Available Equipment at the DNA and Microbe Biofoundry
The Sorbonne University Alliance Biofoundry, also known as the DNA and Microbe Biofoundry within the Paris Biofoundry, is equipped with advanced tools and technologies designed to streamline DNA assembly, microbial transformation, and high-throughput screening. Our state-of-the-art instruments support diverse research projects, enabling precision genetic engineering and comprehensive phenotyping of microorganisms such as bacteria, yeast, and microalgae.
Below is a list of the most important equipment available at our facility, providing researchers with the capabilities necessary to advance innovations in synthetic biology and microbial engineering:
20L Photo-bioreactor
From Synoxis Algae, it is called LUCY. It is a tubular system that uses bubble lift technology to ensure mixing. It operates at temperatures ranging from 15 to 35°C and is pH-controlled by CO2 sparging. The light intensity can reach up to 600 µmol/m²/s, with a customizable light regime. Growth is monitored using a density meter at 880 nm.
Emulsiflex
It is from Avestin, model C3, and is a homogenizer designed to break cells in suspension using a French press-like system. It can operate at pressures up to 2000 psi, lysing cells with minimal oxidation, as there is no air contact with the sample, and with minimal heating. The sample volume ranges from 10 mL to approximately 200 mL.
Cell Sorter
This is the 4-laser version of the CytoFLEX SRT from Beckman. It has a 100 µm aperture, so cells larger than 50 µm are not accepted to prevent clogging. It sorts from 5 mL tubes (down to 1 mL is possible) into a pre-filled 96-well plate or 4 tubes. Sorting is based on forward and side scattering, as well as fluorescence (Ex: 405, 488, 561, 638 nm / Em: 450/45, 525/40, 585/42, 610/20, 660/10, 675/30, 690/50, 710/50, 712/25, 780/60 nm)
QPCR
This equipment is used for fluorescence-based quantitative PCR. It is a QFX Opus 96 from Bio-Rad (CH1: 450-490 nm / 515-530 nm, CH2: 515-535 nm / 560-580 nm, CH3: 560-590 nm / 610-650 nm, CH4: 620-650 nm / 675-690 nm, CH5: 672-684 nm / 705-730 nm) and is compatible with most commonly used fluorophores.
Opentron
An open-source pipetting robot equipped with an 8-channel pipette and 11 SBS deck positions to automate simple and standard protocols. It features a vacuum system for column-based purifications. The robot is compatible with standard labware and has flexible software, including a Python API, making it highly customizable. It can quickly fill a 96-well plate in as little as 22 seconds, ensuring high throughput for various laboratory applications.
Fluorescence kinetics
The Walz Imaging PAM Maxi is a versatile system for chlorophyll fluorescence analysis, providing detailed insights into photosynthetic efficiency. It uses a 450 nm excitation wavelength and supports pulse-modulated excitation and actinic light for precise photosynthetic measurements. The camera used is the IMAG-K6 CCD camera, which features a 2/3″ sensor with a resolution of 1392 x 1040 pixels, offering high sensitivity and image quality for fluorescence imaging. This setup is ideal for analyzing spatial and temporal variations in photosynthetic activity
Colony Picker
It’s a QPIX 420 from Molecular Devices, equipped with a camera to select colonies based on white light or fluorescence. It supports various types of pins to adapt to different colony textures and can restreak colonies onto up to two destination plates, organized either in agar or 96-well formats. The system senses agar height and is compatible with both Omnitrays and circular 90 mm plates.
Biolistic
It’s a Bio-Rad PDS-1000/He, which shoots 0.6 µm high-velocity gold particles onto a petri dish under vacuum. This system can be used for both organellar and nuclear genetic transformation. We currently use 1100 psi rupture disks, but other options ranging from 450 to 1800 psi are available for purchase.
Electroporator
We have several electroporators, ranging from the classic Gene Pulser II from Bio-Rad to the Neon NXT from Thermo Fisher and the Nepa21 from NepaGene. Each system has its own specific features in terms of volume capacity, pulse types, and voltage settings, ensuring that one of them will meet your needs.
· Gene Pulser II (Bio-Rad): Handles sample volumes from 40 µL to 400 µL, with voltage settings ranging from 200 to 3000 V. It offers both exponential decay and square-wave pulse modes for flexibility across different electroporation needs.
· Neon NXT (Thermo Fisher): Designed for very small volumes (down to 10 µL), with customizable pulse width and pulse number. It delivers up to 2500 V, making it highly efficient for electroporating difficult-to-transfect cells.
· Nepa21 (NepaGene): Provides precise control with both high-voltage (up to 2000 V) and low-voltage pulses, capable of applying both positive and negative voltages. It supports volumes from 10 µL to 100 µL, ideal for complex transfections, including delicate cell types.
Cell Counter
This is a Countess II FL from Thermo Fisher, designed for automated cell counting using a dedicated reusable slide and camera-based recognition. It operates on white light, GFP, and Cy5 channels, making it versatile for various cell types. The system is user-friendly, with tunable detection intensity thresholds, roundness, and size parameters to ensure accurate cell counting.
