Biological Systems Research Articles

A Highly Selective and Sensitive Carbazole-Based Fluorescent Probe for Peroxynitrite Detection and Cellular Imaging

Peroxynitrite, a colorless and odorless reactive nitrogen species, plays a critical role in various physiological processes within biological systems. Therefore, developing a reliable method for quantitative detection of peroxynitrite in living systems is essential. In this study, we synthesized a simple, two-step, reaction-based fluorescent probe, designated as EHMC, specifically for peroxynitrite detection. The synthesis involved the use of 4-(9-phenyl-9H-carbazol-3-yl)benzaldehyde as the fluorophore and 2-hydrazineylpyridine as the recognition group, both of which exhibit inherently weak fluorescence. Upon oxidation of the C=N bond by peroxynitrite, EHMC undergoes conversion into an aldehyde, resulting in a significant fluorescence response. EHMC demonstrated high selectivity and sensitivity, achieving a detection limit of 5.43 µM under physiological conditions. Additionally, EHMC was successfully applied to HeLa cellular models, where it exhibited excellent cellular imaging capability for peroxynitrite detection in living systems.

Insights into the efficiencies of different biological treatment systems for pharmaceuticals removal: A review.

This review presents a comprehensive analysis of current research on biological treatment processes for removing pharmaceutical compounds (PhCs) from wastewater. Unlike previous studies on this topic, our study specifically delves into the effectiveness and drawbacks of various treatment approaches such as traditional wastewater treatment facilities (WWTP), membrane bioreactors (MBRs), constructed wetlands (CW), and moving bed biofilm reactors (MBBR). Through the examination and synthesis of information gathered from more than 200 research studies, we have created a comprehensive database that delves into the effectiveness of eliminating 19 particular PhCs, including commonly studied compounds such as acetaminophen, ibuprofen, diclofenac, naproxen, ketoprofen, indomethacin, salicylic acid, codeine, and fenoprofen, amoxicillin, azithromycin, ciprofloxacin, ofloxacin, tetracycline, atenolol, propranolol, and metoprolol. This resource provides a depth and scope of information that was previously lacking in this area of study. Notably, among these pharmaceuticals, azithromycin demonstrated the highest removal rates across all examined treatment systems, with the exception of WWTPs, while carbamazepine consistently exhibited the lowest removal efficiencies across various systems. The analysis showcases the diverse results in removal efficiency impacted by factors such as system configuration, operation specifics, and environmental circumstances. The findings emphasize the critical need for continued innovation and research, specifically recommending the integration of advanced oxidation processes (AOPs) with existing biological treatment methods to improve the breakdown of recalcitrant compounds like carbamazepine. PRACTITIONER POINTS: Persistent pharmaceuticals harm aquatic ecosystems and human health. Biological systems show varying pharmaceutical removal efficiencies. Enhancing HRT and SRT improves removal but adds complexity and costs. Tailored treatment approaches needed based on contaminants and conditions.

A review on protein utilization and its interactions with carbohydrate and lipid from a molecular perspective in aquaculture: An implication beyond growth.

The world's increasing need for protein faces challenges in aquaculture production. New applications and tools will need to be added at every stage of the manufacturing line to attain this expansion sustainably, safely, and effectively. Utilizing experimental methods to increase aquatic animal production has become more common as aquatic biotechnology has advanced. High-throughput omics technologies have been introduced to address these issues, including transcriptomic, metabolomic, proteomic, and genomes. But it also faces many difficulties, like other food manufacturing industries. One of the best and most durable approaches to address these issues is probably to understand nutritional requirements and modify diet based on need. Molecular approaches are a subset of multiomics technology. Previously, most of the published work was devoted to the biochemical aspects of protein-lipid interactions in biological systems. In this review, we explore this idea and highlight various works that fall under the umbrella of nutrigenomics, with a particular emphasis on protein utilization and its interactions with carbohydrates and lipids.

