Green Tech platform
The Green Tech Platform is gathering the equipment and expertise developed at LIST in analytical chemistry, genomics, transcriptomics, proteomics and metabolomics, with a special focus on environmental and plant samples. The platform can perform a range of analytical services and relies on its instrumentation, infrastructure and know-how to offer “à la carte” analyses. The nature of investigated samples is very diverse, including water, soil, plants, microorganisms, cell lines, animal tissues, to name a few. Although the equipment is managed at the platform level, for several activities the expertise is not provided by the platform personnel but can be found in the department for further collaborations.
LIST's partners belong to public and private sectors: universities, research centres, food and feed industries, pharmaceutical companies, water agencies, municipalities.
Equipment
Genomics and Transcriptomics
- General molecular biology labs
- Liquid handling robot for PCR and qPCR set-up (EPmotion 5073 Eppendorf)
- Capillary Sequencer (ABI3500-8 capillaries, Life technologies) for Sanger sequencing and genotyping applications
- Next-generation sequencing : MiSeq (Illumina) for small to medium size genome sequencing (bacterial and fungal genome sequencing, gene expression profiling, amplicon sequencing)
- Real-Time qPCR (ViiA7, Life technologies) 96- and 384-wells plate design, Taqman array plate: Absolute and relation DNA quantification (gene expression profiling, viral RNA and bacterial DNA detection).
- PCR machines (Biometra and Life technologies)
- Chip-based capillary electrophoresis machine to analyse RNA, DNA, and protein (2100 Bioanalyzer, Agilent Technologies)
- Biolistic particle delivery system for transformation (PDS-1000/HEPTA SYSTEM, Bio-Rad Laboratories)
Proteomics
- Gel-based and gel-free analysis: Gel electrophoresis for protein or peptide separation, quantification and/or characterization (2D-DIGE, classical 2D gels, BlueNative gels, 1D gels, western-blotting, off-gel fractionator)
- Fluorescent imaging scanner for gels and plates (Typhoon FLA 9500, GE Healthcare)
- CCD camera for chemiluminescence detection (MiniLAS, GE Healthcare)
- Automatic processing of protein containing gel plugs for further analysis: spot picking (Ettan Spot picker, GE Healthcare), digestion with enzymes and spotting on MALDI targets ( Freedom EVO200, Tecan)
- Preparative chromatography for protein purification (NGC, Bio-rad)
- Matrix-Assisted Laser Desorption and Ionization, for protein identification and de novo peptides sequencing (SCIEX MALDI-ToF/ToF 5800TM)
- Shotgun analysis for identification of peptides / proteins with Ekspert™ nanoLC 425 (micro, nano mode, Eksigent, SCIEX) coupled to high-resolution mass spectrometer TripleTOF® 6600 (SCIEX) and relative quantification.
- Shotgun analysis for identification of peptides / proteins and relative quantification with Ekspert™ nanoLC 425 (micro, nano mode, Eksigent, SCIEX) coupled to high-resolution mass spectrometer TripleTOF® 6600 (SCIEX) and relative quantification.
- SWATH® acquisition on TripleTOF® system for identification and quantitation of complex samples.
- Capillary Electrophoresis CESI-MS (CESI 8000 Plus ESI-MS System, SCIEX) for PTMs analysis, proteoforms, protein conformation and interactions under native conditions.
Environmental chemistry and biochemistry - Metabolomics
- Sample preparation laboratories for the extraction and preconcentration of analytes from various matrices (Solid-Phase Extraction, Quechers, Ultrasonic-Assisted Extraction, Pressured-Fluid Extraction, Soxhlet, Solid-Phase Micro-Extraction, Microwave digestion)
- General analytical instruments: UV-Visible and fluorescence spectrophotometers, TOC/TN analyser, CHNS elemental analyser, Microplate reader
- Anion- and cation-exchange chromatographs (Thermo, Metrohm) with on-line eluent generation, electrochemical suppression and detection by conductivity or amperometry
- Ultra-High Performance Liquid Chromatographs (Waters , Agilent U-HPLC) with Diode-Array, Fluorescence and Light-Scattering detectors
- Inductively Coupled Plasma - Mass Spectrometry (Agilent 7900 ICP-MS) with collision cell and single-particle module for the high-sensitivity analysis of heavy metals, rare-earth elements, alkaline and alkaline-earth metals
- Ultra-High Performance Liquid Chromatographs coupled to tandem Mass Spectrometry (Agilent, SCIEX based on Triple-Quadrupole and Quadrupole-Linear Ion Trap technologies for the targeted analysis of trace contaminants and natural compounds
- Gas chromatographs coupled to single (GC-MS) and tandem mass spectrometry (GC-MS/MS), with multi-purpose autosamplers (liquid injection, large-volume sampling, headspace, Solid-Phase Micro-Extraction, thermal desorption, pyrolysis)
- Ultra-High Performance Liquid Chromatography (UPLC i-class, Waters) coupled with high-resolution mass spectrometer (SCIEX TripleTOF® 6600+) for semi-quantification and characterization of metabolites
Microscopy
- Laser Scanning Microscope (ZEISS, LSM880)
- Hyperspectral Microscope (CytoViva)
- Microtome (LEITZ) ; Cryo-microtome & Vibratome (LEICA MICROSYSTEMS)
- Invertoscopes & Stereomicroscopes
Bioprocess
- BioBench Twin bioreactors (750 mL) ; Pilot scale stirred tank reactors (Biotwin) ; Incubator shakers with bags (Celtainer CT2, CT20) ; Benchtop bioreactors (Biobench Algae 5L & Biobench 7,5L)
- Agitator-Incubators (BRUNSWICK INNOVA 44R)
- Minifors “2” Bioreactors (INFORS 6L)
- Plant Growth Chambers (Weiss Technik Fitotron® SGC 120)
- ASFE Super Fluid Extraction system (WATERS MV10)
- Pilot plants for wastewater treatment (Activated sludge, MBBR, MBR processes from 1 to 10m3)
Software
Dedicated software suites in different domains:
- e.g. CLC Main and Genomics workbench,
- Biogazelle qbase+,
- GeneMapper v5,
- ProteinPilot,
- Mascot Platform (Daemon, Distiller, server),
- MultiQuant v3,
- Chromeleon v7.2,
- MassHunter
applications and Key expertise
| Key expertise | Application domains |
|---|---|
| Identification of organisms in a complex community by genomics or proteomics | Microbiology |
| Identification of proteins from non-sequenced organisms | Plant biology, microbiology, zoology, food safety |
| Quantification of proteins in a complex mixture | Food safety, microbiology, plant biology |
| Characterization of proteins, allergens, food contaminants (organic pollutants, heavy metals) | Allergology, immunology, food safety, pharmaceutical industry |
| High-sensitivity quantification of pesticides and pharmaceuticals in water and environmental samples (e.g. plants, soils, fish, pollen, honey) | Water quality, environmental monitoring, food safety |
| Detection of natural toxins in water and plant samples (mycotoxins, cyanotoxins) | Environmental monitoring, food safety, public health |
| Characterization and profiling of selected metabolites (amino acids, carbohydrates, fatty acids, aroma, off-flavours) | Plant biology, microbiology, food and beverages quality |
| Untargeted semi-quantification and identification of metabolites | Plant biology, pharmacology |
