFP4, and ZFP7 genes were similar to wild-type plants or had only minor differences in plant growth and morphology, probably due to functional redundancy. RNAseq transcript profiling identified ZFP3-controlled gene sets, including targets of ABA signaling with reduced transcript abundance. The largest gene set that was downregulated by ZFP3 encoded regulatory and structural proteins in cell wall biogenesis, cell differentiation, and root hair formation. Chromatin immunoprecipitation confirmed ZFP3 binding to several target promoters.Discussion Our results suggest that ZFP3 and related ZnF proteins can modulate cellular differentiation and plant vegetative development by regulating the expression of genes implicated in cell wall biogenesis.},
	keywords = {EXPRESSION; GENE; INHIBITION; TRANSCRIPTION FACTOR; ABSCISIC-ACID; PLANT DEVELOPMENT; Overexpression; gene silencing; gene overexpression; Arabidopsis thaliana; root hair; gibberellin; trichome initiation; zinc finger protein 3; ZFP5},
	year = {2024},
	eissn = {1664-462X},
	orcid-numbers = {Benyó, Dániel/0000-0002-4537-2866; Zsigmond, Laura/0000-0002-1388-1762}
}

@inproceedings{MTMT:34493120,
	title = {Honfoglalás kori köznépi temetők anyai vonalainak jellemzése, archeogenetikai módszerekkel},
	url = {https://m2.mtmt.hu/api/publication/34493120},
	author = {Maár, Kitti and Neparáczki, Endre and Varga, Gergely István and Kovács, Bence and Maróti, Zoltán and Kalmár, Tibor and Nagy, István and Latinovics, Dóra and Tihanyi, Balázs and Marcsik, Antónia and Kustár, Ágnes and Pálfi, György and Raskó, István and Török, Tibor},
	booktitle = {"Hadak útján" A népvándorláskor fiatal kutatóinak XXIX. konferenciája. = 29th Conference of scholars on the Migration Period},
	doi = {10.55722/Arpad.Kiad.2023.4.2_07},
	unique-id = {34493120},
	abstract = {A régészeti leletekből kinyerhető archaikus DNS vizsgálata fényt deríthet egyének, populációk eredetére és rokoni kapcsolataira. Korábbi munkánk során elsősorban a honfoglalás kori szállási temetők genetikai kapcsolatait derítettük fel régészeti genetikai módszerekkel. A karosi és kenézlői temető együttesek nagy felbontású teljes mitogenom analízise azt mutatta, hogy a honfoglalók anyai ágú vonalai visszavezethetők az eurázsiai sztyeppe távoli részeire: harmaduk Közép-Belső Ázsia területéről származott, kétharmaduk pedig a bronzkori pontusi-kaszpi sztyeppe Poltavka-Potakovka-Szrubnaja kultúráira vezethető vissza. Felvetődött a kérdés, hogy ezek az adatok milyen mértékben vonatkoztathatók a teljes honfoglaló populációra? Hogy ezt a kérdést megválaszoljuk, vizsgálatainkat kiterjesztettük a 10. századi nagyobb sírszámú falusi temetőkre, melyek a honfoglalás kori köznépet rejthetik. A kiválasztott 6 falusi temető mindegyikéből 20-30 egyén anyai vonalait vizsgáltuk. A mintaválasztást elsősorban régészeti és antropológiai adatok alapján végeztük. Mivel a temetők többsége átnyúlik az Árpád-korba és korábbi antropológiai vizsgálatok több temetőben lehetséges népességcserét jeleztek, ezért a korai és a későbbi sírok összehasonlításával a népességcsere kérdésére is választ remélhetünk. A projekt jelen állása szerint csaknem az összes szekvencia adat elkészült és most folyik az adatok filogenetikai és populációgenetikai kiértékelése, ezért az előzetes eredményeket tudjuk bemutatni.},
	keywords = {mitogenom; aDNS; NGS szekvenálás},
	year = {2023},
	pages = {159-170},
	orcid-numbers = {Maár, Kitti/0000-0002-1207-6569; Neparáczki, Endre/0000-0003-3466-0368; Varga, Gergely István/0000-0001-9073-5788; Kovács, Bence/0000-0002-4915-1462; Maróti, Zoltán/0000-0002-0515-117X; Kalmár, Tibor/0000-0002-0419-2009; Tihanyi, Balázs/0000-0001-5124-4468; Marcsik, Antónia/0000-0002-3121-4365; Török, Tibor/0000-0002-2128-1126}
}

