Biological Applications Research Articles

Quantitative Characterization of Gene Regulatory Circuits Associated With Fungal Secondary Metabolism to Discover Novel Natural Products.

Microbial genetic circuits are vital for regulating gene expression and synthesizing bioactive compounds. However, assessing their strength and timing, especially in multicellular fungi, remains challenging. Here, an advanced microfluidic platform is combined with a mathematical model enabling precise characterization of fungal gene regulatory circuits (GRCs) at the single-cell level. Utilizing this platform, the expression intensity and timing of 30 transcription factor-promoter combinations derived from two representative fungal GRCs, using the model fungus Aspergillus nidulans are determined. As a proof of concept, the selected GRC combination is utilized to successfully refactor the biosynthetic pathways of bioactive molecules, precisely control their production, and activate the expression of the silenced biosynthetic gene clusters (BGCs). This study provides insights into microbial gene regulation and highlights the potential of platform in fungal synthetic biology applications and the discovery of novel natural products.

Copper oxide/biopolymer nanocomposites: synthesis and applications, a comprehensive review

Copper oxide particles have a significant role in various fields due to their many properties like special shape, size, and high surface area. Due to their rarity and unique characteristics, such as their large surface area, paramagnetic nature, and ease of separation, Copper oxide nanoparticles have received the greatest attention. Chitosan, Guar Gum, Tamarind, Alginate, starch, cellulose, polysaccharide, etc. are examples of natural biopolymers that have proven to be excellent hosts for the creation of CuO nanoparticles. Long-established fabrication techniques for biopolymer-based CuO nanocomposites include co-precipitations, green synthesis, Solvent Casting Method, Alco thermal method, and Sol-Gel methods. Excellent biological characteristics of Copper oxide/biopolymer nanocomposites include their potent antibacterial activity against a variety of diseases as well as bacteria that are resistant to antibiotics. These characteristics have sparked the creation of numerous strategies with direct biological applications, including customized surfaces with antimicrobial effects, wound dressings, and modified textiles. This study aims to provide the very first biopolymer CuO nanoparticles to be reported in the previous ten years as well as its appealing methodology in diverse applications.

Trifluoroacetic Acid Promotes Umpolung of 2‐Methylindole to Achieve C(sp3)‐H Activation

An umpolung strategy for the C(sp3)‐H aminomethylation of 2‐methylindole has been developed using trifluoroacetic acid to induce the transformation, with aminals serving as precursors of iminium ion. Mechanistic studies have clearly shown that trifluoroacetic acid may play a pivotal role in this strategy. The utilization of readily available starting materials, mild reaction conditions, tolerance to complex functional groups, combine with yields of up to 98% and potential biological applications render this protocol applicable and useful for organic synthesis and medicinal chemistry.

Recent Advances for Synthesis of Benzothiazoles from Arylmethylamines

The benzofused N,S‐containing benzothiazole heterocycles and their scaffolds have remarkable biological and pharmaceutical applications. Attentively, the development towards structurally diverse benzothiazoles via C(sp3)‐H functionalization of arylmethylamines has been the main attraction for synthetic organic chemists. In this review, the various synthetic approaches from C‐H/C‐N bond functionalization of arylmethylamines/amines as a new emerging substrate are described in detail towards the synthesis of substituted benzothiazoles. Furthermore, it gives insights into substrate scope and the reaction mechanistic pathway for the formation of final targeted benzothiazole products.

Self-Replicating Catalytic Hybridization Assembly of Bipedal DNAzyme Walkers for Enhanced Electrochemiluminescence Bioanalysis.

