Rezultaty
The history of technological innovations has demonstrated that the early developers hardly could foresee the various ways the technology would be used and implemented later on To open up all possible narratives of the future we want to invite artists in residency to come and learn in our labs about our mission and give them the opportunity to either carry out an artistic interventions or develop some creative new types of applications of the projects technology
Report on stakeholder involvementFor ellaboration of this report we will involve a number of peers and potential users of the technology such as scientists eg conservational biologists chemists biotechnologists geologists maybe even astrobiologists people form industry small medium and large corporations governance regulatory bodies international organisations like IPCC or CBD and representatives from civil society through workshops and interviews to provide a reality check for the proposed technology
Systems-guided catalogue of sites of intervention with agents delivering NTN reactionsA suite of mathematical and computational approaches ranging from phenomenological to mechanistic will be developed for revisiting the principles that govern the function dynamics and evolution of microbial ecosystems and what allows them to accept new members with novel biochemical properties The way towards topdown synthetic ecology will require new algorithms modeldriven analysis tools and gene function annotation
Report on transposon for converting any Gram-negative bacteria in an HFR strainThis will involve a transposon able to mobilize an entire chromosome though conjugation between a donor and a DNAless recipient For this all the mobtra genes involved in conjugal transfer of superpromiscuous plasmid RP4 will be retrieved from their original genetic frame and assembled as an artificial gene cluster in a miniTn5 transposon vector Upon aquisition of such a transposon any strain will acquire the ability of selftransference and therefore will behave as an HFR strain Highfrequency of recombination that will ease the passing of the genomic information among strains with different degrees of NTN reaction evolution
Proposition of containment needs for microbial agents bearing peribolic reactionsModeling approaches will be adopted to inspect the pluses and minuses of dealing with live —but heavily refactored microbial agents that could propagate through the Biosphere. This will help to determine the needs of containment of the agents at stake. This lower-scale models will help to understand the resilience and optimal yield conditions of designed microorganisms and microbial consortia and create in silico tests of the proposed peribolic reactions.
A merged model of biogeochemical, biological and industrial matter/energy flow in EarthThe concept of Industrial Metabolism traditionally refers in a metaphoric fashion to the physical traffic of material and energy resources through the economic systems as long as similarly to biological metabolism they are processed resulting into goods and waste We wish to go beyond mere metaphores and try to develop actual integrated models of matter and energy flows through the Biosphere and how they could be deliberately or accidentally altered by the introduction at various scales of the NTN reactions entertained in MADONNA and others that could be developed with the same technologies
Detailed report a genetically optimized artificial carboxylase based on evolved Sav isoformsThe reaction conditions that accompany desired carboxylase recations are often different from physiological conditions (defined as pH of approximately 7, aqueous environments, and ambient temperatures) and turnover numbers very low. In order to make such reaction sustainable and to ultimately recruit such reactions into biology, the protein scaffold has to be evolved. Therefore, we will develope an strategy to implement an enzyme engineering trajectory towards a highly efficient Sav-Pd-catalyst for the production of acrylic acid.
Automated generation of metalloenzymes and information capture through a fitness functionWe will take the reaction invented chemically (ie CO2 capture with a metalloenzyme) and and run it in the presence of cells using a chemical droplet robot in which the biological system is programmed to generate peptides that can chelate metal ions to generate ArMs that can be symbiotically selected by the system. This links process engineering to the fitness functions and allows the systems to be linked artificially using such a chem-o-biological robot. The link is software and spectroscopy with chemical feedback. The chemicals can acts as mutagens, and also act as selection agents on the peptides expressed.
Summary and impact of public communication activitiesGiven the fundamental nature of the scope of our project we feel the responsibility to also share this with the general public through a number of science communication formats eg series of short video clips dissemination though web and social media Science Cafe With these formats we do not only aim to inform the public but also to listen to their thoughts and feedback which will be collected consider and eventually be addressed by the project team to alow for a two way communication between science and the public
Responsible innovation. Report of ethics, safety and security tasksReconciliation of geochemical, biological and industrial/human induced global cycles will not only provide a sustainable way of producing and consuming, but will inevitably change the characteristic of the three cycles, diffusing and enlarging the limits of human intervention on the planet. In this report we will ask: what rationale (world view) is behind the projects aim and goal, what other rationales co-exist, which solutions do they provide? What are the ethical dimensions of going forward with the project versus continuing with the unsustainable business-as-usual.
