Behavior Of Biological Systems Research Articles

Protease-Driven Phase Separation of Elastin-Like Polypeptides.

Elastin-like polypeptides (ELPs) are a promising material platform for engineering stimuli-responsive biomaterials, as ELPs undergo phase separation above a tunable transition temperature. ELPs with phase behavior that is isothermally regulated by biological stimuli remain attractive for applications in biological systems. Herein, we report protease-driven phase separation of ELPs. Protease-responsive "cleavable" ELPs comprise a hydrophobic ELP block connected to a hydrophilic ELP block by a protease cleavage site linker. The hydrophilic ELP block acts as a solubility tag for the hydrophobic ELP block, creating a temperature window in which the cleavable ELP reactant is soluble and the proteolytically generated hydrophobic ELP block is insoluble. Within this temperature window, isothermal, protease-driven phase separation occurs when a critical concentration of hydrophobic cleavage product accumulates. Furthermore, protease-driven phase separation is generalizable to four compatible protease-cleavable ELP pairings. This work presents exciting opportunities to regulate ELP phase behavior in biological systems using proteases.

Bioelectronic Delivery of Potassium Ions Controls Membrane Voltage and Growth Dynamics in Bacteria Biofilms

AbstractBioelectrical signaling, or bioelectricity, is crucial in regulating cellular behavior in biological systems. This signaling, involving ion fluxes and changes in membrane potential (Vmem), is particularly important in the growth of bacterial biofilm. Current microfluidic-based methods for studying bacterial colonies are limited in achieving spatiotemporal control over ionic fluxes due to constant flow within the system. To address this limitation, we have developed a platform that integrates biofilm colonies with bioelectronic ion pumps that enable delivery of potassium (K+) ions, allowing for controlled manipulation of local potassium concentration. Our study examines the impact of controlled K+ delivery on bacterial biofilm growth patterns and dynamics. We observed significant changes in Vmem and coordination within the biofilms. Furthermore, we show that localized K + delivery is highly effective in controlling biofilm expansion in a spatially targeted manner. These findings offer insights into the mechanisms underlying bacterial signaling and growth, and suggest potential applications in bioengineering, synthetic biology, and regenerative medicine, where precise control over cellular signaling and subsequent tissue growth is required.

Design patterns for the construction of computational biological models.

Computational biological models have proven to be an invaluable tool for understanding and predicting the behaviour of many biological systems. While it may not be too challenging for experienced researchers to construct such models from scratch, it is not a straightforward task for early stage researchers. Design patterns are well-known techniques widely applied in software engineering as they provide a set of typical solutions to common problems in software design. In this paper, we collect and discuss common patterns that are usually used during the construction and execution of computational biological models. We adopt Petri nets as a modelling language to provide a visual illustration of each pattern; however, the ideas presented in this paper can also be implemented using other modelling formalisms. We provide two case studies for illustration purposes and show how these models can be built up from the presented smaller modules. We hope that the ideas discussed in this paper will help many researchers in building their own future models.

Poly(2-methyl-2-oxazoline) as a polyethylene glycol alternative for lipid nanoparticle formulation

Lipid nanoparticles (LNPs) have emerged as the platform of choice for mRNA delivery. Polyethylene glycol (PEG) is considered a key component of currently approved LNP-based delivery systems as it ensures particle stability and shapes various facets of LNP behavior in biological systems. Whilst PEG has numerous characteristics that are favorable for delivery systems, there is a growing body of evidence that suggests that it is immunogenic. Thus, next-generation mRNA therapeutics are likely to benefit from the identification of PEG alternatives. Towards this end, we have assessed the suitability of poly(2-methyl-2-oxazoline) (PMOZ) for LNP-based mRNA delivery. We compared the properties and bioactivities of PMOZ-containing LNPs to that of a standard composition that includes PEG. Decreasing the percentage of PMOZ in formulations improved transfection efficiency and enhanced the immunostimulatory potential. Reducing the PMOZ density was shown to enhanced antigen-specific T-cell responses in vivo. Interestingly, we found that this was not the case for antibody responses. A direct comparison between LNPs that contain the same amount of PEG or PMOZ strongly suggests that the former induces stronger CD8+ T-cell responses while the latter induces superior neutralizing titers. These findings augur well for the further development of PMOZ as a PEG replacement for LNP-based mRNA delivery approaches.

