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Pentari C, Kosinas C, Nikolaivits E, Dimarogona M, Topakas E. Structural and molecular insights into a bifunctional glycoside hydrolase 30 xylanase specific to glucuronoxylan. Biotechnol Bioeng 2024. [PMID: 38678481 DOI: 10.1002/bit.28731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 04/15/2024] [Accepted: 04/19/2024] [Indexed: 05/01/2024]
Abstract
Glycoside hydrolase (GH) 30 family xylanases are enzymes of biotechnological interest due to their capacity to degrade recalcitrant hemicelluloses, such as glucuronoxylan (GX). This study focuses on a subfamily 7 GH30, TtXyn30A from Thermothelomyces thermophilus, which acts on GX in an "endo" and "exo" mode, releasing methyl-glucuronic acid branched xylooligosaccharides (XOs) and xylobiose, respectively. The crystal structure of inactive TtXyn30A in complex with 23-(4-O-methyl-α-D-glucuronosyl)-xylotriose (UXX), along with biochemical analyses, corroborate the implication of E233, previously identified as alternative catalytic residue, in the hydrolysis of decorated xylan. At the -1 subsite, the xylose adopts a distorted conformation, indicative of the Michaelis complex of TtXyn30AEE with UXX trapped in the semi-functional active site. The most significant structural rearrangements upon substrate binding are observed at residues W127 and E233. The structures with neutral XOs, representing the "exo" function, clearly show the nonspecific binding at aglycon subsites, contrary to glycon sites, where the xylose molecules are accommodated via multiple interactions. Last, an unproductive ligand binding site is found at the interface between the catalytic and the secondary β-domain which is present in all GH30 enzymes. These findings improve current understanding of the mechanism of bifunctional GH30s, with potential applications in the field of enzyme engineering.
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Affiliation(s)
- Christina Pentari
- Industrial Biotechnology & Biocatalysis Group, Biotechnology Laboratory, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
| | - Christos Kosinas
- Laboratory of Structural Biology and Biotechnology, Department of Chemical Engineering, University of Patras, Patras, Greece
| | - Efstratios Nikolaivits
- Industrial Biotechnology & Biocatalysis Group, Biotechnology Laboratory, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
| | - Maria Dimarogona
- Laboratory of Structural Biology and Biotechnology, Department of Chemical Engineering, University of Patras, Patras, Greece
| | - Evangelos Topakas
- Industrial Biotechnology & Biocatalysis Group, Biotechnology Laboratory, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
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2
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Tziouvara O, Petsana M, Kourounis D, Papadaki A, Basdra E, Braliou GG, Boleti H. Characterization of the First Secreted Sorting Nexin Identified in the Leishmania Protists. Int J Mol Sci 2024; 25:4095. [PMID: 38612903 PMCID: PMC11012638 DOI: 10.3390/ijms25074095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 03/19/2024] [Accepted: 03/19/2024] [Indexed: 04/14/2024] Open
Abstract
Proteins of the sorting nexin (SNX) family present a modular structural architecture with a phox homology (PX) phosphoinositide (PI)-binding domain and additional PX structural domains, conferring to them a wide variety of vital eukaryotic cell's functions, from signal transduction to membrane deformation and cargo binding. Although SNXs are well studied in human and yeasts, they are poorly investigated in protists. Herein, is presented the characterization of the first SNX identified in Leishmania protozoan parasites encoded by the LdBPK_352470 gene. In silico secondary and tertiary structure prediction revealed a PX domain on the N-terminal half and a Bin/amphiphysin/Rvs (BAR) domain on the C-terminal half of this protein, with these features classifying it in the SNX-BAR subfamily of SNXs. We named the LdBPK_352470.1 gene product LdSNXi, as it is the first SNX identified in Leishmania (L.) donovani. Its expression was confirmed in L. donovani promastigotes under different cell cycle phases, and it was shown to be secreted in the extracellular medium. Using an in vitro lipid binding assay, it was demonstrated that recombinant (r) LdSNXi (rGST-LdSNXi) tagged with glutathione-S-transferase (GST) binds to the PtdIns3P and PtdIns4P PIs. Using a specific a-LdSNXi antibody and immunofluorescence confocal microscopy, the intracellular localization of endogenous LdSNXi was analyzed in L. donovani promastigotes and axenic amastigotes. Additionally, rLdSNXi tagged with enhanced green fluorescent protein (rLdSNXi-EGFP) was heterologously expressed in transfected HeLa cells and its localization was examined. All observed localizations suggest functions compatible with the postulated SNX identity of LdSNXi. Sequence, structure, and evolutionary analysis revealed high homology between LdSNXi and the human SNX2, while the investigation of protein-protein interactions based on STRING (v.11.5) predicted putative molecular partners of LdSNXi in Leishmania.
