1
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Henaff C, Siepmann J, Siepmann F, Danède F, Avettand-Fènoël MN, Vérin J, Fadel A, Willart JF. Exploration of the physical states of riboflavin (free base) by mechanical milling. Int J Pharm 2023; 645:123416. [PMID: 37716485 DOI: 10.1016/j.ijpharm.2023.123416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 09/11/2023] [Accepted: 09/12/2023] [Indexed: 09/18/2023]
Abstract
Amorphous riboflavin (free base) could be produced for the first time via high energy ball milling of a commercial crystalline form (Form I). Importantly, this solid state amorphization process allowed to circumvent chemical degradation occurring during melting as well as the lack of suitable solvents, which are required for amorphization via spray- or freeze-drying. The amorphous state of riboflavin was thoroughly characterized, revealing a complex recrystallization pattern upon heating, involving two enantiotropic polymorphic forms (II and III) and a dihydrate. The glass transition temperature (Tg) and heat capacity (Cp) jump of the amorphous form were determined as 144 °C and 0.68 J/g/°C. Moreover, the relative physical stability of the different physical states has been elucidated, e.g., at room temperature: I > II > III. The following rank order was observed for the dissolution rates in water at 37 °C during the first 4 h: amorphous > III ≈ II > I. Afterwards, a dihydrate crystallized from the solutions of amorphous and metastable crystalline riboflavin forms, the solubility of which was well above the solubility of the stable FormI.
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Affiliation(s)
- C Henaff
- Univ. Lille, CNRS, INRAE, Centrale Lille, UMR 8207 UMET - Unité Matériaux et Transformations F-59000 Lille, France; Univ. Lille, Inserm, CHU Lille, U1008, F-59000 Lille, France
| | - J Siepmann
- Univ. Lille, Inserm, CHU Lille, U1008, F-59000 Lille, France
| | - F Siepmann
- Univ. Lille, Inserm, CHU Lille, U1008, F-59000 Lille, France
| | - F Danède
- Univ. Lille, CNRS, INRAE, Centrale Lille, UMR 8207 UMET - Unité Matériaux et Transformations F-59000 Lille, France
| | - M-N Avettand-Fènoël
- Univ. Lille, CNRS, INRAE, Centrale Lille, UMR 8207 UMET - Unité Matériaux et Transformations F-59000 Lille, France
| | - J Vérin
- Univ. Lille, Inserm, CHU Lille, U1008, F-59000 Lille, France
| | - A Fadel
- Univ. Lille, CNRS, INRAE, Centrale Lille, Univ. Artois, FR 2638 - IMEC - Institut Michel-Eugène Chevreul, F-59000 Lille, France
| | - J-F Willart
- Univ. Lille, CNRS, INRAE, Centrale Lille, UMR 8207 UMET - Unité Matériaux et Transformations F-59000 Lille, France.
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2
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Castro IG, Shortill SP, Dziurdzik SK, Cadou A, Ganesan S, Valenti R, David Y, Davey M, Mattes C, Thomas FB, Avraham RE, Meyer H, Fadel A, Fenech EJ, Ernst R, Zaremberg V, Levine TP, Stefan C, Conibear E, Schuldiner M. Systematic analysis of membrane contact sites in Saccharomyces cerevisiae uncovers modulators of cellular lipid distribution. eLife 2022; 11:74602. [DOI: 10.7554/elife.74602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 10/19/2022] [Indexed: 11/11/2022] Open
Abstract
Actively maintained close appositions between organelle membranes, also known as contact sites, enable the efficient transfer of biomolecules between cellular compartments. Several such sites have been described as well as their tethering machineries. Despite these advances we are still far from a comprehensive understanding of the function and regulation of most contact sites. To systematically characterize contact site proteomes, we established a high-throughput screening approach in Saccharomyces cerevisiae based on co-localization imaging. We imaged split fluorescence reporters for six different contact sites, several of which are poorly characterized, on the background of 1165 strains expressing a mCherry-tagged yeast protein that has a cellular punctate distribution (a hallmark of contact sites), under regulation of the strong TEF2 promoter. By scoring both co-localization events and effects on reporter size and abundance, we discovered over 100 new potential contact site residents and effectors in yeast. Focusing on several of the newly identified residents, we identified three homologs of Vps13 and Atg2 that are residents of multiple contact sites. These proteins share their lipid transport domain, thus expanding this family of lipid transporters. Analysis of another candidate, Ypr097w, which we now call Lec1 (Lipid-droplet Ergosterol Cortex 1), revealed that this previously uncharacterized protein dynamically shifts between lipid droplets and the cell cortex, and plays a role in regulation of ergosterol distribution in the cell. Overall, our analysis expands the universe of contact site residents and effectors and creates a rich database to mine for new functions, tethers, and regulators.
