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Article ; Online: Evaluation and activity of new porphyrin-peptide cage-type conjugates for the photoinactivation of

Alcaraz, Matthéo / Lyonnais, Sébastien / Ghosh, Chandramouli / Aguilera-Correa, John Jairo / Richeter, Sébastien / Ulrich, Sébastien / Kremer, Laurent

Microbiology spectrum

2024 , Page(s) e0000624

Abstract: Mycobacterium ... ...

Abstract	Mycobacterium abscessus
Language	English
Publishing date	2024-04-15
Publishing country	United States
Document type	Journal Article
ZDB-ID	2807133-5
ISSN	2165-0497 ; 2165-0497
ISSN (online)	2165-0497
ISSN	2165-0497
DOI	10.1128/spectrum.00006-24
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Dynamic Profile of S-Layer Proteins Controls Surface Properties of Emetic

Boutonnet, Cécile / Lyonnais, Sébastien / Alpha-Bazin, Beatrice / Armengaud, Jean / Château, Alice / Duport, Catherine

Frontiers in microbiology

2022 Volume 13, Page(s) 937862

Abstract: Many prokaryotes are covered by a two-dimensional array of proteinaceous subunits. This surface layers (S-layer) is incompletely characterized for many microorganisms. Here, we ... ...

Abstract	Many prokaryotes are covered by a two-dimensional array of proteinaceous subunits. This surface layers (S-layer) is incompletely characterized for many microorganisms. Here, we studied
Language	English
Publishing date	2022-06-29
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2587354-4
ISSN	1664-302X
ISSN	1664-302X
DOI	10.3389/fmicb.2022.937862
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Label-Free Single Nanoparticle Identification and Characterization in Demanding Environment, Including Infectious Emergent Virus.

Nguyen, Minh-Chau / Bonnaud, Peter / Dibsy, Rayane / Maucort, Guillaume / Lyonnais, Sébastien / Muriaux, Delphine / Bon, Pierre

Small (Weinheim an der Bergstrasse, Germany)

2023 Volume 20, Issue 16, Page(s) e2304564

Abstract: Unknown particle screening-including virus and nanoparticles-are keys in medicine, industry, and also in water pollutant determination. Here, RYtov MIcroscopy for Nanoparticles Identification (RYMINI) is introduced, a staining-free, non-invasive, and non- ...

Abstract	Unknown particle screening-including virus and nanoparticles-are keys in medicine, industry, and also in water pollutant determination. Here, RYtov MIcroscopy for Nanoparticles Identification (RYMINI) is introduced, a staining-free, non-invasive, and non-destructive optical approach that is merging holographic label-free 3D tracking with high-sensitivity quantitative phase imaging into a compact optical setup. Dedicated to the identification and then characterization of single nano-object in solution, it is compatible with highly demanding environments, such as level 3 biological laboratories, with high resilience to external source of mechanical and optical noise. Metrological characterization is performed at the level of each single particle on both absorbing and transparent particles as well as on immature and infectious HIV, SARS-CoV-2 and extracellular vesicles in solution. The capability of RYMINI to determine the nature, concentration, size, complex refractive index and mass of each single particle without knowledge or model of the particles' response is demonstrated. The system surpasses 90% accuracy for automatic identification between dielectric/metallic/biological nanoparticles and ≈80% for intraclass chemical determination of metallic and dielectric. It falls down to 50-70% for type determination inside the biological nanoparticle's class.
MeSH term(s)	Nanoparticles/chemistry ; Microscopy/methods ; Metal Nanoparticles ; Viruses ; Holography
Language	English
Publishing date	2023-11-27
Publishing country	Germany
Document type	Journal Article
ZDB-ID	2168935-0
ISSN	1613-6829 ; 1613-6810
ISSN (online)	1613-6829
ISSN	1613-6810
DOI	10.1002/smll.202304564
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Article ; Online: Optimized production and fluorescent labeling of SARS-CoV-2 virus-like particles.

Gourdelier, Manon / Swain, Jitendriya / Arone, Coline / Mouttou, Anita / Bracquemond, David / Merida, Peggy / Saffarian, Saveez / Lyonnais, Sébastien / Favard, Cyril / Muriaux, Delphine

Scientific reports

2022 Volume 12, Issue 1, Page(s) 14651

Abstract: SARS-CoV-2 is an RNA enveloped virus responsible for the COVID-19 pandemic that conducted in 6 million deaths worldwide so far. SARS-CoV-2 particles are mainly composed of the 4 main structural proteins M, N, E and S to form 100 nm diameter viral ... ...