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Affiliation(s)
- Olympia Tziouvara
- Intracellular Parasitism Group, Department of Microbiology, Hellenic Pasteur Institute, 11521 Athens, Greece; (O.T.); (M.P.); (D.K.); (A.P.)
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece;
| | - Marina Petsana
- Intracellular Parasitism Group, Department of Microbiology, Hellenic Pasteur Institute, 11521 Athens, Greece; (O.T.); (M.P.); (D.K.); (A.P.)
- Department of Computer Science and Biomedical Informatics, University of Thessaly, 2–4 Papasiopoulou Str., 35131 Lamia, Greece;
| | - Drosos Kourounis
- Intracellular Parasitism Group, Department of Microbiology, Hellenic Pasteur Institute, 11521 Athens, Greece; (O.T.); (M.P.); (D.K.); (A.P.)
| | - Amalia Papadaki
- Intracellular Parasitism Group, Department of Microbiology, Hellenic Pasteur Institute, 11521 Athens, Greece; (O.T.); (M.P.); (D.K.); (A.P.)
| | - Efthimia Basdra
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece;
| | - Georgia G. Braliou
- Department of Computer Science and Biomedical Informatics, University of Thessaly, 2–4 Papasiopoulou Str., 35131 Lamia, Greece;
| | - Haralabia Boleti
- Intracellular Parasitism Group, Department of Microbiology, Hellenic Pasteur Institute, 11521 Athens, Greece; (O.T.); (M.P.); (D.K.); (A.P.)
- Bioimaging Unit, Hellenic Pasteur Institute, 11521 Athens, Greece
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Manolis GD, Dadoulis GI. Passive Control in a Continuous Beam under a Traveling Heavy Mass: Dynamic Response and Experimental Verification. Sensors (Basel) 2024; 24:573. [PMID: 38257665 PMCID: PMC10820652 DOI: 10.3390/s24020573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 01/15/2024] [Accepted: 01/15/2024] [Indexed: 01/24/2024]
Abstract
The motion of a heavy mass on a bridge span causes vibrations whose magnitude and frequency content depend on the mechanical properties of the structural system, including the magnitude of that mass and its speed of traverse. In order to limit vibrations that could potentially cause damage, a simple passive device configuration, namely the tuned mass damper (TMD), is introduced and its effect on the beam vibrations analyzed. Specifically, a TMD in the form of a single-degree-of-freedom (SDOF) unit comprising a mass and a spring is placed on the span to act as a secondary system for absorbing vibrations from the primary system, i.e., the bridge itself. A Lagrangian energy balance formulation is used to derive the governing equations of motion, followed by an analytical solution using the Laplace transform to investigate the transmission of vibratory energy between primary and secondary systems. Results are given in terms of time histories, Fourier spectra and spectrograms, where the influence of the TMD in reducing vibratory energy is demonstrated. The TMD is placed in the region where the beam's transverse motion is at a maximum, while its mechanical properties are sub-optimal, in the sense that there is no separate damper present and minimal damping is provided by the spring element itself. In parallel with the analysis, a series of experiments involving a simply supported model steel bridge span traversed by a heavy mass are conducted to first gauge the analytical solution and then to confirm the validity of the proposed passive scheme.
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Affiliation(s)
- George D. Manolis
- Laboratory for Experimental Strength of Materials and Structures, School of Civil Engineering, Aristotle University of Thessaloniki, GR-54124 Thessaloniki, Greece;
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Mantovani F, Kitsou K, Paraskevis D, Lagiou P, Magiorkinis G. The interaction of human immunodeficiency virus-1 and human endogenous retroviruses in patients (primary cell cultures) and cell line models. Microbiol Spectr 2023; 11:e0137923. [PMID: 37811936 PMCID: PMC10715072 DOI: 10.1128/spectrum.01379-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 08/24/2023] [Indexed: 10/10/2023] Open
Abstract
IMPORTANCE In this work, we demonstrated that human immunodeficiency virus (HIV) infection leads to the modification of the human endogenous retrovirus (HERV) expression. Differential expression of multiple HERVs was found in peripheral blood mononuclear cells derived from HIV-infected patients compared to healthy donors and HIV-infected T cell cultures compared to non-infected. The effect of HIV presence on HERV expression appears to be more restricted in cells of monocytic origin, as only deregulation of HERV-W and HERV-K (HML-6) was found in these cell cultures after their infection with HIV. Multiple factors contribute to this aberrant HERV expression, and its levels appear to be modified in a time-dependent manner. Further studies and the development of optimized in vitro protocols are warranted to elucidate the interactions between HIV and HERVs in detail.