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Affiliation(s)
| | - Shawn P Shortill
- Centre for Molecular Medicine and Therapeutics, British Columbia Children’s Hospital Research Institute, University of British Columbia
- Department of Medical Genetics, University of British Columbia
| | - Samantha Katarzyna Dziurdzik
- Centre for Molecular Medicine and Therapeutics, British Columbia Children’s Hospital Research Institute, University of British Columbia
- Department of Medical Genetics, University of British Columbia
| | - Angela Cadou
- Laboratory for Molecular Cell Biology, University College London
| | | | - Rosario Valenti
- Department of Molecular Genetics, Weizmann Institute of Science
| | - Yotam David
- Department of Molecular Genetics, Weizmann Institute of Science
| | - Michael Davey
- Centre for Molecular Medicine and Therapeutics, British Columbia Children’s Hospital Research Institute, University of British Columbia
| | - Carsten Mattes
- Medical Biochemistry and Molecular Biology, PZMS, Medical Faculty, Saarland University
| | - Ffion B Thomas
- Laboratory for Molecular Cell Biology, University College London
| | | | - Hadar Meyer
- Department of Molecular Genetics, Weizmann Institute of Science
| | - Amir Fadel
- Department of Molecular Genetics, Weizmann Institute of Science
| | - Emma J Fenech
- Department of Molecular Genetics, Weizmann Institute of Science
| | - Robert Ernst
- Medical Biochemistry and Molecular Biology, PZMS, Medical Faculty, Saarland University
| | | | - Tim P Levine
- UCL Institute of Ophthalmology, University College London
| | | | - Elizabeth Conibear
- Centre for Molecular Medicine and Therapeutics, British Columbia Children’s Hospital Research Institute, University of British Columbia
- Department of Medical Genetics, University of British Columbia
| | - Maya Schuldiner
- Department of Molecular Genetics, Weizmann Institute of Science
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3
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Yifrach E, Holbrook-Smith D, Bürgi J, Othman A, Eisenstein M, van Roermund CW, Visser W, Tirosh A, Rudowitz M, Bibi C, Galor S, Weill U, Fadel A, Peleg Y, Erdmann R, Waterham HR, Wanders RJA, Wilmanns M, Zamboni N, Schuldiner M, Zalckvar E. Systematic multi-level analysis of an organelle proteome reveals new peroxisomal functions. Mol Syst Biol 2022; 18:e11186. [PMID: 36164978 PMCID: PMC9513677 DOI: 10.15252/msb.202211186] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 08/29/2022] [Accepted: 09/05/2022] [Indexed: 11/18/2022] Open
Abstract
Seventy years following the discovery of peroxisomes, their complete proteome, the peroxi‐ome, remains undefined. Uncovering the peroxi‐ome is crucial for understanding peroxisomal activities and cellular metabolism. We used high‐content microscopy to uncover peroxisomal proteins in the model eukaryote – Saccharomyces cerevisiae. This strategy enabled us to expand the known peroxi‐ome by ~40% and paved the way for performing systematic, whole‐organellar proteome assays. By characterizing the sub‐organellar localization and protein targeting dependencies into the organelle, we unveiled non‐canonical targeting routes. Metabolomic analysis of the peroxi‐ome revealed the role of several newly identified resident enzymes. Importantly, we found a regulatory role of peroxisomes during gluconeogenesis, which is fundamental for understanding cellular metabolism. With the current recognition that peroxisomes play a crucial part in organismal physiology, our approach lays the foundation for deep characterization of peroxisome function in health and disease.
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Affiliation(s)
- Eden Yifrach
- Department of Molecular Genetics, The Weizmann Institute of Science, Rehovot, Israel
| | | | - Jérôme Bürgi
- Hamburg Unit c/o DESY, European Molecular Biology Laboratory (EMBL), Hamburg, Germany
| | - Alaa Othman
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Miriam Eisenstein
- Department of Molecular Genetics, The Weizmann Institute of Science, Rehovot, Israel
| | - Carlo Wt van Roermund
- Laboratory Genetic Metabolic Diseases, Department of Clinical Chemistry, Amsterdam Gastroenterology, Endocrinology & Metabolism, Amsterdam University Medical Centers - Location AMC, Amsterdam, The Netherlands
| | - Wouter Visser
- Laboratory Genetic Metabolic Diseases, Department of Clinical Chemistry, Amsterdam Gastroenterology, Endocrinology & Metabolism, Amsterdam University Medical Centers - Location AMC, Amsterdam, The Netherlands
| | - Asa Tirosh
- Life Sciences Core Facilities (LSCF), The Weizmann Institute of Science, Rehovot, Israel
| | - Markus Rudowitz
- Department of Systems Biochemistry, Institute of Biochemistry and Pathobiochemistry, Ruhr-University Bochum, Bochum, Germany
| | - Chen Bibi
- Department of Molecular Genetics, The Weizmann Institute of Science, Rehovot, Israel
| | - Shahar Galor
- Department of Molecular Genetics, The Weizmann Institute of Science, Rehovot, Israel
| | - Uri Weill
- Department of Molecular Genetics, The Weizmann Institute of Science, Rehovot, Israel
| | - Amir Fadel
- Department of Molecular Genetics, The Weizmann Institute of Science, Rehovot, Israel
| | - Yoav Peleg
- Life Sciences Core Facilities (LSCF), The Weizmann Institute of Science, Rehovot, Israel
| | - Ralf Erdmann
- Department of Systems Biochemistry, Institute of Biochemistry and Pathobiochemistry, Ruhr-University Bochum, Bochum, Germany
| | - Hans R Waterham
