DNA Biofoundry

Thermocyclers, Opentrons Lab Robot, 3D printer, Chi.bio mini bioreactor platform and 2L bioreactor for initial scallin-up.

Consulting and integral design of microorganisms, routes and improved prototypes for biotechnological applications. Clients can raise a biological problem and the node team undertakes to study the problem and offer a dossier with possible R&D&i actions. These solutions may later be implemented in the service through a specific agreement following the CSIC contracting models.

Design:

D.1 Metabolic modeling at the genomic scale of individual strains and natural and synthetic microbial communities.

D.2 Systems analysis and definition of the metabolic space of environmental, industrial and medically relevant bacterial strains.

D.3 Design and optimization of strains with biotechnological interest

D.4 Multi-strain modeling of clinical isolates and functional comparison

D.5 Modeling and design of environmental microbial communities, as well as their functional study and identification of key species from metagenomic data from massive sequencing (16S/18S/ITS/Metagenome/Metatranscriptome).

D.6 Modeling and analysis of human microbiome systems for the inference of metabolic interactions

BUILT:

B.1 DNA fragments cloning service

This service offers the cloning of DNA fragments into plasmids using classical molecular biology techniques. Such methodology includes the use of restriction enzymes.

  B.1.1. Cloning modality A. Fragment to clone provided by the user.

  B.1.2. Cloning modality B. Small fragment to clone (less than 1 kb) not provided by the user.

  B.1.3. Cloning modality C. Fragment to clone of large size (~3 kb) not provided by the user.

B.2 DNA Assembly Service by Gibson

This service offers the cloning of DNA fragments using the isothermal assembly technique (Gibson assembly).

1. 3 DNA modular assembly service by MoClo.

This service offers modular transcriptional unit assembly using Golden Standard technology.

  B.3.1. Assembly modality A. Gen to assemble provided by the user.

  B.3.2. Assembly modality B. Gen to assemble of small size (less than 1 kb) not provided by the user.

  B.3.3. Assembly modality C. Gen to assemble large (~3 kb) not provided by user.

TEST:

1. 1 Opentrons robotic workflow design service (OT-2)

This service offers the custom design of workflows based on liquid handling executed using an OT-2 robotic pipettor.

  T.1.1. Design of OT-2 protocols. Conceptualization or modification on Python script of custom protocols.

  T.1.2. Experimental validation of OT-2 protocols. Execution of operation tests on board OT-2 and adjustment of protocols.

T.2 Adaptive Evolution Laboratory (ALE) Service

This service offers the design and execution of adaptive evolution experiments in non-pathogenic model and non-model microorganisms.

  T.2.1. Implementing a manual ALE loop

  T.2.1. Implementation of a robotic ALE cycle

1. 3 3D CAD prototype design and manufacturing service

This service offers the design and manufacture of custom parts.

  T3.3. 3D CAD design

  T3.2. 3D CAD manufacturing