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Affiliation(s)
- Federica Mantovani
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Konstantina Kitsou
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Dimitrios Paraskevis
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Pagona Lagiou
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, Greece
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Gkikas Magiorkinis
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, Greece
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Stavrou M, Chazapis N, Georgakilas V, Couris S. 2D Non-van der Waals Nanoplatelets of Hematene and Magnetene: Nonlinear Optical Response and Optical Limiting Performance from UV to NIR. Chemistry 2023; 29:e202301959. [PMID: 37589720 DOI: 10.1002/chem.202301959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 08/17/2023] [Accepted: 08/17/2023] [Indexed: 08/18/2023]
Abstract
Recently, the preparation of some hematene and magnetene ultrathin non van der Waals (non-vdW) 2D nanoplatelets was reported starting from hematite and magnetite natural iron ores. The present work reports on the determination and evaluation of the nonlinear optical response and the optical limiting (OL) action of these 2D nanoplatelets dispersed in water under ns laser excitation. The obtained results show that both hematene and magnetene exhibit strong nonlinear absorption and refraction, comparable and even larger than those of other van der Waals (vdW) 2D counterpart materials. In addition, due to their strong nonlinear absorption, both hematene and magnetene show exceptional OL performance from the UV to visible, attaining very low values of optical limiting onset (OLon ), comparable and even lower than that of vdW 2D nanomaterials, such as graphene, graphene oxide, other transition metal dichalcogenides like MoS2 , WS2 and MoSe2 , black phosphorous and antimonene. Moreover, hematene was found to exhibit more efficient OL action than magnetene for all the excitation wavelengths studied, attributed to more efficient ligand to metal charge transfer. The present findings open new possibilities for the potential use of these non-vdW 2D materials in photonics and optoelectronics, e. g., as optical limiters and optical switchers.
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Affiliation(s)
- Michalis Stavrou
- Department of Physics, University of Patras University Campus, 26504, Rion, Achaia, Greece
- Institute of Chemical Engineering Sciences (ICE-HT), Foundation for Research and Technology-Hellas (FORTH) Stadiou St, Platani, 26504, Patras, Greece
| | - Nikolaos Chazapis
- Department of Physics, University of Patras University Campus, 26504, Rion, Achaia, Greece
- Institute of Chemical Engineering Sciences (ICE-HT), Foundation for Research and Technology-Hellas (FORTH) Stadiou St, Platani, 26504, Patras, Greece
| | - Vasilios Georgakilas
- Department of Materials Science, University of Patras University Campus, 26504, Rion, Achaia, Greece
| | - Stelios Couris
- Department of Physics, University of Patras University Campus, 26504, Rion, Achaia, Greece
- Institute of Chemical Engineering Sciences (ICE-HT), Foundation for Research and Technology-Hellas (FORTH) Stadiou St, Platani, 26504, Patras, Greece
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Voutyraki C, Choromidis A, Meligkounaki A, Vlachopoulos NA, Theodorou V, Grammenoudi S, Athanasiadis E, Monticelli S, Giangrande A, Delidakis C, Zacharioudaki E. Growth deregulation and interaction with host hemocytes contribute to tumor progression in a Drosophila brain tumor model. Proc Natl Acad Sci U S A 2023; 120:e2221601120. [PMID: 37549261 PMCID: PMC10438840 DOI: 10.1073/pnas.2221601120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 06/27/2023] [Indexed: 08/09/2023] Open
Abstract
Tumors constantly interact with their microenvironment. Here, we present data on a Notch-induced neural stem cell (NSC) tumor in Drosophila, which can be immortalized by serial transplantation in adult hosts. This tumor arises in the larva by virtue of the ability of Notch to suppress early differentiation-promoting factors in NSC progeny. Guided by transcriptome data, we have addressed both tumor-intrinsic and microenvironment-specific factors and how they contribute to tumor growth and host demise. The growth promoting factors Myc, Imp, and Insulin receptor in the tumor cells are important for tumor expansion and killing of the host. From the host's side, hemocytes, professional phagocytic blood cells, are found associated with tumor cells. Phagocytic receptors, like NimC1, are needed in hemocytes to enable them to capture and engulf tumor cells, restricting their growth. In addition to their protective role, hemocytes may also increase the host's morbidity by their propensity to produce damaging extracellular reactive oxygen species.
