Formation of Highly Emissive Anthracene Excimers for Aggregation-Induced Emission/Self-Assembly Directed (Bio)imaging

AIEgens have emerged as a promising alternative to molecular rotors in bioimaging applications. However, transferring the concept of aggregation-induced emission (AIE) from solution to living systems remains a challenge. Given the highly heterogeneous nature and the compartmentalization of the cell, different approaches are needed to control the self-assembly within the crowded intricate cellular environment. Herein, we report for the first time the self-assembly mechanism of an anthracene-guanidine derivative (AG) forming the rare and highly emissive T-shaped dimer in breast cancer cell lines as a proof of concept. This process is highly sensitive to the local environment in terms of polarity, viscosity, and/or water quantity that should enable the use of the AG as a fluorescence lifetime imaging biosensor for intracellular imaging of cellular structures and the monitoring of intracellular state parameters. Different populations of the monomer and T-shaped and π-π dimers were observed in the cell membrane, cytoplasm, and nucleoplasm, related to the local viscosity and presence of water. The T-shaped dimer is formed preferentially in the nucleus because of the higher density and viscosity compared to the cytoplasm. The present results should serve as a precursor for the development of new design strategies for molecular systems for a wide range of applications such as cell viscosity, density, or temperature sensing and imaging.

Proton Hopping in Living Systems

This review focuses on the two-century-old concept of proton hopping. Introduced in 1806 by Grotthuss, it has evolved into an explanation of great diversity in describing many functions in living systems. It is a process involving water, which expands on the belief that life exists only in the presence of water. This review describes the mechanism of the process as it carries information through the water. A focus is initially made on the process of water in the nerve systems. The nature of the process in these systems is described as the passage of proton hopping in living systems. In drug-receptor encounters, proton hopping is initiated, carrying specific information from these specialized encounters. The review continues with an explanation of sleep, arising from an alteration in proton hopping. A similar phenomenon of the effect of general anesthetic agents is described, as they interfere with by proton hopping. Finally, memory functions are addressed in the realm of events carried by proton hopping.

A universal model describing the structure and functions of living systems

Can Life be explained based on the fundamental Laws of Nature? This question is central in Science since its answer could unify Physics and Biology and open new routes for Medicine. The present study introduces a clear and well-documented hypothesis addressing the unified description of all living systems. The proposed universal model is based on two established characteristics of Life. First, the concept of Functional Self-similarity (FSS) is introduced. As shown by several authors, all living systems can be classified in a multi-level hierarchy of increasing complexity. Systems in all hierarchical levels are characterized by a small set of the same attributes defining Life. This observation implies the existence of an elementary living system (i.e., a quantum of Life) having all the necessary functionalities of living systems. Secondly, the non-equilibrium nature of living systems implies that they should be able to process information since such a function is required for reducing entropy. Therefore, all living systems necessarily perform logical operations similar to electronic circuits. This conclusion, which is based on the requirement to overcome the constraints of the Second Law of Thermodynamics, indicates a close correspondence between living systems and information processing machines, namely computers. Consequently, important theoretical principles and concepts regarding computer design may also apply in the study of living systems. The above considerations lead to the Hypothesis of a Universal Architecture (UAH).

The COVID-19 era: No longer business as usual

The paper proposes an alternative cyclical economy based on eco-villages supporting urban hubs to regenerate rural-urban balance based on public education to support eco-facturing, to use Gunter Pauli's concept. The paper sketches an alternative cyclical economy based on eco-villages supporting urban hubs to regenerate rural-urban balance based on eco-facturing. Australia lost over 40 million acres of habitat and at least a billion creatures during the 2019-2020 bushfire season. Africa and Asia are also rapidly urbanizing and rapidly losing habitat. The paper outlines the way in which we could live differently by understanding that production, consumption and regeneration need to follow a natural ecological approach, rather than the current approach to extracting profit at the expense of future generations. Production and regeneration need to be conducted in ways that do not exploit people and the environment. Exchange practices need to ensure that the interests of the few are not expended at the expense of the many.

