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199 results on '"Fiala, Radovan"'

6. Outcome of Application of Cryopreserved Amniotic Membrane Grafts in the Treatment of Chronic Nonhealing Wounds of Different Origins in Polymorbid Patients: A Prospective Multicenter Study

Author

Svobodova, Alzbeta, primary, Horvath, Vojtech, additional, Balogh, Lukas, additional, Zemlickova, Martina, additional, Fiala, Radovan, additional, Burkert, Jan, additional, Brabec, Marek, additional, Stadler, Petr, additional, Lindner, Jaroslav, additional, Bednar, Jan, additional, and Jirsova, Katerina, additional

Published
2023
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11. The healing dynamics of non‐healing wounds using cryo‐preserved amniotic membrane

Author

Svobodova, Alzbeta, primary, Horvath, Vojtech, additional, Smeringaiova, Ingrida, additional, Cabral, Joao Victor, additional, Zemlickova, Martina, additional, Fiala, Radovan, additional, Burkert, Jan, additional, Nemetova, Denisa, additional, Stadler, Petr, additional, Lindner, Jaroslav, additional, Bednar, Jan, additional, and Jirsova, Katerina, additional

Published
2021
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16. The healing dynamics of non‐healing wounds using cryo‐preserved amniotic membrane.

Author

Svobodova, Alzbeta, Horvath, Vojtech, Smeringaiova, Ingrida, Cabral, Joao Victor, Zemlickova, Martina, Fiala, Radovan, Burkert, Jan, Nemetova, Denisa, Stadler, Petr, Lindner, Jaroslav, Bednar, Jan, and Jirsova, Katerina

Subjects
WOUND healing, TRAUMATOLOGY diagnosis, CHRONIC wounds & injuries, AMNION, TREATMENT effectiveness, DESCRIPTIVE statistics, BIOLOGICAL dressings, CRYOPRESERVATION of organs, tissues, etc., WOUND care
Abstract

We evaluated the effect of the application of cryo‐preserved amniotic membrane on the healing of 26 non‐healing wounds (18 patients) with varying aetiologies and baseline sizes (average of 15.4 cm2), which had resisted the standard of care treatment for 6 to 456 weeks (average 88.8 weeks). Based on their average general responses to the application of cryo‐preserved AM, we could differentiate three wound groups. The first healed group was characterised by complete healing (100% wound closure, maximum treatment period 38 weeks) and represented 62% of treated wounds. The wound area reduction of at least 50% was reached for all wounds in this group within the first 10 weeks of treatment. Exactly 19% of the studied wounds responded partially to the treatment (partially healed group), reaching less than 25% of closure in the first 10 weeks and 90% at maximum for extended treatment period (up to 78 weeks). The remaining 19% of treated wounds did not show any reaction to the AM application (unhealed defects). The three groups have different profiles of wound area reduction, which can be used as a guideline in predicting the healing prognosis of non‐healing wounds treated with a cryo‐preserved amniotic membrane. [ABSTRACT FROM AUTHOR]

Published
2022
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18. HERMES – A Software Tool for the Prediction and Analysis of Magnetic-Field-Induced Residual Dipolar Couplings in Nucleic Acids

Author

Giassa, Ilektra Chara, Vavrinská, Andrea, Zelinka, Jiří, Šebera, Jakub, Sychrovský, Vladimír, Boelens, Rolf, Fiala, Radovan, Trantírek, Lukáš, Sub Cellular Protein Chemistry, Sub Algemeen Scheikunde, Cellular Protein Chemistry, and Dep Scheikunde

Subjects
nucleic acids, Chemistry(all), prediction software, Taverne, field-induced residual dipolar couplings, magnetic susceptibility anisotropy, NMR
Abstract

Field-Induced Residual Dipolar Couplings (fiRDC) are a valuable source of long-range information on structure of nucleic acids (NA) in solution. A web application (HERMES) was developed for structure-based prediction and analysis of the (fiRDCs) in NA. fiRDC prediction is based on input 3D model structure(s) of NA and a built-in library of nucleobase-specific magnetic susceptibility tensors and reference geometries. HERMES allows three basic applications: (i) the prediction of fiRDCs for a given structural model of NAs, (ii) the validation of experimental or modeled NA structures using experimentally derived fiRDCs, and (iii) assessment of the oligomeric state of the NA fragment and/or the identification of a molecular NA model that is consistent with experimentally derived fiRDC data. Additionally, the program's built-in routine for rigid body modeling allows the evaluation of relative orientation of domains within NA that is in agreement with experimental fiRDCs.