- Laboratory Genetic Metabolic Diseases, Department of Clinical Chemistry, Amsterdam Gastroenterology, Endocrinology & Metabolism, Amsterdam University Medical Centers - Location AMC, Amsterdam, The Netherlands
| | - Ronald J A Wanders
- Laboratory Genetic Metabolic Diseases, Department of Clinical Chemistry, Amsterdam Gastroenterology, Endocrinology & Metabolism, Amsterdam University Medical Centers - Location AMC, Amsterdam, The Netherlands
| | - Matthias Wilmanns
- Hamburg Unit c/o DESY, European Molecular Biology Laboratory (EMBL), Hamburg, Germany.,University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Nicola Zamboni
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Maya Schuldiner
- Department of Molecular Genetics, The Weizmann Institute of Science, Rehovot, Israel
| | - Einat Zalckvar
- Department of Molecular Genetics, The Weizmann Institute of Science, Rehovot, Israel
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4
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Dahan N, Bykov YS, Boydston EA, Fadel A, Gazi Z, Hochberg-Laufer H, Martenson J, Denic V, Shav-Tal Y, Weissman JS, Aviram N, Zalckvar E, Schuldiner M. Peroxisome function relies on organelle-associated mRNA translation. Sci Adv 2022; 8:eabk2141. [PMID: 35020435 PMCID: PMC8754406 DOI: 10.1126/sciadv.abk2141] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 11/18/2021] [Indexed: 05/26/2023]
Abstract
Crucial metabolic functions of peroxisomes rely on a variety of peroxisomal membrane proteins (PMPs). While mRNA transcripts of PMPs were shown to be colocalized with peroxisomes, the process by which PMPs efficiently couple translation with targeting to the peroxisomal membrane remained elusive. Here, we combine quantitative electron microscopy with proximity-specific ribosome profiling and reveal that translation of specific PMPs occurs on the surface of peroxisomes in the yeast Saccharomyces cerevisiae. This places peroxisomes alongside chloroplasts, mitochondria, and the endoplasmic reticulum as organelles that use localized translation for ensuring correct insertion of hydrophobic proteins into their membranes. Moreover, the correct targeting of these transcripts to peroxisomes is crucial for peroxisomal and cellular function, emphasizing the importance of localized translation for cellular physiology.
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Affiliation(s)
- Noa Dahan
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Yury S. Bykov
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Elizabeth A. Boydston
- Department of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, California Institute for Quantitative Biosciences, Center for RNA Systems Biology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Amir Fadel
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Zohar Gazi
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Hodaya Hochberg-Laufer
- The Mina and Everard Goodman Faculty of Life Sciences, The Bar-Ilan Institute of Nanotechnology and Advanced Materials (BINA), Bar-Ilan University, Ramat Gan 5290002, Israel
| | - James Martenson
- Department of Molecular and Cellular Biology, Harvard University, 52 Oxford St., Cambridge, MA 02138, USA
| | - Vlad Denic
- Department of Molecular and Cellular Biology, Harvard University, 52 Oxford St., Cambridge, MA 02138, USA
| | - Yaron Shav-Tal
- The Mina and Everard Goodman Faculty of Life Sciences, The Bar-Ilan Institute of Nanotechnology and Advanced Materials (BINA), Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Jonathan S. Weissman
- Department of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, California Institute for Quantitative Biosciences, Center for RNA Systems Biology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Naama Aviram
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Einat Zalckvar
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Maya Schuldiner
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
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5
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Eisenberg-Bord M, Zung N, Collado J, Drwesh L, Fenech EJ, Fadel A, Dezorella N, Bykov YS, Rapaport D, Fernandez-Busnadiego R, Schuldiner M. Cnm1 mediates nucleus-mitochondria contact site formation in response to phospholipid levels. J Cell Biol 2021; 220:212719. [PMID: 34694322 PMCID: PMC8548916 DOI: 10.1083/jcb.202104100] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 08/12/2021] [Accepted: 09/21/2021] [Indexed: 12/12/2022] Open
Abstract
Mitochondrial functions are tightly regulated by nuclear activity, requiring extensive communication between these organelles. One way by which organelles can communicate is through contact sites, areas of close apposition held together by tethering molecules. While many contacts have been characterized in yeast, the contact between the nucleus and mitochondria was not previously identified. Using fluorescence and electron microscopy in S. cerevisiae, we demonstrate specific areas of contact between the two organelles. Using a high-throughput screen, we uncover a role for the uncharacterized protein Ybr063c, which we have named Cnm1 (contact nucleus mitochondria 1), as a molecular tether on the nuclear membrane. We show that Cnm1 mediates contact by interacting with Tom70 on mitochondria. Moreover, Cnm1 abundance is regulated by phosphatidylcholine, enabling the coupling of phospholipid homeostasis with contact extent. The discovery of a molecular mechanism that allows mitochondrial crosstalk with the nucleus sets the ground for better understanding of mitochondrial functions in health and disease.