A multiscale model of virus pandemic: Heterogeneous interactive entities in a globally connected world

This paper is devoted to the multidisciplinary modelling of a pandemic initiated by an aggressive virus, specifically the so-called SARS-CoV-2 Severe Acute Respiratory Syndrome, corona virus n.2. The study is developed within a multiscale framework accounting for the interaction of different spatial scales, from the small scale of the virus itself and cells, to the large scale of individuals and further up to the collective behaviour of populations. An interdisciplinary vision is developed thanks to the contributions of epidemiologists, immunologists and economists as well as those of mathematical modellers. The first part of the contents is devoted to understanding the complex features of the system and to the design of a modelling rationale. The modelling approach is treated in the second part of the paper by showing both how the virus propagates into infected individuals, successfully and not successfully recovered, and also the spatial patterns, which are subsequently studied by kinetic and lattice models. The third part reports the contribution of research in the fields of virology, epidemiology, immune competition, and economy focussed also on social behaviours. Finally, a critical analysis is proposed looking ahead to research perspectives.

Advanced Near-Infrared Light for Monitoring and Modulating the Spatiotemporal Dynamics of Cell Functions in Living Systems

Light-based technique, including optical imaging and photoregulation, has become one of the most important tools for both fundamental research and clinical practice, such as cell signal sensing, cancer diagnosis, tissue engineering, drug delivery, visual regulation, neuromodulation, and disease treatment. In particular, low energy near-infrared (NIR, 700-1700 nm) light possesses lower phototoxicity and higher tissue penetration depth in living systems as compared with ultraviolet/visible light, making it a promising tool for in vivo applications. Currently, the NIR light-based imaging and photoregulation strategies have offered a possibility to real-time sense and/or modulate specific cellular events in deep tissues with subcellular accuracy. Herein, the recent progress with respect to NIR light for monitoring and modulating the spatiotemporal dynamics of cell functions in living systems are summarized. In particular, the applications of NIR light-based techniques in cancer theranostics, regenerative medicine, and neuroscience research are systematically introduced and discussed. In addition, the challenges and prospects for NIR light-based cell sensing and regulating techniques are comprehensively discussed.

Adapted or Adaptable: How to Manage Entropy Production?

Adaptable or adapted? Whether it is a question of physical, biological, or even economic systems, this problem arises when all these systems are the location of matter and energy conversion. To this interdisciplinary question, we propose a theoretical framework based on the two principles of thermodynamics. Considering a finite time linear thermodynamic approach, we show that non-equilibrium systems operating in a quasi-static regime are quite deterministic as long as boundary conditions are correctly defined. The Novikov–Curzon–Ahlborn derivation applied to non-endoreversible systems then makes it possible to precisely determine the conditions for obtaining characteristic operating points. As a result, power maximization principle (MPP), entropy minimization principle (mEP), efficiency maximization, or waste minimization states are only specific modalities of system operation. We show that boundary conditions play a major role in defining operating points because they define the intensity of the feedback that ultimately characterizes the operation. Armed with these thermodynamic foundations, we show that the intrinsically most efficient systems are also the most constrained in terms of controlling the entropy and dissipation production. In particular, we show that the best figure of merit necessarily leads to a vanishing production of power. On the other hand, a class of systems emerges, which, although they do not offer extreme efficiency or power, have a wide range of use and therefore marked robustness. It therefore appears that the number of degrees of freedom of the system leads to an optimization of the allocation of entropy production.

Possible Mechanisms of Biological Effects Observed in Living Systems during 2H/1H Isotope Fractionation and Deuterium Interactions with Other Biogenic Isotopes