Published
2020

19. HERMES – A Software Tool for the Prediction and Analysis of Magnetic-Field-Induced Residual Dipolar Couplings in Nucleic Acids

Author

Sub Cellular Protein Chemistry, Sub Algemeen Scheikunde, Cellular Protein Chemistry, Dep Scheikunde, Giassa, Ilektra Chara, Vavrinská, Andrea, Zelinka, Jiří, Šebera, Jakub, Sychrovský, Vladimír, Boelens, Rolf, Fiala, Radovan, Trantírek, Lukáš, Sub Cellular Protein Chemistry, Sub Algemeen Scheikunde, Cellular Protein Chemistry, Dep Scheikunde, Giassa, Ilektra Chara, Vavrinská, Andrea, Zelinka, Jiří, Šebera, Jakub, Sychrovský, Vladimír, Boelens, Rolf, Fiala, Radovan, and Trantírek, Lukáš

Published
2020

20. Insight into formation propensity of pseudocircular DNA G-hairpins

Author

Živković, Martina Lenarčič, primary, Gajarský, Martin, additional, Beková, Kateřina, additional, Stadlbauer, Petr, additional, Vicherek, Lukáš, additional, Petrová, Magdalena, additional, Fiala, Radovan, additional, Rosenberg, Ivan, additional, Šponer, Jiří, additional, Plavec, Janez, additional, and Trantírek, Lukáš, additional

Published
2021
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27. Human heart valve allografts mechanical and morphological properties according to duration of tissue cryopreservation

Author

Fiala, Radovan, Burkert, Jan, Dominik, Jan, and Rosenberg, Josef

Subjects
tkáňová banka, structural changes, mechanické vlastnosti, alograft srdeční chlopně, homograft, mechanical characteristcs, heart valve allograf, tssue banking, strukturální změny, kryoprezervace, homograf, cryopreservaton
Abstract

Background: The aortic and pulmonary allograft heart valves (AHV) are used in the cardiac surgery for replacing the impaired semilunar valves. They are harvested from donor hearts and cryostored in tissue banks. The expiration period was set to 5 years arbitrarily. We hypothesized that their mechanical and structural properties do not reasonably deteriorate after this period. Methods: A total of 64 human AHV (31 aortic and 33 pulmonary) of different length of cryopreservation (fresh, 0-5, 5-10, over 10 years) were sampled to different tissue strips (artery, leaflet, ventriculo-arterial junction, arterial ring) and tested by tensile test with loading velocity 10 mm/min until tissue rupture. Neighbouring regions of tissue were processed histologically and evaluated for elastin and collagen area fraction. The results were evaluated statistically. Results: In aortic AHV, the physical deformation response of wall samples to stress did not changed significantly neither during the process of cryopreservation nor during the first 10 years of storage. In pulmonary AHV, the ultimate strain dropped after 5 years of cryopreservation indicating that pulmonary artery was significantly less deformable at the time of rupture. On the other hand, the ultimate stress was equal during the first 10 years of...

Published
2019

29. RNA folding topology and intermolecular contacts in th AMP-RNA aptamer complex

Author

Jiang, Feng, Fiala, Radovan, Live, David, Kumar, R. Ajay, and Patl, Dinshaw J.