Report on a genetically engineered artificial Fischer-Tropschase enzyme for reduction of CO/CO2 and its expression in vivoGiven that biotinfunctionalized catalysts can be anchored into a streptavidin scaffold this deliverable will report how biotinstreptavidin technology can be exploited selected for incorporation of the Fe4S4 cluster into the genetically encoded protein along with details on characterization of the cofactor and in silico docking studies of the Fe4S4cofactorstreptavidin complex
The aim here is to have the choice of destroying altogether the genetic material of E coli and P putida while preserving the whole of the biochemical networks For this the genes ungdut will be deleted and replaced by a tightly regulated ung dut bicistronic operon inducible upon exposure of cells to an external effector eg 3 methylbenzoate While the lack of ungdut will make many Ts of the genome being replaced by U residues their abrupt expression will cleave the chromosome at multiple sites thus converting the cells in a sort of chemical vesicle These will be excellent vessels to develop NTN reactions and as recipients of heavily mutated and edited artificial chromosomes
Morbidostat for heterotic computation of (bio)chemical problemsThis is about programming evolution by switching between certain combinations of nutrientssubstrates along with a simple deterministic model to compute evolution heterotically This system is an automated continuousculture device that controls substrate concentration to maintain constant growth inhibition The device runs at a certain interval and adds either fresh medium with a high substrate concentration 24dinitrotoluene DNT as the target molecule in our case or without it By giving it pulses of DNT and letting it recover we expect that the ROS produced by faulty reactions by suboptimal dioxygenases will diversify the corresponding DNA sequences until a biochemical solution is found
Genome edited strains of E. coli and P. putida entirely cyborgized for hosting NTN reactionsThe genomes of the two bacterial species adopted in this Project (E. colo and Pseudomonas putida) will be [i] erased of instability determinants and other genes encoding functions considered to be irrelevant for the sake of MADONNA and [ii] endowed with new traits to make them withstand the working conditions of the reactions of interest.
Robotic platform for reverse-reading of chemical reactions into DNAThe coding of DNA in the presence of the process will be reverseread into the system This needs us to generate artificial DNA sequences in the presence of the chemistry and also random peptide synthesis We will build a hybrid digital Complementary metaloxidesemiconductor CMOSdriven synthetic chemical platform to write DNA directly taking advantage of the speed and parallelism of CMOS aiming for GHz write rates on a single strand of DNA within a CMOS nanopore assembler and scale up using PCR this is the reverse of nanopore sequencing
Microdroplet-based environmental simulatorThis will be based on a fully autonomous chemical robot system that is able to generate random physicochemical inputs in microdroplet scale. The droplet behaviours will then be analysed, and ranked using a fitness function. This process is continued through iterated generations. This allows inspecting how the genotype is modulated through an envirotype to express the phenotype of interest.
This Deliverable implies the elaboration of an userfriendly webpage for Communication and Dissemination of Projects activities as well as for internal communication among MADONNA members
This will consist of a document specifying the formats to be followed by the partners for storing the data of interest in a joint repository as well as formal languages for description of actions and constructs
This is about application of complex networks theory to model new metabolic loops brought about by smallscale and largescale peribolism Meso and largescale models of ecosystems incorporating the NTN reactions set by MADONNA will be produced Our ecosystem description incorporates both standard habitats as well as the highenergy fuelpowered counterparts that are defined by large urban centres and industry By incorporating peribolism we will transform these type of wastesink components into new largescale chemical processes thus deeply changing the global dynamics To this goal we will develop a set of mathematical and computational tools that provide a rationale for the expected responses of this global metabolism on different scales
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Elsevier BV
DOI:
10.1016/j.biosystems.2019.104015
Autorzy:
Tas, H., Grozinger, L., Goni-Moreno, A., de Lorenzo, V.
Opublikowane w:
Synthetic Biology, 2021, ISSN 2397-7000
Wydawca:
Oxford University Press
DOI:
10.1093/synbio/ysab024
Autorzy:
Durante-Rodríguez, G., Páez-Espino, D and de Lorenzo, V.
Opublikowane w:
Frontiers in Microbiology, 2021, ISSN 1664-302X
Wydawca:
Frontiers Media
DOI:
10.3389/fmicb.2021.641440
Autorzy:
Pei, L., Garfinkel, M. & Schmidt, M.