This article presents the original descriptions of some recent physics mechanisms (based on the thermodynamic, kinetic, and quantum tunnel effects) providing stable 2H/1H isotope fractionation, leading to the accumulation of particular isotopic forms in intra- or intercellular space, including the molecular effects of deuterium interaction with 18O/17O/16O, 15N/14N, 13C/12C, and other stable biogenic isotopes. These effects were observed mainly at the organelle (mitochondria) and cell levels. A new hypothesis for heavy nonradioactive isotope fractionation in living systems via neutron effect realization is discussed. The comparative analysis of some experimental studies results revealed the following observation: "Isotopic shock" is highly probable and is observed mostly when chemical bonds form between atoms with a summary odd number of neutrons (i.e., bonds with a non-compensated neutron, which correspond to the following equation: Nn - Np = 2k + 1, where k ϵ Z, k is the integer, Z is the set of non-negative integers, Nn is number of neutrons, and Np is number of protons of each individual atom, or in pair of isotopes with a chemical bond). Data on the efficacy and metabolic pathways of the therapy also considered 2H-modified drinking and diet for some diseases, such as Alzheimer's disease, Friedreich's ataxia, mitochondrial disorders, diabetes, cerebral hypoxia, Parkinson's disease, and brain cancer.

Growth and remodelling of living tissues: perspectives, challenges and opportunities

One of the most remarkable differences between classical engineering materials and living matter is the ability of the latter to grow and remodel in response to diverse stimuli. The mechanical behaviour of living matter is governed not only by an elastic or viscoelastic response to loading on short time scales up to several minutes, but also by often crucial growth and remodelling responses on time scales from hours to months. Phenomena of growth and remodelling play important roles, for example during morphogenesis in early life as well as in homeostasis and pathogenesis in adult tissues, which often adapt to changes in their chemo-mechanical environment as a result of ageing, diseases, injury or surgical intervention. Mechano-regulated growth and remodelling are observed in various soft tissues, ranging from tendons and arteries to the eye and brain, but also in bone, lower organisms and plants. Understanding and predicting growth and remodelling of living systems is one of the most important challenges in biomechanics and mechanobiology. This article reviews the current state of growth and remodelling as it applies primarily to soft tissues, and provides a perspective on critical challenges and future directions.

Labelled chemical probes for demonstrating direct target engagement in living systems

Demonstrating target engagement in living systems can help drive successful drug discovery. Target engagement and occupancy studies in cells confirm direct binding of a ligand to its intended target protein and provide the binding affinity. Combined with biomarkers to measure the functional consequences of target engagement, these experiments can increase confidence in the relationship between in vitro pharmacology and observed biological effects. In this review, we focus on chemically and radioactively labelled probes as key reagents for performing such experiments. Using recent examples, we examine how the labelled probes have been employed in combination with unlabelled ligands to quantify target engagement in cells and in animals. Finally, we consider future developments of this emerging methodology.

Dendritic and Axonal Propagation Delays May Shape Neuronal Networks With Plastic Synapses

Biological neuronal networks are highly adaptive and plastic. For instance, spike-timing-dependent plasticity (STDP) is a core mechanism which adapts the synaptic strengths based on the relative timing of pre- and postsynaptic spikes. In various fields of physiology, time delays cause a plethora of biologically relevant dynamical phenomena. However, time delays increase the complexity of model systems together with the computational and theoretical analysis burden. Accordingly, in computational neuronal network studies propagation delays were often neglected. As a downside, a classic STDP rule in oscillatory neurons without propagation delays is unable to give rise to bidirectional synaptic couplings, i.e., loops or uncoupled states. This is at variance with basic experimental results. In this mini review, we focus on recent theoretical studies focusing on how things change in the presence of propagation delays. Realistic propagation delays may lead to the emergence of neuronal activity and synaptic connectivity patterns, which cannot be captured by classic STDP models. In fact, propagation delays determine the inventory of attractor states and shape their basins of attractions. The results reviewed here enable to overcome fundamental discrepancies between theory and experiments. Furthermore, these findings are relevant for the development of therapeutic brain stimulation techniques aiming at shifting the diseased brain to more favorable attractor states.

Structure for energy cycle: a unique status of the second law of thermodynamics for living systems

Distinguishing things from beings, or matters from lives, is a fundamental question. Extending E. Schrödinger's neg-entropy and I. Prigogine's dissipative structure, we propose a chemical kinetic view that the earliest "live" process is embedded essentially in a special interaction between a pair of specific components under a particular, corresponding environmental conditions. The interaction exists as an inter-molecular-force-bond complex (IMFBC) that couples two separate chemical processes: one is the spontaneous formation of the IMFBC driven by a decrease of Gibbs free energy as a dissipative process; while the other is the disassembly of the IMFBC driven thermodynamically by free energy input from the environment. The two chemical processes coupled by the IMFBC originated independently and were considered non-living on Earth, but the IMFBC coupling of the two can be considered as the earliest form of metabolism: the first landmark on the path from things to a being. The dynamic formation and disassembly of the IMFBC, as a composite individual, follows a principle designated as "… structure for energy for structure for energy…", the cycle continues; and for short it will be referred to as "structure for energy cycle". With additional features derived from this starting point, the IMFBC-centered "live" process spontaneously evolved into more complex living organisms with the characteristics currently known.