I-Rheo-optical assay: Measuring the viscoelastic properties of multicellular spheroids

This study introduces a novel mechanobiology assay, named “i-Rheo-optical assay”, that integrates rheology with optical microscopy for analysing the viscoelastic properties of multicellular spheroids. These spheroids serve as three-dimensional models resembling tissue structures. The innovative technique enables real-time observation and quantification of morphological responses to applied stress using a cost-effective microscope coverslip for constant compression force application. By bridging a knowledge gap in biophysical research, which has predominantly focused on the elastic properties while only minimally exploring the viscoelastic nature in multicellular systems, the i-Rheo-optical assay emerges as an effective tool. It facilitates the measurement of broadband viscoelastic compressional moduli in spheroids, here derived from cancer (PANC-1) and non-tumoral (NIH/3T3) cell lines during compression tests.This approach plays a crucial role in elucidating the mechanical properties of spheroids and holds potential for identifying biomarkers to discriminate between healthy tissues and their pathological counterparts. Offering comprehensive insights into the biomechanical behaviour of biological systems, i-Rheo-optical assay marks a significant advancement in tissue engineering, cancer research, and therapeutic development.

Unlocking the Secrets of Liquid-Liquid Interfaces and Phase Equilibria: Exploring the Interplay of Critical Composition, Interfacial Tension, and Mutual Solubility.

This study reveals pivotal insight into liquid-liquid interfaces by demonstrating that the interface composition mirrors that at the critical point. This revelation leads to the formulation of a novel liquid-liquid distribution law and thermodynamic inequality, establishing a direct connection between mutual solubility values and critical compositions. While particularly accurate for regular solutions, the findings exhibit substantial reliability in nonregular systems, supported by experimental data on binary and ternary mixtures. Importantly, the study illustrates that, with known critical compositions, interfacial tension data alone are sufficient for calculating mutual solubilities, providing a practical alternative for assessing molecular solubility. The paper further showcases the versatility of the simple bottle-testing (cloud-testing) method, effectively serving as both a tensiometer and a mutual-solubility meter. This method utilizes established critical composition data to predict the compositions and interfacial tension of coexisting phases concurrently, offering a cost-effective alternative to complex analytical techniques. As a notable outcome, given critical compositions, basic laboratory equipment such as a beaker and a syringe can equivalently function as both a tensiometer and a mutual solubility detector (e.g., GC). The paper also discusses the application of this method in understanding the liquid-liquid phase behavior in biological systems, exemplified by biomolecular condensates or Lewy bodies.

Stability Constants of Tetravalent Germanium Complexes in Aqueous Solution: Small Organic Oxygen and Nitrogen Donor Ligands.

The formation constants of about 100 different complexes of Ge(IV) with some 50 organic, low-molecular-weight ligands, principally bidentate oxygen and/or nitrogen donors, are determined by potentiometric titrations at 25 °C and an ionic strength of 0.1 mol L-1 (KNO3). In the few cases for which literature data are available, these older data are critically discussed and completed in light of our new experimental data. The overall picture emerging from our work is that such complexes are comparatively weak, except when a chelate effect comes into play, as is observed with aminopolyols, α-hydroxocarboxylic acids, and carbohydrate derivatives, where even quantitative chelation of Ge is possible. No binding to amino acids or peptides is detected. An important finding is our evidence for the existence of a bridged dinuclear germanium(IV) tartrate complex in the aqueous phase, whose occurrence in solids was confirmed by X-ray diffraction beforehand. Our work has implications for the general understanding of the aqueous coordination chemistry of Ge, its geochemical cycling, and its behavior in environmental and biological systems. Potentiometric raw data for use by other researchers are publicly accessible in the repository Zenodo at CERN.