Dynamic DNA nanodevices, particularly DNA walkers, have proven to be versatile tools for target recognition, signal conversion, and amplification in biosensing. However, their ability to detect low-abundance analytes in complex biological samples is often compromised by limited amplification depth and severe signal leakage. To address these challenges, we developed a simple yet highly efficient strategy to engineer a self-replicating bipedal DNAzyme (SEDY) walker for sensitive and selective electrochemiluminescence (ECL) bioanalysis. Unlike conventional DNA walkers that are typically constructed by catalytic DNA assembly in a single direction, the SEDY walker integrates a self-replicating feedback mechanism that greatly enhances both the selectivity and sensitivity of bioanalysis. First, the SEDY walker is assembled through a target-triggered, enzyme-free, self-replicating catalytic approach, minimizing the risk of undesired side reactions and signal leakage by simplifying reactant complexity. Furthermore, the SEDY walker features newly exposed trigger sequences that facilitate its autonomous replication, leading to a robust and exponential amplification of its products. Our experiments demonstrate that the SEDY walker can sensitively and selectively detect acetamiprid by navigating specific probes within cross-shaped DNA orbits. The ECL biosensor offers a linear detection range from 1 × 10-15 M to 1 × 10-9 M, with a limit of detection as low as 5.8 × 10-16 M. We anticipate that the SEDY walker will be a powerful tool for detecting various analytes in biological applications.

Deep learning revealed the distribution and evolution patterns for invertible promoters across bacterial lineages.

Invertible promoters (invertons) are crucial regulatory elements in bacteria, facilitating gene expression changes under stress. Despite their importance, their prevalence and the range of regulated gene functions are largely unknown. We introduced DeepInverton, a deep learning model that identifies invertons across a broad phylogenetic spectrum without using sequencing reads. By analyzing 68 733 bacterial genomes and 9382 metagenomes, we have uncovered over 200 000 nonredundant invertons and have also highlighted their abundance in pathogens. Additionally, we identified a post-Cambrian Explosion increase of invertons, paralleling species diversification. Furthermore, we revealed that invertons regulate diverse functions, including antimicrobial resistance and biofilm formation, underscoring their role in environmental adaptation. Notably, the majority of inverton identifications by DeepInverton have been confirmed by the in vitro experiments. The comprehensive inverton profiles have deepened our understanding of invertons at pan-genome and pan-metagenome scales, enabling a broad spectrum of applications in microbial ecology and synthetic biology.

EFIKASI DAN EFEKTIVITAS FORMULASI DAUN MELADA (Piper colubrinum Link) SEBAGAI ATRAKTAN HAMA LALAT BUAH (STUDI KASUS PERTANAMAN CABAI)

Fruit flies ( Bactrocera spp.) represent a group of Plant Pests that can inflict both qualitative and quantitative losses. The utilization of chemical pesticides and the scarcity of Methyl Eugenol continue to pose significant challenges in agriculture. The abundant availability of Melada plants presents an opportunity for the development of an economically viable and environmentally friendly biological attractant. Encapsulation technology based on Maltodextrin and Gum Arabic (MD-GA) formulated with powdered simplicia of Melada leaves F1(02:10), F2(05:10), F3(10:10), and F4(12:10) is employed to enhance the slow-release resistance of volatile compounds. The surface oil content of the four formulations ranges from 0.3% to 9.6%. The encapsulation efficiency value for the four formulations ranges from 70% to 85%. The loading capacity value ranges from 0.7% to 1.3%. The yield value of microcapsule characteristics ranges from 63% to 82%. Morphological analysis reveals a decrease in the number of particles along with the combination of treatment formulations. The size of the microcapsules for the four formulations falls within the range of 201.2 µm–252.6 µm. The effectiveness of the resulting attractant can lure 19-185 fruit flies. The diversity of the fruit fly pest population obtained includes the Bactrocera umbrosa and Bactrocera melastomatos species. The total value of the best formulation for the four treatments ranged from 0.3% to 0.5%. The optimization of the best biological attractant application with high development potential lies in the encapsulation formulations F3 and F4.

