Biological Systems Research Articles

Enhanced Near-infrared Phosphorescent Emission Modulated by Clipping of Metallotweezers in Aqueous Media.

Near-infrared phosphorescent materials have received significant attention due to their potential applications in bioimaging and diagnostics. Although, many types of organic phosphors with near-infrared emission have been developed, the low phosphorescence efficiency in aqueous solution hampers their practical applications in biological systems. Hence, there is an urgent need to develop near-infrared phosphorescent materials with high emission efficiency in aqueous media. Metallotweezers, based on d8 transition metal complexes, emerge as the potential candidates for realizing this objective. Specifically, metallotweezers, featuring two positively charged platinum(II) terpyridine and neutral gold(III) diphenylpyridine pincers on diphenylpyridine spacer, have been designed and synthesized, respectively. The pre-organization effect, rendered by the rigid spacer, enables the resulting metallotweezers to complex with each other, resulting in the formation of clipping complex. The synergistic rigidifying and shielding effects of clipping structure results in enhanced phosphorescent emission intensity. Concurrently, due to phase segregation between the clipping units and the polyethylene glycol tail, the clipping complex undergoes self-assembly in aqueous solution, resulting in phosphorescent emission in the near-infrared region. Overall, non-covalent clipping of metallotweezers illustrated in this study presents a new and effective approach toward near-infrared phosphorescent materials.

Enzymatic Reaction-Coupled, Cooperative Supramolecular Polymerization.

Nature employs sophisticated mechanisms to precisely regulate self-assembly and functions within biological systems, exemplified by the formation of cytoskeletal filaments. Various enzymatic reactions and auxiliary proteins couple with the self-assembly process, meticulously regulating the length and functions of resulting macromolecular structures. In this context, we present a bioinspired, reaction-coupled approach for the controlled supramolecular polymerization in synthetic systems. To achieve this, we employ an enzymatic reaction that interfaces with the adenosine triphosphate (ATP)-templated supramolecular polymerization of naphthalene diimide monomers (NSG). Notably, the enzymatic production of ATP (template) plays a pivotal role in facilitating reaction-controlled, cooperative growth of the NSG monomers. This growth process, in turn, provides positive feedback to the enzymatic production of ATP, creating an ideal reaction-coupled assembly process. The success of this approach is further evident in the living-growth characteristic observed during seeding experiments, marking this method as the pioneering instance where reaction-coupled self-assembly precisely controls the growth kinetics and structural aspects of supramolecular polymers in a predictive manner, akin to biological systems.

The physiological and pathophysiological roles of copper in the nervous system.

Copper is a critical trace element in biological systems due the vast number of essential enzymes that require the metal as a cofactor, including cytochrome c oxidase, superoxide dismutase and dopamine-β-hydroxylase. Due its key role in oxidative metabolism, antioxidant defence and neurotransmitter synthesis, copper is particularly important for neuronal development and proper neuronal function. Moreover, increasing evidence suggests that copper also serves important functions in synaptic and network activity, the regulation of circadian rhythms, and arousal. However, it is important to note that because of copper's ability to redox cycle and generate reactive species, cellular levels of the metal must be tightly regulated to meet cellular needs while avoiding copper-induced oxidative stress. Therefore, it is essential that the intricate system of copper transporters, exporters, copper chaperones and copper trafficking proteins function properly and in coordinate fashion. Indeed, disorders of copper metabolism such as Menkes disease and Wilson disease, as well as diseases linked to dysfunction of copper-requiring enzymes, such as SOD1-linked amyotrophic lateral sclerosis, demonstrate the dramatic neurological consequences of altered copper homeostasis. In this review, we explore the physiological importance of copper in the nervous system as well as pathologies related to improper copper handling.

Gap junctions in Turing-type periodic feather pattern formation.