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Affiliation(s)
| | - Naama Zung
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Javier Collado
- Institute for Neuropathology, Georg August Universität Göttingen, Göttingen, Germany.,Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells," University of Göttingen, Göttingen, Germany
| | - Layla Drwesh
- Interfaculty Institute of Biochemistry, University of Tuebingen, Tuebingen, Germany
| | - Emma J Fenech
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Amir Fadel
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Nili Dezorella
- Electron Microscopy Unit, Chemical Research Support, Weizmann Institute of Science, Rehovot, Israel
| | - Yury S Bykov
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Doron Rapaport
- Interfaculty Institute of Biochemistry, University of Tuebingen, Tuebingen, Germany
| | - Ruben Fernandez-Busnadiego
- Institute for Neuropathology, Georg August Universität Göttingen, Göttingen, Germany.,Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells," University of Göttingen, Göttingen, Germany
| | - Maya Schuldiner
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
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6
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Lemus L, Matić Z, Gal L, Fadel A, Schuldiner M, Goder V. Post-ER degradation of misfolded GPI-anchored proteins is linked with microautophagy. Curr Biol 2021; 31:4025-4037.e5. [PMID: 34314677 DOI: 10.1016/j.cub.2021.06.078] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 06/07/2021] [Accepted: 06/25/2021] [Indexed: 01/08/2023]
Abstract
Glycosylphosphatidylinositol-anchored proteins (GPI-APs) are membrane-conjugated cell-surface proteins with diverse structural, developmental, and signaling functions and clinical relevance. Typically, after biosynthesis and attachment to the preassembled GPI anchor, GPI-APs rapidly leave the endoplasmic reticulum (ER) and rely on post-ER quality control. Terminally misfolded GPI-APs end up inside the vacuole/lysosome for degradation, but their trafficking itinerary to this organelle and the processes linked to their uptake by the vacuole/lysosome remain uncharacterized. In a yeast mutant that is lacking Pep4, a key vacuolar protease, several misfolded model GPI-APs accumulated in the vacuolar membrane. In the same mutant, macroautophagy and the multi-vesicular body (MVB) pathway were intact, hinting at a hitherto-unknown trafficking pathway for the degradation of misfolded GPI-APs. To unravel it, we used a genome-wide screen coupled to high-throughput fluorescence microscopy and followed the fate of the misfolded GPI-AP: Gas1∗. We found that components of the early secretory and endocytic pathways are involved in its targeting to the vacuole and that vacuolar transporter chaperones (VTCs), with roles in microautophagy, negatively affect the vacuolar uptake of Gas1∗. In support, we demonstrate that Gas1∗ internalizes from vacuolar membranes into membrane-bound intravacuolar vesicles prior to degradation. Our data link post-ER degradation with microautophagy.
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Affiliation(s)
- Leticia Lemus
- Department of Genetics, University of Seville, Ave Reina Mercedes, 6, 41012 Seville, Spain.
| | - Zrinka Matić
- Department of Genetics, University of Seville, Ave Reina Mercedes, 6, 41012 Seville, Spain
| | - Lihi Gal
- Department of Molecular Genetics, Meyer Bldg. Room 122, Weizmann Institute of Sciences, 76100 Rehovot, Israel
| | - Amir Fadel
- Department of Molecular Genetics, Meyer Bldg. Room 122, Weizmann Institute of Sciences, 76100 Rehovot, Israel
| | - Maya Schuldiner
- Department of Molecular Genetics, Meyer Bldg. Room 122, Weizmann Institute of Sciences, 76100 Rehovot, Israel
| | - Veit Goder
- Department of Genetics, University of Seville, Ave Reina Mercedes, 6, 41012 Seville, Spain.
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7
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Khelissa S, Gharsallaoui A, Fadel A, Barras A, Jama C, Jbilou F, Chihib NE. Microencapsulation of benzalkonium chloride enhanced its antibacterial and antibiofilm activities against Listeria monocytogenes and Escherichia coli. J Appl Microbiol 2021; 131:1136-1146. [PMID: 33484234 DOI: 10.1111/jam.15010] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 01/11/2021] [Accepted: 01/18/2021] [Indexed: 11/26/2022]
Abstract
AIMS In this study, benzalkonium chloride (BAC) microcapsules were developed for surface disinfection purpose and were evaluated against Listeria monocytogenes and Escherichia coli biofilms. METHODS AND RESULTS Microcapsules were prepared with two different strategies: uncomplexed BAC-microcapsules (UBM) containing BAC and maltodextrins, and complexed BAC-microcapsules (CBM) containing BAC complexed by pectin and maltodextrins. The minimum inhibitory concentrations (MICs) of free and microencapsulated BAC were investigated against two food pathogens: L. monocytogenes and E. coli. The antibiofilm activities of UBM and CBM against L. monocytogenes and E. coli biofilms formed on stainless steel at 37°C were evaluated and compared to BAC used under its free form. MICs of encapsulated BAC were up to fourfold lower than those of free BAC. The UBM and CBM showed higher antibiofilm effect when compared to the free BAC. CONCLUSIONS Overall, results demonstrated that microencapsulation enhanced the antibacterial activity of BAC against L. monocytogenes and E. coli biofilms. SIGNIFICANCE AND IMPACT OF THE STUDY The application of such BAC microcapsule-based delivery systems can improve surface disinfection procedures and reduce the required BAC concentrations and the related cytotoxicity of this antimicrobial compound.