Microbial synthesis of zinc oxide nanoparticles and their potential biological application as an antimicrobial and anticancer agent

Zinc oxide nanoparticles (ZnO-NPs) are a type of metal oxide nanomaterial, recognized as a valuable and adaptable inorganic compound owing to its distinctive physical and chemical properties. Nanosized ZnO particles exhibit substantial antibacterial properties attributable to their diminutive size, which can activate various bactericidal mechanisms within the bacterial cell, including interactions with the bacterial surface or core, the generation of reactive oxygen species (ROS), the release of Zn2+, and potential endocytosis by cells. ZnO NPs nanoparticles were extracellularly produced using pigment extracts from the PP6 strain. Agar well screening indicated that PP6 secondary metabolites possess antibacterial properties. UV–Vis spectroscopy was used to analyze the external growth of nanoparticles. Scanning Electron Microcopy (SEM), Fourier Transform Infrared Spectroscopy (FTIR), and X-ray diffraction (XRD) techniques were employed to analyze the shape, stability, crystalline structure, and coating of strain PP6 ZnO NPs. The PP6 ZnO NPs demonstrated an antibiofilm impact on the bacterial pathogens tested, which was dependent on the dosage. Elevated levels of lipid peroxidation (LPO) and reduced antioxidant activity are indicative of apoptosis in cancer cells. The synthesized ZnO NPs nanoparticles were assessed for their anticancer properties by performing the MTT assay on HT-29 human colorectal adenocarcinoma cells. ZnO NPs nanoparticles exposed to HT-29 cells the viability was reduced significantly in proportion to the concentration of nanoparticles. Additional comprehensive study will be needed to fully understand their mechanism.

3D Bioprinting in Cancer Modeling and Biomedicine: From Print Categories to Biological Applications.

The continuous interaction between tumor cells and the local microenvironment plays a decisive role in tumor development. Selecting effective models to simulate the tumor microenvironment to study the physiological processes of tumorigenesis and progression is extremely important and challenging. Currently, three-dimensional (3D) bioprinting technology makes it possible to replicate a physiologically relevant tumor microenvironment and induce genomic and proteomic expression to better mimic tumors in vivo. Meanwhile, it plays a crucial role in the prevention and treatment of human diseases, contributing to drug delivery and drug screening, tissue development and regenerative medicine. This paper provides an overview of the categories of 3D bioprinting technology, and the recent advances in the bioinks required for printing. In addition, we summarize the current tumor models based on 3D bioprinting and provide an assessment of possible future biological applications.

Current Technologies in Snake Venom Analysis and Applications

This comprehensive review explores the cutting-edge advancements in snake venom research, focusing on the integration of proteomics, genomics, transcriptomics, and bioinformatics. Highlighting the transformative impact of these technologies, the review delves into the genetic and ecological factors driving venom evolution, the complex molecular composition of venoms, and the regulatory mechanisms underlying toxin production. The application of synthetic biology and multi-omics approaches, collectively known as venomics, has revolutionized the field, providing deeper insights into venom function and its therapeutic potential. Despite significant progress, challenges such as the functional characterization of toxins and the development of cost-effective antivenoms remain. This review also discusses the future directions of venom research, emphasizing the need for interdisciplinary collaborations and new technologies (mRNAs, cryo-electron microscopy for structural determinations of toxin complexes, synthetic biology, and other technologies) to fully harness the biomedical potential of venoms and toxins from snakes and other animals.

A Comprehensive Review of Plant-Based Cosmetic Oils (Virgin Coconut Oil, Olive Oil, Argan Oil, and Jojoba Oil): Chemical and Biological Properties and Their Cosmeceutical Applications.