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Affiliation(s)
- Chrysanthi Voutyraki
- Institute of Molecular Biology & Biotechnology, Foundation for Research & Technology Hellas, 70013Heraklion, Crete, Greece
- Department of Biology, University of Crete, 70013Heraklion, Crete, Greece
| | - Alexandros Choromidis
- Institute of Molecular Biology & Biotechnology, Foundation for Research & Technology Hellas, 70013Heraklion, Crete, Greece
- Department of Biology, University of Crete, 70013Heraklion, Crete, Greece
| | - Anastasia Meligkounaki
- Institute of Molecular Biology & Biotechnology, Foundation for Research & Technology Hellas, 70013Heraklion, Crete, Greece
- Department of Biology, University of Crete, 70013Heraklion, Crete, Greece
| | - Nikolaos Andreas Vlachopoulos
- Institute of Molecular Biology & Biotechnology, Foundation for Research & Technology Hellas, 70013Heraklion, Crete, Greece
- Department of Biology, University of Crete, 70013Heraklion, Crete, Greece
| | - Vasiliki Theodorou
- Institute of Molecular Biology & Biotechnology, Foundation for Research & Technology Hellas, 70013Heraklion, Crete, Greece
| | - Sofia Grammenoudi
- Institute for Fundamental Biomedical Research, Biomedical Sciences Research Center Alexander Fleming, 16672Athens, Greece
| | - Emmanouil Athanasiadis
- Greek Genome Centre, Biomedical Research Foundation of the Academy of Athens, 11527Athens, Greece
- Medical Image and Signal Processing Laboratory, Department of Biomedical Engineering, University of West Attica, 12243Athens, Greece
| | - Sara Monticelli
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67400Strasbourg, France
- Centre National de la Recherche Scientifique, UMR7104Strasbourg, France
- Institut National de la Santé et de la Recherche Médicale, U1258Strasbourg, France
- Université de Strasbourg, 67404Strasbourg, France
| | - Angela Giangrande
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67400Strasbourg, France
- Centre National de la Recherche Scientifique, UMR7104Strasbourg, France
- Institut National de la Santé et de la Recherche Médicale, U1258Strasbourg, France
- Université de Strasbourg, 67404Strasbourg, France
| | - Christos Delidakis
- Institute of Molecular Biology & Biotechnology, Foundation for Research & Technology Hellas, 70013Heraklion, Crete, Greece
- Department of Biology, University of Crete, 70013Heraklion, Crete, Greece
| | - Evanthia Zacharioudaki
- Institute of Molecular Biology & Biotechnology, Foundation for Research & Technology Hellas, 70013Heraklion, Crete, Greece
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Ralli E, Spyros A. A Study of Greek Graviera Cheese by NMR-Based Metabolomics. Molecules 2023; 28:5488. [PMID: 37513360 PMCID: PMC10385548 DOI: 10.3390/molecules28145488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Revised: 07/13/2023] [Accepted: 07/14/2023] [Indexed: 07/30/2023] Open
Abstract
Graviera is a very popular yellow hard cheese produced in mainland Greece and the Aegean islands, and in three PDO (protected denomination of origin) locations. Apart from geographic location, type of milk and production practices are also factors that affect cheese composition, and make this dairy product unique in taste and aroma. In this work, 1H nuclear magnetic resonance (NMR) spectroscopy in combination with chemometrics has been used to determine the metabolite profile (40 compounds) of graviera cheese produced in different geographic locations, with emphasis on cheeses produced on the island of Crete. Organic acids and amino acids were the main components quantified in the polar cheese fraction, while the fatty acid (FA) composition of the lipid fraction was also obtained. Analysis of variance (Anova) of the dataset showed that γ-aminobutyric acid (GABA), conjugated linoleic acids (CLA) and linoleic acid differentiate gravieras produced in different areas of Crete, and that the total amino acid content was higher in cheeses produced in eastern Crete. Targeted discriminant analysis models classified gravieras produced in mainland Greece, Cyclades and Crete based on differences in 1,2-diglycerides, sterols, GABA and FA composition. Targeted and untargeted orthogonal partial least squares discriminant analysis (OPLS-DA) models were capable of differentiating gravieras produced in the island of Crete and hold promise as the basis for the authentication of PDO graviera products.