Prioritizing weeds for biological control development in the western USA: Results from the adaptation of the biological control target selection system

Nonnative invasive plants (weeds) negatively impact native ecosystems, and their effects are likely to increase with continuing global trade. Biological weed control has been employed as a cost-effective and sustainable management option for weeds in the USA since 1902. Biological control programs require careful prioritization of target weeds to ensure the most appropriate targets are selected to obtain the greatest beneficial outcomes with available resources. The Biological Control Target Selection (BCTS) system was developed by researchers in South Africa as an objective, transparent approach to prioritizing new weed biological control targets. The BCTS system was recently modified and applied to 295 state-regulated weeds in the western USA for which no biological control agents have yet been released. This paper presents the results of that application, identifying the most suitable candidates for new biological control programs as well as problematic weeds for which the likelihood of successful biological control is low.Top-ranked species in the western USA are biennial or perennial weeds that occur in stable habitats, are established in more than one state, have traits deemed difficult to control with conventional methods, have large negative impacts and no conflicts of interest outside of the horticultural industry, and have substantial information available on potential biocontrol agents. Fifteen of the 20 top-ranked species are already targets of ongoing biological control programs in the USA. When species with current programs are excluded from the analysis, the next 20 top-ranked species largely differ by having less information available on potential biological control agents and having native or economically important congeners in the USA. Results from this framework provide valuable insights to the prioritization of current and future biocontrol research programs in the western USA.

Structurally Colored Photonic Crystal Biomimetic Microstructures for Daytime Radiative Cooling.

Daytime radiative cooling offers a novel solution to the energy crisis, enabling green and efficient thermal management in space. High reflectance in the solar spectrum is essential for passive radiative cooling, rendering dye coloring and similar methods unsuitable for colored coolers. This paper presents a structurally colored photonic crystal biomimetic microstructured radiative cooler. Inspired by natural biological systems, this cooler features a dual-layered microtruncated-cone array structure on the surface and bottom membrane layers. The silver reflector and 3D micrograting surface structure produce continuous iridescent colors through multiple interference effects. Optimized lithographic process enable the fabrication of the ordered dual-layer surface microstructure arrays with precise angular combinations. The dual-layered microtruncated-cone introduces a gradient refractive index, reducing impedance mismatch at the interface. As a result, the radiative cooler achieves high solar spectral reflectance (0.95) and high mid-infrared emissivity (0.95). Notably, the net theoretical cooling power and the subambient temperature drop are 106.9 W m-2 and 7.4 °C, respectively, at an ambient temperature of 40 °C, with a measured average temperature reduction of 6.1 °C under direct sunlight. This performance matches that of advanced radiative coolers, striking a balance between aesthetics and radiative cooling capability.

Senescence, change, and competition: When the desire to pick one model harms our understanding

The question of why we age is a fundamental one. It is about who we are, and it also might have critical practical aspects as we try to find ways to age slower. Or to not age at all. Different reasons point at distinct strategies for the research of anti-ageing drugs. While the main reason why biological systems work as they do is evolution, for quite a while, it was believed that aging required another explanation. Aging seems to harm individuals so much that even if it has group benefits, those benefits were unlikely to be enough. That has led many scientists to propose non-evolutionary explanations as to why we age. But those theories seem to fail at explaining all the data on how species age. Here, I will show that the insistence of finding the one idea that explains it all might be at the root of the difficulty of getting a full picture. By exploring an evolutionary model of aging where locality and temporal changes are fundamental aspects of the problem, I will show that environmental change causes the barrier for group advantages to become much weaker. That weakening might help small group advantages to add up to the point they could make an adaptive difference. To answer why we age, we might have to abandon asking which models are correct. The full answer might come from considering how much each hypothesis behind each existing model, evolutionary and non-evolutionary ones, contributes to the real world’s solution.

The synergistic interaction of fungi with different structural characteristics improves the leaching of lithium from lepidolite

The aim of this study was to explore the improvement of lithium leaching from lepidolite by microbial co-culture, focusing on the synergistic effect of different structural fungi in improving the leaching performance of biological systems. The results showed that in the single leaching experiment, the multicellular fungi and the unicellular yeast showed weak effects. Multicellular fungus is limited by insufficient EPS secretion, while unicellular yeast is non-mycelial organisms with weak acid production capacity and limited effect on minerals. However, in the combined leaching experiment, the interspecific collaboration promoted the synthetic and metabolic activity of the two strains, resulting in changes in the type and content of organic acids, polysaccharides, proteins and humus. The content of citric acid reached the highest value of 16.98g·L-1 at about 22 d, and the EPS secreted by unicellular yeast promoted the mycelium adhesion and mineral wrapping of multicellular fungi. The combined action of the two enhanced the effects of acidification, complexation and mycelium destruction, and improved the leaching effect. This study revealed the synergistic metabolic mechanism of lepidolite leaching by fungi with different structures, verified the effectiveness of microbial co-culture to improve the leaching rate, and provided a basis for industrial application. In addition, the use of co-culture technology has a positive impact on commercial production and environmental protection.

