Biological Signaling Systems Research Articles

Novel thiomaleimide-based fluorescent probe with aggregation-induced emission for detecting H2S

It has been well established that Hydrogen sulfide (H2S) is involved in various pathophysiological processes. Therefore, accurate monitoring H2S levels in vitro or vivo is of great significance in biological systems. Herein, we firstly developed a thiomaleimide-based compound MAL-1 bearing aggregation-induced emission characteristic for selective response toward H2S due to its nucleophilicity. The proposed sensor presented prominent sensitivity and selectivity with low detection limit of 75 nM and pseudo-first-order reaction rate constant of 9.65 × 10−2 s−1, as well as low cytotoxicity which works well in recognizing H2S in real samples and visualizing H2S in living cells. Thus, it could be concluded that the novel thiomaleimide-based probe would be a promising tool for assessing intracellular H2S levels.

The migrasome as a developmental learning paradigm in cell biology.

Migrasome is a newly discovered organelle composed of small vesicular structures enclosed in membrane structures. Since its discovery in 2014, migrasome has attracted increasing attention in cell biology due to its critical role in multiple disease processes. Its pivotal role in various disease processes, including cell migration, intercellular communication, removal of damaged mitochondria, embryogenesis localization, immune cell chemotaxis, and virus transmission, underscores its significance in biological systems. With research on migrasome steadily increasing, it becomes a unique resource for undergraduate cell biology education. For deeper understanding of migrasome, we applied a bibliometric approach. Here we conducted a comprehensive analysis of migrasome research by retrieving relevant literature from databases such as Web of Science, Scopus, and PubMed using the keywords "migrasome" or "migrasomes."Employing CiteSpace software and Prism, we analyzed annual publication trends, identified core authors and institutions, assessed national contributions, examined keywords, and scrutinized highly cited literature related to migrasome research. This study presents a comprehensive overview of migrasome research, elucidating its literature characteristics, key contributors, research hotspots, and emerging trends. By shedding light on the current status and future trajectories of migrasome research, we aim to provide valuable insights for teachers in cell biology education. We propose for the integration of migrasome research into undergraduate curricula to enhance the understanding of cell biology among premedical, medical, and biomedical students, thereby fostering a deeper appreciation for the intricate mechanisms governing cellular behavior and disease processes.

An Ion-Mediated Spiking Chemical Neuron based on Mott Memristor.

Artificial spiking neurons capable of interpreting ionic information into electrical spikes are critical to mimic biological signaling systems. Mott memristors are attractive for constructing artificial spiking neurons due to their simple structure, low energy consumption, and rich neural dynamics. However, challenges remain in achieving ion-mediated spiking and biohybrid-interfacing in Mott neurons. Here, a biomimetic spiking chemical neuron (SCN) utilizing an NbOx Mott memristor and oxide field-effect transistor-type chemical sensor is introduced. The SCN exhibits both excitation and inhibition spiking behaviors toward ionic concentrations akin to biological neural systems. It demonstrates spiking responses across physiological and pathological Na+ concentrations (1-200× 10-3 m). The Na+-mediated SCN enables both frequency encoding and time-to-first-spike coding schemes, illustrating the rich neural dynamics of Mott neuron. In addition, the SCN interfaced with L929 cells facilitates real-time modulation of ion-mediated spiking under both normal and salty cellular microenvironments.

Development and Comprehensive Evaluation of TMR Sensor-Based Magnetrodes.

Due to their compact size and exceptional sensitivity at room temperature, magnetoresistance (MR) sensors have garnered considerable interest in numerous fields, particularly in the detection of weak magnetic signals in biological systems. The "magnetrodes", integrating MR sensors with needle-shaped Si-based substrates, are designed to be inserted into the brain for local magnetic field detection. Although recent research has predominantly focused on giant magnetoresistance (GMR) sensors, tunnel magnetoresistance (TMR) sensors exhibit a significantly higher sensitivity. In this study, we introduce TMR-based magnetrodes featuring TMR sensors at both the tip and midsection of the probe, enabling detection of local magnetic fields at varied spatial positions. To enhance detectivity, we designed and fabricated magnetrodes with varied aspect ratios of the free layer, incorporating diverse junction shapes, quantities, and serial arrangements. Utilizing a custom-built magnetotransport and noise measurement system for characterization, our TMR-based magnetrode demonstrates a limit of detection (LOD) of 300pT/ at 1 kHz. This implies that neuronal spikes can be distinguished with minimal averaging, thereby facilitating the elucidation of their magnetic properties.