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Affiliation(s)
- Evangelia Ralli
- NMR Laboratory, Department of Chemistry, University of Crete, Voutes Campus, 710 03 Heraklion, Crete, Greece
| | - Apostolos Spyros
- NMR Laboratory, Department of Chemistry, University of Crete, Voutes Campus, 710 03 Heraklion, Crete, Greece
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Mantsou A, Papachristou E, Keramidas P, Lamprou P, Pitou M, Papi RM, Dimitriou K, Aggeli A, Choli-Papadopoulou T. Fabrication of a Smart Fibrous Biomaterial That Harbors an Active TGF-β1 Peptide: A Promising Approach for Cartilage Regeneration. Biomedicines 2023; 11:1890. [PMID: 37509529 PMCID: PMC10377373 DOI: 10.3390/biomedicines11071890] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 06/28/2023] [Accepted: 06/30/2023] [Indexed: 07/30/2023] Open
Abstract
The regeneration of articular cartilage remains a serious problem in various pathological conditions such as osteoarthritis, due to the tissue's low self-healing capacity. The latest therapeutic approaches focus on the construction of biomaterials that induce cartilage repair. This research describes the design, synthesis, and investigation of a safe, "smart", fibrous scaffold containing a genetically incorporated active peptide for chondrogenic induction. While possessing specific sequences and the respective mechanical properties from natural fibrous proteins, the fibers also incorporate a Transforming Growth Factor-β1 (TGF-β1)-derived peptide (YYVGRKPK) that can promote chondrogenesis. The scaffold formed stable porous networks with shear-thinning properties at 37 °C, as shown by SEM imaging and rheological characterization, and were proven to be non-toxic to human dental pulp stem cells (hDPSCs). Its chondrogenic capacity was evidenced by a strong increase in the expression of specific chondrogenesis gene markers SOX9, COL2, ACAN, TGFBR1A, and TGFBR2 in cells cultured on "scaffold-TGFβ1" for 21 days and by increased phosphorylation of intracellular signaling proteins Smad-2 and Erk-1/2. Additionally, intense staining of glycosaminoglycans was observed in these cells. According to our results, "scaffold-TGFβ1" is proposed for clinical studies as a safe, injectable treatment for cartilage degeneration.
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Affiliation(s)
- Aglaia Mantsou
- Laboratory of Biochemistry, School of Chemistry, Faculty of Sciences, Aristotle University of Thessaloniki, University Campus, 54124 Thessaloniki, Greece
| | - Eleni Papachristou
- Laboratory of Biochemistry, School of Chemistry, Faculty of Sciences, Aristotle University of Thessaloniki, University Campus, 54124 Thessaloniki, Greece
| | - Panagiotis Keramidas
- Laboratory of Biochemistry, School of Chemistry, Faculty of Sciences, Aristotle University of Thessaloniki, University Campus, 54124 Thessaloniki, Greece
| | - Paraskevas Lamprou
- Laboratory of Biochemistry, School of Chemistry, Faculty of Sciences, Aristotle University of Thessaloniki, University Campus, 54124 Thessaloniki, Greece
| | - Maria Pitou
- Laboratory of Biochemistry, School of Chemistry, Faculty of Sciences, Aristotle University of Thessaloniki, University Campus, 54124 Thessaloniki, Greece
| | - Rigini M Papi
- Laboratory of Biochemistry, School of Chemistry, Faculty of Sciences, Aristotle University of Thessaloniki, University Campus, 54124 Thessaloniki, Greece
| | - Katerina Dimitriou
- Laboratory of Chemical Engineering A', School of Chemical Engineering, Faculty of Engineering, Aristotle University of Thessaloniki, University Campus, 54124 Thessaloniki, Greece
| | - Amalia Aggeli
- Laboratory of Chemical Engineering A', School of Chemical Engineering, Faculty of Engineering, Aristotle University of Thessaloniki, University Campus, 54124 Thessaloniki, Greece
| | - Theodora Choli-Papadopoulou
- Laboratory of Biochemistry, School of Chemistry, Faculty of Sciences, Aristotle University of Thessaloniki, University Campus, 54124 Thessaloniki, Greece
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Anadolu MN, Sun J, Kailasam S, Chalkiadaki K, Krimbacher K, Li JTY, Markova T, Jafarnejad SM, Lefebvre F, Ortega J, Gkogkas CG, Sossin WS. Ribosomes in RNA Granules Are Stalled on mRNA Sequences That Are Consensus Sites for FMRP Association. J Neurosci 2023; 43:2440-2459. [PMID: 36849416 PMCID: PMC10082463 DOI: 10.1523/jneurosci.1002-22.2023] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 02/07/2023] [Accepted: 02/13/2023] [Indexed: 03/01/2023] Open
Abstract