@article{MTMT:34288968,
	title = {CRISPR/Cas9 Mutagenesis through Introducing a Nanoparticle Complex Made of a Cationic Polymer and Nucleic Acids into Maize Protoplasts},
	url = {https://m2.mtmt.hu/api/publication/34288968},
	author = {Nagy, Bettina and Öktem, Ayşegül and Ferenc, Györgyi and Ungor, Ditta Anita and Kalac, Aladina and Kelemen-Valkony, Ildikó and Ayaydin-Fodor, Elfrieda and Nagy, István and Dudits, Dénes and Ayaydin, Ferhan},
	doi = {10.3390/ijms242216137},
	journal-iso = {INT J MOL SCI},
	journal = {INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES},
	volume = {24},
	unique-id = {34288968},
	issn = {1661-6596},
	abstract = {Presently, targeted gene mutagenesis attracts increasing attention both in plant research and crop improvement. In these approaches, successes are largely dependent on the efficiency of the delivery of gene editing components into plant cells. Here, we report the optimization of the cationic polymer poly(2-hydroxypropylene imine) (PHPI)-mediated delivery of plasmid DNAs, or single-stranded oligonucleotides labelled with Cyanine3 (Cy3) or 6-Carboxyfluorescein (6-FAM)-fluorescent dyes into maize protoplasts. Co-delivery of the GFP-expressing plasmid and the Cy3-conjugated oligonucleotides has resulted in the cytoplasmic and nuclear accumulation of the green fluorescent protein and a preferential nuclear localization of oligonucleotides. We show the application of nanoparticle complexes, i.e., “polyplexes” that comprise cationic polymers and nucleic acids, for CRISPR/Cas9 editing of maize cells. Knocking out the functional EGFP gene in transgenic maize protoplasts was achieved through the co-delivery of plasmids encoding components of the editing factors Cas9 (pFGC-pcoCas9) and gRNA (pZmU3-gRNA) after complexing with a cationic polymer (PHPI). Several edited microcalli were identified based on the lack of a GFP fluorescence signal. Multi-base and single-base deletions in the EGFP gene were confirmed using Sanger sequencing. The presented results support the use of the PHPI cationic polymer in plant protoplast-mediated genome editing approaches.},
	year = {2023},
	eissn = {1422-0067},
	orcid-numbers = {Öktem, Ayşegül/0000-0001-7828-999X; Ferenc, Györgyi/0000-0002-3456-319X; Ungor, Ditta Anita/0000-0002-7659-0428}
}

@article{MTMT:34129658,
	title = {Cloning, expression, and biochemical characterisation of a novel endomannanase from Thermobifida alba},
	url = {https://m2.mtmt.hu/api/publication/34129658},
	author = {Luzics, Szabina and Tóth, Ákos and Barna, Teréz and Szabó, Erna and Nagy, I. and Horváth, B. and Nagy, István and Varecza, Zoltán and Batáné Vidács, Ildikó and Kukolya, József},
	doi = {10.1556/066.2023.00186},
	journal-iso = {ACTA ALIMENT},
	journal = {ACTA ALIMENTARIA: AN INTERNATIONAL JOURNAL OF FOOD SCIENCE},
	volume = {52},
	unique-id = {34129658},
	issn = {0139-3006},
	year = {2023},
	eissn = {1588-2535},
	pages = {502-519},
	orcid-numbers = {Batáné Vidács, Ildikó/0000-0003-3019-8030; Kukolya, József/0000-0002-0724-9541}
}