A perspective on bridging scales and design of models using low-dimensional manifolds and data-driven model inference

Systems in nature capable of collective behaviour are nonlinear, operating across several scales. Yet our ability to account for their collective dynamics differs in physics, chemistry and biology. Here, we briefly review the similarities and differences between mathematical modelling of adaptive living systems versus physico-chemical systems. We find that physics-based chemistry modelling and computational neuroscience have a shared interest in developing techniques for model reductions aiming at the identification of a reduced subsystem or slow manifold, capturing the effective dynamics. By contrast, as relations and kinetics between biological molecules are less characterized, current quantitative analysis under the umbrella of bioinformatics focuses on signal extraction, correlation, regression and machine-learning analysis. We argue that model reduction analysis and the ensuing identification of manifolds bridges physics and biology. Furthermore, modelling living systems presents deep challenges as how to reconcile rich molecular data with inherent modelling uncertainties (formalism, variables selection and model parameters). We anticipate a new generative data-driven modelling paradigm constrained by identified governing principles extracted from low-dimensional manifold analysis. The rise of a new generation of models will ultimately connect biology to quantitative mechanistic descriptions, thereby setting the stage for investigating the character of the model language and principles driving living systems.This article is part of the themed issue 'Multiscale modelling at the physics-chemistry-biology interface'.

Bioengineering thermodynamics of biological cells

BACKGROUND

Cells are open complex thermodynamic systems. They can be also regarded as complex engines that execute a series of chemical reactions. Energy transformations, thermo-electro-chemical processes and transports phenomena can occur across the cells membranes. Moreover, cells can also actively modify their behaviours in relation to changes in their environment.

METHODS

Different thermo-electro-biochemical behaviours occur between health and disease states. But, all the living systems waste heat, which is no more than the result of their internal irreversibility. This heat is dissipated into the environment. But, this wasted heat represent also a sort of information, which outflows from the cell toward its environment, completely accessible to any observer.

RESULTS

The analysis of irreversibility related to this wasted heat can represent a new approach to study the behaviour of the cells themselves and to control their behaviours. So, this approach allows us to consider the living systems as black boxes and analyze only the inflows and outflows and their changes in relation to the modification of the environment. Therefore, information on the systems can be obtained by analyzing the changes in the cell heat wasted in relation to external perturbations.

CONCLUSIONS

The bioengineering thermodynamics bases are summarized and used to analyse possible controls of the calls behaviours based on the control of the ions fluxes across the cells membranes.

Ecosystem biogeochemistry considered as a distributed metabolic network ordered by maximum entropy production

We examine the application of the maximum entropy production principle for describing ecosystem biogeochemistry. Since ecosystems can be functionally stable despite changes in species composition, we use a distributed metabolic network for describing biogeochemistry, which synthesizes generic biological structures that catalyse reaction pathways, but is otherwise organism independent. Allocation of biological structure and regulation of biogeochemical reactions is determined via solution of an optimal control problem in which entropy production is maximized. However, because synthesis of biological structures cannot occur if entropy production is maximized instantaneously, we propose that information stored within the metagenome allows biological systems to maximize entropy production when averaged over time. This differs from abiotic systems that maximize entropy production at a point in space-time, which we refer to as the steepest descent pathway. It is the spatio-temporal averaging that allows biological systems to outperform abiotic processes in entropy production, at least in many situations. A simulation of a methanotrophic system is used to demonstrate the approach. We conclude with a brief discussion on the implications of viewing ecosystems as self-organizing molecular machines that function to maximize entropy production at the ecosystem level of organization.