Periodic Reporting for period 3 - ACDC (Artificial Cells with Distributed Cores to Decipher Protein Function)
Berichtszeitraum: 2022-02-01 bis 2023-07-31
We envision a future where ‘chemical apps’ on mobile devices produce on demand valuable compounds for health and performance as well as apps for bioagent threat detection and disease. To take concrete and defined steps toward this future vision, we will exploit the miniaturization provided by lab on a chip technology and construct responsive architectures and metabolism based on living cells and tissues. We will build programmable and re-configurable, (bio)chemical processes, with precision, order, and as hierarchical cellular constructs, in the same way as living systems. We will enable microscale, liquid-based, chemical compartmentalisation (cores), and inter-compartmental (core-core) communication, just as one finds in organelles, cells and tissues. The ACDC project focusses on developing this next generation technology through a detailed workplan that heavily involves the nontrivial tasks of integrating diverse state of the art technologies including microfluidics, microwave resonators, DNA-based supramolecular assembly, in vitro gene expression and the integration of membrane channels into a functional platform.
The overall objective of the ACDC project is to manufacture compartmentalised, liquid-based chemistries, as discrete, yet interactive and multifunctional cores, within micro-scale containment capsules as communicating micro-laboratories.
The overall objective of the ACDC project is to manufacture compartmentalised, liquid-based chemistries, as discrete, yet interactive and multifunctional cores, within micro-scale containment capsules as communicating micro-laboratories.
Objective 1. Produce multifunctional cores and containment capsules through use of 2D/3D printed, multiphase microfluidics.
CU designed and manufactured 3D-printed microfluidic devices to produce ACDC capsules. These devices were implemented with ELV pressure pump technology and thermal controller. Functionality was developed with CU, UNITN and EXP. Core and capsule arrangement and interconnectivity was developed in collaboration with ZHAW. CU also implemented novel control using microwave technology and droplet levitation. ELV developed and beta-tested through the consortium a thermalization system composed of thermal reservoir holders and a chamber.
Objective 2. Demonstrate core-core and core-environment communication together with energy harvesting.
We demonstrated the versatility of core networks in their potential to compartmentalise reaction chemistries which can then be sequenced through the judicial application of communicative elements both cargo-based and cargo-free. We also expanded the breadth of chemistries available to be used within these core networks providing the technology with greater downstream utility. We exploited the connectivity of large, interconnected networks through the creation of digital twins to our wet models. As a proof of principle, cores of various arrangements were made and energy transfer in the form of ATP was demonstrated. Increases in energy-dependent reactions were demonstrated and interestingly these increases were very non-linear, demonstrating the underlying complexities of communication in a three-dimensional compartmentalised system.
Objective 3. Produce reconfigurable capsules based on DNA barcoding.
UNITN executed the production of DNA-labelled capsules, with one step and two step labeling, exploiting 3D microfluidic chips printed in CU and UNITN, with ELV microfluidic flow controller and EXP DNA tags. UNITN also developed the reconfiguration system based on in situ RNA. We also report the effects of phase separation in mixed membranes on the arrangement of assembled vesicles. ZHAW designed an additional simulator that captures the dynamics of assembly.
Objective 4. Build a compiler that translates formally described instances of chemical processes into an ACDC design.
The compiler has been made and demonstrated. In addition, based on a multi-scale simulation environment for life-like process management, we established an intensive collaboration between model builders and experimenters. This multi-scale simulation environment allowed us to perform simulations ranging from the details of the reaction – diffusion processes in the selective binding of containers over studies of spatially heterogeneous reaction environments (e.g. applied to autocatalytic reaction networks) to the geometry of polydisperse aggregates of ACDC containers. In these ways, close contacts between ACDC modelling and ACDC experimentation have been developed.
Objective 5. Test our ACDC technology using small molecule library screening on targeted membrane proteins.
CU determined appropriate core-core/capsule-capsule cargo delivery, reporting and sensing protein/peptide modules to be included in Explora plasmid construction and worked alongside Explora to determine potential and optimal fusion construct arrangements. UNITN completed preparation of the cell-free system, protein pores, and generation of vesicles, integration of pores in their membrane and creation of a standard method to control iron transport inhibition. ZHAW developed the simulator for the 3D structure of cores that will be instrumental for this objective.
Objective 6. Evaluate ACDC emergent technologies and results for potential intellectual property for exploitation.
Ongoing.
Objective 7. Execute targeted dissemination activities to public and stakeholders to enliven ACDC aims and Living Technologies in general
Despite the pandemic, the outreach and training programme conducted by MUSE with ALL consortium members has been carried out without significant delays. Most of the activities have been moved to an online or blended format, such has the Open Talks, Start-up School and Summer School.
In-person activities recommenced with the openings. The two challenges have been an opportunity to engage the artistic community and university students with ACDC themes. A temporary exhibition (not initially planned) was set up to reach a wider public on scientific and artistic reflections on artificial life.
Objective 8. Generate a discussion about the societal and ethical impact of the technologies developed in ACDC and in Living Technologies in general.