Local translation in neurons is partly mediated by the reactivation of stalled polysomes. Stalled polysomes may be enriched within the granule fraction, defined as the pellet of sucrose gradients used to separate polysomes from monosomes. The mechanism of how elongating ribosomes are reversibly stalled and unstalled on mRNAs is still unclear. In the present study, we characterize the ribosomes in the granule fraction using immunoblotting, cryogenic electron microscopy (cryo-EM), and ribosome profiling. We find that this fraction, isolated from 5-d-old rat brains of both sexes, is enriched in proteins implicated in stalled polysome function, such as the fragile X mental retardation protein (FMRP) and Up-frameshift mutation 1 homologue. Cryo-EM analysis of ribosomes in this fraction indicates they are stalled, mainly in the hybrid state. Ribosome profiling of this fraction reveals (1) an enrichment for footprint reads of mRNAs that interact with FMRPs and are associated with stalled polysomes, (2) an abundance of footprint reads derived from mRNAs of cytoskeletal proteins implicated in neuronal development, and (3) increased ribosome occupancy on mRNAs encoding RNA binding proteins. Compared with those usually found in ribosome profiling studies, the footprint reads were longer and were mapped to reproducible peaks in the mRNAs. These peaks were enriched in motifs previously associated with mRNAs cross-linked to FMRP in vivo, independently linking the ribosomes in the granule fraction to the ribosomes associated with FMRP in the cell. The data supports a model in which specific sequences in mRNAs act to stall ribosomes during translation elongation in neurons.SIGNIFICANCE STATEMENT Neurons send mRNAs to synapses in RNA granules, where they are not translated until an appropriate stimulus is given. Here, we characterize a granule fraction obtained from sucrose gradients and show that polysomes in this fraction are stalled on consensus sequences in a specific state of translational arrest with extended ribosome-protected fragments. This finding greatly increases our understanding of how neurons use specialized mechanisms to regulate translation and suggests that many studies on neuronal translation may need to be re-evaluated to include the large fraction of neuronal polysomes found in the pellet of sucrose gradients used to isolate polysomes.
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Affiliation(s)
- Mina N Anadolu
- Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, Quebec H3A 2B4, Canada
| | - Jingyu Sun
- Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec H3A 0C7, Canada
- Centre for Structural Biology, McGill University, Montreal, Quebec H3G 0B1, Canada
| | - Senthilkumar Kailasam
- Canadian Centre for Computational Genomics, McGill University, Montreal, Quebec H3A 0G1, Canada
| | - Kleanthi Chalkiadaki
- Biomedical Research Institute, Foundation for Research and Technology-Hellas, 45110 Ioannina, Greece
| | - Konstanze Krimbacher
- Department of Pharmacology, Medical University of Innsbruck, Innsbruck Austria Division of Biomedical Research, A-6020 Innsbruck, Austria
| | - Jewel T-Y Li
- Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, Quebec H3A 2B4, Canada
| | - Teodora Markova
- Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, Quebec H3A 2B4, Canada
| | - Seyed M Jafarnejad
- Patrick G, Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, Northern Ireland BT9 7AE, United Kingdom
| | - Francois Lefebvre
- Canadian Centre for Computational Genomics, McGill University, Montreal, Quebec H3A 0G1, Canada
| | - Joaquin Ortega
- Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec H3A 0C7, Canada
- Centre for Structural Biology, McGill University, Montreal, Quebec H3G 0B1, Canada
| | - Christos G Gkogkas
- Biomedical Research Institute, Foundation for Research and Technology-Hellas, 45110 Ioannina, Greece
| | - Wayne S Sossin
- Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, Quebec H3A 2B4, Canada
- Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec H3A 0C7, Canada
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Pappa CP, Torofias S, Triantafyllidis KS. Sub-Micro Organosolv Lignin as Bio-Based Epoxy Polymer Component: A Sustainable Curing Agent and Additive. ChemSusChem 2023:e202300076. [PMID: 36912587 DOI: 10.1002/cssc.202300076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 03/11/2023] [Accepted: 03/13/2023] [Indexed: 05/03/2023]
Abstract
Sub-micro organosolv lignin (OBs) isolated from beechwood biomass, comprising of sub-micro sized particles (570 nm) with low molecular weight and dispersity and relatively high total phenolic -OH content, is utilized for the production of bio-based epoxy polymer composites. OBs lignin is incorporated into the glassy epoxy system based on diglycidyl ether of bisphenol A (DGEBA) and aliphatic polyoxypropylene α,ω-diamine (Jeffamine D-230), being utilized both as a curing agent, partially replacing D-230, and as an additive, substituting part of both petroleum-derived components. Up to 12 wt % replacement of D-230 by OBs lignin is achieved, whereas approximately 17 wt % of OBs effectively replaces the conventional epoxy polymer. The incorporation of OBs lignin in the polymeric matrix is achieved without the use of any solvent or previous functionalization. Enhanced properties are obtained, with substantial increases in tensile strength, strain, stiffness, glass transition temperature, antioxidant activity, and resistance to solvents.
