| 1. |
- Schoch, Conrad L., et al.
(author)
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Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi
- 2014
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In: Database: The Journal of Biological Databases and Curation. - : Oxford University Press (OUP). - 1758-0463. ; 2014:bau061, s. 1-21
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Journal article (peer-reviewed)abstract
- DNA phylogenetic comparisons have shown that morphology-based species recognition often underestimates fungal diversity. Therefore, the need for accurate DNA sequence data, tied to both correct taxonomic names and clearly annotated specimen data, has never been greater. Furthermore, the growing number of molecular ecology and microbiome projects using high-throughput sequencing require fast and effective methods for en masse species assignments. In this article, we focus on selecting and re-annotating a set of marker reference sequences that represent each currently accepted order of Fungi. The particular focus is on sequences from the internal transcribed spacer region in the nuclear ribosomal cistron, derived from type specimens and/or ex-type cultures. Re-annotated and verified sequences were deposited in a curated public database at the National Center for Biotechnology Information (NCBI), namely the RefSeq Targeted Loci (RTL) database, and will be visible during routine sequence similarity searches with NR_prefixed accession numbers. A set of standards and protocols is proposed to improve the data quality of new sequences, and we suggest how type and other reference sequences can be used to improve identification of Fungi.
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| 2. |
- Ayoglu, Burcu, et al.
(author)
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Bead Arrays for Antibody and Complement Profiling Reveal Joint Contribution of Antibody Isotypes to C3 Deposition
- 2014
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In: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 9:5, s. e96403-
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Journal article (peer-reviewed)abstract
- The development of antigen arrays has provided researchers with great tools to identify reactivities against self or foreign antigens from body fluids. Yet, these approaches mostly do not address antibody isotypes and their effector functions even though these are key points for a more detailed understanding of disease processes. Here, we present a bead array-based assay for a multiplexed determination of antigen-specific antibody levels in parallel with their properties for complement activation. We measured the deposition of C3 fragments from serum samples to reflect the degree of complement activation via all three complement activation pathways. We utilized the assay on a bead array containing native and citrullinated peptide antigens to investigate the levels of IgG, IgM and IgA autoantibodies along with their complement activating properties in serum samples of 41 rheumatoid arthritis patients and 40 controls. Our analysis revealed significantly higher IgG reactivity against the citrullinated fibrinogen beta and filaggrin peptides as well as an IgA reactivity that was exclusive for citrullinated fibrinogen b peptide and C3 deposition in rheumatoid arthritis patients. In addition, we characterized the humoral immune response against the viral EBNA-1 antigen to demonstrate the applicability of this assay beyond autoimmune conditions. We observed that particular buffer compositions were demanded for separate measurement of antibody reactivity and complement activation, as detection of antigen-antibody complexes appeared to be masked due to C3 deposition. We also found that rheumatoid factors of IgM isotype altered C3 deposition and introduced false-positive reactivities against EBNA-1 antigen. In conclusion, the presented bead-based assay setup can be utilized to profile antibody reactivities and immune-complex induced complement activation in a high-throughput manner and could facilitate the understanding and diagnosis of several diseases where complement activation plays role in the pathomechanism.
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| 3. |
- Nagy, Laszlo G., et al.
(author)
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The evolution of autodigestion in the mushroom family Psathyrellaceae (Agaricales) inferred from Maximum Likelihood and Bayesian methods
- 2010
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In: Molecular Phylogenetics and Evolution. - 1055-7903. ; 57, s. 1037-1048
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Journal article (peer-reviewed)abstract
- Recently developed comparative phylogenetic methods offer a wide spectrum of applications in evolutionary biology, although it is generally accepted that their statistical properties are incompletely known. Here, we examine and compare the statistical power of the ML and Bayesian methods with regard to selection of best-fit models of fruiting-body evolution and hypothesis testing of ancestral states on a real-life data set of a physiological trait (autodigestion) in the family Psathyrellaceae. Our phylogenies are based on the first multigene data set generated for the family. Two different coding regimes (binary and multistate) and two data sets differing in taxon sampling density are examined. The Bayesian method outperformed Maximum Likelihood with regard to statistical power in all analyses. This is particularly evident if the signal in the data is weak, i.e. in cases when the ML approach does not provide support to choose among competing hypotheses. Results based on binary and multistate coding differed only modestly, although it was evident that multistate analyses were less conclusive in all cases. It seems that increased taxon sampling density has favourable effects on inference of ancestral states, while model parameters are influenced to a smaller extent. The model best fitting our data implies that the rate of losses of deliquescence equals zero, although model selection in ML does not provide proper support to reject three of the four candidate models. The results also support the hypothesis that non-deliquescence (lack of autodigestion) has been ancestral in Psathyrellaceae, and that deliquescent fruiting bodies represent the preferred state, having evolved independently several times during evolution.