Abstract	SARS-CoV-2 is an RNA enveloped virus responsible for the COVID-19 pandemic that conducted in 6 million deaths worldwide so far. SARS-CoV-2 particles are mainly composed of the 4 main structural proteins M, N, E and S to form 100 nm diameter viral particles. Based on productive assays, we propose an optimal transfected plasmid ratio mimicking the viral RNA ratio in infected cells. This allows SARS-CoV-2 Virus-Like Particle (VLPs) formation composed of the viral structural proteins M, N, E and mature S. Furthermore, fluorescent or photoconvertible VLPs were generated by adding a fluorescent protein tag on N or M mixing with unlabeled viral proteins and characterized by western blots, atomic force microscopy coupled to fluorescence and immuno-spotting. Thanks to live fluorescence and super-resolution microscopies, we quantified VLPs size and concentration. SARS-CoV-2 VLPs present a diameter of 110 and 140 nm respectively for MNE-VLPs and MNES-VLPs with a concentration of 10e12 VLP/ml. In this condition, we were able to establish the incorporation of the Spike in the fluorescent VLPs. Finally, the Spike functionality was assessed by monitoring fluorescent MNES-VLPs docking and internalization in human pulmonary cells expressing or not the receptor hACE2. Results show a preferential maturation of S on N(GFP) labeled VLPs and an hACE2-dependent VLP internalization and a potential fusion in host cells. This work provides new insights on the use of non-fluorescent and fluorescent VLPs to study and visualize the SARS-CoV-2 viral life cycle in a safe environment (BSL-2 instead of BSL-3). Moreover, optimized SARS-CoV-2 VLP production can be further adapted to vaccine design strategies.
MeSH term(s)	Fluorescence ; Humans ; SARS-CoV-2/isolation & purification ; Viral Structural Proteins ; Virion/isolation & purification
Chemical Substances	Viral Structural Proteins
Language	English
Publishing date	2022-08-27
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-022-18681-z
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Validation of flavivirus infectious clones carrying fluorescent markers for antiviral drug screening and replication studies.

Cherkashchenko, Liubov / Gros, Nathalie / Trausch, Alice / Neyret, Aymeric / Hénaut, Mathilde / Dubois, Gregor / Villeneuve, Matthieu / Chable-Bessia, Christine / Lyonnais, Sébastien / Merits, Andres / Muriaux, Delphine

Frontiers in microbiology

2023 Volume 14, Page(s) 1201640

Abstract: Flaviviruses have emerged as major arthropod-transmitted pathogens and represent an increasing public health problem worldwide. High-throughput screening can be facilitated using viruses that easily express detectable marker proteins. Therefore, ... ...

Abstract	Flaviviruses have emerged as major arthropod-transmitted pathogens and represent an increasing public health problem worldwide. High-throughput screening can be facilitated using viruses that easily express detectable marker proteins. Therefore, developing molecular tools, such as reporter-carrying versions of flaviviruses, for studying viral replication and screening antiviral compounds represents a top priority. However, the engineering of flaviviruses carrying either fluorescent or luminescent reporters remains challenging due to the genetic instability caused by marker insertion; therefore, new approaches to overcome these limitations are needed. Here, we describe reverse genetic methods that include the design and validation of infectious clones of Zika, Kunjin, and Dengue viruses harboring different reporter genes for infection, rescue, imaging, and morphology using super-resolution microscopy. It was observed that different flavivirus constructs with identical designs displayed strikingly different genetic stabilities, and corresponding virions resembled wild-type virus particles in shape and size. A successful strategy was assessed to increase the stability of rescued reporter virus and permit antiviral drug screening based on quantitative automated fluorescence microscopy and replication studies.
Language	English
Publishing date	2023-09-15
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2587354-4
ISSN	1664-302X
ISSN	1664-302X
DOI	10.3389/fmicb.2023.1201640
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Structural analysis of the Candida albicans mitochondrial DNA maintenance factor Gcf1p reveals a dynamic DNA-bridging mechanism.

Tarrés-Solé, Aleix / Battistini, Federica / Gerhold, Joachim M / Piétrement, Olivier / Martínez-García, Belén / Ruiz-López, Elena / Lyonnais, Sébastien / Bernadó, Pau / Roca, Joaquim / Orozco, Modesto / Le Cam, Eric / Sedman, Juhan / Solà, Maria

Nucleic acids research

2023 Volume 51, Issue 11, Page(s) 5864–5882

Abstract: The compaction of mitochondrial DNA (mtDNA) is regulated by architectural HMG-box proteins whose limited cross-species similarity suggests diverse underlying mechanisms. Viability of Candida albicans, a human antibiotic-resistant mucosal pathogen, is ... ...