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Affiliation(s)
- S Khelissa
- Univ Lille, CNRS, INRAE, Centrale Lille, UMR 8207 - UMET - Unité Matériaux et Transformations, Lille, France
| | - A Gharsallaoui
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, LAGEPP UMR 5007, Villeurbanne, France
| | - A Fadel
- Univ Lille, CNRS, INRAE, Centrale Lille, Université d'Artois, FR 2638 - IMEC -Institut Michel-Eugène Chevreul, Lille, France
| | - A Barras
- Univ Lille, CNRS, Centrale Lille Univ. Polytechnique Hauts-de-France, UMR 8520-IEMN, Lille, France
| | - C Jama
- Univ Lille, CNRS, INRAE, Centrale Lille, UMR 8207 - UMET - Unité Matériaux et Transformations, Lille, France
| | | | - N-E Chihib
- Univ Lille, CNRS, INRAE, Centrale Lille, UMR 8207 - UMET - Unité Matériaux et Transformations, Lille, France
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8
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Schummer A, Maier R, Gabay-Maskit S, Hansen T, Mühlhäuser WWD, Suppanz I, Fadel A, Schuldiner M, Girzalsky W, Oeljeklaus S, Zalckvar E, Erdmann R, Warscheid B. Pex14p Phosphorylation Modulates Import of Citrate Synthase 2 Into Peroxisomes in Saccharomyces cerevisiae. Front Cell Dev Biol 2020; 8:549451. [PMID: 33042991 PMCID: PMC7522779 DOI: 10.3389/fcell.2020.549451] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 08/25/2020] [Indexed: 12/16/2022] Open
Abstract
The peroxisomal biogenesis factor Pex14p is an essential component of the peroxisomal matrix protein import machinery. Together with Pex13p and Pex17p, it is part of the membrane-associated peroxisomal docking complex in yeast, facilitating the binding of cargo-loaded receptor proteins for translocation of cargo proteins into the peroxisome. Furthermore, Pex14p is part of peroxisomal import pores. The central role of Pex14p in peroxisomal matrix protein import processes renders it an obvious target for regulatory mechanisms such as protein phosphorylation. To explore this possibility, we examined the state of Pex14p phosphorylation in Saccharomyces cerevisiae. Phos-tag-SDS-PAGE of Pex14p affinity-purified from solubilized membranes revealed Pex14p as multi-phosphorylated protein. Using mass spectrometry, we identified 16 phosphorylation sites, with phosphorylation hot spots located in the N- and C-terminal regions of Pex14p. Analysis of phosphomimicking and non-phosphorylatable variants of Pex14p revealed a decreased import of GFP carrying a peroxisomal targeting signal type 1, indicating a functional relevance of Pex14p phosphorylation in peroxisomal matrix protein import. We show that this effect can be ascribed to the phosphomimicking mutation at serine 266 of Pex14p (Pex14p-S266D). We further screened the subcellular distribution of 23 native GFP-tagged peroxisomal matrix proteins by high-content fluorescence microscopy. Only Cit2p, the peroxisomal isoform of citrate synthase, was affected in the Pex14p-S266D mutant, showing increased cytosolic localization. Cit2p is part of the glyoxylate cycle, which is required for the production of essential carbohydrates when yeast is grown on non-fermentable carbon sources. Pex14p-S266 phosphosite mutants showed reversed growth phenotypes in oleic acid and ethanol with acetyl-CoA formed in peroxisomes and the cytosol, respectively. Overexpression of Cit2p rescued the growth phenotype of yeast cells expressing Pex14p-S266D in oleic acid. Our data indicate that phosphorylation of Pex14p at S266 provides a mechanism for controlling the peroxisomal import of Cit2p, which helps S. cerevisiae cells to adjust their carbohydrate metabolism according to the nutritional conditions.
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Affiliation(s)
- Andreas Schummer
- Faculty of Biology, Biochemistry and Functional Proteomics, Institute of Biology II, University of Freiburg, Freiburg, Germany
| | - Renate Maier
- Faculty of Biology, Biochemistry and Functional Proteomics, Institute of Biology II, University of Freiburg, Freiburg, Germany
| | - Shiran Gabay-Maskit
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Tobias Hansen
- Faculty of Medicine, System Biochemistry, Institute of Biochemistry and Pathobiochemistry, Ruhr-University Bochum, Bochum, Germany
| | - Wignand W D Mühlhäuser
- Faculty of Biology, Biochemistry and Functional Proteomics, Institute of Biology II, University of Freiburg, Freiburg, Germany
| | - Ida Suppanz
- Faculty of Biology, Biochemistry and Functional Proteomics, Institute of Biology II, University of Freiburg, Freiburg, Germany
| | - Amir Fadel
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Maya Schuldiner
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Wolfgang Girzalsky
- Faculty of Medicine, System Biochemistry, Institute of Biochemistry and Pathobiochemistry, Ruhr-University Bochum, Bochum, Germany
| | - Silke Oeljeklaus
- Faculty of Biology, Biochemistry and Functional Proteomics, Institute of Biology II, University of Freiburg, Freiburg, Germany.,Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
| | - Einat Zalckvar
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Ralf Erdmann
- Faculty of Medicine, System Biochemistry, Institute of Biochemistry and Pathobiochemistry, Ruhr-University Bochum, Bochum, Germany
| | - Bettina Warscheid
- Faculty of Biology, Biochemistry and Functional Proteomics, Institute of Biology II, University of Freiburg, Freiburg, Germany.,Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
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9
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Weill U, Cohen N, Fadel A, Ben-Dor S, Schuldiner M. Protein Topology Prediction Algorithms Systematically Investigated in the Yeast Saccharomyces cerevisiae. Bioessays 2019; 41:e1800252. [PMID: 31297843 DOI: 10.1002/bies.201800252] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2018] [Revised: 05/05/2019] [Indexed: 11/09/2022]
Abstract
Membrane proteins perform a variety of functions, all crucially dependent on their orientation in the membrane. However, neither the exact number of transmembrane domains (TMDs) nor the topology of most proteins have been experimentally determined. Due to this, most scientists rely primarily on prediction algorithms to determine topology and TMD assignments. Since these can give contradictory results, single-algorithm-based predictions are unreliable. To map the extent of potential misanalysis, the predictions of nine algorithms on the yeast proteome are compared and it is found that they have little agreement when predicting TMD number and termini orientation. To view all predictions in parallel, a webpage called TopologYeast: http://www.weizmann.ac.il/molgen/TopologYeast was created. Each algorithm is compared with experimental data and a poor agreement is found. The analysis suggests that more systematic data on protein topology are required to increase the training sets for prediction algorithms and to have accurate knowledge of membrane protein topology.
