11. |
12. Under fungal attack on a metalliferous soil: ROS or not ROS? Insights from Silene paradoxa L. growing under copper stressCosimo Taiti, Elisabetta Giorni, Ilaria Colzi, Sara Pignattelli, Nadia Bazihizina, Antonella Buccianti, Simone Luti, Luigia Pazzagli, Stefano Mancuso, Cristina Gonnelli, 2016, izvirni znanstveni članek Opis: We investigated how the adaptation to metalliferous environments can influence the plant response to biotic stress. In a metallicolous and a non-metallicolous population of Silene paradoxa the induction of oxidative stress and the production of callose and volatiles were evaluated in the presence of copper and of the PAMP fungal protein cerato-platanin, separately and in combination. Our results showed incompatibility between the ordinary ROS-mediated response to fungal attack and the acquired mechanisms of preventing oxidative stress in the tolerant population. A similar situation was also demonstrated by the sensitive population growing in the presence of copper but, in this case, with a lack of certain responses, such as callose production. In addition, in terms of the joint behaviour of emitted volatiles, multivariate statistics showed that not only did the populations respond differently to the presence of
copper or biotic stress, but also that the biotic and abiotic stresses interacted in different ways in the two populations.
Our results demonstrated that the same incompatibility of hyperaccumulators in ROS-mediated biotic stress signals also seemed to be exhibited by the excluder metallophyte, but without the advantage of being able to rely on the elemental defence for plant protection from natural enemies.
Ključne besede: Biotic interactions
Callose
Heavy metals
Oxidative stress
VOCs
Objavljeno v RUNG: 20.04.2020; Ogledov: 3428; Prenosov: 0
Gradivo ima več datotek! Več... |
13. Structural and functional determinants of TDP-43 aggregation : DissertationSanja Škaro, 2019, doktorska disertacija Opis: TDP-43 (TAR DNA-binding protein) is an hnRNP that was identified as the main component of the brain inclusions characteristically found in patients suffering of Amyotrophic Lateral Sclerosis and Frontotemporal Lobar Degeneration. As an hnRNP protein, TDP-43 fulfills diverse roles in mRNA metabolism, localization and transport. Structurally, TDP-43 is composed of a well conserved N terminal domain (NTD), two RRM domains of which RRM1 is necessary for recognizing and binding to its target, UG rich RNA sequences, and the C-terminal domain (CTD) which is a Glycine rich domain. The CTD also contains a Q/N rich region that plays a key role in protein aggregation and interaction with another hnRNP proteins and polyglutamine repeats. This thesis focus on the structural determinants involved in the different TDP-43 interactions with itself and with other hnRNPs. Both the carboxyl and amino terminal domains are involved in these interactions. We have mapped the regions more relevant for the function of TDP-43 and for the aggregation process characteristic of the pathological pathway leading to neurodegeneration. We have started to further study the N-terminal domain. Previous results in our laboratory using a cellular aggregation model have shown that the N-terminal domain is also necessary for sequestering the endogenous TDP-43 into the aggregates. In particular, the intact NTD, specifically residues 1 to 77, have been shown to be needed to efficiently recruit TDP-43 monomers into these aggregates. We have extended our knowledge of NTD structure and function, by assessing the behavior of a series of proteins in which key structural features (α-helix and β-sheets) were modified and TDP-43 splicing function together with structure via NMR were analyzed. It was found that by disrupting protein secondary structure in the NTD (mutation in α-helix NTD-31V/R-32T/R) the capacity of the aggregates to sequester enough TDP-43 to induce loss of function was lost.In fact, this protein is also unable to recovery TDP-43 functionality when it is disrupted due to sequestration of the endogenous TDP-43 in add back experiments. Disturbing protein stability through substitution of residues in α-helix also affects its ability to form an active conformation. On the other hand, synthesis of hybrid peptides containing certain NTD and CTD segments was performed in order to see if they are capable to bind to the TDP-43 aggregates. However, it has been shown that these synthetic peptides have a greater ability to induce TDP-43 aggregation than to bind to them, probably due to specific functional characteristics of NTD and CTD segments used for their synthesis.The main focus of the thesis was on the C-terminal domain sequences involved in protein-protein interaction, misfolding and aggregation.A comparison of human, mouse, zebrafish, Annelida, flatworms and Drosophila showed a very strong conservation of the NTD and RRMs, but the C terminal regions of human and other TDP-43 orthologues are very different.I have studied Human and Drosophila melanogaster orthologues, because Drosophila orthologue contains different paralogs of TDP-43.Through a series of deletions and mutations it was shown that the shorter paralog of Drosophila TDP-43 (TBPH-RA) is more active than the longer one (TBPH-RC), and that this is due to a combination of two factors: 1. TBPH-RC by itself aggregates more than TBPH-RA, 2. The functionality of TBPH-RC is downregulated by intramolecular interactions in the C terminal domain. Apparently there is a cation-π interaction involving Tryptophan and Arginine in TBPH-RC that has a high relevance to the protein function and is lacking in the TBPH-RA.Overall this data has identified structural features essential for the proper function of TDP-43.In addition, we have also identified sequences that are critical in the pathological aggregation process of TDP-43 that lead to the characteristic brain inclusions in ALS and FTLD and to the loss of functionality
Ključne besede: TDP-43 structural determinants, hybrid peptides, protein-protein interactions, intramolecular interaction, cation-π interaction, Drosophila orthologues.
