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Adonias GL, Siljak H, Balasubramaniam S, Barros MT. In silico modelling of neuron signal impact of cytokine storm-induced demyelination. Open Biol 2024; 14:240138. [PMID: 39226928 DOI: 10.1098/rsob.240138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Revised: 07/16/2024] [Accepted: 07/17/2024] [Indexed: 09/05/2024] Open
Abstract
In this study, we develop an in silico model of a neuron's behaviour under demyelination caused by a cytokine storm to investigate the effects of viral infections in the brain. We use a comprehensive model to measure how cytokine-induced demyelination affects the propagation of action potential (AP) signals within a neuron. We analysed the effects of neuron-neuron communications by applying information and communication theory at different levels of demyelination. Our simulations demonstrate that virus-induced degeneration can play a role in the signal power and spiking rate, which compromise the propagation and processing of information between neurons. We propose a transfer function to model the weakening effects on the AP. Our results show that demyelination induced by a cytokine storm not only degrades the signal but also impairs its propagation within the axon. Our proposed in silico model can analyse virus-induced neurodegeneration and enhance our understanding of virus-induced demyelination.
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Affiliation(s)
- Geoflly L Adonias
- Walton Institute for Information and Communication Systems Science, South East Technology University , Waterford, Ireland
| | - Harun Siljak
- Department of Electronic and Electrical Engineering, Trinity College Dublin , Dublin, Ireland
| | | | - Michael Taynnan Barros
- School of Computer Science and Electronic Engineering, University of Essex , Colchester, UK
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2
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Qian X, Angerbauer S, Egan M, Renzo MD, Haselmayr W. A Molecular Communication Perspective on Synchronization of Coupled Microfluidic-Spectroscopy. IEEE Trans Nanobioscience 2024; 23:458-471. [PMID: 38564355 DOI: 10.1109/tnb.2024.3384082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
A challenge for real-time monitoring of biochemical processes, such as cells, is detection of biologically relevant molecules. This is due to the fact that spectroscopy methods for detection may perturb the cellular environment. One approach to overcome this problem is coupled microfluidic-spectroscopy, where a microfluidic output channel is introduced in order to observe biologically relevant molecules. This approach allows for non-passive spectroscopy methods, such as mass spectrometry, to identify the structure of molecules released by the cell. Due to the non-negligible length of the microfluidic channel, when a sequence of stimuli are applied to a cell it is not straightforward to determine which spectroscopy samples correspond to a given stimulus. In this paper, we propose a solution to this problem by taking a molecular communication (MC) perspective on the coupled microfluidic-spectroscopy system. In particular, assignment of samples to a stimulus is viewed as a synchronization problem. We develop two new algorithms for synchronization in this context and carry out a detailed theoretical and numerical study of their performance. Our results show improvements over maximum-likelihood synchronization algorithms in terms of detection performance when there are uncertainties in the composition of the microfluidic channel.
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Ventura J, Llopis-Lorente A, Abdelmohsen LKEA, van Hest JCM, Martínez-Máñez R. Models of Chemical Communication for Micro/Nanoparticles. Acc Chem Res 2024; 57:815-830. [PMID: 38427324 PMCID: PMC10956390 DOI: 10.1021/acs.accounts.3c00619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 02/12/2024] [Accepted: 02/13/2024] [Indexed: 03/02/2024]
Abstract
Engineering chemical communication between micro/nanosystems (via the exchange of chemical messengers) is receiving increasing attention from the scientific community. Although a number of micro- and nanodevices (e.g., drug carriers, sensors, and artificial cells) have been developed in the last decades, engineering communication at the micro/nanoscale is a recent emergent topic. In fact, most of the studies in this research area have been published within the last 10 years. Inspired by nature─where information is exchanged by means of molecules─the development of chemical communication strategies holds wide implications as it may provide breakthroughs in many areas including nanotechnology, artificial cell research, biomedicine, biotechnology, and ICT. Published examples rely on nanotechnology and synthetic biology for the creation of micro- and nanodevices that can communicate. Communication enables the construction of new complex systems capable of performing advanced coordinated tasks that go beyond those carried out by individual entities. In addition, the possibility to communicate between synthetic and living systems can further advance our understanding of biochemical processes and provide completely new tailored therapeutic and diagnostic strategies, ways to tune cellular behavior, and new biotechnological tools. In this Account, we summarize advances by our laboratories (and others) in the engineering of chemical communication of micro- and nanoparticles. This Account is structured to provide researchers from different fields with general strategies and common ground for the rational design of future communication networks at the micro/nanoscale. First, we cover the basis of and describe enabling technologies to engineer particles with communication capabilities. Next, we rationalize general models of chemical communication. These models vary from simple linear communication (transmission of information between two points) to more complex pathways such as interactive communication and multicomponent communication (involving several entities). Using illustrative experimental designs, we demonstrate the realization of these models which involve communication not only between engineered micro/nanoparticles but also between particles and living systems. Finally, we discuss the current state of the topic and the future challenges to be addressed.