Periodic patterning requires coordinated cell-cell interactions at the tissue level. Turing showed, using mathematical modeling, how spatial patterns could arise from the reactions of a diffusive activator-inhibitor pair in an initially homogenous 2D field. Most activators and inhibitors studied in biological systems are proteins, and the roles of cell-cell interaction, ions, bioelectricity, etc. are only now being identified. Gap junctions (GJs) mediate direct exchanges of ions or small molecules between cells, enabling rapid long-distance communications in a cell collective. They are therefore good candidates for propagating nonprotein-based patterning signals that may act according to the Turing principles. Here, we explore the possible roles of GJs in Turing-type patterning using feather pattern formation as a model. We found 7 of the 12 investigated GJ isoforms are highly dynamically expressed in the developing chicken skin. In ovo functional perturbations of the GJ isoform, connexin 30, by siRNA and the dominant-negative mutant applied before placode development led to disrupted primary feather bud formation. Interestingly, inhibition of gap junctional intercellular communication (GJIC) in the ex vivo skin explant culture allowed the sequential emergence of new feather buds at specific spatial locations relative to the existing primary buds. The results suggest that GJIC may facilitate the propagation of long-distance inhibitory signals. Thus, inhibition of GJs may stimulate Turing-type periodic feather pattern formation during chick skin development, and the removal of GJ activity would enable the emergence of new feather buds if the local environment were competent and the threshold to form buds was reached. We further propose Turing-based computational simulations that can predict the sequential appearance of these ectopic buds. Our models demonstrate how a Turing activator-inhibitor system can continue to generate patterns in the competent morphogenetic field when the level of intercellular communication at the tissue scale is modulated.

Mapping protein-protein interactions by mass spectrometry.

Protein-protein interactions (PPIs) are essential for numerous biological activities, including signal transduction, transcription control, and metabolism. They play a pivotal role in the organization and function of the proteome, and their perturbation is associated with various diseases, such as cancer, neurodegeneration, and infectious diseases. Recent advances in mass spectrometry (MS)-based protein interactomics have significantly expanded our understanding of the PPIs in cells, with techniques that continue to improve in terms of sensitivity, and specificity providing new opportunities for the study of PPIs in diverse biological systems. These techniques differ depending on the type of interaction being studied, with each approach having its set of advantages, disadvantages, and applicability. This review highlights recent advances in enrichment methodologies for interactomes before MS analysis and compares their unique features and specifications. It emphasizes prospects for further improvement and their potential applications in advancing our knowledge of PPIs in various biological contexts.

GRouNdGAN: GRN-guided simulation of single-cell RNA-seq data using causal generative adversarial networks

We introduce GRouNdGAN, a gene regulatory network (GRN)-guided reference-based causal implicit generative model for simulating single-cell RNA-seq data, in silico perturbation experiments, and benchmarking GRN inference methods. Through the imposition of a user-defined GRN in its architecture, GRouNdGAN simulates steady-state and transient-state single-cell datasets where genes are causally expressed under the control of their regulating transcription factors (TFs). Training on six experimental reference datasets, we show that our model captures non-linear TF-gene dependencies and preserves gene identities, cell trajectories, pseudo-time ordering, and technical and biological noise, with no user manipulation and only implicit parameterization. GRouNdGAN can synthesize cells under new conditions to perform in silico TF knockout experiments. Benchmarking various GRN inference algorithms reveals that GRouNdGAN effectively bridges the existing gap between simulated and biological data benchmarks of GRN inference algorithms, providing gold standard ground truth GRNs and realistic cells corresponding to the biological system of interest.

Conjugated Polymer/Recombinant Escherichia coli Biohybrid Systems for Photobiocatalytic Hydrogen Production.

Biohybrid photocatalysts are composite materials that combine the efficient light-absorbing properties of synthetic materials with the highly evolved metabolic pathways and self-repair mechanisms of biological systems. Here, we show the potential of conjugated polymers as photosensitizers in biohybrid systems by combining a series of polymer nanoparticles with engineered Escherichia coli cells. Under simulated solar light irradiation, the biohybrid system consisting of fluorene/dibenzo [b,d]thiophene sulfone copolymer (LP41) and recombinant E. coli (i.e., a LP41/HydA BL21 biohybrid) shows a sacrificial hydrogen evolution rate of 3.442 mmol g-1 h-1 (normalized to polymer amount). It is over 30 times higher than the polymer photocatalyst alone (0.105 mmol g-1 h-1), while no detectable hydrogen was generated from the E. coli cells alone, demonstrating the strong synergy between the polymer nanoparticles and bacterial cells. The differences in the physical interactions between synthetic materials and microorganisms, as well as redox energy level alignment, elucidate the trends in photochemical activity. Our results suggest that organic semiconductors may offer advantages, such as solution processability, low toxicity, and more tunable surface interactions with the biological components over inorganic materials.