Innovative approaches to fractional modeling: Aboodh transform for the Keller-Segel equation

<abstract><p>This study focuses on developing efficient numerical techniques for solving the fractional Keller-Segel (KS) model, which is critical in explaining chemotaxis events. Within the Caputo operator framework, the study applied two unique methodologies: The Aboodh residual power series method (ARPSM) and the Aboodh transform iteration method (ATIM). These approaches were used to find precise solutions to the fractional KS equation, resulting in a better understanding of chemotactic behavior in biological systems. The comparative examination of the ARPSM and ATIM revealed their distinct strengths and applications in solving complicated fractional models. The work advances numerical approaches for fractional differential equations and improves our understanding of chemotaxis dynamics using a precise modeling approach.</p></abstract>

Boolean model of the gene regulatory network of Pseudomonas aeruginosa CCBH4851.

Pseudomonas aeruginosa infections are one of the leading causes of death in immunocompromised patients with cystic fibrosis, diabetes, and lung diseases such as pneumonia and bronchiectasis. Furthermore, P. aeruginosa is one of the main multidrug-resistant bacteria responsible for nosocomial infections worldwide, including the multidrug-resistant CCBH4851 strain isolated in Brazil. One way to analyze their dynamic cellular behavior is through computational modeling of the gene regulatory network, which represents interactions between regulatory genes and their targets. For this purpose, Boolean models are important predictive tools to analyze these interactions. They are one of the most commonly used methods for studying complex dynamic behavior in biological systems. Therefore, this research consists of building a Boolean model of the gene regulatory network of P. aeruginosa CCBH4851 using data from RNA-seq experiments. Next, the basins of attraction are estimated, as these regions and the transitions between them can help identify the attractors, representing long-term behavior in the Boolean model. The essential genes of the basins were associated with the phenotypes of the bacteria for two conditions: biofilm formation and polymyxin B treatment. Overall, the Boolean model and the analysis method proposed in this work can identify promising control actions and indicate potential therapeutic targets, which can help pinpoint new drugs and intervention strategies.

Modeling and simulation of Lac-Operon using reaction-diffusion master equation on heterogeneous parallel platforms

The Lac-Operon is a pivotal molecular mechanism controlling gene expression in response to presence or absence of lactose. Mastering its dynamics aids cellular comprehension and gene circuit design. Employing the multi-particle diffusion reaction-diffusion master equation (MPD-RDME), we model gene expression kinetics. This couples with the Gillespie algorithm-driven Next sub-volume method for particle reactions and diffusion, enabling predictive time-course molecule concentration insights via RDME and Gillespie. Such insights inform experimentation and elucidate cellular operations. Particularly, inducible operon kinetics, like Lac-Operon, hold applications in recombinant protein production and gene therapy. Our work constructs a Lac-Operon gene expression model utilizing MPD-RDME and Next sub-volume on a Heterogeneous Parallel Platform (HPP). Implementation employs the combination of host and GPU, and host and homogeneous GPU pairs. Simulation speed, affected by external inducers, repressor count, and lattice spacing, is compared. Protein and mRNA count under various conditions were simulated on host, GPU, and GPU pairs. Results display 75 %–80 % speed enhancement on the HPP compared to host and GPU combination. This adaptable method extends to explore diverse gene circuits, unraveling molecular-level biological system behaviors.

