Article
Biochemistry & Molecular Biology
David Canadell, Nicolas Ortiz-Vaquerizas, Sira Mogas-Diez, Eulalia de Nadal, Javier Macia, Francesc Posas
Summary: This article introduces an architecture for reprogrammable biological circuits, aiming to achieve flexibility and scalability of complex cell-based computing devices through minimal cell engineering. By external reprogramming, simple logic responses can be realized without further cell engineering or rearrangements. Additionally, the inclusion of a memory module significantly improves the digital response of the devices.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Multidisciplinary Sciences
Tianchi Chen, M. Ali Al-Radhawi, Christopher A. Voigt, Eduardo D. Sontag
Summary: A design for genetically encoded counters using repressor-based circuits is proposed, allowing for scalable computation and bypassing limitations on maximal circuit genes per cell. The design utilizes distributed computation with specialized cell types and connector modules for interconnecting single-bit counters to achieve an N-bit counter. An optimization framework is used to determine gate parameters and guide the construction of novel gates, moving towards circuits capable of finite automaton computation akin to central processing units.
Article
Multidisciplinary Sciences
Luna Rizik, Loai Danial, Mouna Habib, Ron Weiss, Ramez Daniel
Summary: Researchers have utilized the perceptgene technology to create synthetic gene circuits based on the computational properties of neuronal networks. These circuits can perform non-binary logic computation and signal processing, and can be modified for different tasks by adjusting parameters.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Noreen Wauford, Akshay Patel, Jesse Tordoff, Casper Enghuus, Andrew Jin, Jack Toppen, Melissa L. Kemp, Ron Weiss
Summary: During development, cells undergo symmetry breaking and self-organize into complex structures. This study presents a stochastic genetic switch that is tunable by small molecules, allowing for programmable symmetry breaking, commitment to downstream cell fates, and morphological self-organization. The switch can control the cell-cell adhesion properties and generate a wide variety of 3D morphologies. The findings provide new insights into the relationship between cell-cell adhesion strengths and downstream morphologies, and suggest that programmable symmetry breaking could be used in complex tissue and organoid engineering.
Article
Multidisciplinary Sciences
Vladimir Nikolic, Moriah Echlin, Boris Aguilar, Ilya Shmulevich
Summary: The capacity of cells to process information is used in various applications. Single cell engineering has limitations, so synthetic biologists have started to engineer multicellular systems. Reservoir computing is introduced to further advance information processing in synthetic multicellular systems.
Article
Computer Science, Hardware & Architecture
Marzieh Gerami, Mohammad Eshghi, Modjtaba Emadi-Baygi, Fatemeh Elahian, Mehdi Hosseinzadeh
Summary: Researching biological circuit design and simulation, it was found that among different architectures of biomultiplexers, the Full-NOR design offers the shortest execution time, with a significant decrease in the number of promoters and genes.
JOURNAL OF SUPERCOMPUTING
(2021)
Article
Biology
Miha Moskon, Ziga Pusnik, Nikolaj Zimic, Miha Mraz
Summary: Applications in synthetic biology often require engineered computing structures that can be programmed to process information. The design of programmable biological circuits, inspired by field-programmable gate array (FPGA) circuits, allows configurations to be changed in vivo without additional genetic engineering. These circuits are based on distributed cellular computing modules, making biological implementation easier to achieve.
COMPUTERS IN BIOLOGY AND MEDICINE
(2021)
Article
Multidisciplinary Sciences
Ximing Li, Luna Rizik, Valeriia Kravchik, Maria Khoury, Netanel Korin, Ramez Daniel
Summary: Complex biological systems involve cells acting collectively to solve sophisticated tasks, while researchers have implemented neural network-like computing in bacterial consortia for pattern recognition.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Sira Mogas-Diez, Eva Gonzalez-Flo, Javier Macia
Summary: Efforts have been made to build printable cellular devices for different purposes, using concentration of biological signals for information encoding in 2D circuits. By printing cellular circuits on paper surfaces, a feasible and reliable industrial production for multiple applications can be achieved.
NATURE COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Janvie Manhas, Hailey Edelstein, Joshua N. Leonard, Leonardo Morsut
Summary: Researchers have repurposed natural receptors to engineer synthetic receptors that enable cells to detect and respond to their environments. By improving and integrating protein-based receptors and signal-processing components, customized functions and programming can be achieved.