Abstract	The compaction of mitochondrial DNA (mtDNA) is regulated by architectural HMG-box proteins whose limited cross-species similarity suggests diverse underlying mechanisms. Viability of Candida albicans, a human antibiotic-resistant mucosal pathogen, is compromised by altering mtDNA regulators. Among them, there is the mtDNA maintenance factor Gcf1p, which differs in sequence and structure from its human and Saccharomyces cerevisiae counterparts, TFAM and Abf2p. Our crystallographic, biophysical, biochemical and computational analysis showed that Gcf1p forms dynamic protein/DNA multimers by a combined action of an N-terminal unstructured tail and a long helix. Furthermore, an HMG-box domain canonically binds the minor groove and dramatically bends the DNA while, unprecedentedly, a second HMG-box binds the major groove without imposing distortions. This architectural protein thus uses its multiple domains to bridge co-aligned DNA segments without altering the DNA topology, revealing a new mechanism of mtDNA condensation.
MeSH term(s)	Humans ; Candida albicans/genetics ; Candida albicans/metabolism ; DNA, Mitochondrial/metabolism ; DNA-Binding Proteins/metabolism ; Mitochondria/metabolism ; Mitochondrial Proteins/metabolism ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae/metabolism ; Transcription Factors/metabolism ; Fungal Proteins/metabolism
Chemical Substances	DNA, Mitochondrial ; DNA-Binding Proteins ; Mitochondrial Proteins ; Transcription Factors ; Fungal Proteins
Language	English
Publishing date	2023-05-18
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	186809-3
ISSN	1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
ISSN (online)	1362-4962 ; 1362-4954
ISSN	0301-5610 ; 0305-1048
DOI	10.1093/nar/gkad397
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Optimized production and fluorescent labeling of SARS-CoV-2 virus-like particles

Manon Gourdelier / Jitendriya Swain / Coline Arone / Anita Mouttou / David Bracquemond / Peggy Merida / Saveez Saffarian / Sébastien Lyonnais / Cyril Favard / Delphine Muriaux

Scientific Reports, Vol 12, Iss 1, Pp 1-

2022 Volume 15

Abstract: Abstract SARS-CoV-2 is an RNA enveloped virus responsible for the COVID-19 pandemic that conducted in 6 million deaths worldwide so far. SARS-CoV-2 particles are mainly composed of the 4 main structural proteins M, N, E and S to form 100 nm diameter ... ...

Abstract	Abstract SARS-CoV-2 is an RNA enveloped virus responsible for the COVID-19 pandemic that conducted in 6 million deaths worldwide so far. SARS-CoV-2 particles are mainly composed of the 4 main structural proteins M, N, E and S to form 100 nm diameter viral particles. Based on productive assays, we propose an optimal transfected plasmid ratio mimicking the viral RNA ratio in infected cells. This allows SARS-CoV-2 Virus-Like Particle (VLPs) formation composed of the viral structural proteins M, N, E and mature S. Furthermore, fluorescent or photoconvertible VLPs were generated by adding a fluorescent protein tag on N or M mixing with unlabeled viral proteins and characterized by western blots, atomic force microscopy coupled to fluorescence and immuno-spotting. Thanks to live fluorescence and super-resolution microscopies, we quantified VLPs size and concentration. SARS-CoV-2 VLPs present a diameter of 110 and 140 nm respectively for MNE-VLPs and MNES-VLPs with a concentration of 10e12 VLP/ml. In this condition, we were able to establish the incorporation of the Spike in the fluorescent VLPs. Finally, the Spike functionality was assessed by monitoring fluorescent MNES-VLPs docking and internalization in human pulmonary cells expressing or not the receptor hACE2. Results show a preferential maturation of S on N(GFP) labeled VLPs and an hACE2-dependent VLP internalization and a potential fusion in host cells. This work provides new insights on the use of non-fluorescent and fluorescent VLPs to study and visualize the SARS-CoV-2 viral life cycle in a safe environment (BSL-2 instead of BSL-3). Moreover, optimized SARS-CoV-2 VLP production can be further adapted to vaccine design strategies.
Keywords	Medicine ; R ; Science ; Q
Subject code	670
Language	English
Publishing date	2022-08-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Apport de la microscopie de fluorescence super-résolue : dans l’intimité des virus !