A rhodamine-based fluorescent probe for specific recognition of mitochondrial cysteine

Cysteine (Cys) is of great significance in biological systems and in the process of mitochondrial function. Highly selective and specificity recognizable probes for mitochondrial Cys are still in demand. In this work, a new fluorescent probe for detecting mitochondrial Cys was developed based on a rhodamine derivative. In this probe, acrylate unit was selected as group of Cys recognition and quaternized pyridinium moiety was utilized as mitochondrial targeting group. The probe showed colorless in daylight and extremely weak fluorescence in 365 nm due to its spirolactone structure when Cys did not exist. In the presence of Cys, the probe exhibited orange in daylight and produced intensely green fluorescence in 365 nm owing to the formation of the conjugated xanthene structure. The probe exhibited specific recognition for Cys. There was an excellent linear relationship between fluorescence intensity at 540 nm of the probe and the Cys concentration from 4.0 × 10-8 to 1.0 × 10-5 mol⋅L-1. And the detection limit was estimated to be 1.57 × 10-8 mol/L. Moreover, the probe was almost non-cytotoxic, possessed targeting-mitochondria ability and could sense Cys at the cellular level. The good bioimaging ability makes the probe a potential tool for studying mitochondrial Cys in biological samples.

A new oxidative pathway of nitric oxide production from oximes in plants

Nitric oxide (NO) is an essential reactive oxygen species and a signal molecule in plants. Although several studies have proposed the occurrence of oxidative NO production, only reductive routes for NO production, such as the nitrate (NO-3) -upper-reductase pathway, have been evidenced to date in land plants. However, plants grown axenically with ammonium as the sole source of nitrogen exhibit contents of nitrite and NO3−, evidencing the existence of a metabolic pathway for oxidative production of NO. We hypothesized that oximes, such as indole-3-acetaldoxime (IAOx), a precursor to indole-3-acetic acid, are intermediate oxidation products in NO synthesis. We detected the production of NO from IAOx and other oximes catalyzed by peroxidase (POD) enzyme using both 4-amino-5-methylamino-2′,7′-difluorescein fluorescence and chemiluminescence. Flavins stimulated the reaction, while superoxide dismutase inhibited it. Interestingly, mouse NO synthase can also use IAOx to produce NO at a lower rate than POD. We provided a full mechanism for POD-dependent NO production from IAOx consistent with the experimental data and supported by density functional theory calculations. We showed that the addition of IAOx to extracts from Medicago truncatula increased the in vitro production of NO, while in vivo supplementation of IAOx and other oximes increased the number of lateral roots, as shown for NO donors, and a more than 10-fold increase in IAOx dehydratase expression. Furthermore, we found that in vivo supplementation of IAOx increased NO production in Arabidopsis thaliana wild-type plants, while prx33-34 mutant plants, defective in POD33-34, had reduced production. Our data show that the release of NO by IAOx, as well as its auxinic effect, explain the superroot phenotype. Collectively, our study reveals that plants produce NO utilizing diverse molecules such as oximes, POD, and flavins, which are widely distributed in the plant kingdom, thus introducing a long-awaited oxidative pathway to NO production in plants. This knowledge has essential implications for understanding signaling in biological systems.