A panel discussion led by Rudolf Füchslin with 5 panelists was held on this topic, as part of the Wivace 2021 workshop on September 15th, 2021 at ZHAW in Winterthur, Switzerland, which was organized by the ZHAW group of the ACDC consortium. The report
has been condensed to a paper (published in the proceedings of WIVACE 21). MUSE organised an Open Talk about ethics in science and technology and an ethics discussion with students during the second challenge. An ethics report of the ACDC project has been submitted.
CU designed and manufactured 3D-printed microfluidic devices to produce ACDC capsules. These devices were implemented with ELV pressure pump technology and thermal controller. Functionality was developed with CU, UNITN and EXP. Core and capsule arrangement and interconnectivity was developed in collaboration with ZHAW. CU also implemented novel control using microwave technology and droplet levitation. ELV developed and beta-tested through the consortium a thermalization system composed of thermal reservoir holders and a chamber.
Objective 2. Demonstrate core-core and core-environment communication together with energy harvesting.
We demonstrated the versatility of core networks in their potential to compartmentalise reaction chemistries which can then be sequenced through the judicial application of communicative elements both cargo-based and cargo-free. We also expanded the breadth of chemistries available to be used within these core networks providing the technology with greater downstream utility. We exploited the connectivity of large, interconnected networks through the creation of digital twins to our wet models. As a proof of principle, cores of various arrangements were made and energy transfer in the form of ATP was demonstrated. Increases in energy-dependent reactions were demonstrated and interestingly these increases were very non-linear, demonstrating the underlying complexities of communication in a three-dimensional compartmentalised system.
Objective 3. Produce reconfigurable capsules based on DNA barcoding.
UNITN executed the production of DNA-labelled capsules, with one step and two step labeling, exploiting 3D microfluidic chips printed in CU and UNITN, with ELV microfluidic flow controller and EXP DNA tags. UNITN also developed the reconfiguration system based on in situ RNA. We also report the effects of phase separation in mixed membranes on the arrangement of assembled vesicles. ZHAW designed an additional simulator that captures the dynamics of assembly.
Objective 4. Build a compiler that translates formally described instances of chemical processes into an ACDC design.
The compiler has been made and demonstrated. In addition, based on a multi-scale simulation environment for life-like process management, we established an intensive collaboration between model builders and experimenters. This multi-scale simulation environment allowed us to perform simulations ranging from the details of the reaction – diffusion processes in the selective binding of containers over studies of spatially heterogeneous reaction environments (e.g. applied to autocatalytic reaction networks) to the geometry of polydisperse aggregates of ACDC containers. In these ways, close contacts between ACDC modelling and ACDC experimentation have been developed.
Objective 5. Test our ACDC technology using small molecule library screening on targeted membrane proteins.
CU determined appropriate core-core/capsule-capsule cargo delivery, reporting and sensing protein/peptide modules to be included in Explora plasmid construction and worked alongside Explora to determine potential and optimal fusion construct arrangements. UNITN completed preparation of the cell-free system, protein pores, and generation of vesicles, integration of pores in their membrane and creation of a standard method to control iron transport inhibition. ZHAW developed the simulator for the 3D structure of cores that will be instrumental for this objective.
Objective 6. Evaluate ACDC emergent technologies and results for potential intellectual property for exploitation.
Ongoing.
Objective 7. Execute targeted dissemination activities to public and stakeholders to enliven ACDC aims and Living Technologies in general
Despite the pandemic, the outreach and training programme conducted by MUSE with ALL consortium members has been carried out without significant delays. Most of the activities have been moved to an online or blended format, such has the Open Talks, Start-up School and Summer School.
In-person activities recommenced with the openings. The two challenges have been an opportunity to engage the artistic community and university students with ACDC themes. A temporary exhibition (not initially planned) was set up to reach a wider public on scientific and artistic reflections on artificial life.
Objective 8. Generate a discussion about the societal and ethical impact of the technologies developed in ACDC and in Living Technologies in general.
A panel discussion led by Rudolf Füchslin with 5 panelists was held on this topic, as part of the Wivace 2021 workshop on September 15th, 2021 at ZHAW in Winterthur, Switzerland, which was organized by the ZHAW group of the ACDC consortium. The report
has been condensed to a paper (published in the proceedings of WIVACE 21). MUSE organised an Open Talk about ethics in science and technology and an ethics discussion with students during the second challenge. An ethics report of the ACDC project has been submitted.
We have achieved progress beyond the state of the art with regard to several areas. 1. 3D printed fluidics, 2. reconfigurable systems, 3. chemical compiling. 4. microwave technology as appiled to artificial cells. These new results are disseminated in public access reports, publications, presentations, and public forum discussions. We expect scientific impact in the areas of soft-matter physics, complex systems, and custom small scale manufacturing. We have developed these new artificial cell technologies such that we are now proceeding with applications towards cellular systems including cancer mediation and early stage cancer detection. With the development of these new trusts, we expect a large impact of our budding technologies on the health sector, improving the lives of people in the EU and around the world.