Structural Biology Services
Provided to you by instruct
Contact
Instruct-ERIC
isidore@instruct-eric.org
Nanobody discovery
- 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.
Crystallography
- Crystallisation of Proteins and Nucleic Acids
- High-throughput Crystallisation
- CrystalDirect Online Crystallography protein-to-structure pipeline
- IceBEAR crystallography pipelines (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 production for Structural Biology
- Protein expression
- Cloning
- High throughput expression
- Protein purification
Molecular Biophysics
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)
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 and Super-Resolution Microscopy for Structural Biology applications (Instruct)
- Single-molecule detection with fluorescence microscopy techniques: using widefield microscopy such as TIRF, super-resolution methods SMLM (STORM, GSD/GSDIM, PALM, PAINT)
Mass Spectrometry
- 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
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
Electron Microscopy techniques for Structural Biology
- 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
Magnetic Resonance Techniques
- 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 Structural Biology Techniques
- X-ray crystallography
- Biological small angle scattering (Bio-SAXS),
- X-ray imaging from synchrotron sources
- XChem Fragment Screening
- Fragment screening through automated CrystalDirect Pipeline
ISIDORe Services in action:
The intrinsically disordered SARS-CoV-2 nucleoprotein in dynamic complex with its viral partner nsp3a. doi: 10.1126/sciadv.abm4034.
PDB-REDO
Procedure to optimise crystallographic structure models, providing algorithms that make a fully automated decision-making system for refinement, rebuilding and validation.
- PDB-REDO
IMAGING SERVICES
Provided to you by Euro-BioImaging & VetBioNet
Contact
Arina RYBINA
arina.rybina@eurobioimaging.eu
How imaging technologies contribute to understanding viruses
Imaging technologies used to understand COVID-19 infection
Imaging techniques and COVID19 diagnosis
Understanding SARS-CoV-2 replication cycle in human cells
Light Microscopy & Advanced Light Microscopy for Biological Imaging
Fluorescence microscopy
- Laser scanning confocal microscopy (LSCM/CLSM)
- Spinning disc confocal microscopy (SDCM)
- Light sheet microscopy (LSM) and lattice light sheet microscopy (LLSM)
- Structured illumination microscopy (SIM)
- Widefield microscopy: Total internal reflection fluorescence microscopy (TIRF), Deconvolution widefield microscopy (DWM)
- Increased resolution confocal microscopy/Image scanning microscopy
- Two-Photon Microscopy/Multi-photon microscopy systems
Fluorescence Nanoscopy
- Stimulated Emission Depletion Microscopy (STED)
- Single-molecule localisation microscopy techniques (SMLM): STORM, GSD/GSDIM, PALM
- Reversible optical fluorescence transitions (RESOLFT)
- Super-resolution localization microscopy – localization super-resolution experiments (SMLM: dSTORM, GSDIM, STORM, PALM, PAINT), particle tracking, standard wide-field epifluorescence and TIRF microscopy, transmission microscopy.
Functional Imaging and Specialized Technologies
- High-throughput microscopy (HTM)/High content screening (HCS), RNAi screens
- Protein dynamics and interactions (FRET, FCS, FCCS, FLIM, FRAP)
- Multi-photon microscopy
- High resolution episcopic microscopy (HREM)
- Photomanipulation
- High speed imaging
- Feedback microscopy
- Cryo-FM
Mesoscopic Imaging
- Light Sheet mesoscopic imaging: Single-plane illumination microscopy (SPIM), dSLSM
- Optical projection tomography (OPT)
Label-free Imaging
- Quantitative phase imaging (QPI)
- Raman spectroscopy
- Coherent Anti-Stokes Raman Scattering microscopy (CARS)
- Mass Spectrometry based Imaging (MSI)
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
Virus morphology: Insights from super-resolution fluorescence microscopy
doi: 10.1016/j.csbj.2021.10.038
Electron microscopy for Biological Imaging / Ultrastructural Analysis in 2D & 3D
- 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
Correlative Light Microscopy & Electron Microscopy for Biological Imaging
- 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
- 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
Animal imaging (multimodal imaging of small animals)
- 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 Monitoring
- 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
- Histopathology
Image Data & Image Analysis
- Image data analysis
- 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
Sequencing SERVICES
Provided to you by Emergen
Contacts
Common genome sequencing technologies (whole SARS-CoV-2 genome sequencing)
- Illumina technology, COVIDSEQ strategy, Novaseq sequencer, 750 genomes per lane , 1500 genomes per run, one run per week
- Oxford Nanopore technology, ARTIC or MIDNIGHT amplicon strategy, GridIon sequencer, 96 genomes per flow cell, 5 flowcells per instrument, two runs per week
- Urgent SARS-CoV-2 genome sequencing: Oxford Nanopore technology, Artic strategy, GridIon sequencer, 10 genomes in 8 hours.
ISIDORe Services in action
Evaluation of NGS-Based Approaches for SARS-CoV-2 Whole Genome Characterisation
doi:10.1093/ve/veaa075
Metagenome sequencing
- 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 (AP-HP CHU Henri Mondor Technologie patent and accreditation)
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
Metatranscriptome sequencing
- 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