Subjects
RNA -- Research, Adenylic acid -- Research, Molecular structure -- Analysis, Biological sciences, Chemistry
Abstract

Nuclear magnetic resonance spectroscopy of the AMP-RNA aptamer complex reveals an internal loop and bulge which bind the AMP. The helical stems consists of GG mismatches that form from either direction of the internal loop/bulge segment. The purine ring of AMP is found between A10 and G11 of the internal loop whereas the stems in the G8-A9-A10-AMP segment are stacked on each other, and contains a G7G11 mismatch pair at the terminal end. The AMP ligand is stabilized by a hydrogen bond, with the sugar ring located in the minor groove of the rightward helical stem.

Published
1996

30. Solution conformation of the (-)-trans-anti-benzo(c)phenanthrene-dA ((BPh)dA) adduct opposite dT in a DNA duplex: Intercalation of the covalently attached benzo(c)phenanthrenyl ring to the 3'-side of the adduct site and comparison with the (+)-trans-anti-(BPh)dA opposite dT stereoisomer

Author

Cosman, Monique, Laryea, Alfred, Fiala, Radovan, Hingerty, Brian E., Amin, Shantu, Geacintov, Nicholas E., Broyde, Suse, and Patel, Dinshaw J.

Subjects
Polycyclic aromatic compounds -- Research, Conformational analysis -- Observations, Stereoisomers -- Analysis, Biological sciences, Chemistry
Abstract

Examination of the solution structures of the (-)-trans-anti-benzo(c)phenanthrene-dA((BPh)dA) adduct opposite dT in a DNA duplex by a combined two-dimensional NMR-molecular mechanics approach reveals intercalation of the covalently attached benzo(c)phenanthrenyl ring with the 3'-side of the (-)-trans-anti-(BPh)dA adduct site. A comparative study reveals that the direction of this intercalation is opposite to that observed in the solution structure of the (+)-trans-anti-(BPh)dA opposite dT stereiosomers.

Published
1995

31. Solution conformation of the (+)-trans-anti-(BP)dG adduct opposite a deletion site in a DNA duplex: intercalation of the covalently attached benzo(a)pyrene into the helix with base displacement of the modified deoxyguanosine in to the major groove

Author

Cosman, Monique, Fiala, Radovan, Hingerty, Brian E., Amin, Shantu, Geacintov, Nicholas E., Broyde, Suse, and Patel, Dinshaw J.

Subjects
DNA -- Research, Molecular structure -- Analysis, Biological sciences, Chemistry
Abstract

NMR and molecular mechanics studies of the solution structure of (+)-trans-anti-(BP)dG adduct present opposite the deletion site in DNA oligomer duplex reveal the occurrence of benzo(a)pyrene ring intercalation into the base pair-displaced helix of the (BP)dG6 deoxyguanosine base and displays numerous shifted proton resonances. The intercalation site is wedge-shaped but narrows in the dG16-dG17 position of the deletion-containing strand. Solution structure of the intercalated 11-mer duplex does not correlate with the previously proposed structure where the pyrene ring localizes to the minor groove and does not affect the Watson-Crick base pairing.

Published
1994

32. Solution conformation of the (+)-cis-anti-(BP)dG adduct opposite a deletion site in a DNA duplex: intercalation of the covalently attached benzo(a)pyrene into the helix with base displacement of the modified deoxyguanosine into the minor groove

Author

Cosman, Monique, Fiala, Radovan, Hingerty, Brian E., Amin, Shantu, Geacintov, Nicholas E., Broyde, Suse, and Patel, Dinshaw J.

Subjects
DNA -- Research, Chromosome deletion -- Analysis, Biological sciences, Chemistry
Abstract

Use of molecular mechanics and NMR to analyze the solution structure of (+)-cis-anti-(BP)dG adduct present opposite the deletion site of a DNA duplex show that the benzo(a)pyrene ring intercalates into the helix that is present opposite the deletion site, while the altered deoxyguanosine base undergoes displacement to the minor groove. The intercalation site has a wedge shape while the benzo(a)pyrene ring stacks over the Watson-Crick dG.dC base pairs. However, during the intercalation of (+)-trans-anti-(BP)dG, the modified base displaces into the major groove unlike the minor groove displacement of the base during (+)-cis-anti(BP)dG intercalation.