@article{MTMT:33723348,
	title = {CUTIS-SEQ, a flexible bilocus sequence typing scheme that provides high resolution of Cutibacterium acnes strains across all subspecies},
	url = {https://m2.mtmt.hu/api/publication/33723348},
	author = {McLaughlin, Joseph and Nagy, István and Miliotis, Georgios and McDowell, Andrew},
	doi = {10.1016/j.anaerobe.2022.102671},
	journal-iso = {ANAEROBE},
	journal = {ANAEROBE},
	volume = {79},
	unique-id = {33723348},
	issn = {1075-9964},
	abstract = {Objectives: A `high resolution' Single Locus Sequence Typing (SLST) scheme has been described for the anaerobic skin bacterium Cutibacterium acnes that seemingly discriminates sequence types (STs) to a level commensurate with previously described Multilocus Sequence Typing (MLST) methods (MLST4; MLST8; MLST9). However, no quantifiable evaluation of SLST versus MLST for differentiation of C. acnes strains, especially in relation to the subspecies of the bacterium, known as C. acnes subsp. acnes (type I), C. acnes subsp. defendens (type II) and C. acnes subsp. elongatum (type III), has been performed which is vital given its increasing use. To address this, we examined the discriminatory power of SLST versus MLST with a large group of isolates representative of all subspecies. Methods: Simpson's index of diversity (D) was used for quantitative comparison of the resolving power of the SLST and MLST schemes for 186 isolates of C. acnes covering all three subspecies. Results: When strains were considered collectively, SLST and all three MLST approaches had similar D values > 90%. However, at the subspecies level there were significant differences between the methods, most strikingly a reduced discrimination of type II and type III strains (D <80%) by SLST versus MLST8, and to a lesser extent MLST4. The MLST9 method also performed poorly for type II strains (D <70%), but did display the best results for type I (D= 90%). By combining the SLST locus with the camp2 gene sequence to create a novel and flexible high-resolution Bilocus Sequence Typing (BLST) scheme, known as CUTIS-SEQ typing (CUTIbacterium acneS BilocuS sEQuence Typing), we achieved improved resolution at both species and, critically, subspp. levels. Conclusions: CUTIS-SEQ provides an opportunity to improve differentiation of C. acnes isolates by SLST without significantly impacting laboratory workload, or compromising application to complex biological communities. A CUTIS-SEQ isolate database is now available as part of the C. acnes PubMLST database at https://pubmlst.org. (c) 2022 The Authors. Published by Elsevier Ltd. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).},
	keywords = {DISCRIMINATION; RECOMBINATION; MLST; cutibacterium acnes; SLST; PROPIONIBACTERIUM-ACNES},
	year = {2023},
	eissn = {1095-8274},
	orcid-numbers = {Miliotis, Georgios/0000-0002-0944-2206}
}

@article{MTMT:33708483,
	title = {Prolonged activity of the transposase helper may raise safety concerns during DNA transposon-based gene therapy},
	url = {https://m2.mtmt.hu/api/publication/33708483},
	author = {Imre, Gergely and Takács, Bertalan Vilmos and Czipa, Erik and Drubi, Andrea and Jaksa, Gábor and Latinovics, Dóra and Nagy, Andrea and Karkas, Réka and Hudoba, Liza and Vásárhelyi, Bálint Márk and Pankotai-Bodó, Gabriella and Blastyák, András and Hegedűs, Zoltán and Germán, Péter and Bálint, Balázs and Ahmed Abdullah, Khaldoon Sadiq and Kopasz, Anna Georgina and Kovács, Anita Kármen and Nagy, László and Sükösd, Farkas and Pintér, Lajos and Rülicke, Thomas and Barta, Endre and Nagy, István and Haracska, Lajos and Mátés, Lajos},
	doi = {10.1016/j.omtm.2023.03.003},
	journal-iso = {MOL THER-METH CLIN D},
	journal = {MOLECULAR THERAPY-METHODS AND CLINICAL DEVELOPMENT},
	volume = {29},
	unique-id = {33708483},
	year = {2023},
	eissn = {2329-0501},
	pages = {145-159},
	orcid-numbers = {Vásárhelyi, Bálint Márk/0000-0003-1782-8691; Kovács, Anita Kármen/0000-0001-9805-1647}
}