Arone, Coline / Dibsy, Rayane / Inamdar, Kaushik / Lyonnais, Sébastien / Arhel, Nathalie J / Favard, Cyril / Muriaux, Delphine

Virologie (Montrouge, France)

2021 Volume 25, Issue 3, Page(s) 153–167

Abstract: The recent revolution in optical fluorescence microscopy, supported by the optimization of both spatial resolution and acquisition speed, led to the ability to visualize nano-scaled objects. Currently, the use of a new generation of super-resolution ... ...

Title translation	Illuminating the nanoscopic world of viruses by fluorescence super-resolution microscopy.
Abstract	The recent revolution in optical fluorescence microscopy, supported by the optimization of both spatial resolution and acquisition speed, led to the ability to visualize nano-scaled objects. Currently, the use of a new generation of super-resolution fluorescence microscopes coupled to improved fluorescent probes gives the possibility to study the replicative cycle of viruses in living cells, at the single-virus and molecule level. In this review, after a brief chronological description of these new approaches, we highlight several examples of super-resolution microscopies that have allowed to revisit our understanding of several human viruses and of host-pathogen interactions.
Language	French
Publishing date	2021-07-08
Publishing country	France
Document type	English Abstract ; Journal Article
ZDB-ID	2118387-9
ISSN	1950-6961 ; 1267-8694
ISSN (online)	1950-6961
ISSN	1267-8694
DOI	10.1684/vir.2021.0907
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Article: Illuminating the nanoscopic world of viruses by fluorescence super-resolution microscopy.

Arone, Coline / Dibsy, Rayane / Inamdar, Kaushik / Lyonnais, Sébastien / Arhel, Nathalie J / Favard, Cyril / Muriaux, Delphine

Virologie (Montrouge, France)

2021 Volume 25, Issue 3, Page(s) 47–60

Abstract	The recent revolution in optical fluorescence microscopy, supported by the optimization of both spatial resolution and acquisition speed, led to the ability to visualize nano-scaled objects. Currently, the use of a new generation of super-resolution fluorescence microscopes coupled to improved fluorescent probes gives the possibility to study the replicative cycle of viruses in living cells, at the single-virus and molecule level. In this review, after a brief chronological description of these new approaches, we highlight several examples of super-resolution microscopies that have allowed to revisit our understanding of several human viruses and of host-pathogen interactions.
MeSH term(s)	Fluorescent Dyes ; Humans ; Microscopy, Fluorescence ; Single Molecule Imaging ; Viruses
Chemical Substances	Fluorescent Dyes
Language	English
Publishing date	2021-07-09
Publishing country	France
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	2118387-9
ISSN	1950-6961 ; 1267-8694
ISSN (online)	1950-6961
ISSN	1267-8694
DOI	10.1684/vir.2021.0908
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Article ; Online: Atomic force microscopy analysis of native infectious and inactivated SARS-CoV-2 virions.

Lyonnais, Sébastien / Hénaut, Mathilde / Neyret, Aymeric / Merida, Peggy / Cazevieille, Chantal / Gros, Nathalie / Chable-Bessia, Christine / Muriaux, Delphine

Scientific reports

2021 Volume 11, Issue 1, Page(s) 11885

Abstract: SARS-CoV-2 is an enveloped virus responsible for the Coronavirus Disease 2019 (COVID-19) pandemic. Here, single viruses were analyzed by atomic force microscopy (AFM) operating directly in a level 3 biosafety (BSL3) facility, which appeared as a fast and ...

Abstract	SARS-CoV-2 is an enveloped virus responsible for the Coronavirus Disease 2019 (COVID-19) pandemic. Here, single viruses were analyzed by atomic force microscopy (AFM) operating directly in a level 3 biosafety (BSL3) facility, which appeared as a fast and powerful method to assess at the nanoscale level and in 3D infectious virus morphology in its native conformation, or upon inactivation treatments. AFM imaging reveals structurally intact infectious and inactivated SARS-CoV-2 upon low concentration of formaldehyde treatment. This protocol combining AFM and plaque assays allows the preparation of intact inactivated SARS-CoV-2 particles for safe use of samples out of level 3 laboratory to accelerate researches against the COVID-19 pandemic. Overall, we illustrate how adapted BSL3-AFM is a remarkable toolbox for rapid and direct virus analysis based on nanoscale morphology.
MeSH term(s)	Animals ; COVID-19/virology ; Chlorocebus aethiops ; Humans ; Microscopy, Atomic Force ; SARS-CoV-2/physiology ; SARS-CoV-2/ultrastructure ; Vero Cells ; Virion/physiology ; Virion/ultrastructure ; Virus Inactivation
Language	English
Publishing date	2021-06-04
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-021-91371-4
Database	MEDical Literature Analysis and Retrieval System OnLINE

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