Analytical services

• Generation and characterisation of conformational nanobodies (to facilitate the structural analysis of proteins that are notoriously difficult to purify, to crystallize or to study by another method.)
• Rapid selection of nanobodies by screening/affinity maturation

• Crystallisation of Proteins and Nucleic Acids
• High-throughput Crystallisation
• CrystalDirect Online Crystallography protein-to-structure pipeline 
• IceBear crystallography data management (data management, crystallization, data collection)

ISIDORe Services in action:
Structural analysis of the SARS-CoV-2 methyltransferase complex involved in RNA cap creation bound to sinefungin. doi.org/10.1038/s41467-020-17495-9

• Protein expression 
• Cloning 
• High throughput expression
• Protein purification
• Biomolecular complex purification

 Wide range of techniques to study the biophysical characterization of the structure, function and stability of biological macromolecules like proteins, nucleic acids, lipids and their complexes; as well as the kinetic and thermodynamic parameters of their interaction.

• Circular Dichroism
  • Differential Scanning Fluorescence
  • Differential Scanning Calorimetry
  • Dynamic Light Scattering
  • UV/Vis Spectrometry
  • Microscale Thermophoresis
  • Surface Plasmon Resonance,
  • High Throughput Biolayer Interferometry
  • Isothermal titration Calorimetry
  • Antibody screening in patient sera (Robotein automated Bimolecular analysis platform)
  • SEC-MALS (multi-angle light scattering)

ISIDORe Services in action:
Poor antibody response to BioNTech/Pfizer COVID-19 vaccination in SARS-CoV-2 naïve residents of nursing homes. doi:10.1093/cid/ciab998

• Single-molecule detection with fluorescence microscopy techniques: using widefield microscopy such as TIRF, super-resolution methods SMLM (STORM, GSD/GSDIM, PALM, PAINT)

• Native mass spectrometry
• Single cell mass spectrometry 
• Proteomic mass spectrometry with possibility for plasma proteome analysis including monitoring of viral and immune response proteins, analysis of single viral proteins and binding to drugs and antibodies
• Glycan analysis by Mass spectrometry
• GC-MS for the analysis of cuticle thickness to test insecticide resistance in mosquitoes

ISIDORe Services in action:
ICAM-1 induced re-arrangements of capsid and genome prime rhinovirus 14 for activation and uncoating. doi.org/10.1073/pnas.2024251118

• Scanning electron microscopy (SEM) 
• Transmission electron microscopy (TEM)
• Cryogenic electron microscopy (Cryo-EM)
• Electron Microscopy Data Processing Services
• Electron tomography
• Cryo-Electron tomography
• Cryo-Correlative Light and EM

ISIDORe Services in action:
Immunization with synthetic SARS-CoV-2 S glycoprotein virus-like particles protects macaques from infection. doi: 10.1016/j.xcrm.2022.100528
In situ structural analysis of SARS-CoV-2 spike reveals flexibility mediated by three hinges. doi: 10.1126/science.abd5223

• Solution NMR
• Solid state NMR
• Fragment-screening by NMR
• NMR metabolomic
• NMR-based screening of protein-drug interactions
• Glycan analysis by NMR

ISIDORe Services in action:
The intrinsically disordered SARS-CoV-2 nucleoprotein in dynamic complex with its viral partner nsp3a. doi: 10.1126/sciadv.abm4034
In-Cell NMR Spectroscopy of Functional Riboswitch Aptamers in Eukaryotic Cells. doi:10.1002/anie.202007184

• X-ray crystallography
• Biological small angle scattering (Bio-SAXS), 
• X-ray imaging from synchrotron sources
• XChem Fragment Screening

ISIDORe Services in action:
The intrinsically disordered SARS-CoV-2 nucleoprotein in dynamic complex with its viral partner nsp3a. doi: 10.1126/sciadv.abm4034.

Procedure to optimise crystallographic structure models, providing algorithms that make a fully automated decision-making system for refinement, rebuilding and validation.

• PDB-REDO

AlphaFold models enriched with ligands and co-factors.

• Alphafill

ISIDORe Services in action

3DClusterViSu: 3D clustering analysis of super-resolution microscopy data by 3D Voronoi tessellations. doi:10.1093/bioinformatics/bty200. Microscopy-based assay for semi-quantitative detection of SARS-CoV-2 specific antibodies in human sera
doi: 10.1002/bies.202000257

Integrative Imaging Reveals SARS-CoV-2-Induced Reshaping of Subcellular Morphologies doi.org/10.1016/j.chom.2020.11.003

A spatial multi-scale fluorescence microscopy toolbox discloses entry checkpoints of SARS-CoV-2 variants in Vero E6 cells

Virus morphology: Insights from super-resolution fluorescence microscopy
doi: 10.1016/j.csbj.2021.10.038

• Atomic force microscopy (AFM)