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Affiliation(s)
- Uri Weill
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Nir Cohen
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Amir Fadel
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Shifra Ben-Dor
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Maya Schuldiner
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 7610001, Israel
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Woldemichael AK, Alwan F, Hassen A, Kazibwe F, Fadel A. P6.023 Cross - Border HIV & AIDS Intervention Programme in Seven East African Countries (2008 – 2012). Br J Vener Dis 2013. [DOI: 10.1136/sextrans-2013-051184.1177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Bdeir, Abolfotouh, Mukhtar A, Omer H, Ali D, Khateeb MA, Tayyeb AE, Fadel A, Farah I, Odeh R, Rabai R, Tayiem, Al Dossari H. SHA 058. Predictors of in-hospital mortality in patients with heart failure at King Abdulaziz Medical City Cardiac Center – Riyadh, Saudi Arabia. J Saudi Heart Assoc 2011. [DOI: 10.1016/j.jsha.2011.02.059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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Wallqvist A, Fukunishi Y, Murphy LR, Fadel A, Levy RM. Iterative sequence/secondary structure search for protein homologs: comparison with amino acid sequence alignments and application to fold recognition in genome databases. Bioinformatics 2000; 16:988-1002. [PMID: 11159310 DOI: 10.1093/bioinformatics/16.11.988] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION Sequence alignment techniques have been developed into extremely powerful tools for identifying the folding families and function of proteins in newly sequenced genomes. For a sufficiently low sequence identity it is necessary to incorporate additional structural information to positively detect homologous proteins. We have carried out an extensive analysis of the effectiveness of incorporating secondary structure information directly into the alignments for fold recognition and identification of distant protein homologs. A secondary structure similarity matrix based on a database of three-dimensionally aligned proteins was first constructed. An iterative application of dynamic programming was used which incorporates linear combinations of amino acid and secondary structure sequence similarity scores. Initially, only primary sequence information is used. Subsequently contributions from secondary structure are phased in and new homologous proteins are positively identified if their scores are consistent with the predetermined error rate. RESULTS We used the SCOP40 database, where only PDB sequences that have 40% homology or less are included, to calibrate homology detection by the combined amino acid and secondary structure sequence alignments. Combining predicted secondary structure with sequence information results in a 8-15% increase in homology detection within SCOP40 relative to the pairwise alignments using only amino acid sequence data at an error rate of 0.01 errors per query; a 35% increase is observed when the actual secondary structure sequences are used. Incorporating predicted secondary structure information in the analysis of six small genomes yields an improvement in the homology detection of approximately 20% over SSEARCH pairwise alignments, but no improvement in the total number of homologs detected over PSI-BLAST, at an error rate of 0.01 errors per query. However, because the pairwise alignments based on combinations of amino acid and secondary structure similarity are different from those produced by PSI-BLAST and the error rates can be calibrated, it is possible to combine the results of both searches. An additional 25% relative improvement in the number of genes identified at an error rate of 0.01 is observed when the data is pooled in this way. Similarly for the SCOP40 dataset, PSI-BLAST detected 15% of all possible homologs, whereas the pooled results increased the total number of homologs detected to 19%. These results are compared with recent reports of homology detection using sequence profiling methods. AVAILABILITY Secondary structure alignment homepage at http://lutece.rutgers.edu/ssas CONTACT anders@rutchem.rutgers.edu; ronlevy@lutece.rutgers.edu SUPPLEMENTARY INFORMATION Genome sequence/structure alignment results at http://lutece.rutgers.edu/ss_fold_predictions.
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Affiliation(s)
- A Wallqvist
- Department of Chemistry, Rutgers University, Wright-Rieman Laboratories, 610 Taylor Rd, Piscataway, NJ 08854-8087, USA.