Renewable Carbohydrates: Advancements in Sustainable Glucose Production and Optimization

This study explores and optimizes glucose production through various biochemical processes and assesses the potential of diverse feedstock sources to meet the growing demand for renewable carbohydrates. It focuses on glucose production's significance in biological systems and industrial applications, analyzing pathways like enzymatic hydrolysis of polysaccharides and acid hydrolysis of biomass. The kinetics of glucose production are examined, encompassing kinetic models for enzymatic hydrolysis, acid hydrolysis, and fermentation processes. Factors influencing reaction kinetics are explored, and experimental techniques for kinetic parameter estimation are discussed. To address sustainability and resource utilization challenges, the study investigates locally sourced materials like agricultural residues, forest biomass, algal biomass, and food waste as renewable feedstock sources. Optimization strategies for glucose production are presented, using statistical design of experiments and response surface methodology. Techno-economic analysis and life cycle assessments provide a holistic evaluation of environmental and economic aspects associated with glucose production processes. The study's comprehensive approach to glucose production, encompassing both technological advancements and sustainability considerations, offers insights into enzymatic, acid hydrolysis, and fermentation processes, as well as comparing diverse feedstock sources. This knowledge can foster further advancements in the field, benefit industries, and encourage policymakers to promote the integration of renewable carbohydrates in the broader bioeconomy. The research contributes to the global shift towards a greener and more sustainable future, where glucose production plays a key role in building a resilient and eco-conscious society.

Electrochemical oxidation of guanosine: Mechanistic insights and direct detection in weakly supported media

Guanosine, a purine nucleoside, is a potential biomarker of oxidative stress and central nervous system diseases. In this study, we investigate the oxidation of guanosine using a combination of voltammetric measurements at stationary and hydrodynamic electrodes, at both macro- and micro-scales, along with DFT calculations, shedding light on its complex reaction mechanism of significance in biological systems. In addition to providing mechanistic insights, we present the development of an electrochemical sensor for guanosine detection using a carbon fiber microelectrode. This sensor can be applied to samples with low ionic strength and exhibits two linear detection ranges in the absence of added supporting electrolyte: 0.0067 – 0.12 mM and 0.12 – 1.00 mM with the sensitivities of 1.40 ± 0.03 nA mM−1 and 0.05 ± 0.003 nA mM−1, respectively, and the limit of detection of (3sB/m) 0.002 mM. The sensor was validated in synthetic urine samples, showing a %recovery of 99.71 ± 4.02 % (RSD = 4.95 %), indicating its suitability for direct guanosine measurements in the complex matrices.

Positron Emission Tomography Using 64-Copper as a Tracer for the Study of Copper-Related Disorders.

Copper is an essential trace element, functioning in catalysis and signaling in biological systems. Radiolabeled copper has been used for decades in studying basic human and animal copper metabolism and copper-related disorders, such as Wilson disease (WD) and Menke's disease. A recent addition to this toolkit is 64-copper (64Cu) positron emission tomography (PET), combining the accurate anatomical imaging of modern computed tomography (CT) or magnetic resonance imaging (MRI) scanners with the biodistribution of the 64Cu PET tracer signal. This allows the in vivo tracking of copper fluxes and kinetics, thereby directly visualizing human and animal copper organ traffic and metabolism. Consequently, 64Cu PET is well-suited for evaluating clinical and preclinical treatment effects and has already demonstrated the ability to diagnose WD accurately. Furthermore, 64Cu PET/CT studies have proven valuable in other scientific areas like cancer and stroke research. The present article shows how to perform 64Cu PET/CT or PET/MR in humans. Procedures for 64Cu handling, patient preparation, and scanner setup are demonstrated here.

Ion-tunable antiambipolarity in mixed ion–electron conducting polymers enables biorealistic organic electrochemical neurons

Biointegrated neuromorphic hardware holds promise for new protocols to record/regulate signalling in biological systems. Making such artificial neural circuits successful requires minimal device/circuit complexity and ion-based operating mechanisms akin to those found in biology. Artificial spiking neurons, based on silicon-based complementary metal-oxide semiconductors or negative differential resistance device circuits, can emulate several neural features but are complicated to fabricate, not biocompatible and lack ion-/chemical-based modulation features. Here we report a biorealistic conductance-based organic electrochemical neuron (c-OECN) using a mixed ion–electron conducting ladder-type polymer with stable ion-tunable antiambipolarity. The latter is used to emulate the activation/inactivation of sodium channels and delayed activation of potassium channels of biological neurons. These c-OECNs can spike at bioplausible frequencies nearing 100 Hz, emulate most critical biological neural features, demonstrate stochastic spiking and enable neurotransmitter-/amino acid-/ion-based spiking modulation, which is then used to stimulate biological nerves in vivo. These combined features are impossible to achieve using previous technologies.