Streptavidin‐Biotin Complexes as Tools for Modulating an Important DNA Epigenetic Modification†

Comprehensive SummaryDNA 5‐formylcytosine (5fC) is a prominent epigenetic modification within biological systems. Recent investigations have shed light on its pivotal role in governing cell fate, gene expression, and disease pathways. However, our comprehension of the precise control of the 5fC site structure to influence its functionality remains limited. In this study, we have successfully achieved precise control over 5fC activity by harnessing the interaction between streptavidin and biotin. This research underscores the potential application of interactions between biomacromolecules and small molecules in advancing the field of DNA epigenetic functional regulation.

Dynamic Near‐Infrared Circularly Polarized Luminescence Encoded by Transient Supramolecular Chiral Assemblies

Circularly polarized luminescence (CPL) is promising for applications in many fields. However, most systems involving CPL are within the visible range; near‒infrared (NIR) CPL‒active materials, especially those that exhibit high glum values and can be controlled spatially and temporally, are rare. Herein, dynamic NIR‒CPL with a glum value of 2.5[[EQUATION]]10‒2 was achieved through supramolecular coassembly and energy transfer strategies. The chiral assemblies formed by the coassembly between adenosine triphosphate (ATP) and a pyrene derivative exhibit a red CPL signal (glum of 10‒3). The further introduction of sulfo‒cyanine5 resulted in a cooperative energy transfer process, which not only aroused the NIR CPL but also increased the glum value to 10‒2. Temporal control of these chiral assemblies was realized by introducing alkaline phosphatase to fabricate a biomimetic enzyme‒catalyzed network, allowing the dynamic NIR CPL signal to be turned on. Based on these enzyme‐regulated temporally controllable dynamic CPL‐active chiral assemblies, a multilevel information encryption system was further developed. Our work provides a pioneering example for constructing dynamic NIR CPL materials holding the ability to perform temporal control via the supramolecular assembly strategy, which is expected to aid in the design of supramolecular complex systems that more closely resemble natural biological systems.

Dynamic Near-Infrared Circularly Polarized Luminescence Encoded by Transient Supramolecular Chiral Assemblies.

Circularly polarized luminescence (CPL) is promising for applications in many fields. However, most systems involving CPL are within the visible range; near‒infrared (NIR) CPL‒active materials, especially those that exhibit high glum values and can be controlled spatially and temporally, are rare. Herein, dynamic NIR‒CPL with a glum value of 2.5[[EQUATION]]10‒2 was achieved through supramolecular coassembly and energy transfer strategies. The chiral assemblies formed by the coassembly between adenosine triphosphate (ATP) and a pyrene derivative exhibit a red CPL signal (glum of 10‒3). The further introduction of sulfo‒cyanine5 resulted in a cooperative energy transfer process, which not only aroused the NIR CPL but also increased the glum value to 10‒2. Temporal control of these chiral assemblies was realized by introducing alkaline phosphatase to fabricate a biomimetic enzyme‒catalyzed network, allowing the dynamic NIR CPL signal to be turned on. Based on these enzyme-regulated temporally controllable dynamic CPL-active chiral assemblies, a multilevel information encryption system was further developed. Our work provides a pioneering example for constructing dynamic NIR CPL materials holding the ability to perform temporal control via the supramolecular assembly strategy, which is expected to aid in the design of supramolecular complex systems that more closely resemble natural biological systems.

Mechanistic Insights Behind the Self-Assembly of Human Insulin under the Influence of Surface-Engineered Gold Nanoparticles.

