Biotechnologies and Environmental Analytics Platform
From bioprocesses and water quality to food safety and plant biology, the Biotechnologies and Environmental Analytics Platform (BEAP) offers cutting-edge equipment and expertise in analytical chemistry, omics technologies and bioprocessing to scientists, industry and public stakeholders. Eager to provide a tailor-made approach, BEAP engineers enable to analyse numerous types of samples ranging from water, soil, plants and microorganisms to animal tissues. The bioreactor facilities allow providing a research infrastructure for end-to-end bioprocess development (up to TRL5), including upscaling of production volumes up to 50L and downstream processing. It is currently used for yeast, bacteria and plant cell cultures, in order to produce biomass, proteins, secondary metabolites and other high added value compounds.
The support provided by BEAP team members includes the scientific and technical expertise and knowledge of engineers, as well as the implementation, manipulation and maintenance of state-of-the-art equipment.
KEY EXPERTISE
Bioprocessing
Optimisation of processes, on-demand medium formulation, upscaling of existing or newly developed processes, as well as production, purification and characterisation of enzymes.
Sample preparation
To perform analyses in the domains of e.g. water quality, food safety, quality control or plant biology.
Omics
Quantitative and qualitative analysis of molecules such as DNA, RNA, proteins and/or peptides and metabolites in microorganisms, plants or animal samples.
Analytical science
Analysis of primary and secondary metabolites, determination of targeted xenobiotics or natural compounds in various environmental or biological matrices (water, food, plants, etc), from trace contaminants to major elements.
MAIN APPLICATION AREAS
- Production of biomass for the probiotic sector, e.g. with Probiotics
- Optimisation of process and custom-made cultivation media (service)
- Production of enzymes or secondary metabolites in volumes up to 50L (service)
- Water quality or food safety: determination of targeted xenobiotics or natural compounds from trace contaminants to major elements
- Quantitative and qualitative analysis of molecules such as DNA, RNA, proteins and/or peptides and metabolites in environmental or living samples, e.g. SMARTWALL, ECOTREE.
- Purification and characterisation of enzymes, e.g. CABERNET
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
- 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 (IPGphor III, HPE™ FlatTop Tower, 2D-DIGE, classical 2D gels, BlueNative gels, 1D gels, western-blotting, off-gel fractionator), Fluorescent imaging scanner (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.
- 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
- 1 x 3L Photobioreactors (Biobench)
- 6x 5L WV Benchtop bioreactors (Biobench)
- 8x Benchtop bioreactors (Minifors 2) 8x 4L WV vessels + 8x 2L WV vessels
- 4x 2L WV Benchtop bioreactors (Biobench)
- 8x 0,5L WV Benchtop bioreactors (Biobench)
- 3x 10L WV Wave-shaking incubator (Celltainer)
- 2x 45L WV Pilot scale stirred tank bioreactors (BioTwin)
- 1x Solid-state fermentation bioreactors 2,4 L WV( (Labfors 5 solids and enzymatic)
- 1x orbital-shaking incubator (Minitron)
- 2x orbital-shaking incubators (Ecotron)
- 6x orbital-shaking incubators (INNOVA 44R)
- 1x Large volume centrifugator (Sorval BIOS 16 SP)
- 1x Autoclave (Systec VX-150)
- 16x Optical density probe (CGQBioR)
- 4x Optical density probe (Dencytee)
- 1x Sonicator (BioruptorPlus)
- 1x Tangential flow filtration system (TFF) (Sartoflow Smart)
- 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 v2.6.1 (Daemon, Distiller, server)
- MultiQuant v3
- Chromeleon v7.2
- MassHunter
- EVE (Infors)
- Minitabs
- CGQuant (Aquilabiolab)
- ArcAIR (Hamilton)
SELECTED PUBLICATIONS
- Deletion of bglC triggers a genetic compensation response by awakening the expression of alternative beta-glucosidase. Biochim Biophys Acta Gene Regul Mech. Deflandre B, Thiébaut N, Planckaert S, Jourdan S, Anderssen S, Hanikenne M, Devreese B, Francis I, Rigali S. (2020). 1863(10):194615. doi: 10.1016/j.bbagrm.2020.194615.