In situ investigation of the oxidation of a phospholipid monolayer by reactive oxygen species

The oxidation of membrane lipids has been widely studied for several decades owing to its significance in biological systems. However, despite its damaging physiological impact and its known role in many diseases, relatively little is understood about the specific structural consequences of oxidative action, particularly in vivo. In this work, a combination of sum-frequency generation spectroscopy, surface tensiometry, and surface-selective infrared spectroscopies are used to gain deeper insight into the oxidation of phospholipids by reactive oxygen species generated in situ. Oxidation is achieved by employing the Fenton reaction to convert physiological levels of H2O2 into OH and HO2 radicals in proximity to the headgroups of lipid monolayers at the air-water interface. By temporally monitoring the surface tension and spectroscopic changes at the interface as the oxidation proceeds, the impact of oxidation on the structure, conformation, and intermolecular interactions within the membrane has been revealed.

Geographic and record-based pesticide exposure assessment, biologic exposure signatures, and chronic disease modelling in California

Background and Aims: For the past 50 years, California has been recording agricultural pesticide applications in a pesticide use reports (PUR) database; i.e. documenting use for several hundred pesticide active ingredients. These data can be employed in exposure assessment purposes targeting specific pesticides and pesticide mixtures and study a range of adverse health outcomes. Methods: In collaboration with M. Cockburn at USC, my team at UCLA has generated a geographic information system tool that uses these records in conjunction with land use data to generate spatio-temporal exposure measures for the California population living near agricultural applications. Over the past 2 decades we have used this tool kit to estimate pesticide related health effects including studies of adverse birth outcomes, autism, cerebral palsy, childhood brain cancers, Parkinson’s and Alzheimer’s disease. Results: I will present and discuss common as well as special challenges for exposure assessment and the results of the studies we conducted in the past 2 decades. Furthermore, we investigated whether long- or shorter-term exposures to agricultural use pesticides assessed with the PUR tools generate exposure signals in biological systems and bio-fluids, i.e. relying on human blood samples from older adult residents of central California to examine metabolomic patterns, methylation changes, and influences that certain pesticides have on the gut microbiome. Using integrative omics analyses, we also examined overlap between pesticide-associated biologic pathways and pathways known to be perturbed in certain diseases. Conclusions: These studies help to systematically identify physiologic responses to chronic pesticide exposures. Eventually this will help to better understand how low-level chronic pesticide exposures may contribute to chronic brain diseases in real world exposure scenarios. Keywords: pesticides, exposure assessment, Parkinson’s disease, neurodevelopment, multi-omics

Nitrogenated Holey Graphene (C2N-h2D): An excellent sensor for neurotransmitter amino acids

Interactions of amino acids with organic surfaces are highly relevant to the development of modern synthetic biomaterials with biocompatibility and low biotoxicity. Biomolecule-surface interactions vary differently according to the molecule orientation, charge state, and distance from the surface. Furthermore, the electron transfer through molecule/surface could also play a key role in biological recognition and signaling systems. Here, using density functional theory (DFT), we investigated the interactions of three neurotransmitter amino acids (NAAs), namely, glycine (Gly), γ-aminobutyric acid (Gaba), and glutamate (Glu), onto a nanosheet of holey nitrogenated graphene (C2N-h2D). In general, the interactions between amino acids and carbon-based surfaces are mediated through weak van der Waals interactions. However, based on interaction energy and charge density difference calculations, there is a strong physisorption process between NAAs and the C2N structure. In particular, Gaba and Glu can act as exclusive electron donor and acceptor, respectively. Our calculations also reveal that, by changing the orientations from neutral to zwitterionic, the Gly molecule changes from a donor to a strong acceptor of electrons. In the case of electron donation, the resistivity on the C2N surface should be reduced. These findings indicate that the C2N surface is an excellent candidate for high-performance biosensor applications. From the band structure point of view, the NAAs molecules introduce occupied flat bands within the bandgap of the C2N single layer, while the surface energy levels keep the bulk characteristics of the semiconductor system. Finally, the optical absorption spectrum of NAAs-C2N systems reveals that these NAAs seem to improve the photoactivity performance of the C2N structure, with the appearance of intraband transitions.