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| 4. |
- Papp, Dóra, et al.
(author)
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Structural water stabilizes protein motifs in liquid protein phase: The folding mechanism of short β-sheets coupled to phase transition
- 2021
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In: International Journal of Molecular Sciences. - : MDPI AG. - 1661-6596 .- 1422-0067. ; 22:16
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Journal article (peer-reviewed)abstract
- Macromolecular associates, such as membraneless organelles or lipid-protein assemblies, provide a hydrophobic environment, i.e., a liquid protein phase (LP), where folding preferences can be drastically altered. LP as well as the associated phase change from water (W) is an intriguing phenomenon related to numerous biological processes and also possesses potential in nanotechnological applications. However, the energetic effects of a hydrophobic yet water-containing environment on protein folding are poorly understood. Here, we focus on small β-sheets, the key motifs of proteins, undergoing structural changes in liquid–liquid phase separation (LLPS) and also model the mechanism of energy-coupled unfolding, e.g., in proteases, during W → LP transition. Due to the importance of the accurate description for hydrogen bonding patterns, the employed models were studied by using quantum mechanical calculations. The results demonstrate that unfolding is energetically less favored in LP by ~0.3–0.5 kcal·mol−1 per residue in which the difference further increased by the presence of explicit structural water molecules, where the folded state was preferred by ~1.2–2.3 kcal·mol−1 per residue relative to that in W. Energetics at the LP/W interfaces was also addressed by theoretical isodesmic reactions. While the models predict folded state preference in LP, the unfolding from LP to W renders the process highly favorable since the unfolded end state has >1 kcal·mol−1 per residue excess stabilization.
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| 5. |
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| 6. |
- Papp, Gergely, 1985, et al.
(author)
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The effect of magnetic perturbations on runaway dynamics
- 2013
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In: Proceeding of the13th IAEA Technical Meeting on Energetic Particles in Magnetic Confinement Systems. ; , s. IAEA-F1-TM-44766 / I12-
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Conference paper (peer-reviewed)abstract
- Disruptions in large tokamaks can lead to the generation of a relativistic runaway (RE) electron beam that may cause serious damage to the first wall. To suppress the RE beamthe application of resonant magnetic perturbations (RMP) has been suggested. We investigate the effect of resonant magnetic perturbations by simulating the RE drift orbits inmagnetostatic perturbed fields and calculating the transport and orbit losses for various particle energies and different magnetic perturbation configurations. In the simulations we use model configurations with the planned ITER RMP system and solve the relativistic, gyro-averaged drift equations for the runaway electrons including radiation losses and collisions. The results indicate that runaway electrons are rapidly lost from regions where thenormalised perturbation amplitude δB/B is larger than ∼0.1% in a properly chosen perturbation geometry. This corresponds to the outer half of the confinement volume in ITER. We show that despite the chaotic magnetic topology the ensemble behaviour can only be approximated by a diffusion process.
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| 7. |
- Papp, Gergely, 1985, et al.
(author)
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The effect of the ITER-like wall on runaway electron generation in JET
- 2013
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In: Nuclear Fusion. - : IOP Publishing. - 0029-5515 .- 1741-4326. ; 53:12
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Journal article (peer-reviewed)abstract
- This paper investigates the effect of the ITER-like wall (ILW) on runaway electron (RE) generation through a comparative study of similar slow argon injection JET disruptions, performed with different wall materials. In the carbon wall case, a RE plateau is observed, while in the ITER-like wall case, the current quench is slower and the runaway current is negligibly small. The aim of the paper is to shed light on the reason for these differences by detailed numerical modelling to study which factors affected the RE formation. The post-disruption current profile is calculated by a one-dimensional model of electric field, temperature and runaway current taking into account the impurity injection. Scans of various impurity contents are performed and agreement with the experimental scenarios is obtained for reasonable argon and wall impurity contents. Our modelling shows that the reason for the changed RE dynamics is a complex, combined effect of the differences in plasma parameter profiles, the radiation characteristics of beryllium and carbon, and the difference of the injected argon amount. These together lead to a significantly higher Dreicer generation rate in the carbon wall case, which is less prone to being suppressed by RE loss mechanisms. The results indicate that the differences are greatly reduced above ~50% argon content, suggesting that significant RE current is expected in future massive gas injection experiments on both JET and ITER.
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