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001-es BibID:	BIBFORM072517
035-os BibID:	(cikkazonosító)158 (WoS)000426305200003 (Scopus)85042425048
Első szerző:	Ivády Gergely (laboratóriumi szakorvos)
Cím:	Analytical parameters and validation of homopolymer detection in a pyrosequencing-based next generation sequencing system / Ivády Gergely, Madar László, Dzsudzsák Erika, Koczok Katalin, Kappelmayer János, Krulisova Veronika, Macek Milan, Horváth Attila, Balogh István
Dátum:	2018
ISSN:	1471-2164
Megjegyzések:	BackgroundCurrent technologies in next-generation sequencing are offering high throughput reads at low costs, but still suffer from various sequencing errors. Although pyro- and ion semiconductor sequencing both have the advantage of delivering long and high quality reads, problems might occur when sequencing homopolymer-containing regions, since the repeating identical bases are going to incorporate during the same synthesis cycle, which leads to uncertainty in base calling. The aim of this study was to evaluate the analytical performance of a pyrosequencing-based next-generation sequencing system in detecting homopolymer sequences using homopolymer-preintegrated plasmid constructs and human DNA samples originating from patients with cystic fibrosis.ResultsIn the plasmid system average correct genotyping was 95.8% in 4-mers, 87.4% in 5-mers and 72.1% in 6-mers. Despite the experienced low genotyping accuracy in 5- and 6-mers, it was possible to generate amplicons with more than a 90% adequate detection rate in every homopolymer tract. When homopolymers in the CFTR gene were sequenced average accuracy was 89.3%, but varied in a wide range (52.2 ? 99.1%). In all but one case, an optimal amplicon-sequencing primer combination could be identified. In that single case (7A tract in exon 14 (c.2046_2052)), none of the tested primer sets produced the required analytical performance.ConclusionsOur results show that pyrosequencing is the most reliable in case of 4-mers and as homopolymer length gradually increases, accuracy deteriorates. With careful primer selection, the NGS system was able to correctly genotype all but one of the homopolymers in the CFTR gene. In conclusion, we configured a plasmid test system that can be used to assess genotyping accuracy of NGS devices and developed an accurate NGS assay for the molecular diagnosis of CF using self-designed primers for amplification and sequencing.
Tárgyszavak:	Orvostudományok Elméleti orvostudományok idegen nyelvű folyóiratközlemény külföldi lapban folyóiratcikk Pyrosequencing Homopolymer detection Cystic fibrosis
Megjelenés:	BMC Genomics. - 19 (2018), p. 1-8. -
További szerzők:	Madar László (1972-) (klinikai laboratóriumi kutató) Dzsudzsák Erika Koczok Katalin (1979-) (labororvos) Kappelmayer János (1960-) (laboratóriumi szakorvos) Krulisova, Veronika Macek Jr., Milan Horváth Attila (1988-) (programtervező informatikus) Balogh István (1972-) (molekuláris biológus, genetikus)
Pályázati támogatás:	K109076 OTKA GINOP-2.3.2-15-2016-00039 GINOP
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001-es BibID:	BIBFORM097910
035-os BibID:	(cikkazonosító)310
Első szerző:	Nagy Nikoletta Andrea (biológus)
Cím:	Draft genome of a biparental beetle species, Lethrus apterus / Nagy Nikoletta A., Rácz Rita, Rimington Oliver, Póliska Szilárd, Orozco-terWengel Pablo, Bruford Michael W., Barta Zoltán
Dátum:	2021
ISSN:	1471-2164
Tárgyszavak:	Orvostudományok Klinikai orvostudományok idegen nyelvű folyóiratközlemény külföldi lapban folyóiratcikk
Megjelenés:	BMC Genomics. - 22 : 1 (2021). -
További szerzők:	Rácz Rita (1989-) (biológus) Rimington, Oliver Póliska Szilárd (1978-) (biológus) Orozco-terWengel, Pablo Bruford, Michael W. Barta Zoltán (1967-) (biológus, zoológus)
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001-es BibID:	BIBFORM081935
035-os BibID:	(WOS)000499182500001 (Scopus)85075277364
Első szerző:	Szabó Krisztina (molekuláris biológus)
Cím:	Deletion of the fungus specific protein phosphatase Z1 exaggerates the oxidative stress response in Candida albicans / Krisztina Szabó, Ágnes Jakab, Szilárd Póliska, Katalin Petrényi, Katalin Kovács, Lama Hasan Bou Issa, Tamás Emri, István Pócsi, Viktor Dombrádi
Dátum:	2019
ISSN:	1471-2164
Megjegyzések:	Background:Candida albicansis an opportunistic pathogen which is responsible for widespread nosocomialinfections. It encompasses a fungus specific serine/threonine protein phosphatase gene, CaPPZ1 that is involvedin cation transport, cell wall integrity, oxidative stress response, morphological transition, and virulence accordingto the phenotypes of thecappz1deletion mutant.Results:We demonstrated that a short-term treatment with a sublethal concentration oftert-butyl hydroperoxidesuppressed the growth of the fungal cells without affecting their viability, both in thecappz1mutant and in thegenetically matching QMY23 control strains. To reveal the gene expression changes behind the above observationswe carried out a global transcriptome analysis. We used a pilot DNA microarray hybridization together withextensive RNA sequencing, and confirmed our results by quantitative RT-PCR. Novel functions of the CaPpz1enzyme and oxidative stress mechanisms have been unraveled. The numbers of genes affected as well as theamplitudes of the transcript level changes indicated that the deletion of the phosphatase sensitized the responseofC. albicansto oxidative stress conditions in important physiological functions like membrane transport, cellsurface interactions, oxidation-reduction processes, translation and RNA metabolism.Conclusions:We conclude that in the wild typeC. albicansCaPPZ1 has a protective role against oxidative damage.We suggest that the specific inhibition of this phosphatase combined with mild oxidative treatment could be afeasible approach to topical antifungal therapy.