Agency, Goal-Directed Behavior, and Part-Whole Relationships in Biological Systems

In this essay we aim to present some considerations regarding a minimal but concrete notion of agency and goal-directed behavior that are useful for characterizing biological systems at different scales. These considerations are a particular perspective, bringing together concepts from dynamical systems, combinatorial problem-solving, and connectionist learning with an emphasis on the relationship between parts and wholes. This perspective affords some ways to think about agents that are concrete and quantifiable, and relevant to some important biological issues. Instead of advocating for a strict definition of minimally agential characteristics, we focus on how (even for a modest notion of agency) the agency of a system can be more than the sum of the agency of its parts. We quantify this in terms of the problem-solving competency of a system with respect to resolution of the frustrations between its parts. This requires goal-directed behavior in the sense of delayed gratification, i.e., taking dynamical trajectories that forego short-term gains (or sustain short-term stress or frustration) in favor of long-term gains. In order for this competency to belong to the system (rather than to its parts or given by its construction or design), it can involve distributed systemic knowledge that is acquired through experience, i.e., changes in the organization of the relationships among its parts (without presupposing a system-level reward function for such changes). This conception of agency helps us think about the ways in which cells, organisms, and perhaps other biological scales, can be agential (i.e., more agential than their parts) in a quantifiable sense, without denying that the behavior of the whole depends on the behaviors of the parts in their current organization.

Distilling identifiable and interpretable dynamic models from biological data.

Mechanistic dynamical models allow us to study the behavior of complex biological systems. They can provide an objective and quantitative understanding that would be difficult to achieve through other means. However, the systematic development of these models is a non-trivial exercise and an open problem in computational biology. Currently, many research efforts are focused on model discovery, i.e. automating the development of interpretable models from data. One of the main frameworks is sparse regression, where the sparse identification of nonlinear dynamics (SINDy) algorithm and its variants have enjoyed great success. SINDy-PI is an extension which allows the discovery of rational nonlinear terms, thus enabling the identification of kinetic functions common in biochemical networks, such as Michaelis-Menten. SINDy-PI also pays special attention to the recovery of parsimonious models (Occam's razor). Here we focus on biological models composed of sets of deterministic nonlinear ordinary differential equations. We present a methodology that, combined with SINDy-PI, allows the automatic discovery of structurally identifiable and observable models which are also mechanistically interpretable. The lack of structural identifiability and observability makes it impossible to uniquely infer parameter and state variables, which can compromise the usefulness of a model by distorting its mechanistic significance and hampering its ability to produce biological insights. We illustrate the performance of our method with six case studies. We find that, despite enforcing sparsity, SINDy-PI sometimes yields models that are unidentifiable. In these cases we show how our method transforms their equations in order to obtain a structurally identifiable and observable model which is also interpretable.

Spreading behavior of biological SIR system of a COVID-19 disease through a fast Taylor wavelet based numerical algorithm

In this paper, we provide a unique, cost-effective numerical method for solving the SIR model of a COVID-19 disease using the method of Taylor wavelets and collocation technique. The model’s mathematical structure is represented by an ordered collection of ordinary differential equations that are nonlinear. We use the functional matrix of integration of Fibonacci wavelets to translate the given model into a set of computational equations, which we next simplify using the Newton–Raphson method. The given model is solved using the proposed method under various conditions to analyze the outcomes graphically and numerically as well. To demonstrate the efficiency and easy applicability of the method, we have also made a numerical comparison of the solution with some other methods in tables. The behavior of the approximate solutions of susceptible, infectible, and recovery curves under the proposed method is analyzed. MATLAB software is used to perform all the related calculations.

A fractional-order visual neural network for collision sensing in noisy and dynamic scenes

Autonomously sensing collision threats in intelligent mobile machines is a significant challenge. Inspired by the perfect collision sensing system of locusts, various neural networks based on lobular giant motion detectors (LGMD) have been proposed. These networks use integer-order differential operators to simulate the simple and efficient visual neural system of locusts. However, some biological studies have shown that the neurodynamics of neuronal response should be fractional-order, and fractional-order differential operators can accurately describe the biological logic brain neural response process. In view of this, firstly, this paper uses a fractional-order differential operator to simulate the membrane potential response of neurons, and a new fractional-order LGMD collision sensing visual neural network is proposed. This network is designed to accurately detect looming objects and generate reliable response spikes. Then, through experimental analysis, a range [0.36, 0.4] of order in the fractional-order system is given, which is considered to be a reasonable interval for modeling the behavior of biological nervous systems. This maybe contribute to the study of the locust’s fractional-order biological nervous system. Finally, the network was systematically tested in noisy and complex dynamic environments. The experimental results demonstrated that the fractional-order LGMD visual neural network generated responses with high adaptability and reliability, showcasing significantly improved collision detection performance.