Opublikowane w:
Nature Communications, 2022, ISSN 2041-1723
Wydawca:
Nature Publishing Group
DOI:
10.1038/s41467-022-29889-y
Autorzy:
Kim, J., Goñi-Moreno, A., de Lorenzo, V.
Opublikowane w:
mBio, 2021, ISSN 2150-7511
Wydawca:
American Society for Microbiology
DOI:
10.1128/mbio.03685-20
Autorzy:
Akkaya, Ö., Aparicio, T., Perez-Pantoja, D., de Lorenzo, V.
Opublikowane w:
Environmental Microbiology, 2020, ISSN 1462-2912
Wydawca:
Blackwell Publishing Inc.
DOI:
10.1111/1462-2920.15384
Autorzy:
Miguel Berdugo, Manuel Delgado-Baquerizo, Santiago Soliveres, Rocío Hernández-Clemente, Yanchuang Zhao, Juan J. Gaitán, Nicolas Gross, Hugo Saiz, Vincent Maire, Anika Lehmann, Matthias C. Rillig, Ricard V. Solé, Fernando T. Maestre
Opublikowane w:
Science, Numer 367/6479, 2020, Strona(/y) 787-790, ISSN 0036-8075
Wydawca:
American Association for the Advancement of Science
DOI:
10.1126/science.aay5958
Autorzy:
Silbert, J., de Lorenzo, V. and Aparicio, T.
Opublikowane w:
ACS Synthetic Biology, 2021, ISSN 2161-5063
Wydawca:
American Chemical Society
DOI:
10.1021/acssynbio.0c00611
Autorzy:
Algar, E., Al-Ramahi, Y., de Lorenzo, V. and Martínez-García, E.
Opublikowane w:
ChemBioChem, 2020, ISSN 1439-7633
Wydawca:
John Wiley & Sons
DOI:
10.1002/cbic.202000330
Autorzy:
Aparicio, T., Silbert, J., Cepeda, S. and de Lorenzo, V.
Opublikowane w:
BioDesign Research, 2022, ISSN 2693-1257
Wydawca:
American Association for the Advancement of Science
DOI:
10.34133/2022/9850305
Autorzy:
Solé, R. and Levin, S.
Opublikowane w:
Philosophical Transactions of the Royal Society B,, 2022, ISSN 0962-8436
Wydawca:
Royal Society of London
DOI:
10.1098/rstb.2021.0376
Autorzy:
Martínez-García, E., Fraile, S., Rodríguez-Espeso, R., Vecchietti, D., Bertoni, G., de Lorenzo, V.
Opublikowane w:
ACS Synthetic Biology, 2020, ISSN 2161-5063
Wydawca:
American Chemical Society
DOI:
10.1021/acssynbio.0c00272
Autorzy:
Nikel, P.I., Benedetti, I., Wirth, N.T., de Lorenzo, V. and Calles, B.
Opublikowane w:
Microbial Biotechnology, 2022, ISSN 1751-7915
Wydawca:
John Wiley & Sons
DOI:
10.1111/1751-7915.14063
Autorzy:
Doran, David; Abul-Haija, Yousef M.; Cronin, Leroy
Opublikowane w:
Angewandte Chemie (International Ed. in English), Numer 1, 2019
Wydawca:
American Chemical Society (ACS), Chinese Chemical Society, Chemical Society of Japan, German Chemical Society (GDCh) and the Royal Society of Chemistry
DOI:
10.26434/chemrxiv.7712297.v1
Autorzy:
Aparicio, T., de Lorenzo, V., Martínez-García, E.
Opublikowane w:
Recombineering. Methods in Molecular Biology, 2022, ISBN 978-1-0716-2233-9
Wydawca:
Springer Nature
DOI:
10.1007/978-1-0716-2233-9_4
Autorzy:
Markus Schmidt, Nediljko Budisa
Opublikowane w:
Art as We Don’t Know It, 2020, Strona(/y) 20-36, ISBN 978-952-60-8823-5
Wydawca:
Aalto University Press
Autorzy:
Víctor de Lorenzo, Hiren Joshi
Opublikowane w:
Consequences of Microbial Interactions with Hydrocarbons, Oils, and Lipids: Biodegradation and Bioremediation, 2019, Strona(/y) 1-15, ISBN 978-3-319-44535-9
Wydawca:
Springer International Publishing
DOI:
10.1007/978-3-319-44535-9_25-1
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