1. Instruct-ERIC network : biophysical characterization of antigen-nanobody complexesClaudia D'Ercole, 2024, objavljeni povzetek znanstvenega prispevka na konferenci Opis: Forest environments are exposed to multiple stressful factors of both abiotic and biotic nature which may lead to their massive decline [1]. Understanding the molecular mechanisms of specific stress conditions and monitoring the fluctuations of reliable forest plant biomarkers with affordable methods would be instrumental for assessing stress levels over the time. Ascorbate peroxidase (APX) represents a suitable plant biomarker. APX is a hydrogen peroxide-scavenging enzyme the critical role of which has been described in several plants, both herbaceous and woody. Its activity generally increases under oxidative stress during which its peroxide detoxifying function is part of the wider ascorbate-glutathione cycle [2]. The development of reagents to detect such fluctuations would help the evaluation of plant physiological conditions. In this study, nanobodies (Nbs) targeting APX have been identified. Nbs correspond to the variable domain of heavy chain-only antibodies derived from camelids. They are small (15 kDa), stable, and can be easily produced in bacteria fused to different protein tags according to the downstream applications [3]. After their isolation by biopanning against soluble APX, they have been produced and underwent a biophysical characterization in combination with their antigen (APX-Nb complex) to identify the best binders in terms of stability and affinity. The protein complex characterization was supported by Instruct-ERIC and mainly performed at the BIOCEV institute of Prague. Data from Mass Photometry and Dynamic Light scattering evidenced the formation of the protein complexes, whereas the preliminary data of Hydrogen-Deuterium Exchange Mass Spectrometry, performed with the aim of identifying the residues involved in the paratope/epitope interface, were insufficient to clarify the issue and rather suggested that the interaction has low affinity. This indication was then confirmed by ELISA assay. The combination of multiple methods allowed a comprehensive sample characterization which will require further structural analyses to provide a complete picture of the APX-Nb complex.
[1] G. Marie. B. C. M. B. C. Walters, “Forest decline and tree mortality in a southeastern Ohio oak-hickory forest,” Ohio Journal of Science , vol. 97, 1997.
[2] O. Chew, J. Whelan, and A. H. Millar, “Molecular Definition of the Ascorbate-Glutathione Cycle in Arabidopsis Mitochondria Reveals Dual Targeting of Antioxidant Defenses in Plants,” Journal of Biological Chemistry, vol. 278, no. 47, 2003, doi: 10.1074/jbc.M307525200.
[3] S. Muyldermans, “A guide to: generation and design of nanobodies,” FEBS J, vol. 288, no. 7, pp. 2084–2102, Apr. 2021, doi: 10.1111/febs.15515.
Ključne besede: nanobody, ascorbate peroxidase, plant stress, protein complex, biophysical methodologies
Objavljeno v RUNG: 31.05.2024; Ogledov: 118; Prenosov: 0
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4. ULTRAFAST ELECTRON DYNAMICS IN CORRELATED SYSTEMS PROBED BY TIME-RESOLVED PHOTOEMISSION SPECTROSCOPYTanusree Saha, 2023, doktorska disertacija Opis: Complex systems in condensed matter are characterized by strong coupling
between different degrees of freedom constituting a solid. In materials
described by many-body physics, these interactions may lead to
the formation of new ground states such as excitonic insulators, Mott
insulators, and charge and spin density waves. However, the inherent
complexity in such materials poses a challenge to identifying the
dominant interactions governing these phases using equilibrium studies.
Owing to the distinct timescales associated with the elementary interactions,
such complexities can be readily addressed in the non-equilibrium
regime. Additionally, these materials might also show the emergence
of new, metastable “hidden“ phases under non-equilibrium. The thesis
investigates the ultrafast timescales of fundamental interactions in candidate
systems by employing time-and angle-resolved photoemission spectroscopy
in the femtosecond time domain. In the (supposed) excitonic
insulator model system Ta2NiSe5, the timescale of band gap closure
and the dependence of rise time (of the photoemission signal) on the
photoexcitation strength point to a predominantly electronic origin of
the band gap at the Fermi level. The charge density wave (CDW) -
Mott insulator 1T-TaS2 undergoes photoinduced phase transition to two
different phases. The initial one is a transient phase which resembles
the systems’s high temperature equilibrium phase, followed by a long-lived
“hidden“ phase with a different CDW amplitude and is primarily
driven by the CDW lattice order. For the spin density wave system
CaFe2As2 where multiple bands contribute in the formation of Fermi surfaces,
selective photoexcitation was used to disentangle the role played
by different electron orbitals. By varying the polarization of photoexcitation
pulses, it is observed that dxz/dyz orbitals primarily contribute to
the magnetic ordering while the dxy orbitals have dominant role in the
structural order. The findings of the present study provide deeper perspectives
on the underlying interactions in complex ground phases of
matter, therefore, initiating further experimental and theoretical studies
on such materials.