The Effects of Tomato Intercropping with Medicinal Aromatic Plants Combined with Trichoderma Applications in Organic Cultivation

To increase biodiversity in tomato cultivation, two herbal aromatic plants, thyme (Thymus vulgaris) and basil (Ocimum basilicum L.), were introduced as companion plants. Their role was to improve crop plant growth and stress resistance. Moreover, the effect of the soil application of Trichoderma microbial preparations on tomato growth parameters and yield, in combination with companion plants, was studied. Ligno-cellulose multi-layer microcapsules with Trichoderma atroviride TRS14 spores (MIC14) and the commercial preparation Trianum G (TG) were used as microbial preparations. This experiment was carried out in a certified organic field. Tomato plants were intercropped with thyme or basil in the arrangement of two tomato rows alternating with one herbal row. In all intercropping arrangements and in the control (tomato plants grown without herbs), subplots were sectioned. The soil in the subplots was amended with the MIC14 and TG preparations used at a concentration of 104 spores g−1 of the soil and planted with tomato transplants. No control measures were applied during tomato growing, and the plants were naturally infected with late blight. Tomato plant growth parameters and yield were assessed, and late blight severity was monitored. The degree of soil colonization by Trichoderma fungi and the effect of these applications on soil microbial activity and biodiversity (dehydrogenases activity, EcoPlates AWCD, and Shannon index) were evaluated. The results clearly showed a significant influence of thyme and basil on tomato growth and yield in organic production. The cultivation of thyme adjacent to tomatoes had a beneficial effect on the development of the root system and the number of flowers and fruits on the crop plants. Basil, on the other hand, clearly decreased tomato yield and adversely affected the effect of Trichoderma applications by reducing root system development. Moreover, basil as a companion plant increased late blight symptoms. Both Trichoderma strains colonized soil, but they had no significant effect on the microbial activity or metabolic potential measured on the EcoPlates with the use of the BIOLOG system. However, a decrease in dehydrogenases activity was noted. In organic cultivation, the Trichoderma preparations used had no significant effect on tomato yield, opposite to its increase in integrated tomato production.

Vanillic acid ameliorates diethyl phthalate and bisphenol S-induced oxidative stress and neuroinflammation in the hippocampus of experimental rats.

Long-term adverse effects on human health are caused by exogenous compounds that alter the functions of biological systems, especially neuroendocrine disruptors like diethyl phthalate (DEP) and bisphenol S (BPS). Although vanillic acid (VA) has pertinent neuropharmacological characteristics, its effect against DEP + BPS-induced neurotoxicity has not been explored. This study proposed that VA may offer protection against the neurotoxicity caused by DEP + BPS. Thirty male Wistar rats were randomly distributed across five groups: a control group receiving DMSO, a group exposed to a mixture of BPS and DEP, two BPS + DEP-exposed groups treated with VA at doses of 25 mg/kg or 50 mg/kg, and a nonexposed group treated with 50 mg VA/kg. After 21 days, the hippocampal tissues were processed for biochemical analyses. Our results indicate that exposure to DEP + BPS upregulated neurosignaling mediators (NTPDase, ADA, MAO-A, and Ca2+), inhibited others (AChE and Ca2+/Mg2+-ATPase), decreased hippocampus antioxidants (GSH, GPx, CAT, and SOD), and elevated markers of oxidative stress/damage (NO, H2O2, MDA, and AOPP). AR, BAX, TNF-α, BAK1, and IL-1β expressions were upregulated, while IL-10 and BDNF expressions were downregulated. NF-κB and caspase-3/9 pathways were also upregulated. Co-treatment with vanillic acid remarkably precluded these neurotoxic outcomes by improving neurosignaling, augmenting antioxidant status, abrogating oxidative damage, inflammation (TNF-α, IL-1β), and apoptosis (BAX, BAK1, caspase-3/9). Vanillic acid also restored IL-10 and BDNF levels, thereby exhibiting neuroprotective effects, corroborated by histological examinations. We posit vanillic acid as a safe and effective therapeutic agent against neurotoxicity occasioned by exposure to neuroendocrine disruptors.