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Gervois P, Chopin-Delannoy S, Fadel A, Dubois G, Kosykh V, Fruchart JC, Najïb J, Laudet V, Staels B. Fibrates increase human REV-ERBalpha expression in liver via a novel peroxisome proliferator-activated receptor response element. Mol Endocrinol 1999; 13:400-9. [PMID: 10076997 DOI: 10.1210/mend.13.3.0248] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Fibrates are widely used hypolipidemic drugs that act by modulating the expression of genes involved in lipid and lipoprotein metabolism. Whereas the activation of gene transcription by fibrates occurs via the nuclear receptor peroxisome proliferator-activated receptor-alpha (PPARalpha) interacting with response elements consisting of a direct repeat of the AGGTCA motif spaced by one nucleotide (DR1), the mechanisms of negative gene regulation by fibrates and PPARalpha are largely unknown. In the present study, we demonstrate that fibrates induce the expression of the nuclear receptor Rev-erbalpha, a negative regulator of gene transcription. Fibrates increase Rev-erbalpha mRNA levels both in primary human hepatocytes and in HepG2 hepatoblastoma cells. In HepG2 cells, fibrates furthermore induce Rev-erbalpha protein synthesis rates. Transfection studies with reporter constructs driven by the human Rev-erbalpha promoter revealed that fibrates induce Rev-erbalpha expression at the transcriptional level via PPARalpha. Site-directed mutagenesis experiments identified a PPAR response element that coincides with the previously identified Rev-erbalpha negative autoregulatory Rev-DR2 element. Electromobility shift assay experiments indicated that PPARalpha binds as heterodimer with 9-cis-retinoic acid receptor to a subset of DR2 elements 5' flanked by an A/T-rich sequence such as in the Rev-DR2. PPARalpha and Rev-erbalpha bind with similar affinities to the Rev-DR2 site. In conclusion, these data demonstrate human Rev-erbalpha as a PPARalpha target gene and identify a subset of DR2 sites as novel PPARalpha response elements. Finally, the PPARalpha and Rev-erbalpha signaling pathways cross-talk through competition for binding to those response elements.
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Affiliation(s)
- P Gervois
- U.325 INSERM, Département d'Athérosclérose, Institut Pasteur de Lille and The Faculté de Pharmacie, Université de Lille II, France
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14
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Staels B, Koenig W, Habib A, Merval R, Lebret M, Torra IP, Delerive P, Fadel A, Chinetti G, Fruchart JC, Najib J, Maclouf J, Tedgui A. Activation of human aortic smooth-muscle cells is inhibited by PPARalpha but not by PPARgamma activators. Nature 1998; 393:790-3. [PMID: 9655393 DOI: 10.1038/31701] [Citation(s) in RCA: 868] [Impact Index Per Article: 33.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Peroxisome proliferator-activated receptors (PPARs) are key players in lipid and glucose metabolism and are implicated in metabolic disorders predisposing to atherosclerosis, such as dyslipidaemia and diabetes. Whereas PPARgamma promotes lipid storage by regulating adipocyte differentiation, PPARalpha stimulates the beta-oxidative degradation of fatty acids. PPARalpha-deficient mice show a prolonged response to inflammatory stimuli, suggesting that PPARalpha is also a modulator of inflammation. Hypolipidaemic fibrate drugs are PPARalpha ligands that inhibit the progressive formation of atherosclerotic lesions, which involves chronic inflammatory processes, even in the absence of their atherogenic lipoprotein-lowering effect. Here we show that PPARalpha is expressed in human aortic smooth-muscle cells, which participate in plaque formation and post-angioplasty re-stenosis. In these smooth-muscle cells, we find that PPARalpha ligands, and not PPARgamma ligands, inhibit interleukin-1-induced production of interleukin-6 and prostaglandin and expression of cyclooxygenase-2. This inhibition of cyclooxygenase-2 induction occurs transcriptionally as a result of PPARalpha repression of NF-kappaB signalling. In hyperlipidaemic patients, fenofibrate treatment decreases the plasma concentrations of interleukin-6, fibrinogen and C-reactive protein. We conclude that activators of PPARalpha inhibit the inflammatory response of aortic smooth-muscle cells and decrease the concentration of plasma acute-phase proteins, indicating that PPARalpha in the vascular wall may influence the process of atherosclerosis and re-stenosis.
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MESH Headings
- Acute-Phase Proteins/metabolism
- Animals
- Anti-Inflammatory Agents/pharmacology
- Aorta/cytology
- Aorta/drug effects
- Aorta/enzymology
- Aorta/pathology
- COS Cells
- Coronary Disease/blood
- Cyclooxygenase 2
- Cyclooxygenase 2 Inhibitors
- Cyclooxygenase Inhibitors/pharmacology
- Fenofibrate/pharmacology
- Gemfibrozil/pharmacology
- Gene Expression Regulation, Enzymologic
- Humans
- Hyperlipidemias/blood
- Hypolipidemic Agents/pharmacology
- Inflammation/enzymology
- Inflammation/metabolism
- Interleukin-1/metabolism
- Interleukin-6/biosynthesis
- Isoenzymes/biosynthesis
- Isoenzymes/genetics
- Membrane Proteins
- Muscle, Smooth, Vascular/drug effects
- Muscle, Smooth, Vascular/pathology
- Muscle, Smooth, Vascular/physiology
- NF-kappa B/metabolism
- Prostaglandin-Endoperoxide Synthases/biosynthesis
- Prostaglandin-Endoperoxide Synthases/genetics
- Prostaglandins/biosynthesis
- Pyrimidines/pharmacology
- Receptors, Cytoplasmic and Nuclear/biosynthesis
- Receptors, Cytoplasmic and Nuclear/chemistry
- Receptors, Cytoplasmic and Nuclear/physiology
- Rosiglitazone
- Thiazoles/pharmacology
- Thiazolidinediones
- Transcription Factors/biosynthesis
- Transcription Factors/chemistry
- Transcription Factors/physiology
- Transcription, Genetic
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Affiliation(s)
- B Staels
- U325 INSERM, Département d'Athérosclérose, Institut Pasteur, Lille, France.