@article{MTMT:33632100,
	title = {Plasticity and stereotypic rewiring of the transcriptome upon bacterial evolution of antibiotic resistance},
	url = {https://m2.mtmt.hu/api/publication/33632100},
	author = {Grézal, Gábor and Spohn, Réka and Méhi, Orsolya Katinka and Dunai, Anett and Lázár, Viktória and Bálint, Balázs and Nagy, István and Pál, Csaba and Papp, Balázs},
	doi = {10.1093/molbev/msad020},
	journal-iso = {MOL BIOL EVOL},
	journal = {MOLECULAR BIOLOGY AND EVOLUTION},
	volume = {40},
	unique-id = {33632100},
	issn = {0737-4038},
	abstract = {Bacterial evolution of antibiotic resistance frequently has deleterious side effects on microbial growth, virulence, and susceptibility to other antimicrobial agents. However, it is unclear how these trade-offs could be utilized for manipulating antibiotic resistance in the clinic, not least because the underlying molecular mechanisms are poorly understood. Using laboratory evolution, we demonstrate that clinically relevant resistance mutations in Escherichia coli constitutively rewire a large fraction of the transcriptome in a repeatable and stereotypic manner. Strikingly, lineages adapted to functionally distinct antibiotics and having no resistance mutations in common show a wide range of parallel gene expression changes that alter oxidative stress response, iron homeostasis, and the composition of the bacterial outer membrane and cell surface. These common physiological alterations are associated with changes in cell morphology and enhanced sensitivity to antimicrobial peptides. Finally, the constitutive transcriptomic changes induced by resistance mutations are largely distinct from those induced by antibiotic stresses in the wild-type. This indicates a limited role for genetic assimilation of the induced antibiotic stress response during resistance evolution. Our work suggests that diverse resistance mutations converge on similar global transcriptomic states that shape genetic susceptibility to antimicrobial compounds.},
	year = {2023},
	eissn = {1537-1719},
	orcid-numbers = {Grézal, Gábor/0000-0003-1685-4791; Méhi, Orsolya Katinka/0009-0004-7918-913X}
}

@article{MTMT:33125064,
	title = {Global alteration of colonic microRNAome landscape associated with inflammatory bowel disease},
	url = {https://m2.mtmt.hu/api/publication/33125064},
	author = {Boros, Éva and Hegedűs, Zoltán and Kellermayer, Zoltán and Balogh, Péter and Nagy, István},
	doi = {10.3389/fimmu.2022.991346},
	journal-iso = {FRONT IMMUNOL},
	journal = {FRONTIERS IN IMMUNOLOGY},
	volume = {13},
	unique-id = {33125064},
	issn = {1664-3224},
	abstract = {Inflammatory Bowel Disease (IBD) is characterized by chronic inflammation of the gastrointestinal tract that associates with, among others, increased risk of colorectal cancer. There is a growing evidence that miRNAs have important roles in pathological processes, such as inflammation or carcinogenesis. Understanding the molecular mechanisms such as alterations in microRNAome upon chronic intestinal inflammation is critical for understanding the exact pathomechanism of IBD. Hence, we conducted a genome wide microRNAome analysis by applying miRNA-Seq in a rat model of experimental colitis, validated the data by QPCR, examined the expression of a selection of precursor and mature miRNAs, performed in depth biological interpretation using Ingenuity Pathway Analysis and tested the obtained results on samples derived from human patients. We identified specific, interdependent expression pattern of activator/repressor transcription factors, miRNAs and their direct targets in the inflamed colon samples. Particularly, decreased expression of the miR-200 family members (miR-200a/b/c,-141, and -429) and miR-27b correlates with the reduced level of their enhancers (HNF1B, E2F1), elevated expression of their repressors (ZEB2, NFKB1) and increased expression of their target genes (ZEB2, RUNX1). Moreover, the marked upregulation of six miR-27b target genes (IFI16, GCA, CYP1B1, RUNX1, MEF2C and MMP13) in the inflamed colon tissues is a possible direct consequence of the lack of repression due to the downregulated miRNA-27b expression. Our data indicate that changes in microRNAome are associated with the pathophysiology of IBD, consequently, microRNAs offer potential targets for the diagnosis, prognosis and treatment of IBD.},
	year = {2022},
	eissn = {1664-3224}
}

@misc{MTMT:33074997,
	title = {Whole genome analysis sheds light on the genetic origin of Huns, Avars and conquering Hungarians},
	url = {https://m2.mtmt.hu/api/publication/33074997},
	author = {Maróti, Zoltán and Neparáczki, Endre and Schütz, Oszkár and Maár, Kitti and Varga, Gergely István and Kovács, Bence and Kalmár, Tibor and Nyerki, Emil and Nagy, István and Latinovics, Dóra and Tihanyi, Balázs and Marcsik, Antónia and Pálfi, György and Bernert, Zsolt and Gallina, József Zsolt and Horváth, Ciprian and Varga, Sándor and Költő, László and Raskó, István and L. Nagy, Péter and Balogh, Csilla and Zink, Albert and Maixner, Frank and Götherström, Anders and George, Robert and Szalontai, Csaba and Szenthe, Gergely Pál and Gáll, Erwin and P. Kiss, Attila and Rácz, Attila and Gulyás, Bence and Ny. Kovacsóczy, Bernadett and Gaál, Sándor Szilárd and Tomka, Péter and Török, Tibor},
	unique-id = {33074997},
	year = {2022},
	pages = {1-26},
	orcid-numbers = {Maróti, Zoltán/0000-0002-0515-117X; Neparáczki, Endre/0000-0003-3466-0368; Schütz, Oszkár/0000-0001-5521-3044; Maár, Kitti/0000-0002-1207-6569; Varga, Gergely István/0000-0001-9073-5788; Kovács, Bence/0000-0002-4915-1462; Kalmár, Tibor/0000-0002-0419-2009; Nyerki, Emil/0000-0003-1168-763X; Tihanyi, Balázs/0000-0001-5124-4468; Marcsik, Antónia/0000-0002-3121-4365; Balogh, Csilla/0000-0002-9161-1653; Török, Tibor/0000-0002-2128-1126}
}