Slow-fast dynamics in non-linear enzyme cascades gives rise to spatial multiscaling.

Slow-fast dynamics in a well-mixed biological system is known to be associated with functional modularity with temporal hierarchy of processes. Yet, the significance of slow-fast dynamics in spatially distributed reaction-diffusion systems remains to be clarified.We assessed such systems with slow-fast dynamics, such as blood coagulation and predator-prey models to identify spatial patterns with independent parametric regulation, and performed their reaction-rate based sensitivity analysis with the help of computational one-dimensional reaction-diffusion models.In blood coagulation, spatial distribution of fibrin had two scales: a larger region with a high and almost constant fibrin concentration (corresponding to solid blood clot) and a narrow transition zone, where fibrin concentration decayed to zero (semi-liquid clot). Slow variables (e.g., the concentration of the coagulation factor IXa) regulated the clot size (large scale), while fast variables (e.g., concentrations of thrombin and factor Xa) regulated the thickness of the gel-to-liquid transition zone (small scale). Analysis of the simplified model of blood coagulation, composed only of factor X and IX activation, and of the predator-prey model confirmed this finding to be sufficiently general, and revealed that the limitation of fast enzyme production (due to precursor depletion or to kinetics with saturation) was crucial for this multi-scaling. Independent regulation of spatial scales also required species with slow kinetics to be upstream from species with fast kinetics.The shared slow-fast dynamics of the examined systems endow them with the ability to form spatial patterns, representing a new mechanism complementing the Turing-type and the Positional Information type pattern formation.

Dual-locked NIR fluorescent probe for detection of GSH and lipid droplets and its bioimaging application in cancer model

Fluorescence probes with outstanding merits have wide applications in tumor diagnosis. However, most of these probes can only detect single tumor biomarker, potentially generating “false positive” signals within intricate biological systems. In contrast, the dual-locked fluorescent probes triggered by two response factors can effectively address the aforementioned limitations. In this work, we fabricated a novel coumarin-based NIR fluorescent probe (CP-GSH), demonstrating dual-responsiveness to high glutathione (GSH) concentrations and high viscosity. Specifically, the probe showed strong fluorescence enhancement at 675 nm ∼ 725 nm in the simultaneous presence of GSH and high viscosity, whereas the presence of either GSH or high viscosity alone could not induce a noticeable change in fluorescence intensity of CP-GSH. More importantly, the bioimaging experiments further validated CP-GSH triggered by endogenous GSH possessed excellent targeting capability towards lipid droplets (LDs), which could be utilized to effective discriminate between cancer cells and normal cells. This work proposes a promising strategy for the design of dual-locked probe for tumor imaging.

Temperature Dependent Photoluminescence Properties of a Y2Ge2O7:Tb3+ phosphors. A dual band ratiometric luminescent thermometer

A series of green light emitting Y2Ge2O7:xTb3+ phosphors (x = 0.2, 0.5, 1.0, 2.0 and 4.0mol%) were obtained via the solid-state reaction method. The single phase was confirmed by XRD technique. The photoluminescence (PL) excitation spectrum, emission spectra at room and as a function of temperature, decay curves of phosphors were studied in detail. The emission spectra show typical emissions of Tb3+ ions, whose relative intensities change with the ion concentration or UV excitation. A shift of the CIE chromaticity coordinates from blueish to green region was observed. The emission decay curves are compatible with a single type of Tb3+ activator. The obtained internal Quantum Yield (iQY) increase with the terbium concentration, up to 10.0% for sample with 4.0mol%. In addition, the relative sensitivity values (Sr) for samples with 1.0 and 2.0mol% reached 0.97 and 2.02%K-1, respectively. These high thermal sensitivities obtained, in comparison with other Tb3+ based optical temperature sensors, in biophysical temperature range (30–45 °C), illustrates the potential use of Y2Ge2O7:xTb3+ phosphors in the design of efficient FIR luminescent thermometers for biological systems or other industrial applications.