Dental Materials for Oral Microbiota Dysbiosis: An Update.

The balance or dysbiosis of the microbial community is a major factor in maintaining human health or causing disease. The unique microenvironment of the oral cavity provides optimal conditions for colonization and proliferation of microbiota, regulated through complex biological signaling systems and interactions with the host. Once the oral microbiota is out of balance, microorganisms produce virulence factors and metabolites, which will cause dental caries, periodontal disease, etc. Microbial metabolism and host immune response change the local microenvironment in turn and further promote the excessive proliferation of dominant microbes in dysbiosis. As the product of interdisciplinary development of materials science, stomatology, and biomedical engineering, oral biomaterials are playing an increasingly important role in regulating the balance of the oral microbiome and treating oral diseases. In this perspective, we discuss the mechanisms underlying the pathogenesis of oral microbiota dysbiosis and introduce emerging materials focusing on oral microbiota dysbiosis in recent years, including inorganic materials, organic materials, and some biomolecules. In addition, the limitations of the current study and possible research trends are also summarized. It is hoped that this review can provide reference and enlightenment for subsequent research on effective treatment strategies for diseases related to oral microbiota dysbiosis.

Excited-state geometry relaxation of pyrene-modified cellulose nanocrystals under UV-light excitation for detecting Fe3+

Abstract Capturing and detecting Fe3+ ions in aqueous solution is of great significance in biological systems as well as the water treatment industry. Herein, pyrene-modified cellulose nanocrystal (CNC-1-Pyr) acting as a fluorescent probe was prepared by a one-step esterification reaction, which shows geometry relaxation under UV-light excitation. Experiments and density functional theory-based simulations revealed that the structural geometry relaxation is controlled by the electron excitation and fluorescence emission. The S1 state of CNC-1-Pyr provides a conformation match for coordination with Fe3+ under the excitation of UV light, facilitating the detecting and capturing of Fe3+ efficiently.

Multi-omics insights into host-viral response and pathogenesis in Crimean-Congo hemorrhagic fever viruses for novel therapeutic target.

The pathogenesis and host-viral interactions of the Crimean-Congo hemorrhagic fever orthonairovirus (CCHFV) are convoluted and not well evaluated. Application of the multi-omics system biology approaches, including biological network analysis in elucidating the complex host-viral response, interrogates the viral pathogenesis. The present study aimed to fingerprint the system-level alterations during acute CCHFV-infection and the cellular immune responses during productive CCHFV-replication in vitro. We used system-wide network-based system biology analysis of peripheral blood mononuclear cells (PBMCs) from a longitudinal cohort of CCHF patients during the acute phase of infection and after one year of recovery (convalescent phase) followed by untargeted quantitative proteomics analysis of the most permissive CCHFV-infected Huh7 and SW13 cells. In the RNAseq analysis of the PBMCs, comparing the acute and convalescent-phase, we observed system-level host's metabolic reprogramming towards central carbon and energy metabolism (CCEM) with distinct upregulation of oxidative phosphorylation (OXPHOS) during CCHFV-infection. Upon application of network-based system biology methods, negative coordination of the biological signaling systems like FOXO/Notch axis and Akt/mTOR/HIF-1 signaling with metabolic pathways during CCHFV-infection were observed. The temporal quantitative proteomics in Huh7 showed a dynamic change in the CCEM over time and concordant with the cross-sectional proteomics in SW13 cells. By blocking the two key CCEM pathways, glycolysis and glutaminolysis, viral replication was inhibited in vitro. Activation of key interferon stimulating genes during infection suggested the role of type I and II interferon-mediated antiviral mechanisms both at the system level and during progressive replication.