@article{MTMT:32853231,
	title = {The genetic origin of Huns, Avars, and conquering Hungarians},
	url = {https://m2.mtmt.hu/api/publication/32853231},
	author = {Maróti, Zoltán and Neparáczki, Endre and Schütz, Oszkár and Maár, Kitti and Varga, Gergely István and Kovács, Bence and Kalmár, Tibor and Nyerki, Emil and Nagy, István and Latinovics, Dóra and Tihanyi, Balázs and Marcsik, Antónia and Pálfi, György and Bernert, Zsolt and Gallina, József Zsolt and Horváth, Ciprian and Varga, Sándor and Költő, László and Raskó, István and Nagy, Péter L. and Balogh, Csilla and Zink, Albert and Maixner, Frank and Götherström, Anders and George, Robert and Szalontai, Csaba and Szenthe, Gergely Pál and Gáll, Erwin and Kiss P., Attila and Gulyás, Bence and Kovacsóczy, Bernadett and Gál, Szilárd Sándor and Tomka, Péter and Török, Tibor},
	doi = {10.1016/j.cub.2022.04.093},
	journal-iso = {CURR BIOL},
	journal = {CURRENT BIOLOGY},
	volume = {32},
	unique-id = {32853231},
	issn = {0960-9822},
	abstract = {Huns, Avars, and conquering Hungarians were migration-period nomadic tribal confederations that arrived in three successive waves in the Carpathian Basin between the 5th and 9th centuries. Based on the historical data, each of these groups are thought to have arrived from Asia, although their exact origin and relation to other ancient and modern populations have been debated. Recently, hundreds of ancient genomes were analyzed from Central Asia, Mongolia, and China, from which we aimed to identify putative source populations for the above-mentioned groups. In this study, we have sequenced 9 Hun, 143 Avar, and 113 Hungarian conquest period samples and identified three core populations, representing immigrants from each period with no recent European ancestry. Our results reveal that this “immigrant core” of both Huns and Avars likely originated in present day Mongolia, and their origin can be traced back to Xiongnus (Asian Huns), as suggested by several historians. On the other hand, the “immigrant core” of the conquering Hungarians derived from an earlier admixture of Mansis, early Sarmatians, and descendants of late Xiongnus. We have also shown that a common “proto-Ugric” gene pool appeared in the Bronze Age from the admixture of Mezhovskaya and Nganasan people, supporting genetic and linguistic data. In addition, we detected shared Hun-related ancestry in numerous Avar and Hungarian conquest period genetic outliers, indicating a genetic link between these successive nomadic groups. Aside from the immigrant core groups, we identified that the majority of the individuals from each period were local residents harboring “native European” ancestry.},
	keywords = {ancient DNA; F-STATISTICS; Carpathian Basin; Migration period; Ugric; qpAdm modeling; Asian Hun},
	year = {2022},
	eissn = {1879-0445},
	pages = {2858-2870.e7},
	orcid-numbers = {Maróti, Zoltán/0000-0002-0515-117X; Neparáczki, Endre/0000-0003-3466-0368; Schütz, Oszkár/0000-0001-5521-3044; Maár, Kitti/0000-0002-1207-6569; Varga, Gergely István/0000-0001-9073-5788; Kovács, Bence/0000-0002-4915-1462; Kalmár, Tibor/0000-0002-0419-2009; Nyerki, Emil/0000-0003-1168-763X; Tihanyi, Balázs/0000-0001-5124-4468; Marcsik, Antónia/0000-0002-3121-4365; Balogh, Csilla/0000-0002-9161-1653; Gulyás, Bence/0000-0002-7682-2065; Török, Tibor/0000-0002-2128-1126}
}