Discovery of anti-tumor agent targeted MetAP-2 using a special turn-on fluorescent probe

Methionine aminopeptidase 2 (MetAP-2) catalyzes the removal of methionine from the amino-terminus of proteins or peptides and is a known target for anti-tumor therapy. In this study, we developed an enzyme-activated fluorescent probe, DDAO-BMT, specifically for the real-time detection of endogenous MetAP-2. This probe enables the determination of extracellular MetAP-2 activity and visual monitoring of intracellular MetAP-2. Additionally, Sappan Lignum was identified as an active herbal medicine against MetAP-2, with brazilin identified as its key active constituent. Brazilin also exhibited a significant anti-tumor effect, including the inhibition on proliferation, migration, and invasion of tumor cells, and the preliminary mechanism of its activity against cancer has been elucidated. The use of this probe facilitates the monitoring of endogenous MetAP-2 in complex biological system, aiding in the discovery of novel active compounds for cancer treatment.

Strategies for Top-Down Hydrogen Deuterium Exchange-Mass Spectrometry: A Mini Review and Perspective.

Hydrogen deuterium-exchange mass spectrometry (HDX-MS) is commonly used in the study of protein dynamics and protein interactions. By measuring the isotopic exchange of backbone amide hydrogens in solution, HDX-MS offers valuable structural insights into challenging biological systems. Traditional HDX-MS approaches utilize bottom-up (BU) proteomics, in which deuterated proteins are digested before MS analysis. BU-HDX enables the characterization of proteins with various sizes in simple protein mixtures or complex biological samples such as cell lysates. However, BU methods are inherently limited by the inability to resolve protein sub-populations arising from different protein conformations, such as those arising from post-translational modifications (PTMs). Alternatively, top-down (TD) HDX-MS detects the global deuterium uptake at the intact proteoform level, allowing direct probing of structural changes due to protein-protein interactions, PTMs, or conformational changes. Combining TD-HDX-MS with electron-based fragmentation techniques, such as electron capture dissociation (ECD) and electron transfer dissociation (ETD), has demonstrated the feasibility of studying intact protein interactions with amino acid-level resolution. Here, we present a brief overview of methodologies, limitations, and applications of TD-HDX-MS using direct infusion techniques and LC-based approaches. Furthermore, we conclude with a perspective on the future directions for TD-HDX-MS.

Directionality theory and the origin of life.

The origin of cellular life can be described in terms of the transition from inorganic matter to the emergence of cooperative assemblies of organic matter: DNA and proteins, capable of replication and metabolism. Directionality theory is a mathematical theory of the collective behaviour of networks of organic matter: activated macromolecules, cells and higher organisms. Evolutionary entropy, a generalization of the thermodynamic entropy of Boltzmann, is a statistical measure of the cooperativity of the biotic components. The cornerstone of Directionality theory is the Entropic Principle of Evolution: evolutionary entropy increases in systems driven by a stable energy source, and decreases in systems subject to a fluctuating energy source. This article invokes the Entropic Principle of Evolution-an extension to biological systems of the Second Law of Thermodynamics-to provide an adaptive rationale for the following sequence of transformations that define the emergence of cellular life: (i) the self-assembly of activated macromolecules from inorganic matter; (ii) the emergence of an RNA world, defined by RNA molecules with catalytic and replicative properties; and (iii) the origin of cellular life, the integration of the three carbon-based polymers-DNA, proteins and lipids, to generate a metabolic and replicative unit.