Plant-based oils, such as coconut, olive, argan, and jojoba, are abundant in natural emollients and vital fatty acids that hydrate and moisturize the skin. They shield the surface, stop moisture loss, and maintain suppleness of, the skin. They are rich in vitamins, nutrients, and antioxidants that nourish the skin. Virgin coconut oil (VCO) is used as a functional food due to its tremendous health benefits, and olive oil is well-known for its cosmetic and culinary applications. Argan oil contains many antioxidants, vital fatty acids, and vitamin E, while jojoba oil is an excellent moisturizer and conditioner. Plant-based oils can be extracted using various techniques including conventional and chemical extraction methods, and each will affect the yield and quality. Traditional methods like mechanical pressing are less efficient, whereas extraction methods such as pressurized liquid and supercritical fluid extraction may give higher yields and better quality. The chemical composition of olive oil primarily consists of saturated fatty acids (SFAs), polyunsaturated fatty acids (PUFAs), and monounsaturated fatty acids (MUFAs). Argan oil is rich in tocopherols, containing between 60 and 90 mg per 100 g, with only 19 g/100 g of argan oil's fatty acids saturated. Jojoba oil is liquid wax comprising over 98% triglyceride esters, pure waxes, vitamins, and sterols. This review focuses on the chemical and biological properties, production processes, and applications of natural cosmetic oils (virgin coconut oil, olive oil, argan oil, and jojoba oil), emphasizing their usage in skin care and cosmeceutical products.

High-Yield Production of SiV-Doped Nanodiamonds for Spectroscopy and Sensing Applications.

Nanodiamonds (NDs) containing optically active centers have gained significant relevance as the material of choice for biological, optoelectronic, and quantum applications. However, current production methods lag behind their real needs. This study introduces two CVD-based approaches for fabricating NDs with optically active silicon-vacancy (SiV) color centers: bottom-up (BU) and top-down (TD) methods. The BU approach generates nanoporous diamond films with a core-shell structure, while the TD method employs molten-salt thermal etching to create uniform porous structures from nanocrystalline diamond films. Comprehensive characterization using advanced techniques revealed distinct morphologies and optical properties for each approach. The BU method yielded higher-quality diamond phases with top-surface incorporation of SiV centers, while the TD method demonstrated efficient nondiamond phase removal. Ultrasonic disintegration of both porous films produced NDs ranging from 40 to 500 nm, with unique morphologies characteristic of each approach. Photoluminescence measurements confirmed SiV centers (738 nm) in all NDs, exhibiting sensitivity to surface terminations, particularly in BU samples. Temperature-resolved spectroscopy shows the potential of the fabricated NDs for nano thermometry over a wide range of temperatures up to 100 °C. The zero-phonon line shows 0.022 ± 0.003 nm/K sensitivity, while the line width exhibits 0.068 ± 0.004 nm/K broadening. The presented BU and TD methods offer significant advantages over existing techniques, including streamlined production processes, high-yield ND synthesis with tailored properties, and the potential for scalable, cost-effective manufacturing.

Water-Soluble Chitosan-Europium Hybrid Sensor for Singlet Oxygen Detection.

The ability to effectively monitor singlet oxygen (1O2) with fluorescence probes in biological systems is severely restricted mainly by the background autofluorescence of these systems. Though the application of lanthanide complexes as 1O2 monitors successfully resolves this problem with time-gated luminescence measurements, the insolubility of these complexes in an aqueous medium heavily limits their application in biological systems. Here, we present a water-soluble 1O2 sensor based on a chitosan-europium hybrid material. A procedure for the modification of chitosan to expand its solubility to neutral and basic pH, while maintaining its free active amine groups, is described. These are then coupled covalently to a europium-based probe for the detection of 1O2. The resulting hybrid sensor is readily soluble in water across the pH scale and efficiently signals the presence of 1O2 at physiological pH, with the characteristic Eu3+ emission at 611 nm yielding up to a 15-fold increase in emission intensity and a decay time of 332 μs. Being of particular interest for time-gated measurements, this long decay time, coupled with the biocompatibility of chitosan, describes a material with potential biological applications, where 1O2 plays a vital role.