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Affiliation(s)
- Christina P Pappa
- Department of Chemistry, Aristotle University of Thessaloniki, Thessaloniki, 54124, Greece
| | - Stylianos Torofias
- Department of Chemistry, Aristotle University of Thessaloniki, Thessaloniki, 54124, Greece
| | - Konstantinos S Triantafyllidis
- Department of Chemistry, Aristotle University of Thessaloniki, Thessaloniki, 54124, Greece
- Center for Interdisciplinary Research and Innovation (CIRI-AUTH), Thessaloniki, 57001, Greece
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Papadopoulou ES, Bachtsevani E, Papazlatani CV, Rousidou C, Brouziotis A, Lampronikou E, Tsiknia M, Vasileiadis S, Ipsilantis I, Menkissoglu-Spiroudi U, Ehaliotis C, Philippot L, Nicol GW, Karpouzas DG. The Effects of Quinone Imine, a New Potent Nitrification Inhibitor, Dicyandiamide, and Nitrapyrin on Target and Off-Target Soil Microbiota. Microbiol Spectr 2022; 10:e0240321. [PMID: 35856708 PMCID: PMC9431271 DOI: 10.1128/spectrum.02403-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 06/24/2022] [Indexed: 11/26/2022] Open
Abstract
Dicyandiamide (DCD) and nitrapyrin (NP) are nitrification inhibitors (NIs) used in agriculture for over 40 years. Recently, ethoxyquin (EQ) was proposed as a novel potential NI, acting through its derivative quinone imine (QI). Still, the specific activity of these NIs on the different groups of ammonia-oxidizing microorganisms (AOM), and mostly their effects on other soil microbiota remain unknown. We determined the impact of QI, and comparatively of DCD and NP, applied at two doses (regular versus high), on the function, diversity, and dynamics of target (AOM), functionally associated (nitrite-oxidizing bacteria-NOB), and off-target prokaryotic and fungal communities in two soils mainly differing in pH (5.4 versus 7.9). QI was equally effective to DCD but more effective than NP in inhibiting nitrification in the acidic soil, while in the alkaline soil QI was less efficient than DCD and NP. This was attributed to the higher activity of QI toward AOA prevailing in the acidic soil. All NIs induced significant effects on the composition of the AOB community in both soils, unlike AOA, which were less responsive. Beyond on-target effects, we noted an inhibitory effect of all NIs on the abundance of NOB in the alkaline soil, with Nitrobacter being more sensitive than Nitrospira. QI, unlike the other NIs, induced significant changes in the composition of the bacterial and fungal communities in both soils. Our findings have serious implications for the efficiency and future use of NIs on agriculture and provide unprecedented evidence for the potential off-target effects of NIs on soil microbiota. IMPORTANCE NIs could improve N use efficiency and decelerate N cycling. Still, we know little about their activity on the distinct AOM groups and about their effects on off-target soil microorganisms. Here, we studied the behavior of a new potent NI, QI, compared to established NIs. We show that (i) the variable efficacy of NIs across soils with different pH reflects differences in the inherent specific activity of the NIs to AOA and AOB; (ii) beyond AOM, NIs exhibit negative effects on other nitrifiers, like NOB; (iii) QI was the sole NI that significantly affected prokaryotic and fungal diversity. Our findings (i) highlight the need for novel NI strategies that consider the variable sensitivity of AOM groups to the different NIs (ii) identify QI as a potent AOA inhibitor, and (iii) stress the need for monitoring NIs' impact on off-target soil microorganisms to ensure sustainable N fertilizers use and soil ecosystem functioning.