Objavljeno v RUNG: 22.07.2019; Ogledov: 3359; Prenosov: 190
 Celotno besedilo (6,84 MB) |
14. On spin description of water-biopolymer interactions: theory and experiment of reentrant order-disorder transition.Artem Badasyan, predavanje na tuji univerzi Opis: The experimental studies of biopolymer conformations have reached an unprecedented level of
detailization during the past decade and allow now to study single molecules in vivo [1]. Processing of
experimental data essentially relies on theoretical approaches to conformational transitions in
biopolymers [2]. However, the models that are currently used, originate from the early 1960's and
contain several unjustified assumptions, widely accepted at that time. Thus, the view on the
conformational transitions in the polypeptides as a two-state process has very limited applicability
because the all-or-none transition mechanism takes place only in short polypeptides with sizes
comparable to the spatial correlation length; the original formulation of Zimm-Bragg model is
phenomenological and does not allow for a microscopic model for water; the implicit consideration of
the water-polypeptide interactions through the ansatz about the quadratic dependence of free energy
difference on temperature can only be justified through the assumption of an ideal gas with a constant
heat capacity. To get rid of these deficiencies, we augment the Hamiltonian formulation [3] of the
Zimm-Bragg model [4] with the term describing the water-polypeptide interactions [5]. The analytical
solution of the model results in a formula, ready to be fit to Circular Dichroism (CD) data for both heat
and cold denaturation. On the example of several sets of experimental data we show, that our formula
results in a significantly better fit, as compared to the existing approaches. Moreover, the application
of our procedure allows to compare the strengths of inter- and intra-molecular H-bonds, an
information, inaccessible before.
Ključne besede: helix-coil transition, water-polypeptide interactions
Objavljeno v RUNG: 13.03.2019; Ogledov: 3213; Prenosov: 0
Gradivo ima več datotek! Več... |
15. |
16. Particle Physics with the Pierre Auger ObservatoryTanguy Pierog, Andrej Filipčič, Samo Stanič, Darko Veberič, Danilo Zavrtanik, Marko Zavrtanik, 2014, objavljeni znanstveni prispevek na konferenci Ključne besede: Pierre Auger Observatory, extensive air showers, hadronic interactions, proton-air inelastic cross-section
Objavljeno v RUNG: 27.06.2017; Ogledov: 4017; Prenosov: 0
Gradivo ima več datotek! Več... |
17. Particle physics at the Pierre Auger ObservatoryJan Ebr, Andrej Filipčič, Ahmed Saleh, Samo Stanič, Darko Veberič, Serguei Vorobiov, Danilo Zavrtanik, Marko Zavrtanik, 2014, objavljeni znanstveni prispevek na konferenci Ključne besede: Pierre Auger Observatory, extensive air showers, hadronic interactions, proton-air cross section
Objavljeno v RUNG: 20.06.2017; Ogledov: 4567; Prenosov: 206
Celotno besedilo (1,02 MB) |
18. |
19. Measurement of the muon content in air showers at the Pierre Auger ObservatoryLaura Collica, Andrej Filipčič, Gašper Kukec Mezek, Ahmed Saleh, Samo Stanič, Marta Trini, Darko Veberič, Serguei Vorobiov, Lili Yang, Danilo Zavrtanik, Marko Zavrtanik, 2015, objavljeni znanstveni prispevek na konferenci Opis: The muon content of extensive air showers is an
observable sensitive to the primary composition and to
the hadronic interaction properties. We present here
different methods which allow us to estimate the muon number
at the ground level and the muon production depth by
exploiting the measurement of the longitudinal, lateral and
temporal distribution of particles in air showers recorded at
the Pierre Auger Observatory. The results, obtained at about
10[sup]19 eV (E[inf]CM ∼ 140 TeV center-of-mass energy for
proton primaries), are compared to the predictions
of LHC-tuned hadronic interaction models with different primary
masses and suggest a deficit in the muon content at the
ground predicted by simulations. The Pierre Auger Observatory
uses water-Cherenkov detectors to measure particle
densities at the ground and therefore has a good
sensitivity to the muon content of air showers. Moreover, due
to its hybrid design, the combination of muon measurements with
other independent mass composition analyses such as Xmax
provides additional constraints on hadronic interaction models.
Ključne besede: Pierre Auger Observatory, ultra-high energy cosmic rays, muons, mass composition, hadronic interactions
Objavljeno v RUNG: 03.03.2016; Ogledov: 4790; Prenosov: 218
Celotno besedilo (298,46 KB) |