Elucidating the underlying principles of amyloid protein self-assembly at nanobio interfaces is extremely challenging due to the diversity in physicochemical properties of nanomaterials and their physical interactions with biological systems. It is, therefore, important to develop nanoscale materials with dynamic features and heterogeneities. In this work, through engineering of hierarchical polyethylene glycol (PEG) structures on gold nanoparticle (GNP) surfaces, tailored nanomaterials with different surface properties and conformations (GNPs-PEG) are created for modulating the self-assembly of a widely studied protein, insulin, under amyloidogenic conditions. Important biophysical studies including thioflavin T (ThT) binding, circular dichroism (CD), surface plasmon resonance (SPR), and atomic force microscopy (AFM) showed that higher-molecular weight GNPs-PEG triggered the formation of amyloid fibrils by promoting adsorption of proteins at nanoparticle surfaces and favoring primary nucleation rate. Moreover, the modulation of fibrillation kinetics reduces the overall toxicity of insulin oligomers and fibrils. In addition, the interaction between the PEG polymer and amyloidogenic insulin examined using MD simulations revealed major changes in the secondary structural elements of the B chain of insulin. The experimental findings provide molecular-level descriptions of how the PEGylated nanoparticle surface modulates protein adsorption and drives the self-assembly of insulin. This facile approach provides a new avenue for systematically altering the binding affinities on nanoscale surfaces by tailoring their topologies for examining adsorption-induced fibrillogenesis phenomena of amyloid proteins. Together, this study suggests the role of nanobio interfaces during surface-induced heterogeneous nucleation as a primary target for designing therapeutic interventions for amyloid-related neurodegenerative disorders.

Spike timing-based coding in neuromimetic tactile system enables dynamic object classification.

Rapid processing of tactile information is essential to human haptic exploration and dexterous object manipulation. Conventional electronic skins generate frames of tactile signals upon interaction with objects. Unfortunately, they are generally ill-suited for efficient coding of temporal information and rapid feature extraction. In this work, we report a neuromorphic tactile system that uses spike timing, especially the first-spike timing, to code dynamic tactile information about touch and grasp. This strategy enables the system to seamlessly code highly dynamic information with millisecond temporal resolution on par with the biological nervous system, yielding dynamic extraction of tactile features. Upon interaction with objects, the system rapidly classifies them in the initial phase of touch and grasp, thus paving the way to fast tactile feedback desired for neuro-robotics and neuro-prosthetics.

Highly focused beam generated with a height tuned micro-optical structure for high contrast microscopic imaging

Light sheet illumination technology improves the signal-to-noise ratio, resolution, and reduces scattered backgrounds for biological microscopic detection system. Here, we developed a novel micro-optical structure to produce a focused and uniform beam for the enhancement of imaging contrast. The beam intensity and working distance can be modified by adjusting the height and period of the structure. Our experiments successfully recorded structured light illumination, demonstrating the ability of the structure to capture high-contrast imaging data. We compared the light fields generated with and without the structure to assess the imaging quality, revealing a maximum 4.78-fold improvement in the signal-to-noise ratio. This work provides a potential method for high-resolution and high-contrast light sheet fluorescence microscopic detection.

A Novel Technique for Solving the Nonlinear Fractional-Order Smoking Model

In the study of biological systems, nonlinear models are commonly employed, although exact solutions are often unattainable. Therefore, it is imperative to develop techniques that offer approximate solutions. This study utilizes the Elzaki residual power series method (ERPSM) to analyze the fractional nonlinear smoking model concerning the Caputo derivative. The outcomes of the proposed technique exhibit good agreement with the Laplace decomposition method, demonstrating that our technique is an excellent alternative to various series solution methods. Our approach utilizes the simple limit principle at zero, making it the easiest way to extract series solutions, while variational iteration, Adomian decomposition, and homotopy perturbation methods require integration. Moreover, our technique is also superior to the residual method by eliminating the need for derivatives, as fractional integration and differentiation are particularly challenging in fractional contexts. Significantly, our technique is simpler than other series solution techniques by not relying on Adomian’s and He’s polynomials, thereby offering a more efficient way of solving nonlinear problems.

