Integrative Biology

The Integrative Biology Facility is gathering the equipment and expertise developed at the LIST in genomics, transcriptomics, proteomics and metabolomics. More specifically, the facility is targeting environmental and plant samples. The type of analysis can be broader and performed ‘à la carte’. The nature of samples is very diverse, and encompassing matrices such as plant cell walls, rodent blood samples or microorganisms in wine must, to name a few. Indeed protocols can be adapted or even developed, depending on the samples sent by our partners: e.g. universities, research centres, food or feed industries, pharmaceutical companies. 

Equipment

Genomics-transcriptomics

  • General molecular biology and biochemistry lab for sample preparation
  • 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)

Proteomics

  • Gel electrophoresis for protein or peptide separation, quantification or characterization (2D-DIGE, classical 2D gels, BlueNative gels, 1D gels, western-blotting, off-gel fractionator)
  • Fluorescent imaging for gels, membranes, microplates and divers samples with a Typhoon FLA 9500 (GE Healthcare)
  • CCD camera for chemilumiscence detection (MiniLAS, GE Healthcare)
  • Automatic processing of gel plugs, protein complexes or purified proteins for further analysis: spot picking (Ettan Spot picker, GE Healthcare), digestion with enzymes (Tecan EVO200) and spotting on MALDI targets (EVO200, Tecan)
  • Identification of proteins or peptides by mass spectrometry, either MALDI or ESI based (TOF/TOF 5800 and Triple TOF 5600+, Sciex)
  • De novo peptides sequencing
  • Control of purified proteins
  • Liquid chromatography (nanoLC 2D, Eksigent) coupled with high-resolution mass spectrometer for quantification and characterization of proteins and peptides in solution with or without fractionation

Metabolomics

  • Ultra-High Performance Liquid Chromatography (UPLC, Waters) coupled with high-resolution mass spectrometer (Triple TOF 5600+, Sciex) for semi-quantification and characterization of metabolites

Other equipment

  • Dedicated software in different domains: e.g. CLC Main and Genomics workbench, Biogazelle qbase+, GeneMapper v5, ProteinPilot, Mascot Platform (Daemon, Distiller, server)

 

Key expertise and possible applications

Key expertiseSome possible applications
Characterization of proteins, allergens, food contaminantsAllergology, immunology, food safety, pharmaceutical industry
Quantification of proteins in a complex mixtureFood safety, microbiology, plant biology
Identification of organisms in a complex community by genomics or proteomicsMicrobiology
Identification of proteins from non-sequenced organismsPlant biology, microbiology, zoology, food safety
Semi-quantification and identification of metabolitesPlant biology, pharmacology

 

Contact

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Dr Jenny RENAUT
Send an e-mail

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