Divalent transition metal complexes with mixed of β-enaminone and N,O-donor ligands: synthesis, characterization and biological assessment

This study extensively describes the synthesizing and characterizing of new β-enaminone complexes derived from dimedone and amines coordinated with transition metals Fe(II), Co(II), Ni(II), and Cu(II), also two ligand's metformin (Met) and 8-hydroxyquinoline (8-hq). These were determined via FT-IR, 1H-NMR, electron and mass spectroscopy, molar electrical conductivity, thermal analysis (TGA, DTA and DSC) and characterized by metal content determination (%), magnetic susceptibility and elemental analysis (C.H.N.) and SEM technique. The measurements indicate that the complexes have six coordination numbers, where the β-enaminone is coordinated as tetradentate ligand through the two nitrogen atoms and the two oxygen atoms beside metformin is coordinated through the two nitrogen atoms and 8-hydroxyquinoline is coordinated by oxygen and nitrogen atoms as bidentate ligands. The conductance suggests that all complexes have electrolytic behavior, being conductive in a ratio of (1:2). SEM results revealed the presence of nanostructures on sample surfaces. The biological activity of the prepared ligands and complexes are studied in different concentrations for four types of bacteria Staphylococcus aureus has (+G) and Escherichia coli, Pseudomonas aeruginosa, Klebsiella have (-G), well as, the influence of the fungus. The ligands have disparate effectiveness while complexes have high effectiveness inhibiting the bacteria and fungus. KEY WORDS: Mixed ligand systems, Dimedone, β-Enaminone ligands, Transition metals, Biological application Bull. Chem. Soc. Ethiop. 2025, 39(1), 65-78. DOI: https://dx.doi.org/10.4314/bcse.v39i1.5

Europium-Infused Polystyrene Nanoparticles for Enhanced Bacterial Labeling in Microscopic Imaging

Luminescence microscopic imaging has become an indispensable tool in diagnostics and therapeutics. Lanthanide luminescent complexes (LLCs) have proven to be invaluable in this endeavor due to certain attractive characteristics such as long decay times, large Richardson shifts and narrow emission bands. However, the insolubility of these complexes and the negative effects of the aqueous environment on their photophysical properties still restrict their biological applications. By embedding luminescent Eu3+ complexes into polystyrene nanoparticles (NPs), these complexes can not only maintain their photophysical properties, but even enhance them. This leads to exceptionally high quantum yields (> 90 %) and decay times ( >800 μs). In addition, the surfaces of the NPs described here are covered with primary amine groups, which may be exploited for various interesting bioconjugation chemistries. In the present application, they were modified with N-hydroxysuccinimide (NHS) esters and then coupled either electrostatically or covalently to both, Gram-positive and Gram-negative bacteria, labeling them for luminescence microscopic imaging. This, to the best of our knowledge, is the first report of polymer NPs infused with LLCs for bacteria labeling.

A hovering bubble with a spontaneous horizontal oscillation

Active matters, characterized by multi-mode motions, have been emerging for both engineering and biological applications. Generally, active objects rely on the symmetry-broken structures, compositions, or interfacial activities through a physical or chemical approach. Here, we report an active bubble spontaneously hovering with a horizontal oscillation at the solid/liquid interface by impacting a stationary laser beam into a liquid through a transparent solid cover. This spontaneous oscillation mode of the bubble synchronizes with that of the interfacial temperature and hydrodynamical flow. A physical mechanism is proposed, and the scaling analysis of the oscillation frequency agrees well with experiments in various liquids under different laser powers. Additionally, the bubble trajectory rotates azimuthally, arising from the symmetry breaking of the vortex pair accompanying the oscillation. Moreover, the double pendulum of oscillation bubbles has been demonstrated, achieving a preferable oscillation direction in a controllable way. These findings would not only advance our understanding of active matters but also shed light on the bubble-mediated technological applications, such as microrobots and drug deliveries.