NATURE CHEMICAL BIOLOGY
(2022)
Review
Plant Sciences
Marta Vazquez-Vilar, Sara Selma, Diego Orzaez
Summary: The possibility of engineering plants with augmented capabilities has fascinated plant biotechnologists since its origins, and it has become even more relevant in present times due to climate change and population growth. Synthetic biology has provided tools for constructing synthetic gene circuits (SGCs) in plant biotechnology, allowing the manipulation of environmental or endogenous inputs to generate new physiological outputs. This review aims to categorize the components of SGCs into sensor, processor, and actuator modules and discuss the latest advances and challenges in their design, providing a framework for exchanging DNA parts and information in plant synthetic biology.
JOURNAL OF EXPERIMENTAL BOTANY
(2023)
Review
Biotechnology & Applied Microbiology
Dmytro Kukhtar, Martin Fussenegger
Summary: Synthetic biology has traditionally focused on single cell systems, such as bacteria, yeast, or mammalian cells, for introducing new or altered functionality. This article extends the field of synthetic biology to nematodes, particularly the well-studied organism Caenorhabditis elegans, as a practical platform for developing applications in a multicellular context. The authors review transgenesis techniques for nematodes and discuss the application of synthetic biology principles in constructing nematode gene switches and genetic devices for controlling motility. Potential applications of engineered nematodes are also discussed.
BIOTECHNOLOGY AND BIOENGINEERING
(2023)
Review
Computer Science, Artificial Intelligence
Miha Moskon, Roman Komac, Nikolaj Zimic, Miha Mraz
Summary: Synthetic biology has evolved from focusing on uncoupled monoclonal cellular populations to coupled intercellular circuits composed of engineered cellular modules. The shift is towards building networks of different strains to create more complex biological processing systems. This transition aims to advance the field towards constructing multicellular biological processors and exploring potential applications in neural computing.
NEURAL COMPUTING & APPLICATIONS
(2021)
Review
Biochemical Research Methods
Heather S. Deter, Ting Lu
Summary: Synthetic microbial consortia are at the forefront of synthetic biology, promising versatile engineering of cellular functions through coordination of intercellular interactions. Researchers have studied building blocks for intercellular communication, unidirectional positive and negative interactions, and have developed bidirectional interactions towards complex communities.
CURRENT OPINION IN BIOTECHNOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Davide Ribezzi, Marieme Gueye, Sammy Florczak, Franziska Dusi, Dieuwke de Vos, Francesca Manente, Andreas Hierholzer, Martin Fussenegger, Massimiliano Caiazzo, Torsten Blunk, Jos Malda, Riccardo Levato
Summary: A novel technique called Embedded Extrusion-Volumetric Printing (EmVP) is introduced, combining extrusion bioprinting and layer-less, ultra-fast volumetric bioprinting. Light-responsive microgels are developed as bioresins for light-based volumetric bioprinting, providing a microporous environment for cell homing and self-organization. EmVP is used to create complex synthetic biology-inspired intercellular communication models, where adipocyte differentiation is regulated by optogenetic-engineered pancreatic cells.
ADVANCED MATERIALS
(2023)
Article
Multidisciplinary Sciences
Blai Vidiella, Antoni Guillamon, Josep Sardanyes, Victor Maull, Jordi Pla, Nuria Conde, Ricard Sole
Summary: This paper presents an engineered gene network that displays self-organized criticality (SOC) behavior in living cells, poising them close to a critical state. The authors discuss the potential implications of this state on cellular dynamics and behavior.
NATURE COMMUNICATIONS
(2021)
Article
Biology
Guim Aguade-Gorgorio, Stuart Kauffman, Ricard Sole
Summary: Phenotypic switching in cancer cells is a common phenomenon across tumor types and plays a crucial role in tumor evolution and therapy resistance. A mathematical framework has been developed to understand the dynamics of phenotypic switching, which provides insights for the success of combination therapies targeting both replication and phenotypic transitions.
BULLETIN OF MATHEMATICAL BIOLOGY
(2022)
Article
Ecology
Miguel Berdugo, Blai Vidiella, Ricard V. Sole, Fernando T. Maestre
Summary: With ongoing climate change, the probability of exceeding aridity thresholds in drylands and experiencing abrupt ecosystem changes is higher than ever. By identifying different mechanisms causing aridity thresholds and potential amplification mechanisms, we can develop specific hypotheses to bridge knowledge gaps and focus on monitoring and adapting to abrupt ecosystem changes in global drylands.
FUNCTIONAL ECOLOGY
(2022)
Article
Oncology
Radoslav Janostiak, Ariadna Torres-Sanchez, Francesc Posas, Eulalia de Nadal
Summary: This review summarizes the recent research on the function and regulation of Rb1. Rb1 is an important tumor suppressor protein that regulates cell cycle and cancer development through post-translational modifications. We discuss potential approaches to design novel anticancer therapies by harnessing these modifications.