Tárgyszavak:	Orvostudományok Elméleti orvostudományok idegen nyelvű folyóiratközlemény külföldi lapban folyóiratcikk Candida albicans Protein phosphatase Z1 Deletion mutant Oxidative stress tert-butyl hydoperoxide Transcriptome DNA microarray RNA-Seq Quantitative RT-PCR
Megjelenés:	Bmc Genomics. - 20 (2019), p. 1-17. -
További szerzők:	Jakab Ágnes (1987-) (biológus) Póliska Szilárd (1978-) (biológus) Petrényi Katalin (1988-) (Ph.D hallgató) Kovács Katalin (1978-) (biokémikus) Issa, Lama Hasan Bou Emri Tamás (1969-) (biológus) Pócsi István (1961-) (vegyész) Dombrádi Viktor (1953-) (biokémikus)
Pályázati támogatás:	NKFIH-K108989 NKFIH EFOP-3.6.1-16-2016-00022 EFOP
Internet cím:	Intézményi repozitóriumban (DEA) tárolt változat
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001-es BibID:	BIBFORM049100
Első szerző:	Veréb Zoltán (immunológus, mikrobiológus, molekuláris biológus)
Cím:	Comparison of upstream regulators in human ex vivo cultured cornea limbal epithelial stem cells and differentiated corneal epithelial cells / Zoltán Veréb, Réka Albert, Szilárd Póliska, Ole Kristoffer Olstad, Saeed Akhtar, Morten C. Moe, Goran Petrovski
Dátum:	2013
ISSN:	1471-2164
Megjegyzések:	BACKGROUND:The surface of the human eye is covered by corneal epithelial cells (CECs) which regenerate from a small population of limbal epithelial stem cells (LESCs). Cell therapy with LESCs is a non-penetrating treatment for preventing blindness due to LESC deficiency or dysfunction. Our aim was to identify new putative molecular markers and upstream regulators in the LESCs and associated molecular pathways.RESULTS:Genome-wide microarray transcriptional profiling was used to compare LESCs to differentiated human CECs. Ingenuity-based pathway analysis was applied to identify upstream regulators and pathways specific to LESCs. ELISA and flow cytometry were used to measure secreted and surface expressed proteins, respectively. More than 2 fold increase and decrease in expression could be found in 1830 genes between the two cell types. A number of molecules functioning in cellular movement (381), proliferation (567), development (552), death and survival (520), and cell-to-cell signaling (290) were detected having top biological functions in LESCs and several of these were confirmed by flow cytometric surface protein analysis. Custom-selected gene groups related to stemness, differentiation, cell adhesion, cytokines and growth factors as well as angiogenesis could be analyzed. The results show that LESCs play a key role not only in epithelial differentiation and tissue repair, but also in controlling angiogenesis and extracellular matrix integrity. Some pro-inflammatory cytokines were found to be important in stemness-, differentiation- and angiogenesis-related biological functions: IL-6 and IL-8 participated in most of these biological pathways as validated by their secretion from LESC cultures.CONCLUSIONS:The gene and molecular pathways may provide a more specific understanding of the signaling molecules associated with LESCs, therefore, help better identify and use these cells in the treatment of ocular surface diseases.
Tárgyszavak:	Orvostudományok Elméleti orvostudományok idegen nyelvű folyóiratközlemény külföldi lapban Limbal epithelial stem cells Corneal epithelial cells Gene array Upstream regulators Cytokines Cell adhesion IL-6 IL-8 Angiogenesis
Megjelenés:	BMC Genomics. - 14 : 1 (2013), p. [1-33]. -
További szerzők:	Albert Réka (1986-) Póliska Szilárd (1978-) (biológus) Olstad, Ole Kristoffer Akhtar, Saeed (1949-) (molekuláris biológus) Moe, Morten C. Petrovski, Goran (1975-) (orvos)
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