1. Instruct-ERIC network : biophysical characterization of antigen-nanobody complexesClaudia D'Ercole, 2024, published scientific conference contribution abstract Abstract: 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.
Keywords: nanobody, ascorbate peroxidase, plant stress, protein complex, biophysical methodologies
Published in RUNG: 31.05.2024; Views: 134; Downloads: 0
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2. A practical guide for the quality evaluation of fluobodies/chromobodiesUrša Štrancar, Claudia D'Ercole, Lucia Cikatricisová, Mirna Nakić, Matteo De March, Ario De Marco, 2024, original scientific article Keywords: fluorescent proteins, protein stability, protein degradation
Published in RUNG: 16.05.2024; Views: 226; Downloads: 2
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3. Biological applications of synthetic binders isolated from a conceptually new adhiron libraryClaudia D'Ercole, Matteo De March, Gianluca Veggiani, Sandra Oloketuyi, Rossella Svigelj, Ario De Marco, 2023, original scientific article Keywords: synthetic library, adhirons, affimers, C-reactive protein, SpyCatcher
Published in RUNG: 17.10.2023; Views: 887; Downloads: 3
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6. Macroporous epoxy-based monoliths functionalized with anti-CD63 nanobodies for effective isolation of extracellular vesicles in urineJulia Neumair, Claudia D'Ercole, Matteo De March, Martin Elsner, Michael Seidel, Ario De Marco, 2023, original scientific article Keywords: extracellular vesicles, monolith chromatography, nanobodies, functionalitazion strategies
Published in RUNG: 27.03.2023; Views: 1256; Downloads: 11
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7. Real-time monitoring of Arundo donax response to saline stress through the application of in vivo sensing technologyJanni Michela, Claudia Cocozza, Federico Brilli, Sara Pignattelli, Filippo Vurro, Nicola Coppede, Manuele Bettelli, Davide Calestani, Francesco Loreto, Andrea Zappettini, 2021, original scientific article Abstract: One of the main impacts of climate change on agriculture production is the dramatic increase of saline (Na+) content in substrate, that will impair crop performance and productivity. Here we demonstrate how the application of smart technologies such as an in vivo sensor, termed bioristor, allows to continuously monitor in real-time the dynamic changes of ion concentration in the sap of Arundo donax L. (common name giant reed or giant cane), when exposed to a progressive salinity stress. Data collected in vivo by bioristor sensors inserted at two different heights into A. donax stems enabled us to detect the early phases of stress response upon increasing salinity. Indeed, the continuous time-series of data recorded by the bioristor returned a specific signal which correlated with Na+ content in leaves of Na-stressed plants, opening a new perspective for its application as a tool for in vivo plant phenotyping and selection of genotypes more suitable for the exploitation of saline soils.
Keywords: Arundo donax, saline stress, vivo sensing technology
Published in RUNG: 17.12.2021; Views: 1790; Downloads: 18
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8. "Umetnost je zgodovina napak, ki pa so poetične, ki delujejo kot nekaj izvirnega. Za vsemi napakmi se skrivajo zgodbe." : "UMETNOST JE ZGODOVINA NAPAK, KI PA SO POETIČNE, KI DELUJEJO KOT NEKAJ IZVIRNEGA. ZA VSEMI NAPAKMI SE SKRIVAJO ZGODBE."2021, radio or television broadcast, podcast, interview, press conference Abstract: Med gosti letošnjega festivala Fabula – Literature sveta je leta 1984 rojena italijanska pisateljica Claudia Durastanti. V slovenščino imamo preveden njen roman Tujka, avtofikcijsko pripoved, ki se začne z odraščanjem ob gluhih starših; odvija se od New Yorka, prek revne južne Italije do Rima in Londona – hkrati pa gre za razmisleke o identiteti, umetnosti in življenju.
Keywords: italijanske pisateljice, romani, intervjuji
Published in RUNG: 05.11.2021; Views: 1658; Downloads: 7
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10. Silver nanoparticles enter the tree stem faster through leaves than through rootsClaudia Cocozza, Annalisa Perone, Cristiana Giordano, Maria Cristina Salvatici, Sara Pignattelli, Aida Raio, Marcus Schaub, Kruno Sever, John L. Innes, Roberto Tognetti, Paolo Cherubini, 2019, original scientific article Abstract: A major environmental pollution problem is the release into the atmosphere of particulate matter, including nanoparticles (NPs), which causes serious hazards to human and ecosystem health, particularly in urban areas. However, knowledge about the uptake, translocation and accumulation of NPs in plant tissues is almost completely lacking. The uptake of silver nanoparticles (Ag-NPs) and their transport and accumulation in the leaves, stems and roots of three different tree species, downy oak (Quercus pubescens Willd.), Scots pine (Pinus sylvestris L.) and black poplar (Populus nigra L.), were assessed. In the experiment, Ag- NPs were supplied separately to the leaves (via spraying, the foliar treatment) and roots (via watering, the root treatment) of the three species. Uptake, transport and accumulation of Ag were investigated through spectroscopy. The concentration of Ag in the stem was higher in the foliar than in the root treatment, and
in poplar more than in oak and pine. Foliar treatment with Ag-NPs reduced aboveground biomass and stem length in poplars, but not in oaks or pines. Species-specific signals of oxidative stress were observed; foliar treatment of oak caused the accumulation of H2O2 in leaves, and both foliar and root treatments of poplar led to increased O2− in leaves.
Ag-NPs affected leaf and root bacteria and fungi; in the case of leaves, foliar treatment reduced bacterial populations in
oak and poplar and fungi populations in pine, and in the case of roots, root treatment reduced bacteria and increased fungi in poplar. Species-specific mechanisms of interaction, transport, allocation and storage of NPs in trees were found.
We demonstrated definitively that NPs enter into the tree stem through leaves faster than through roots in all of the
investigated tree species.
Keywords: Ag-NPs, pathway of uptake, Pinus sylvestris L., Populus nigra L., Quercus pubescens Willd.
Published in RUNG: 20.04.2020; Views: 3003; Downloads: 0
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