Article
Biochemistry & Molecular Biology
Carlos Jimenez, Roberta Antonelli, Mariona Nadal-Ribelles, Laura Devis-Jauregui, Pablo Latorre, Carme Sole, Marc Masanas, Adria Molero-Valenzuela, Aroa Soriano, Josep Sanchez de Toledo, David Llobet-Navas, Josep Roma, Francesc Posas, Eulalia de Nadal, Soledad Gallego, Lucas Moreno, Miguel F. Segura
Summary: Loss of function of mSWI/SNF complexes in neuroblastoma impairs cell proliferation and inhibits tumor invasion and metastasis. Disruption of the BAF complex results in epigenetic repression of invasion-related genes, significantly inhibiting neuroblastoma metastasis. These findings provide important insights for the development of new therapeutic strategies targeting mSWI/SNF complexes in neuroblastoma.
Article
Cell Biology
Arnau Ulsamer, Adrian Martinez-Limon, Sina Bader, Sara Rodriguez-Acebes, Raimundo Freire, Juan Mendez, Eulalia de Nadal, Francesc Posas
Summary: The stress-activated protein kinases (SAPKs) and their functional homologs, such as Mrc1 and Claspin, play a protective role in preventing DNA damage during S-phase in both yeast and mammals.
Article
Biochemistry & Molecular Biology
Pol Picon-Pages, Monica Bosch-Morato, Laia Subirana, Francisca Rubio-Moscardo, Biuse Guivernau, Hugo Fanlo-Ucar, Melisa Ece Zeylan, Simge Senyuz, Victor Herrera-Fernandez, Ruben Vicente, Jose M. Fernandez-Fernandez, Jordi Garcia-Ojalvo, Attila Gursoy, Ozlem Keskin, Baldomero Oliva, Francesc Posas, Eulalia de Nadal, Francisco J. Munoz
Summary: Alzheimer's disease is caused by misfolded amyloid beta-peptide (Aβ) forming beta-sheets, but there are currently no treatments available to prevent it. Through a genome-wide screen in Saccharomyces cerevisiae, we identified 81 mammalian orthologue genes that enhance Aβ(1-42) toxicity and 157 that provide protection. Further studies revealed that calcium regulation, protein translation, and mitochondrial activity were the main cellular functions affected by Aβ oligomers (oAβ). We focused on SURF4, a protein that regulates the store-operated calcium channel (SOCE), and found that it contributes to oAβ(1-42) neurotoxicity by decreasing SOCE activity.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
David Canadell, Nicolas Ortiz-Vaquerizas, Sira Mogas-Diez, Eulalia de Nadal, Javier Macia, Francesc Posas
Summary: This article introduces an architecture for reprogrammable biological circuits, aiming to achieve flexibility and scalability of complex cell-based computing devices through minimal cell engineering. By external reprogramming, simple logic responses can be realized without further cell engineering or rearrangements. Additionally, the inclusion of a memory module significantly improves the digital response of the devices.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Multidisciplinary Sciences
Maximilian Mosbacher, Sung Sik Lee, Gilad Yaakov, Mariona Nadal-Ribelles, Eulalia de Nadal, Frank van Drogen, Francesc Posas, Matthias Peter, Manfred Claassen
Summary: This study characterizes the regulation of MAP kinase Hog1 in Saccharomyces cerevisiae and reveals a mixed phosphorylation mechanism regulated by a positive feedback loop. Simulations show that this mechanism is necessary for full sensitivity to stimuli and robustness to perturbations.
NATURE COMMUNICATIONS
(2023)
Review
Biotechnology & Applied Microbiology
Eulalia de Nadal, Francesc Posas
Summary: Cells coordinate their intracellular activities in response to changes in the extracellular environment for their survival and proliferation. The high-osmolarity glycerol (HOG) pathway in yeast is responsible for the response to high osmolarity, leading to temporary cell cycle arrest, adjustment of transcription and translation patterns, and regulation of metabolism.
FEMS YEAST RESEARCH
(2022)
Article
Genetics & Heredity
Pablo Latorre, Rene Bottcher, Mariona Nadal-Ribelles, Constance H. Li, Carme Sole, Gerard Martinez-Cebrian, Paul C. Boutros, Francesc Posas, Eulalia de Nadal
Summary: This study investigates the stress-responsive mechanisms of Saccharomyces cerevisiae to osmotic stress and identifies the features of osmostress-responsive genes. The study also demonstrates that these features can predict osmostress-responsive genes in humans, although the importance of these features may differ. These findings provide a comprehensive understanding of the regulation of stress-responsive gene expression across eukaryotes.
NAR GENOMICS AND BIOINFORMATICS
(2022)