Design, construction and evaluation of collaborative bio-system of Vibrio fluvialis with Chlorella sorokiniana for treating actual printing and dyeing wastewater

Treating actual printing and dyeing wastewater (APDW) using bacteria/algae collaborative is considered an eco-friendly and cost-effective strategy. In this study, Vibrio fluvialis (V. fluvialis) and Chlorella sorokiniana (C. sorokiniana) were isolated from APDW and used to construct the bacteria/algae collaborative treatment system (BACTS) for treating APDW. The results showed that the V. fluvialis / C. sorokiniana collaborative treatment could achieve removal rates of 87.31 % for TP, 73.23 % for COD, and 35 % for dyes under the optimized conditions (V. fluvialis first added, C. sorokiniana followed, V. fluvialis / C. sorokiniana inoculation ratio of 1:2, pH 6.5 and light intensity 8,000 Lux). The APDW water quality improved 55.6 % after the V. fluvialis / C. sorokiniana collaborative treatment. Additionally, the collaborative system generated a significant amount of high-value products (27.63 % lipid yield, 81.1 mg/g polysaccharide and 16.62 mg/g protein). The transcriptome analysis demonstrated that the expression of various enzymes such as laccases, peroxidases and azoreductases, etc. related pathways in V. fluvialis / C. sorokiniana involved in textile dyes degradation and biotransformation. This study provides an efficient and low-cost treatment method for APDW through a novel synergistic biological system of bacteria and algae.

An interdisciplinary research field transformed into an intermedial science exploration programme: how to explore neurotronics research and development in a school student laboratory programme

Abstract This work presents the development and implementation of an interdisciplinary and intermedial science outreach programme designed for school students. The programme integrates biological systems and technological advancements to provide students with hands-on laboratory experiences and immersive media, including virtual reality videos and augmented reality posters. Through a co-creation process involving scientists and educators, the programme aims to enhance students understanding of bio-inspired information pathways and neurogenesis. Preliminary evaluations indicate high engagement and educational value, suggesting that such interdisciplinary approaches can significantly enrich science education. Graphical abstract

Demographics of co-ageing complex systems: from infected worms to chess games.

Ageing, as defined in terms of the slope of the probability of death versus time (hazard curve), is a generic phenomenon observed in nearly all complex systems. Theoretical models of ageing predict hazard curves that monotonically increase in time, in discrepancy with the peculiar ups and downs observed empirically. Here we introduce the concept of co-ageing, where the demographic trajectories of multiple cohorts couple together, and show that co-ageing dynamics can account for the anomalous hazard curves exhibited by some species. In our model, multiple interdependency networks inflict damage on one other proportional to their number of functional nodes. We then fit our model predictions to three datasets describing (i) co-ageing worm-pathogen populations and (ii) competing tree species. Lastly, we collect data on the mortality statistics of (iii) chess games to demonstrate that co-ageing dynamics is not exclusive to biological systems.

Markov field network model of multi-modal data predicts effects of immune system perturbations on intravenous BCG vaccination in macaques.

Analysis of multi-modal datasets can identify multi-scale interactions underlying biological systems but can be beset by spurious connections due to indirect impacts propagating through an unmapped biological network. For example, studies in macaques have shown that Bacillus Calmette-Guerin (BCG) vaccination by an intravenous route protects against tuberculosis, correlating with changes across various immune data modes. To eliminate spurious correlations and identify critical immune interactions in a public multi-modal dataset (systems serology, cytokines, and cytometry) of vaccinated macaques, we applied Markov fields (MFs), a data-driven approach that explains vaccine efficacy and immune correlations via multivariate network paths, without requiring large numbers of samples (i.e., macaques) relative to multivariate features. We find that integrating multiple data modes with MFs helps remove spurious connections. Finally, we used the MF to predict outcomes of perturbations at various immune nodes, including an experimentally validated B cell depletion that induced network-wide shifts without reducing vaccine protection.

Random-Coupled Neural Network

Improving the efficiency of current neural networks and modeling them on biological neural systems have become prominent research directions in recent years. The pulse-coupled neural network (PCNN) is widely used to mimic the computational characteristics of the human brain in computer vision and neural network fields. However, PCNN faces limitations such as limited neural connections, high computational costs, and a lack of stochastic properties. This study proposes a random-coupled neural network (RCNN) to address these limitations. RCNN employs a stochastic inactivation process, selectively inactivating neural connections using a random inactivation weight matrix. This method reduces the computational burden and allows for extensive neural connections. RCNN encodes constant stimuli as periodic spike trains and periodic stimuli as chaotic spike trains, reflecting the information encoding characteristics of biological neural systems. Our experiments applied RCNN to image segmentation and fusion tasks, demonstrating its robustness, efficiency, and high noise resistance. Results indicate that RCNN surpasses traditional methods in performance across these applications.