CCL

Összesen 5 találat.
#/oldal:
Részletezés:
Rendezés:

1.

001-es BibID:BIBFORM079797
035-os BibID:(cikkazonosító)398 (WoS)000475910500002 (Scopus)85069472612
Első szerző:Csősz Éva (biokémikus, molekuláris biológus)
Cím:Analysis of networks of host proteins in the early time points following HIV transduction / Éva Csősz, Ferenc Tóth, Mohamed Mahdi, George Tsaprailis, Miklós Emri, József Tőzsér
Dátum:2019
ISSN:1471-2105
Megjegyzések:Background: Utilization of quantitative proteomics data on the network level is still a challenge in proteomics data analysis. Currently existing models use sophisticated, sometimes hard to implement analysis techniques. Our aim was to generate a relatively simple strategy for quantitative proteomics data analysis in order to utilize as much of the data generated in a proteomics experiment as possible. Results: In this study, we applied label-free proteomics, and generated a network model utilizing both qualitative, and quantitative data, in order to examine the early host response to Human Immunodeficiency Virus type 1 (HIV-1). A weighted network model was generated based on the amount of proteins measured by mass spectrometry, and analysis of weighted networks and functional sub-networks revealed upregulation of proteins involved in translation, transcription, and DNA condensation in the early phase of the viral life-cycle. Conclusion: A relatively simple strategy for network analysis was created and applied to examine the effect of HIV-1 on host cellular proteome. We believe that our model may prove beneficial in creating algorithms, allowing for both quantitative and qualitative studies of proteome change in various biological and pathological processes by quantitative mass spectrometry.
Tárgyszavak:Természettudományok Biológiai tudományok idegen nyelvű folyóiratközlemény külföldi lapban
folyóiratcikk
weighted network
quantitative proteomics
host response
HIV-1
Megjelenés:Bmc Bioinformatics. - 20 (2019), p. 1-18. -
További szerzők:Tóth Ferenc (1980-) (molekuláris biológus) Mahdi, Mohamed (1979-) (orvos, tudományos segédmunkatárs) Tsaprailis, George Emri Miklós (1962-) (fizikus) Tőzsér József (1959-) (molekuláris biológus, biokémikus, vegyész)
Pályázati támogatás:GINOP-2.3.3-15-2016-00020
GINOP
Bolyai János Kutatói Ösztöndíj
MTA
Felsőoktatási Intézményi Kiválósági Program
Egyéb
NKFI-6, 125238
Egyéb
NIEHS - ES06694
Egyéb
NIH/NCI - CA023074
Egyéb
NIH/NCRR - 1S10 RR028868-01
Egyéb
Internet cím:Intézményi repozitóriumban (DEA) tárolt változat
DOI
Borító:

2.

001-es BibID:BIBFORM050899
035-os BibID:PMID:24044430 Article ID: 275
Első szerző:Mótyán János András (biokémikus, molekuláris biológus)
Cím:A molecular model of the full-length human NOD-like receptor family CARD domain containing 5 (NLRC5) protein / János András Mótyán, Péter Bagossi, Szilvia Benkő, József Tőzsér
Dátum:2013
ISSN:1471-2105
Megjegyzések:Pattern recognition receptors of the immune system have key roles in the regulation of pathways after the recognition of microbial- and danger-associated molecular patterns in vertebrates. Members of NOD-like receptor (NLR) family typically function intracellularly. The NOD-like receptor family CARD domain containing 5 (NLRC5) is the largest member of this family that also contains the largest number of leucine-rich repeats (LRRs).Due to the lack of crystal structures of full-length NLRs, projects have been initiated with the aim to model certain or all members of the family, but systematic studies did not model the full-length NLRC5 due to its unique domain architecture.Our aim was to analyze the LRR sequences of NLRC5 and some NLRC5-related proteins and to build a model for the full-length human NLRC5 by homology modeling. RESULTS: LRR sequences of NLRC5 were aligned and were compared with the consensus pattern of ribonuclease inhibitor protein (RI)-like LRR subfamily. Two types of alternating consensus patterns previously identified for RI repeats were also found in NLRC5. A homology model for full-length human NLRC5 was prepared and, besides the closed conformation of monomeric NLRC5, a heptameric platform was also modeled for the opened conformational NLRC5 monomers. CONCLUSIONS: Identification of consensus patterns of leucine-rich repeat sequences helped to identify LRRs in NLRC5 and to predict their number and position within the protein. In spite of the lack of fully adequate template structures, the presence of an untypical CARD domain and unusually high number of LRRs in NLRC5, we were able to construct a homology model for both the monomeric and homo-heptameric full-length human NLRC5 protein.
Tárgyszavak:Orvostudományok Elméleti orvostudományok idegen nyelvű folyóiratközlemény külföldi lapban
NLRC5
Molecular modeling
LRR protein
NOD-like receptor
Megjelenés:BMC Bioinformatics 14 : 1 (2013), p. 1-11. -
További szerzők:Bagossi Péter (1966-2011) (biokémikus, vegyész) Benkő Szilvia (1973-) (molekuláris biológus) Tőzsér József (1959-) (molekuláris biológus, biokémikus, vegyész)
Internet cím:Szerző által megadott URL
DOI
Intézményi repozitóriumban (DEA) tárolt változat
Borító:

3.