- An apoplastic fluid extraction method for the characterization of grapevine leaves proteome and metabolome from a single sample. Figueiredo J, Cavaco A.R, Guerra‐Guimarães L, Leclercq C.C, Renaut J, Cunha J, Eiras‐Dias J, Cordeiro C, Matos R, Sousa Silva M, Figueiredo A. (2020). Physiologia plantarum, DOI: 10.1111/ppl.13198.
- Molecular investigation of Tuscan sweet cherries sampled over three years: gene expression analysis coupled to metabolomics and proteomics. (2020). Guerriero G, Berni R, Charton S, Planchon S, Legay S, Romi M, Cantini C, Cai G, Hausman JF, Renaut J. Horticulture Research
- Primary Metabolism Is Distinctly Modulated by Plant Resistance Inducers in Coffea arabica Leaves Infected by Hemileia vastatrix. Possa KF, Silva JAG, Resende MLV, Tenente R, Pinheiro C, Chaves I, Planchon S, Monteiro ACA, Renaut J, Carvalho MAF, Ricardo CP, Guerra-Guimarães L. (2020). Front Plant Sci. 11:309. doi: 10.3389/fpls.2020.00309. PMID: 32265962; PMCID: PMC7099052
- Protein changes as robust signatures of fish chronic stress: a proteomics approach to fish welfare research. Raposo de Magalhães C, Schrama D, Farinha AP, Revets D, Kuehn A, Planchon S, Rodrigues PM, Cerqueira M. (2020). BMC Genomics. 21(1):309. doi: 10.1186/s12864-020-6728-4.
- The effects of improving low dietary protein utilization on the proteome of lamb tissues. Ribeiro DM, Planchon S, Leclercq CC, Dentinho MTP, Bessa RJB, Santos-Silva J, Paulos K, Jerónimo E, Renaut J, Almeida AM. (2020). J Proteomics. 223:103798. doi: 10.1016/j.jprot.2020.103798.
- Impact of heat treatment on the acid induced gelation of brewers' spent grain protein isolates. Soukoulis C, Hellebois T, Gaiani C, Planchon S, Renaut J. (2020). Food Hydrocolloids, vol. 113, art. no. 106531, 2021, doi:10.1016/j.foodhyd.2020.106531.
- Phospholipase A2 Triggers Anaphylaxis to Snake Venom by Repeated Skin Sensitization-A Case Report. Swiontek K, Planchon S, Ollert M, Eyer F, Fischer J, Hilger C. (2020). J Investig Allergol Clin Immunol. doi: 10.18176/jiaci.0545.
- Soluble silver ions from silver nanoparticles induce a polarised secretion of interleukin-8 in differentiated Caco-2 cells. Polet M, Laloux L, Cambier S, Ziebel J, Gutleb A, Schneider YJ. (2020). Toxicology Letters. 325(14-24) DOI: 10.1016/j.toxlet.2020.02.004.
- Long-Term Cd Exposure Alters the Metabolite Profile in Stem Tissue of Medicago sativa. Gutsch A, Hendrix S, Guerriero G, Renaut J, Lutts S, Alseekh S, Fernie AR, Hausman JF, Vangronsveld J, Cuypers A, Sergeant K. (2020). Cells. 9(12):2707. doi: 10.3390/cells9122707
- Expression Analysis of Cell Wall-Related Genes in the Plant Pathogenic Fungus Drechslera teres. Backes A, Hausman JF, Renaut J, Ait Barka E, Jacquard C, Guerriero G. (2020). Genes (Basel). 11(3):300. doi: 10.3390/genes11030300.