Ključne besede: complex systems, charge density wave, excitonic insulator, metastable phase, Mott insulator, non-equilibrium, spin density wave, timescales, time- and angle-resolved photoemission, ultrafast dynamics
Objavljeno v RUNG: 01.06.2023; Ogledov: 1505; Prenosov: 29
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8. Correlation between FeCl2 electrolyte conductivity and electrolysis efficiencyUroš Luin, Matjaž Valant, Iztok Arčon, 2022, objavljeni povzetek znanstvenega prispevka na konferenci Opis: The electrolysis efficiency is an important aspect of the Power-to-Solid energy storage technology (EST) based
on the iron chloride electrochemical cycle [1]. This cycle employs an aqueous FeCl2 catholyte solution for the
electro-reduction of iron. The metal iron deposits on the cathode. The energy is stored as a difference in the
redox potential of iron species. Hydrogen, as an energy carrier, is released on demand over a fully controlled
hydrogen evolution reaction between metallic Fe0 and HCl (aq) [1]. Due to these characteristics, the cycle is
suitable for long-term high-capacity and high-power energy storage. In a previous work [2] we revealed that
the electrolyte conductivity linearly increases with temperature. Contrary, the correlation between the
electrolyte concentration and efficiency is not so straightforward. Unexpectedly small efficiency variations were
found between 1 and 2.5 mol dm-3 FeCl2 (aq) followed by an abrupt efficiency drop at higher concentrations.
To explain the behavior of the observed trends and elucidate the role of FeCl2 (aq) complex ionic species we
performed in situ X-ray absorption studies. We made a dedicated experimental setup, consisting of a tubular
oven and PMMA liquid absorption cell, and performed the measurements at the DESY synchrotron P65
beamline. The XAS investigation covered XANES and EXAFS analyses of FeCl2 (aq) at different
concentrations (1 - 4 molL-1) and temperatures (25 - 80 °C). We found that at low temperature and low FeCl2
concentration the octahedral first coordination sphere around Fe is occupied by one Cl ion at a distance of 2.33
(±0.02) Å and five water molecules at a distance of 2.095 (±0.005) Å [3]. The structure of the ionic complex
gradually changes with an increase in temperature and/or concentration. The apical water molecule is
substituted by a chlorine ion to yield a neutral Fe[Cl2(H2O)4]0. The transition from the single charged
Fe[Cl(H2O)5]+ to the neutral Fe[Cl2(H2O)4]0 causes a significant drop in the solution conductivity, which well
correlates with the existing conductivity models [3].
[1] M. Valant, “Procedure for electric energy storage in solid matter. United States Patent and
Trademark Office. Patent No. US20200308715,” Patent No. US20200308715, 2021.
[2] U. Luin and M. Valant, “Electrolysis energy efficiency of highly concentrated FeCl2 solutions
for power-to-solid energy storage technology,” J. Solid State Electrochem., vol. 26, no. 4, pp.
929–938, Apr. 2022, doi: 10.1007/S10008-022-05132-Y.
[3] U. Luin, I. Arčon, and M. Valant, “Structure and Population of Complex Ionic Species in
FeCl2 Aqueous Solution by X-ray Absorption Spectroscopy,” Molecules, vol. 27, no. 3, 2022,
doi: 10.3390/molecules27030642.
Ključne besede: Iron chloride electrochemical cycle, Power-to-Solid energy storage, XANES, EXAFS, electrical
conductivity, electrolyte complex ionic species structure and population
Objavljeno v RUNG: 26.09.2022; Ogledov: 1755; Prenosov: 0 (1 glas)
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10. Graph based feature extraction and classification of wet and dry cough signals: A machine learning approachMohanachandran Nair Sindhu Swapna, 2021, izvirni znanstveni članek Opis: This article proposes a unique approach to bring out the potential of graph-based features to reveal the
hidden signatures of wet (WE) and dry (DE) cough signals, which are the suggestive symptoms of various
respiratory ailments like COVID 19. The spectral and complex network analyses of 115 cough signals are
employed for perceiving the airflow dynamics through the infected respiratory tract while coughing. The
different phases of WE and DE are observed from their time-domain signals, indicating the operation of the
glottis. The wavelet analysis of WE shows a frequency spread due to the turbulence in the respiratory tract.
The complex network features namely degree centrality, eigenvector centrality, transitivity, graph density
and graph entropy not only distinguish WE and DE but also reveal the associated airflow dynamics. A better
distinguishability between WE and DE is obtained through the supervised machine learning techniques
(MLTs)—quadratic support vector machine and neural net pattern recognition (NN), when compared to
the unsupervised MLT, principal component analysis. The 93.90% classification accuracy with a precision
of 97.00% suggests NN as a better classifier using complex network features. The study opens up the
possibility of complex network analysis in remote auscultation.
Ključne besede: wet cough, dry cough, complex network, quadratic SVM, neural net
Objavljeno v RUNG: 30.06.2022; Ogledov: 1180; Prenosov: 0
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