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Affiliation(s)
- Evangelia S. Papadopoulou
- Laboratory of Plant and Environmental Biotechnology, Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
- Laboratory of Environmental Microbiology, Department of Environmental Sciences, University of Thessaly, Larissa, Greece
| | - Eleftheria Bachtsevani
- Laboratory of Plant and Environmental Biotechnology, Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
| | - Christina V. Papazlatani
- Laboratory of Plant and Environmental Biotechnology, Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
| | - Constantina Rousidou
- Laboratory of Plant and Environmental Biotechnology, Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
| | - Antonios Brouziotis
- Laboratory of Plant and Environmental Biotechnology, Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
| | - Eleni Lampronikou
- Laboratory of Plant and Environmental Biotechnology, Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
| | - Myrto Tsiknia
- Laboratory of Soils and Agricultural Chemistry, Agricultural University of Athens, Athens, Greece
| | - Sotirios Vasileiadis
- Laboratory of Plant and Environmental Biotechnology, Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
| | - Ioannis Ipsilantis
- Laboratory of Soil Sciences, School of Agriculture, Forestry and Environment, Faculty of Agriculture, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Urania Menkissoglu-Spiroudi
- Pesticide Science Laboratory, School of Agriculture, Forestry and Environment, Faculty of Agriculture, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Constantinos Ehaliotis
- Laboratory of Soils and Agricultural Chemistry, Agricultural University of Athens, Athens, Greece
| | - Laurent Philippot
- Université Bourgogne Franche-Comté, INRAE, AgroSup Dijon, Agroécologie, Dijon, France
| | - Graeme W. Nicol
- Environmental Microbial Genomics Group, Laboratoire Ampère, École Centrale de Lyon, CNRS UMR 5005, Université de Lyon, Lyon, France
| | - Dimitrios G. Karpouzas
- Laboratory of Plant and Environmental Biotechnology, Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
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Pezoulas VC, Kourou KD, Kalatzis F, Exarchos TP, Zampeli E, Gandolfo S, Goules A, Baldini C, Skopouli F, De Vita S, Tzioufas AG, Fotiadis DI. Overcoming the Barriers That Obscure the Interlinking and Analysis of Clinical Data Through Harmonization and Incremental Learning. IEEE Open J Eng Med Biol 2020; 1:83-90. [PMID: 35402941 PMCID: PMC8940202 DOI: 10.1109/ojemb.2020.2981258] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Revised: 02/23/2020] [Accepted: 03/09/2020] [Indexed: 11/22/2022] Open
Abstract
Goal: To present a framework for data sharing, curation, harmonization and federated data analytics to solve open issues in healthcare, such as, the development of robust disease prediction models. Methods: Data curation is applied to remove data inconsistencies. Lexical and semantic matching methods are used to align the structure of the heterogeneous, curated cohort data along with incremental learning algorithms including class imbalance handling and hyperparameter optimization to enable the development of disease prediction models. Results: The applicability of the framework is demonstrated in a case study of primary Sjögren's Syndrome, yielding harmonized data with increased quality and more than 85% agreement, along with lymphoma prediction models with more than 80% sensitivity and specificity. Conclusions: The framework provides data quality, harmonization and analytics workflows that can enhance the statistical power of heterogeneous clinical data and enables the development of robust models for disease prediction.
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Affiliation(s)
- Vasileios C Pezoulas
- Unit of Medical Technology and Intelligent Information Systems, Department of Materials Science and EngineeringUniversity of Ioannina GR45110 Ioannina Greece
| | - Konstantina D Kourou
- Unit of Medical Technology and Intelligent Information Systems, Department of Materials Science and EngineeringUniversity of Ioannina GR45110 Ioannina Greece
- Department of Biological Applications and TechnologyUniversity of Ioannina GR45110 Ioannina Greece
| | - Fanis Kalatzis
- Unit of Medical Technology and Intelligent Information Systems, Department of Materials Science and EngineeringUniversity of Ioannina GR45110 Ioannina Greece
| | - Themis P Exarchos
- Department of InformaticsIonian University GR49100 Corfu Greece
- Unit of Medical Technology and Intelligent Information Systems, Department of Materials Science and EngineeringUniversity of Ioannina GR45100 Ioannina Greece
| | - Evi Zampeli
- Institute for Systemic Autoimmune and Neurological Diseases GR11743 Athens Greece
| | - Saviana Gandolfo
- Clinic of Rheumatology, Department of Medical and Biological SciencesUdine University IT33100 Udine Italy
| | - Andreas Goules
- Department of Pathophysiology, School of MedicineUniversity of Athens GR15772 Athens Greece
| | - Chiara Baldini
- Department of Clinical and Experimental MedicineUniversity of Pisa Pisa IT56126 Italy
| | - Fotini Skopouli
- Department of Internal Medicine and Clinical ImmunologyEuroclinic Hospital GR11521 Athens Greece
| | - Salvatore De Vita
- Clinic of Rheumatology, Department of Medical and Biological SciencesUdine University IT33100 Udine Italy
| | - Athanasios G Tzioufas
- Department of Pathophysiology, School of MedicineUniversity of Athens GR15772 Athens Greece
| | - Dimitrios I Fotiadis
- Unit of Medical Technology and Intelligent Information Systems, Department of Materials Science and EngineeringUniversity of Ioannina GR45110 Ioannina Greece
- Department of Biomedical ResearchFORTH-IMBB GR45110 Ioannina Greece
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