Polystyrene nanoplastics mediate oxidative stress, senescence, and apoptosis in a human alveolar epithelial cell line

BackgroundNanoplastics, an emerging form of pollution, are easily consumed by organisms and pose a significant threat to biological functions due to their size, expansive surface area, and potent ability to penetrate biological systems. Recent findings indicate an increasing presence of airborne nanoplastics in atmospheric samples, such as polystyrene (PS), raising concerns about potential risks to the human respiratory system.MethodsThis study investigates the impact of 800 nm diameter-PS nanoparticles (PS-NPs) on A549, a human lung adenocarcinoma cell line, examining cell viability, redox balance, senescence, apoptosis, and internalization. We also analyzed the expression of hallmark genes of these processes.ResultsWe demonstrated that PS-NPs of 800 nm in diameter significantly affected cell viability, inducing oxidative stress, cellular senescence, and apoptosis. PS-NPs also penetrated the cytoplasm of A549 cells. These nanoparticles triggered the transcription of genes comprised in the antioxidant network [SOD1 (protein name: superoxide dismutase 1, soluble), SOD2 (protein name: superoxide dismutase 2, mitochondrial), CAT (protein name: catalase), Gpx1 (protein name: glutathione peroxidase 1), and HMOX1 (protein name: heme oxygenase 1)], senescence-associated secretory phenotype [Cdkn1a (protein name: cyclin-dependent kinase inhibitor 1A), IL1A (protein name: interleukin 1 alpha), IL1B (protein name: interleukin 1 beta), IL6 (protein name: interleukin 6), and CXCL8 (protein name: C-X-C motif chemokine ligand 8)], and others involved in the apoptosis modulation [BAX (protein name: Bcl2 associated X, apoptosis regulator), CASP3 (protein name: caspase 3), and BCL2 (protein name: Bcl2, apoptosis regulator)].ConclusionCollectively, this investigation underscores the importance of concentration (dose-dependent effect) and exposure duration as pivotal factors in assessing the toxic effects of PS-NPs on alveolar epithelial cells. Greater attention needs to be directed toward comprehending the risks of cancer development associated with air pollution and the ensuing environmental toxicological impacts on humans and other terrestrial mammals.

Tiny Organs, Big Impact: How Microfluidic Organ-on-Chip Technology Is Revolutionizing Mucosal Tissues and Vasculature

Organ-on-chip (OOC) technology has gained importance for biomedical studies and drug development. This technology involves microfluidic devices that mimic the structure and function of specific human organs or tissues. OOCs are a promising alternative to traditional cell-based models and animals, as they provide a more representative experimental model of human physiology. By creating a microenvironment that closely resembles in vivo conditions, OOC platforms enable the study of intricate interactions between different cells as well as a better understanding of the underlying mechanisms pertaining to diseases. OOCs can be integrated with other technologies, such as sensors and imaging systems to monitor real-time responses and gather extensive data on tissue behavior. Despite these advances, OOCs for many organs are in their initial stages of development, with several challenges yet to be overcome. These include improving the complexity and maturity of these cellular models, enhancing their reproducibility, standardization, and scaling them up for high-throughput uses. Nonetheless, OOCs hold great promise in advancing biomedical research, drug discovery, and personalized medicine, benefiting human health and well-being. Here, we review several recent OOCs that attempt to overcome some of these challenges. These OOCs with unique applications can be engineered to model organ systems such as the stomach, cornea, blood vessels, and mouth, allowing for analyses and investigations under more realistic conditions. With this, these models can lead to the discovery of potential therapeutic interventions. In this review, we express the significance of the relationship between mucosal tissues and vasculature in organ-on-chip (OOC) systems. This interconnection mirrors the intricate physiological interactions observed in the human body, making it crucial for achieving accurate and meaningful representations of biological processes within OOC models. Vasculature delivers essential nutrients and oxygen to mucosal tissues, ensuring their proper function and survival. This exchange is critical for maintaining the health and integrity of mucosal barriers. This review will discuss the OOCs used to represent the mucosal architecture and vasculature, and it can encourage us to think of ways in which the integration of both can better mimic the complexities of biological systems and gain deeper insights into various physiological and pathological processes. This will help to facilitate the development of more accurate predictive models, which are invaluable for advancing our understanding of disease mechanisms and developing novel therapeutic interventions.