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Boucard V, Dumas P, Sigwalt P, Guérin P, Fadel A. Living stereospecific and enantioasymmetric polymerization of methylthiirane initiated by various bis(alkyl-S-cysteinato)cadmium. Eur Polym J 1996. [DOI: 10.1016/0014-3057(95)00155-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Abstract
Diallyl sulfide, a major flavor ingredient from garlic, was previously shown to inhibit chemically induced carcinogenesis and cytotoxicity in animal model systems. It modulated cytochrome P-450 compositions by inactivating P-450 2E1 and inducing P-450 2B1. The present studies examined the inhibition of P-450 2E1 mediated p-nitrophenol hydroxylase activity by diallyl sulfide and its putative metabolites diallyl sulfoxide and diallyl sulfone (DASO2). Each compound displayed competitive inhibition of p-nitrophenol hydroxylase activity in incubations using liver microsomes from acetone-pretreated male Sprague-Dawley rats. Preincubation of the microsomes with DASO2 inactivated p-nitrophenol hydroxylase activity in a process that was time- and NADPH-dependent and saturable, exhibited pseudo-first-order kinetics, was protected by alternate substrate, was accompanied by a loss of microsomal P-450-CO binding spectrum, and was unaffected by exogenous nucleophile. The Ki value for DASO2 was 188 microM and the maximal rate of inactivation was 0.32 min-1. DASO2 was ineffective in the inactivation of ethoxyresorufin dealkylase, pentoxyresorufin dealkylase, or benzphetamine demethylase activity. Purified P-450 2E1 in a reconstituted system was inactivated in a time- and NADPH-dependent manner by DASO2. The metabolic conversion of diallyl sulfide to the sulfoxide and sulfone was observed in vivo and in vitro. The results suggest that diallyl sulfide inhibits the metabolism of P-450 2E1 substrates by competitive inhibition mechanisms and by inactivating P-450 2E1 via a suicide-inhibitory action of DASO2.
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Affiliation(s)
- J F Brady
- Laboratory for Cancer Research, College of Pharmacy, Rutgers University, Piscataway, New Jersey 08855
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Yang CS, Ishizaki H, Lee MJ, Wade D, Fadel A. Deuterium isotope effect in the interaction of N-nitrosodimethylamine, ethanol, and related compounds with cytochrome P-450IIE1. Chem Res Toxicol 1991; 4:408-13. [PMID: 1912326 DOI: 10.1021/tx00022a002] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Deuteration of N-nitrosodimethylamine (NDMA) decreases its carcinogenicity and produces an isotope effect on its metabolism. Our previous results showed that deuteration causes a 5-fold increase in the apparent Km, but not the Vmax, for the demethylation and denitrosation of NDMA in microsomes. In the present work, we studied the nature of this deuterium isotope effect with several compounds using acetone-induced microsomes as a source of cytochrome P-450IIE1. In the microsomal N-nitrosodiethylamine deethylase reaction, NDMA and [2H6]NDMA were competitive inhibitors and displayed apparent Ki values of 59 and 441 mM, respectively, showing an isotope effect of 0.13. Similarly, in the p-nitrophenol hydroxylase reaction, a deuterium isotope effect of 0.21 on the Ki was observed. With acetone as an inhibitor for p-nitrophenol hydroxylase, the isotope effect on the Ki was 0.11. Similar deuterium isotope effects were also observed with acetone and dimethylformamide as competitive inhibitors for NDMA demethylase. When the oxidation of ethanol, [1,1-2H2]ethanol, [2,2,2-2H3]ethanol, and [2H6]ethanol was compared, an isotope effect of about 5 was found in the Vmax/Km due to the deuteration of the methylene group (carbon 1) but not due to the methyl group. However, the Vmax was not affected. A corresponding deuterium isotope effect was observed in the Ki when these compounds were used as competitive inhibitors for the NDMA demethylase reaction. The results demonstrate that deuteration of NDMA, ethanol, and related compounds results in an increase in the Km or Ki with little change in the Vmax of P-450IIE1-catalyzed reactions. The molecular basis of this isotope effect is discussed.
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Affiliation(s)
- C S Yang
- Department of Chemical Biology and Pharmacognosy, College of Pharmacy, Rutgers University, Piscataway, New Jersey 08855-0789
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Fadel A, Salaun J. Anhydrous ferric chloride dispersed on silica gel induced ring enlargement of tertiary cycloalkanols. II : a convenient homologation of cycloalkanones, preparation of spiro systems and propella -γ-lactones. Tetrahedron 1985. [DOI: 10.1016/s0040-4020(01)96528-7] [Citation(s) in RCA: 34] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Salaün J, Fadel A, Conia J. Ring enlargement of 1-hydroxycylopropyl carbinol derivatives induced by lithium chloride. A convenient synthesis of 2-alkynylcyclobutanones. Tetrahedron Lett 1979. [DOI: 10.1016/s0040-4039(01)86169-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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