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Affiliation(s)
- Jordi Ventura
- Instituto
Interuniversitario de Investigación de Reconocimiento Molecular
y Desarrollo Tecnológico (IDM), Universitat
Politècnica de València, Universitat de València, Camino de Vera
s/n, 46022 València, Spain
| | - Antoni Llopis-Lorente
- Instituto
Interuniversitario de Investigación de Reconocimiento Molecular
y Desarrollo Tecnológico (IDM), Universitat
Politècnica de València, Universitat de València, Camino de Vera
s/n, 46022 València, Spain
- CIBER
de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Loai K. E. A. Abdelmohsen
- Department
of Chemical Engineering & Chemistry, Department of Biomedical
Engineering, Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, Het Kranenveld 14, 5600 MB Eindhoven, The Netherlands
| | - Jan C. M. van Hest
- Department
of Chemical Engineering & Chemistry, Department of Biomedical
Engineering, Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, Het Kranenveld 14, 5600 MB Eindhoven, The Netherlands
| | - Ramón Martínez-Máñez
- Instituto
Interuniversitario de Investigación de Reconocimiento Molecular
y Desarrollo Tecnológico (IDM), Universitat
Politècnica de València, Universitat de València, Camino de Vera
s/n, 46022 València, Spain
- Unidad
Mixta de Investigación en Nanomedicina y Sensores, Universitat Politècnica de València,
Instituto de Investigación Sanitaria La Fe, Av Fernando Abril Martorell 106, 46026 Valencia, Spain
- Unidad
Mixta UPV-CIPF de Investigación en Mecanismos de Enfermedades
y Nanomedicina, Universitat Politècnica
de València, Centro
de Investigación Príncipe Felipe, C/Eduardo Primo Yúfera
3, 46100 Valencia, Spain
- CIBER
de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Instituto de Salud Carlos III, 28029 Madrid, Spain
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Lingam M. Information Transmission via Molecular Communication in Astrobiological Environments. ASTROBIOLOGY 2024; 24:84-99. [PMID: 38109216 DOI: 10.1089/ast.2023.0069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2023]
Abstract
The ubiquity of information transmission via molecular communication between cells is comprehensively documented on Earth; this phenomenon might even have played a vital role in the origin(s) and early evolution of life. Motivated by these considerations, a simple model for molecular communication entailing the diffusion of signaling molecules from transmitter to receiver is elucidated. The channel capacity C (maximal rate of information transmission) and an optimistic heuristic estimate of the actual information transmission rate ℐ are derived for this communication system; the two quantities, especially the latter, are demonstrated to be broadly consistent with laboratory experiments and more sophisticated theoretical models. The channel capacity exhibits a potentially weak dependence on environmental parameters, whereas the actual information transmission rate may scale with the intercellular distance d as ℐ ∝ d-4 and could vary substantially across settings. These two variables are roughly calculated for diverse astrobiological environments, ranging from Earth's upper oceans (C ∼ 3.1 × 103 bits/s; ℐ ∼ 4.7 × 10-2 bits/s) and deep sea hydrothermal vents (C ∼ 4.2 × 103 bits/s; ℐ ∼ 1.2 × 10-1 bits/s) to the hydrocarbon lakes and seas of Titan (C ∼ 3.8 × 103 bits/s; ℐ ∼ 2.6 × 10-1 bits/s).
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Affiliation(s)
- Manasvi Lingam
- Department of Aerospace, Physics and Space Sciences, Florida Institute of Technology, Melbourne, Florida, USA
- Department of Physics, The University of Texas at Austin, Austin, Texas, USA
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Stano P. Chemical Systems for Wetware Artificial Life: Selected Perspectives in Synthetic Cell Research. Int J Mol Sci 2023; 24:14138. [PMID: 37762444 PMCID: PMC10532297 DOI: 10.3390/ijms241814138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 09/07/2023] [Accepted: 09/11/2023] [Indexed: 09/29/2023] Open
Abstract
The recent and important advances in bottom-up synthetic biology (SB), in particular in the field of the so-called "synthetic cells" (SCs) (or "artificial cells", or "protocells"), lead us to consider the role of wetware technologies in the "Sciences of Artificial", where they constitute the third pillar, alongside the more well-known pillars hardware (robotics) and software (Artificial Intelligence, AI). In this article, it will be highlighted how wetware approaches can help to model life and cognition from a unique perspective, complementary to robotics and AI. It is suggested that, through SB, it is possible to explore novel forms of bio-inspired technologies and systems, in particular chemical AI. Furthermore, attention is paid to the concept of semantic information and its quantification, following the strategy recently introduced by Kolchinsky and Wolpert. Semantic information, in turn, is linked to the processes of generation of "meaning", interpreted here through the lens of autonomy and cognition in artificial systems, emphasizing its role in chemical ones.