001-es BibID:BIBFORM003489
035-os BibID:(scopus)54549105754 (wos)000260487500001
Első szerző:Roszik János (biofizikus)
Cím:AccPbFRET : an ImageJ plugin for semi-automatic, fully corrected analysis of acceptor photobleaching FRET images / Roszik János, Szöllősi János, Vereb György
Dátum:2008
Megjegyzések:The acceptor photobleaching fluorescence resonance energy transfer (FRET) method is widely used for monitoring molecular interactions in cells. This method of FRET, while among those with the simplest mathematics, is robust, self-controlled and independent of fluorophore amounts and ratios. RESULTS: AccPbFRET is a user-friendly, efficient ImageJ plugin which allows fully corrected, pixel-wise calculation and detailed, ROI (region of interest)-based analysis of FRET efficiencies in microscopic images. Furthermore, automatic registration and semi-automatic analysis of large image sets is provided, which are not available in any existing FRET evaluation software. CONCLUSIONS: Despite of the widespread applicability of the acceptor photobleaching FRET technique, this is the first paper where all possible sources of major errors of the measurement and analysis are considered, and AccPbFRET is the only program which provides the complete suite of corrections - for registering image pairs, for unwanted photobleaching of the donor, for cross-talk of the acceptor and/or its photoproduct to the donor channel and for partial photobleaching of the acceptor. The program efficiently speeds up the analysis of large image sets even for novice users and is freely available.
Tárgyszavak:Természettudományok Biológiai tudományok idegen nyelvű folyóiratközlemény külföldi lapban
folyóiratcikk
acceptor photobleaching
FRET
CLSM
software
Megjelenés:BMC Bioinformatics. - 9 : 1 (2008), p. 346. -
További szerzők:Szöllősi János (1953-) (biofizikus) Vereb György (1965-) (biofizikus, orvos)
Internet cím:elektronikus változat
DOI
elektronikus változat
Borító:

4.

001-es BibID:BIBFORM018163
Első szerző:Sebestyén Endre
Cím:DoOPSearch : a web-based tool for finding and analysing common conserved motifs in the promoter regions of different chordate and plant genes / Sebestyén Endre, Nagy Tibor, Suhai Sándor, Barta Endre
Dátum:2009
ISSN:1471-2105
Megjegyzések:The comparative genomic analysis of a large number of orthologous promoter regions of the chordate and plant genes from the DoOP databases shows thousands of conserved motifs. Most of these motifs differ from any known transcription factor binding site (TFBS). To identify common conserved motifs, we need a specific tool to be able to search amongst them. Since conserved motifs from the DoOP databases are linked to genes, the result of such a search can give a list of genes that are potentially regulated by the same transcription factor(s). Results We have developed a new tool called DoOPSearch http://doopsearch.abc.hu webcite for the analysis of the conserved motifs in the promoter regions of chordate or plant genes. We used the orthologous promoters of the DoOP database to extract thousands of conserved motifs from different taxonomic groups. The advantage of this approach is that different sets of conserved motifs might be found depending on how broad the taxonomic coverage of the underlying orthologous promoter sequence collection is (consider e.g. primates vs. mammals or Brassicaceae vs. Viridiplantae). The DoOPSearch tool allows the users to search these motif collections or the promoter regions of DoOP with user supplied query sequences or any of the conserved motifs from the DoOP database. To find overrepresented gene ontologies, the gene lists obtained can be analysed further using a modified version of the GeneMerge program. Conclusion We present here a comparative genomics based promoter analysis tool. Our system is based on a unique collection of conserved promoter motifs characteristic of different taxonomic groups. We offer both a command line and a web-based tool for searching in these motif collections using user specified queries. These can be either short promoter sequences or consensus sequences of known transcription factor binding sites. The GeneMerge analysis of the search results allows the user to identify statistically overrepresented Gene Ontology terms that might provide a clue on the function of the motifs and genes.
Tárgyszavak:Orvostudományok Elméleti orvostudományok konferenciacikk
Megjelenés:Bmc Bioinformatics [electronic resource]. - 10 : Suppl.6. (2009), p. S6. -
További szerzők:Nagy Tibor (Gödöllő) Suhai Sándor Barta Endre (1963-) (molekuláris biológus)
Internet cím:Szerző által megadott URL
DOI
Intézményi repozitóriumban (DEA) tárolt változat
Borító:

5.

001-es BibID:BIBFORM002428
Első szerző:Thallinger, Gerhard G.
Cím:TAMEE : data management and analysis for tissue microarrays / Thallinger G. G., Baumgartner K., Pirklbauer M., Uray M., Pauritsch E., Méhes G., Buck C. R., Zatloukal K., Trajanoski Z.
Dátum:2007
Tárgyszavak:Orvostudományok Elméleti orvostudományok idegen nyelvű folyóiratközlemény külföldi lapban
külföldön készült közlemény
Megjelenés:BMC Bioinformatics 8 (2007), p. 81-92. -
További szerzők:Baumgartner, Kerstin Pirklbauer, Martin Uray, Martina Pauritsch, Elke Méhes Gábor (1966-) (patológus) Buck, Charles R. Zatloukal, Kurt Trajanoski, Zlatko
Internet cím:elektronikus változat
DOI
Borító:
Rekordok letöltése1