Published
1994

33. Solution conformation of the (+)-trans-anti-(BPh)dA adduct opposite dT in a DNA duplex: intercalation of the covalently attached benzo(c)phenanthrene to the 5'-side of the adduct site without disruption of the modified base pair

Author

Cosman, Monique, Fiala, Radovan, Hingerty, Brian E., Laryea, Alfred, Lee, Hongmee, Harvey, Ronald G., Amin, Shantu, Geacintov, Nicholas E., Broyde, Suse, and Patel, Dinshaw

Subjects
Polycyclic aromatic hydrocarbons -- Research, Nuclear magnetic resonance spectroscopy -- Usage, Nucleic acids -- Analysis, Biological sciences, Chemistry
Abstract

Two dimensional NMR methods, together with energy minimization computations, were used to examine the solution structure of (+)-trans-anti-(BPh)dA adduct located opposite the dT in the sequence context d(C5-(BPh)A6-C7)-d-(G16-T17-G18) at the 11-mer duplex level. The (BPh)dA dT base pair was not terminated when the covalently bound benzo (c) phenanthrenyl intercalated to the 5'-part of the (Bph)dA adduct region.

Published
1993

34. Solution conformation of the (+)-cis-anti-(BP)dG adduct in a DNA duplex: intercalation of the covalently attached benzo(a)pyrenyl rring into the helix and displacement of the modified deoxyguanosine

Author

Cosman, Monique, Santos, Carlos de los, Fiala, Radovan, Hingerty, Brian E., Ibanez, Victor, Luna, Ernestina, Harvey, Ronald, Geacintov, Nicholas E., Broyde, Suse, and Patel, Dinshaw J.

Subjects
Benzopyrene -- Research, DNA -- Research, Nucleotide sequence -- Research, Biological sciences, Chemistry
Abstract

The structure of the (+)-cis-anti(BP)dG adduct designated opposite dC in solution with a DNA oligomer duplex was analyzed usin NMR-energy minimization calculations. Results indicated intercalation between specific Watson-Crick base pairs and the benzopyrene ring of (BP)dG6 in a right handed helix. Shifted protein resonances was observed in the intercalative structure because of ring current effects of the deoxyguanosine and pyrenyl rings of the adduct. These data showed a base-displayed intercalation type form for a polycyclic aromatic hydrocarbon fixed to the deoxyguanosine adduct at the DNA oligomer level.

Published
1993

36. Monitoring DNA–Ligand Interactions in Living Human Cells Using NMR Spectroscopy

Author

Krafcikova, Michaela, primary, Dzatko, Simon, additional, Caron, Coralie, additional, Granzhan, Anton, additional, Fiala, Radovan, additional, Loja, Tomas, additional, Teulade-Fichou, Marie-Paule, additional, Fessl, Tomas, additional, Hänsel-Hertsch, Robert, additional, Mergny, Jean-Louis, additional, Foldynova-Trantirkova, Silvie, additional, and Trantirek, Lukas, additional

Published
2019
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37. Ascorbigen A-NMR identification

Author

Sychrovský, Vladimír, primary, Šaman, David, additional, Fiala, Radovan, additional, Humpa, Otakar, additional, Sýkora, Jan, additional, Kessler, Pavel, additional, Blechta, Vratislav, additional, Dobrev, Petre, additional, and Schraml, Jan, additional

Published
2019
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39. Structural changes arising from different thawing protocols on cryopreserved human allograft’s aortic valve leaflets

Author

Novotny, Robert, primary, Slizova, Dasa, additional, Hlubocky, Jaroslav, additional, Krs, Otakar, additional, Spatenka, Jaroslav, additional, BURKERT, Jan, additional, Fiala, Radovan, additional, Mitas, Petr, additional, Mericka, Pavel, additional, Spacek, Miroslav, additional, Hlubocka, Zuzana, additional, and Lindner, Jaroslav, additional

Published
2018
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44. Spectral density mapping at multiple magnetic fields suitable for C-13 NMR relaxation studies