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Affiliation(s)
- Pasquale Stano
- Department of Biological and Environmental Sciences and Technologies (DiSTeBA), University of Salento, 73100 Lecce, Italy
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Lingam M, Frank A, Balbi A. Planetary Scale Information Transmission in the Biosphere and Technosphere: Limits and Evolution. Life (Basel) 2023; 13:1850. [PMID: 37763254 PMCID: PMC10532900 DOI: 10.3390/life13091850] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 08/24/2023] [Accepted: 08/29/2023] [Indexed: 09/29/2023] Open
Abstract
Information transmission via communication between agents is ubiquitous on Earth, and is a vital facet of living systems. In this paper, we aim to quantify this rate of information transmission associated with Earth's biosphere and technosphere (i.e., a measure of global information flow) by means of a heuristic order-of-magnitude model. By adopting ostensibly conservative values for the salient parameters, we estimate that the global information transmission rate for the biosphere might be ∼1024 bits/s, and that it may perhaps exceed the corresponding rate for the current technosphere by ∼9 orders of magnitude. However, under the equivocal assumption of sustained exponential growth, we find that information transmission in the technosphere can potentially surpass that of the biosphere ∼90 years in the future, reflecting its increasing dominance.
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Affiliation(s)
- Manasvi Lingam
- Department of Aerospace, Physics and Space Sciences, Florida Institute of Technology, Melbourne, FL 32901, USA
- Department of Physics and Institute for Fusion Studies, The University of Texas at Austin, Austin, TX 78712, USA
| | - Adam Frank
- Department of Physics and Astronomy, University of Rochester, Rochester, NY 14620, USA
| | - Amedeo Balbi
- Dipartimento di Fisica, Università di Roma “Tor Vergata”, 00133 Roma, Italy
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Stano P, Gentili PL, Damiano L, Magarini M. A Role for Bottom-Up Synthetic Cells in the Internet of Bio-Nano Things? Molecules 2023; 28:5564. [PMID: 37513436 PMCID: PMC10385758 DOI: 10.3390/molecules28145564] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Revised: 06/29/2023] [Accepted: 07/18/2023] [Indexed: 07/30/2023] Open
Abstract
The potential role of bottom-up Synthetic Cells (SCs) in the Internet of Bio-Nano Things (IoBNT) is discussed. In particular, this perspective paper focuses on the growing interest in networks of biological and/or artificial objects at the micro- and nanoscale (cells and subcellular parts, microelectrodes, microvessels, etc.), whereby communication takes place in an unconventional manner, i.e., via chemical signaling. The resulting "molecular communication" (MC) scenario paves the way to the development of innovative technologies that have the potential to impact biotechnology, nanomedicine, and related fields. The scenario that relies on the interconnection of natural and artificial entities is briefly introduced, highlighting how Synthetic Biology (SB) plays a central role. SB allows the construction of various types of SCs that can be designed, tailored, and programmed according to specific predefined requirements. In particular, "bottom-up" SCs are briefly described by commenting on the principles of their design and fabrication and their features (in particular, the capacity to exchange chemicals with other SCs or with natural biological cells). Although bottom-up SCs still have low complexity and thus basic functionalities, here, we introduce their potential role in the IoBNT. This perspective paper aims to stimulate interest in and discussion on the presented topics. The article also includes commentaries on MC, semantic information, minimal cognition, wetware neuromorphic engineering, and chemical social robotics, with the specific potential they can bring to the IoBNT.
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Affiliation(s)
- Pasquale Stano
- Department of Biological and Environmental Sciences and Technologies (DiSTeBA), University of Salento, 73100 Lecce, Italy
| | - Pier Luigi Gentili
- Dipartimento di Chimica, Biologia e Biotecnologie, Università degli Studi di Perugia, 06123 Perugia, Italy
| | - Luisa Damiano
- Department of Communication, Arts and Media, IULM University, 20143 Milan, Italy
| | - Maurizio Magarini
- Department of Electronics, Information and Bioengineering, Politecnico di Milano, 20133 Milan, Italy
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