Effects of Exposure to Electromagnetic Fields (EMFs) on Biological Systems

Electromagnetic Field (EMF) is a natural phenomenon; however, anthropogenic activities have significantly shifted its equilibrium, leading to potential deleterious effects on biological systems. As technology becomes more integrated into daily life, the increased use of electronic devices has contributed to a rise in man-made EMF exposure. This exposure can affect biological systems on physiological and molecular levels, raising concerns about its potential effects on animal development, reproductive systems, and overall ecosystem health. The review explores the physiological effects of exposure to static, extremely low-frequency (ELF), and radiofrequency (RF) fields, analyzing how EMF impacts oxidative stress, reproductive physiology, cardiovascular function, brain and nervous system activity, and DNA/RNA integrity. It also acknowledges the emerging concern of EMF in aquatic environments, where underwater power supplies and extensive underwater cable networks are sources of EMF exposure that may affect marine and freshwater species. The potential effects on marine life include disruptions to migratory patterns, altered reproductive cycles, and changes in aquatic biodiversity. The review acknowledges that research on EMF has improved over time, but significant gaps and information remain. It emphasizes the need for immediate attention to address the challenges and opportunities in this field.

Bioinspired Liquid Metal based Soft Humanoid Robots.

The pursuit of constructing humanoid robots to replicate the anatomical structures and capabilities of human beings has been a long-standing significant undertaking and especially garnered tremendous attention in recent years. However, despite the progress made over recent decades, humanoid robots have predominantly been confined to those rigid metallic structures, which however starkly contrast with the inherent flexibility observed in biological systems. To better innovate this area, the present article systematically explores the value and potential of liquid metals and their derivatives in facilitating a crucial transition towards soft humanoid robots. Through a comprehensive interpretation of bionics, we present an overview of liquid metals' multifaceted roles as essential components in constructing advanced humanoid robots - functioning as soft actuators, sensors, power sources, logical devices, circuit systems, and even transformable skeletal structures. We conceived that the integration of these components with flexible structures, facilitated by the unique properties of liquid metals, can create unexpected versatile functionalities and behaviors to better fulfill human needs. Finally, we envision a revolution in humanoid robots, transitioning from metallic frameworks to hybrid soft-rigid structures resembling that of biological tissues. This article is expected to provide fundamental guidance for the coming research, thereby advancing the area. This article is protected by copyright. All rights reserved.

A Novel Near-Infrared Fluorescent Probe for the Detection of Endogenous Peroxynitrite (ONOO-) in Living Cells.

In this study, we present a novel near-infrared (NIR) fluorescent probe Nile-ONO designed for the selective and sensitive detection of ONOO-. The probe Nile-ONO employed Nile red as the fluorophore, with diphenylphosphinate serving as the reaction site. In the presence of ONOO-, the probe Nile-ONO exhibits remarkable fluorescence enhancement at 659nm, with a response time of less than 20min and a low detection limit of 0.32 µM. Importantly, MTT assays demonstrate low cytotoxicity in living cells. Furthermore, Nile-ONO has excellent imaging capabilities for endogenous ONOO-. Overall, this work introduces a valuable new method for the rapid detection of ONOO- in biological systems.

An enhanced bio‐inspired energy‐efficient localization routing for mobile wireless sensor network

SummaryEnvironmental disasters such as earthquakes, tsunamis, floods, and landslides disrupt natural resources, human casualties, and so on. Early warning and alert of such events will help for preparedness to avoid human and economic causalities. Managing a disaster or emergency scenario is a difficult endeavor. These episodes of mass devastation, whether caused by natural disasters or man‐made disasters, result in massive losses of money, property, and lives as a result of inadequate response by the government and management authorities. As a result, actions must be taken to avoid these circumstances from occurring by discovering the causes of these catastrophes in advance and providing swift rescue procedures once the crisis happens. In a disaster situation, communication plays a vital role, and a lot of people turn towards it as a source of information conveyance/delivery for controlling the situation. Even these communication networks are damaged and incur tremendous losses during disasters. All the communication networks, including mobile wireless sensor networks (WSNs) deployed for communication, also suffer huge damage and face many challenges during disasters. Nature appears to deal with these issues well. WSN is inspired by several biological systems and processes that have intrinsically attractive properties such as adaptation, self‐organization, and self‐healing. In this paper, we proposed an enhanced bio‐inspired energy‐efficient localization (EBEEL) routing for Mobile WSN. The main focus of the proposed EBEEL algorithm is to overcome the challenges faced by peer‐existing routing protocols such as data aggregation, limited bandwidth, scalability, data redundancy, energy consumption, packet drops, load balancing, and Quality of Service (QoS).