Stochastic resonance in a single autapse–coupled neuron

The signal detection ability of nervous system is highly associated with nonlinear and collective behaviors in neuronal medium. Neuronal noise, which occurs as natural endogenous fluctuations in brain activity, is the most salient factor influencing this ability. Experimental and theoretical research suggests that noise is beneficial, not detrimental, for regular functioning of nervous system. In this regard, there is a general agreement that noise at an adequate intensity can engage rhythmic activity in brain and noise-induced oscillations enhances performance of the weak signal processing, especially when frequency of the signal is around that of the noise-induced rhythmic oscillation. This behavior in biological neural systems is explained by the notion of “stochastic resonance”. Another factor that plays a key role in regulating neuronal behaviors, including motor and cognitive tasks by maintaining signaling between cells, is characteristics of synapses different in structure and functioning. Here, we study stochastic resonance in Hodgkin–Huxley neuron that has a peculiar synaptic connection called autapse, known as a biophysical feedback mechanism, under presynaptic noise originating from superposition of inhibitory and excitatory Poisson bombardment. Our results show that, under certain conditions, autapse dynamics are able to improve the weak signal detection performance of Hodgkin–Huxley neuron via stochastic resonance. This study provides novel insights into functional role of autapse in neural information processing by revealing a biophysical aspect of stochastic resonance with numerical computations.

From Brain Models to Robotic Embodied Cognition: How Does Biological Plausibility Inform Neuromorphic Systems?

We examine the challenging "marriage" between computational efficiency and biological plausibility-A crucial node in the domain of spiking neural networks at the intersection of neuroscience, artificial intelligence, and robotics. Through a transdisciplinary review, we retrace the historical and most recent constraining influences that these parallel fields have exerted on descriptive analysis of the brain, construction of predictive brain models, and ultimately, the embodiment of neural networks in an enacted robotic agent. We study models of Spiking Neural Networks (SNN) as the central means enabling autonomous and intelligent behaviors in biological systems. We then provide a critical comparison of the available hardware and software to emulate SNNs for investigating biological entities and their application on artificial systems. Neuromorphics is identified as a promising tool to embody SNNs in real physical systems and different neuromorphic chips are compared. The concepts required for describing SNNs are dissected and contextualized in the new no man's land between cognitive neuroscience and artificial intelligence. Although there are recent reviews on the application of neuromorphic computing in various modules of the guidance, navigation, and control of robotic systems, the focus of this paper is more on closing the cognition loop in SNN-embodied robotics. We argue that biologically viable spiking neuronal models used for electroencephalogram signals are excellent candidates for furthering our knowledge of the explainability of SNNs. We complete our survey by reviewing different robotic modules that can benefit from neuromorphic hardware, e.g., perception (with a focus on vision), localization, and cognition. We conclude that the tradeoff between symbolic computational power and biological plausibility of hardware can be best addressed by neuromorphics, whose presence in neurorobotics provides an accountable empirical testbench for investigating synthetic and natural embodied cognition. We argue this is where both theoretical and empirical future work should converge in multidisciplinary efforts involving neuroscience, artificial intelligence, and robotics.