Author

Kaderavek, Pavel, Zapletal, Vojtech, Fiala, Radovan, Srb, Pavel, Padrta, Petr, Precechtelova, Jana Pavlikova, Soltesova, Maria, Kowalewski, Jozef, Widmalm, Göran, Chmelik, Josef, Sklenar, Vladimir, and Zidek, Lukas

Subjects
Nucleic acids, Relaxation, Magnetic field, Physical Sciences, Chemical Sciences, Carbohydrates, Fysik, Biologiska vetenskaper, Kemi, Biological Sciences, Spectral density function, Nuclear magnetic resonance
Abstract

Standard spectral density mapping protocols, well suited for the analysis of N-15 relaxation rates, introduce significant systematic errors when applied to C-13 relaxation data, especially if the dynamics is dominated by motions with short correlation times (small molecules, dynamic residues of macromolecules). A possibility to improve the accuracy by employing cross-correlated relaxation rates and on measurements taken at several magnetic fields has been examined. A suite of protocols for analyzing such data has been developed and their performance tested. Applicability of the proposed protocols is documented in two case studies, spectral density mapping of a uniformly labeled RNA hairpin and of a selectively labeled disaccharide exhibiting highly anisotropic tumbling. Combination of auto- and cross-correlated relaxation data acquired at three magnetic fields was applied in the former case in order to separate effects of fast motions and conformational or chemical exchange. An approach using auto-correlated relaxation rates acquired at five magnetic fields, applicable to anisotropically moving molecules, was used in the latter case. The results were compared with a more advanced analysis of data obtained by interpolation of auto-correlated relaxation rates measured at seven magnetic fields, and with the spectral density mapping of cross-correlated relaxation rates. The results showed that sufficiently accurate values of auto- and cross-correlated spectral density functions at zero and C-13 frequencies can be obtained from data acquired at three magnetic fields for uniformly C-13-labeled molecules with a moderate anisotropy of the rotational diffusion tensor. Analysis of auto-correlated relaxation rates at five magnetic fields represents an alternative for molecules undergoing highly anisotropic motions.

Published
2016

47. Structure of a Stable G-Hairpin

Author

Gajarský, Martin, primary, Živković, Martina Lenarčič, additional, Stadlbauer, Petr, additional, Pagano, Bruno, additional, Fiala, Radovan, additional, Amato, Jussara, additional, Tomáška, L’ubomír, additional, Šponer, Jiří, additional, Plavec, Janez, additional, and Trantírek, Lukáš, additional

Published
2017
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49. Erratum to: Impact of nucleic acid self-alignment in a strong magnetic field on the interpretation of indirect spin-spin interactions

Author

Sub Cellular Protein Chemistry, Sub NMR Spectroscopy, NMR Spectroscopy, Vavrinská, Andrea, Zelinka, Jiří, Šebera, Jakub, Sychrovský, Vladimír, Fiala, Radovan, Boelens, Rolf, Sklenář, Vladimír, Trantírek, Lukáš, Sub Cellular Protein Chemistry, Sub NMR Spectroscopy, NMR Spectroscopy, Vavrinská, Andrea, Zelinka, Jiří, Šebera, Jakub, Sychrovský, Vladimír, Fiala, Radovan, Boelens, Rolf, Sklenář, Vladimír, and Trantírek, Lukáš

Published
2016

50. Impact of nucleic acid self-alignment in a strong magnetic field on the interpretation of indirect spin-spin interactions

Author

Sub Cellular Protein Chemistry, Sub NMR Spectroscopy, NMR Spectroscopy, Cellular Protein Chemistry, Vavrinska, Andrea, Zelinka, Jiří, Šebera, Jakub, Sychrovský, Vladimír, Fiala, Radovan, Boelens, Rolf, Sklenář, Vladimír, Trantírek, Lukáš, Sub Cellular Protein Chemistry, Sub NMR Spectroscopy, NMR Spectroscopy, Cellular Protein Chemistry, Vavrinska, Andrea, Zelinka, Jiří, Šebera, Jakub, Sychrovský, Vladimír, Fiala, Radovan, Boelens, Rolf, Sklenář, Vladimír, and Trantírek, Lukáš

Published
2016

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