• Scanning electron microscopy (SEM), including 3D SEM of plastic embedded samples
• Array tomography
• Focused-ion-beam scanning EM (FIB-SEM)
• Serial Block Face Scanning EM (SBF-SEM or SBEM)
• Transmission Electron Microscopy, including Serial section TEM (ssTEM)
• TEM tomography, STEM tomography
• Cryogenic electron Microscopy (Cryo-EM: Cryo-ET, Cryo-SEM, Cryo-FIB, Cryo-TEM)
• Immuno-electron microscopy (immunogold labelling of Tokuyasu cryosections)

ISIDORe Services in action

Integrative Imaging Reveals SARS-CoV-2-Induced Reshaping of Subcellular Morphologies doi.org/10.1016/j.chom.2020.11.003

SARS-CoV-2 infection induces the dedifferentiation of multiciliated cells and impairs mucociliary clearance doi.org/10.1038/s41467-021-24521-x

• CLEM from live cells to plastic sections (“live” CLEM)
• Correlative light-electron microscopy from live cells to 3D plastic embedded samples
• Intravital CLEM
• High accuracy on section CLEM
• CLEM on Tokuyasu sections
• CryoCLEM

ISIDORe Services in action

Post-correlation on-lamella cryo-CLEM reveals the membrane architecture of lamellar bodies doi.org/10.1038/s42003-020-01567-z

• Phase contrast X ray imaging (PCI)

ISIDORe Services in action

3D virtual pathohistology of lung tissue from Covid-19 patients based on phase contrast X-ray tomography doi: 10.7554/eLife.60408

• Multimodal imaging of small animals
• In vivo optical imaging
• Intravital microscopy
• Magnetic Resonance Imaging (MRI)
• Ultra-sound imaging (US)
• Computed tomography (CT)
• Nuclear imaging (PET, SPECT)
• Bimodal technologies
• Provision of imaging probes/tracers

• Animal behaviour monitoring
  • Quantitative spatial-temporal monitoring of individual animals and groups using TrackLab or EthoVision XT software (computer vision, UWB, GPS sensors)
  • Computer-aided monitoring: Registration and analysis of manual observations of animals directly or with video feeds/films, potentially including synchronization of data streams, e.g., of physiology by means of The Observer XT
• Animal physiology monitoring
  • Body temperature (combined with other variables as required), physiology sensors dependent on the animal species and variables required

• Histopathology

• Biological and Bio-Medical Image data analysis, including consultation and development of novel analysis and visualisation solutions
• AI and Machine Learning (ML)
• Medical Image Data Archiving

ISIDORe Services in action

Integrative Imaging Reveals SARS-CoV-2-Induced Reshaping of Subcellular Morphologies doi.org/10.1016/j.chom.2020.11.003

Microscopy-based assay for semi-quantitative detection of SARS-CoV-2 specific antibodies in human sera doi: 10.1002/bies.202000257

• Illumina technology**
• Oxford Nanopore technology
• Bacterial Genome Sequencing

ISIDORe Services in action

Evaluation of NGS-Based Approaches for SARS-CoV-2 Whole Genome Characterisation
doi:10.1093/ve/veaa075

• Shotgun metagenome sequencing (AP-HP CHU Henri Mondor Technologie patent and accreditation): identification of any microorganism (up to 100/week)
• Viral metagenome sequencing: identification of any virus (up to 100/week)
• 16S rRNA metagenome sequencing

• Pan-pathogen surveillance through shotgun metagenomics

ISIDORe Services in action

Identification of necrotizing dermohypodermitis and fasciitis causative microbial agents and microbiota by targeted and shotgun metagenomics
doi: 10.1111/bjd.18611

Inclusion-Body Encephalitis Detected and Characterized by Standardized and Validated Shotgun Metagenomic Approach
doi: 10.3201/eid2609.200366

Fatal Encephalitis Caused by Cristoli virus, a New Emerging Member of the Orthobunyavirus genus of the Peribunyaviridae family
doi: 10.3201/eid2606.191431

Comparison of Nucleic Acid Extraction Methods for a Viral Metagenomics Analysis of Respiratory Viruses. Microorganisms
doi: 10.3390/microorganisms8101539

Metagenomic Investigation of Torque Teno Mini Virus-SH in Hematological Patients
doi: 10.3389/fmicb.2019.01898

Metagenomic Next-Generation Sequencing Reveals Individual Composition and Dynamics of Anelloviruses during Autologous Stem Cell Transplant Recipient Management
doi:10.3390/v10110633

Quality Control Implementation for Universal Characterization of DNA and RNA Viruses in Clinical Respiratory Samples Using Single Metagenomic Next-Generation Sequencing Workflow
doi:10.1186/s12879-018-3446-5

• Viral metatranscriptomic – Whole genome sequencing of RNA viruses, including SARS-CoV-2 (up to 100 /week)

ISIDORe Services in action

Evaluation of NGS-Based Approaches for SARS-CoV-2 Whole Genome Characterisation
doi:10.1093/ve/veaa075

• Small RNA Illumina sequencing**
• Long read DNA sequencing by Nanopore**
• RNAseq total transcriptome Illumina sequencing**
• Genotyping of mosquitoes, insecticide resistance and detection of pathogens

ISIDORe Services in action

Evaluation of NGS-Based Approaches for SARS-CoV-2 Whole Genome Characterisation
doi:10.1093/ve/veaa075