Suppression of cell-cell variation by cooperative interaction of phosphatase and response regulator

In bacterial chemotaxis, the output of chemosensing, the concentration of the response regulator CheY-P that was constantly adjusted by the opposing action of the kinase CheA and the phosphatase CheZ, serves as the input of the ultrasensitive flagellar motor that drives bacterial motility. The steady-state kinase activity exhibits large cell-to-cell variation that may result in similar variation in CheY-P concentration. Here, we found that the in vivo phosphatase activity is highly cooperative with respect to CheY-P concentration, and this suppresses the cell-to-cell variation of CheY-P concentration so that it falls within the operational range of the flagellar motor. Therefore, the cooperativity of the CheZ and CheY-P interaction we identified here provided a mechanism of robust coupling between the output of chemosensing and the input of the flagellar motor. Suppression of cell heterogeneity by cooperativity of protein-protein interaction is likely a common feature in many biological signaling systems.

Low-molecular-mass labile metal pools in Escherichia coli: advances using chromatography and mass spectrometry

Labile low-molecular-mass (LMM) transition metal complexes play essential roles in metal ion trafficking, regulation, and signalling in biological systems, yet their chemical identities remain largely unknown due to their rapid ligand-exchange rates and weak M–L bonds. Here, an Escherichia coli cytosol isolation procedure was developed that was devoid of detergents, strongly coordinating buffers, and EDTA. The interaction of the metal ions from these complexes with a SEC column was minimized by pre-loading the column with 67ZnSO4 and then monitoring 66Zn and other metals by inductively coupled plasma mass spectrometry (ICP-MS) when investigating cytosolic ultrafiltration flow-through-solutions (FTSs). Endogenous cytosolic salts suppressed ESI-MS signals, making the detection of metal complexes difficult. FTSs contained ca. 80 µM Fe, 15 µM Ni, 13 µM Zn, 10 µM Cu, and 1.4 µM Mn (after correcting for dilution during cytosol isolation). FTSs exhibited 2–5 Fe, at least 2 Ni, 2–5 Zn, 2–4 Cu, and at least 2 Mn species with apparent masses between 300 and 5000 Da. Fe(ATP), Fe(GSH), and Zn(GSH) standards were passed through the column to assess their presence in FTS. Major LMM sulfur- and phosphorus-containing species were identified. These included reduced and oxidized glutathione, methionine, cysteine, orthophosphate, and common mono- and di-nucleotides such as ATP, ADP, AMP, and NADH. FTSs from cells grown in media supplemented with one of these metal salts exhibited increased peak intensity for the supplemented metal indicating that the size of the labile metal pools in E. coli is sensitive to the concentration of nutrient metals.

Long-range mechanical signaling in biological systems.

Cells can respond to signals generated by other cells that are remarkably far away. Studies from at least the 1920's showed that cells move toward each other when the distance between them is on the order of a millimeter, which is many times the cell diameter. Chemical signals generated by molecules diffusing from the cell surface would move too slowly and dissipate too fast to account for these effects, suggesting that they might be physical rather than biochemical. The non-linear elastic responses of sparsely connected networks of stiff or semiflexible filament such as those that form the extracellular matrix (ECM) and the cytoskeleton have unusual properties that suggest multiple mechanisms for long-range signaling in biological tissues. These include not only direct force transmission, but also highly non-uniform local deformations, and force-generated changes in fiber alignment and density. Defining how fibrous networks respond to cell-generated forces can help design new methods to characterize abnormal tissues and can guide development of improved biomimetic materials.

Cenote-Taker 2 democratizes virus discovery and sequence annotation.

Viruses, despite their great abundance and significance in biological systems, remain largely mysterious. Indeed, the vast majority of the perhaps hundreds of millions of viral species on the planet remain undiscovered. Additionally, many viruses deposited in central databases like GenBank and RefSeq are littered with genes annotated as 'hypothetical protein' or the equivalent. Cenote-Taker 2, a virus discovery and annotation tool available on command line and with a graphical user interface with free high-performance computation access, utilizes highly sensitive models of hallmark virus genes to discover familiar or divergent viral sequences from user-input contigs. Additionally, Cenote-Taker 2 uses a flexible set of modules to automatically annotate the sequence features of contigs, providing more gene information than comparable tools. The outputs include readable and interactive genome maps, virome summary tables, and files that can be directly submitted to GenBank. We expect Cenote-Taker 2 to facilitate virus discovery, annotation, and expansion of the known virome.