Bioinspired Vertical Transistors from Artificial Synapse to Neuromorphic System

Neuromorphic devices emulating the brain functionality have achieved a substantial scientific leap in the last decade. Among them, neuromorphic vertical transistors have attracted extensive interests due to their abilities of mitigating physical channel‐length limitations and developing new‐generation 3D integrated electronics. In this review, the recent advances and major trends in the field of emerging neuromorphic devices based on vertical transistor are focused on. It has been started with a brief introduction of biological nervous system and neuromorphic behaviors. Next, the latest advances in the development of vertical transistor and shed light on bio‐related neuromorphic applications are discussed. They are discussed in detail from the aspects of materials and potential applications. Finally, future research challenges in neuromorphic vertical transistor are briefly summarized, and their prospects are discussed.

Multi-omics regulatory network inference in the presence of missing data.

A key problem in systems biology is the discovery of regulatory mechanisms that drive phenotypic behaviour of complex biological systems in the form of multi-level networks. Modern multi-omics profiling techniques probe these fundamental regulatory networks but are often hampered by experimental restrictions leading to missing data or partially measured omics types for subsets of individuals due to cost restrictions. In such scenarios, in which missing data is present, classical computational approaches to infer regulatory networks are limited. In recent years, approaches have been proposed to infer sparse regression models in the presence of missing information. Nevertheless, these methods have not been adopted for regulatory network inference yet. In this study, we integrated regression-based methods that can handle missingness into KiMONo, a Knowledge guided Multi-Omics Network inference approach, and benchmarked their performance on commonly encountered missing data scenarios in single- and multi-omics studies. Overall, two-step approaches that explicitly handle missingness performed best for a wide range of random- and block-missingness scenarios on imbalanced omics-layers dimensions, while methods implicitly handling missingness performed best on balanced omics-layers dimensions. Our results show that robust multi-omics network inference in the presence of missing data with KiMONo is feasible and thus allows users to leverage available multi-omics data to its full extent.

Resonant frequency of coronavirus: The tensegrity approach

COVID-19 is a worldwide health hazard. In discovering a fully efficient vaccination for continually evolving viruses, alternatives such as the sonication treatment methods, which have seen encouraging outcomes in disinfection and medical therapies, are worth exploring. Such treatments incapacitate microbes or diseased cells by selectively invoking large deformation at the resonant frequency that initiates structural failure. Nevertheless, due to biodiversity, the precise range of resonant frequencies for different biological bodies can be widely varying, its determination of which is best achieved with the cost-effective computational simulation approach. The paper proposes, therefore, the numerical determination of the resonant frequency of the coronavirus employing the tensegrity method, due to its efficacy in modeling various biomechanical behaviors of different biological bodies and systems. Initiating from successfully verifying the resonant frequency with existing findings, the model then determines the operative sonication frequencies range for the resonant state of the virus. At these sonication frequencies, the modal analysis exhibits a large structurally destructive deformation of the coronavirus. For practical convenience, the operative range of sonication resonant frequencies of the coronavirus has been mapped alongside healthy human cells. These findings offer an alternative technological avenue in combating the COVID-19 progressive threat.

Insight into response characteristics and inhibition mechanisms of anammox granular sludge to polyethylene terephthalate microplastics exposure

Currently, in-depth understanding of response characteristics and mechanisms of anammox process under microplastics (MPs) stress remains quite limited. This study investigated the influence of 0.1–1.0 g/L polyethylene terephthalate (PET) on anammox granular sludge (AnGS). Compared with the control, 0.1–0.2 g/L PET did not significantly affect the anammox efficiency, while the anammox activity decreased by 16.2% at 1.0 g/L PET. Integrity coefficient and transmission electron microscopy analysis demonstrated that the strength and structural stability of the AnGS became weaken following exposure to 1.0 g/L PET. With the PET increasing, the abundance of anammox genera and genes related to energy metabolism and cofactors and vitamins metabolism decreased. The reactive oxygen species generated in the interaction between microbial cells and PET resulting in cellular oxidative stress was responsible for inhibiting anammox. These findings give novel insights into the anammox behavior in biological nitrogen removal systems treating PET-loaded nitrogenous wastewater.