Infrastructure

At the Centre for Synthetic Biology, state-of-the-art infrastructure is available for the processing of (engineered) microbes and enzymes, and the identification of (new) products in a high-throughput fashion.

All auxiliary instrumentation and infrastructure that is necessary for correct execution of planned experiments with the below-mentioned instrumentation is also made available to CF users whenever needed. This includes laminar flows, autoclave, shakers, incubation chamber, barcode printer, freeze dryer, etc.

Advanced analytical equipment

HPAEC-PAD

Two dual High-Performance Anion Exchange Chromatography (HPAEC) instruments with Pulsed Amperometric Detection (PAD) from Dionex / Thermo Fisher Scientific, which are specialized for carbohydrate analysis. Different columns available for separation of mono-, di-, oligo- and polysaccharides. The instruments are equipped with an autosampler that can work with both HPLC-vials (0.2 ml and 1 mL, with split septum cap, which can be obtained from us at purchase cost or we provide you the details for purchase) and 96 well plates (microtiter and deepwell plates).

The sample requirements are:

Linear concentration range is normally 1-100 μM.
Samples are diluted in ultrapure water (18.2 MΩ.cm water resistivity, e.g. milliQ water).
The samples need to be clean:
- No strong anions (e.g Cl-, F-, because they ruin the column): if anions would be present, we can provide special filters to remove them (at purchase cost or provide you the product number.
- No precipitate: we strongly advise centrifuging samples before diluting them to ensure that potential precipitate is not transferred.

UPLC/HPLC

Ultra High-Performance Liquid Chromatography equipped with photodiode array detection (PDA) and mass spectrometry (MS) from Shimadzu for separation and detection of metabolite and small biomolecules (e.g., secondar metabolites, lipids, glycolipids, organic compounds, ...). Different columns available for separation of a diverse range aan biomolecules.

Equipped a dual pump system (incl. degassing units), a cooled autosampler (for 334 samples), a broad range column oven (range: 10°C below room temperature to 85°C) with place for 6 columns, hereby allowing analysis of a broad range of diverse molecules.
The UPLC is equipped with different detectors:
1. Mass Spectrometry (MS) detector with ultrafast scanning speed (15,000 u/sec) in two modes of ionization, namely ESI (Electrospray ionization) and APCI (Atmospheric Pressure Chemical Ionization) for macromolecules and small polar molecules, respectively.
2. Photo Diode Array Detector with deuterium and tungsten lamps for UV/VIS detection in the range between 190 to 800 nm in high-resolution and/or high-sensitivity mode.

High-Performance Liquid Chromatography equipped with refractive index (RI) detector, ultraviolet (UV) detector and evaporative light-scattering detector (ELSD) for separation and detection of small biomolecules (e.g., secondar metabolites, lipids, glycolipids, organic compounds, ...). Different columns available for separation of a diverse range aan biomolecules.

Equipped a dual pump system (incl. degassing units), a cooled autosampler (for 334 samples), a broad range column oven (range: 10°C below room temperature to 85°C) with place for 6 columns, hereby allowing analysis of a broad range of diverse molecules.
The UPLC is equipped with the following detectors for detection of small biomolecules:
1. Refractive Index (RI) detector,
2. Ultraviolet (UV) detector,
3. Evaporative Light-Scattering Detector (ELSD) for small biomolecules.

Multimode plate readers

Three multimode microtitre plate readers (Tecan) are available, which are specialized for massive screening assays in synthetic biology:

With monochromator-based wavelength selection
Absorbance (UV – NIR & wavelength scanning)
Fluorescence with bottom reading module
Linear and orbital shaking, amplitude selectable (1-6 mm in 0.5 mm steps)
Temperature control from 5 °C above ambient up to 42 °C

High-throughput robotic systems

Biofoundry platform

A custom-made robotics platform (Revvity) for flexible high-throughput cloning and on-line screening. Different modules are combined through a flexible robotic arm.

PerkinElmer (now Revvity) explorer^TM G3 workstation iX20 module configured with:

Control PC running plate::works^TM scheduling and control software
Plate::handler^TM Flex 750 EXT collaborative SCARA robot
With servo gripper on 1m linear axis rail
4‐position lid handler
Barcode reader
Monitor/keyboard arm
iX20 TRESPA instrument tables with integrated LED status lights
iX20 system enclosure with HEPA filter
plate storage - 3x PerkinElmer 21 position plate shelfs tall

Cloning module

PerkinElmer JANUS G3 standard 8‐tip and rail gripper liquid handler)
PerkinElmer PlateStak
two heating blocks on-deck (Inheco CPAC Ultraflat HT 2‐TEC (4‐110°C))
PCR unit - Biometra TRobot 96 thermal cycler
centrifuge - Agilent Vspin centrifuge
plate sealer - KBiosystems WASP sealer

Screening module

8 Inheco Incubator Shaker MP (ambient +5K to 80°C, shaking 400‐1800 rpm)
plate reader: fluorescence (monochromator), optical density (stand-alone possible) - PerkinElmer EnSight
colony picker (stand-alone possible) - KBiosystems K63 colony picker- With tray hive, HEPA filter and UV sterilization lamp