Involvement of Molecular Mechanism and Biological Activities of Pemirolast: A Therapeutic Review

: This review paper aims to investigate the therapeutic benefits of pemirolast across different medical conditions, including asthma, allergic rhinitis, cancer, conjunctivitis, etc. The prevalence of allergic conditions has risen in recent decades, primarily attributed to environmental factors. This paper explores the role of pemirolast in managing and mitigating these diseases, shedding light on its potential applications in the context of evolving environmental influences. : This review paper investigates the diverse biological activities exhibited by pemirolast, encompassing its roles as an antimicrobial, analgesic, antiviral, anti-inflammatory, antioxidant, antihistamine, mast cell stabilizer, anti-tubercular, anticancer, anti-asthmatic, anti-malarial, diuretic, antianxiety, and antifungal agent. The positive outcomes of pemirolast application in various diseases are highlighted, showcasing its potential across a spectrum of medical conditions. : The pharmacological impact of pemirolast extends to diverse inflammatory mediators, enzymes, and hormones associated with various diseases. Pemirolast demonstrates inhibitory effects on key elements such as eosinophil activation, histamine, leukotriene, IgE, mast cells, basophils, prostaglandin, interleukin, T-helper cells, macrophage T-cells, neutrophils, tryptase, T-lymphocytes, interferons I-III, Amyloid β (Aβ) peptide, dsRNA transcription, GABA, dopamine, serotonin, and norepinephrine. This comprehensive exploration underscores pemirolast inhibitory actions across disorders, emphasizing its potential therapeutic relevance in diverse pathological conditions. : This review paper illuminates pemirolast potassium's versatile biological and therapeutic applications across various diseases. The potential synergies of combining pemirolast with buspirone, ritanserin, theophylline, and capreomycin are explored, showcasing its ability to elicit beneficial responses in addressing diverse ailments.

MMLmiRLocNet: miRNA Subcellular Localization Prediction based on Multi-view Multi-label Learning for Drug Design.

Identifying subcellular localization of microRNAs (miRNAs) is essential for comprehensive understanding of cellular function and has significant implications for drug design. In the past, several computational methods for miRNA subcellular localization is being used for uncovering multiple facets of RNA function to facilitate the biological applications. Unfortunately, most existing classification methods rely on a single sequencebased view, making the effective fusion of data from multiple heterogeneous networks a primary challenge. Inspired by multi-view multi-label learning strategy, we propose a computational method, named MMLmiRLocNet, for predicting the subcellular localizations of miRNAs. The MMLmiRLocNet predictor extracts multi-perspective sequence representations by analyzing lexical, syntactic, and semantic aspects of biological sequences. Specifically, it integrates lexical attributes derived from k-mer physicochemical profiles, syntactic characteristics obtained via word2vec embeddings, and semantic representations generated by pre-trained feature embeddings. Finally, module for extracting multi-view consensus-level features and specific-level features was constructed to capture consensus and specific features from various perspectives. The full connection networks are utilized as the output module to predict the miRNA subcellular localization. Experimental results suggest that MMLmiRLocNet outperforms existing methods in terms of F1, subACC, and Accuracy, and achieves best performance with the help of multi-view consensus features and specific features extract network.

Histone Methylation-Mediated Reproductive Toxicity to Consumer Product Chemicals in Caenorhabditis elegans: An Epigenetic Adverse Outcome Pathway (AOP).

The significance of histone methylation in epigenetic inheritance underscores its relevance to disease and the chronic effects of environmental chemicals. However, limited evidence of the causal relationships between chemically induced epigenetic changes and organismal-level effects hinders the application of epigenetic markers in ecotoxicological assessments. This study explored the contribution of repressive histone marks to reproductive toxicity induced by chemicals in consumer products in Caenorhabditis elegans, applying the adverse outcome pathway (AOP) framework. Triclosan (TCS) and tetrabromobisphenol A (TBBPA) exposures caused reproductive toxicity and altered histone methyltransferase (HMT) and histone demethylase (HDM) activities, increasing the level of trimethylation of H3K9 and H3K27. Notably, treatment with an H3K27-specific HMT inhibitor alleviated reproductive defects and the transcriptional response of genes related to vitellogenin, xenobiotic metabolism, and oxidative stress. Comparison of points of departure (PODs) based on calculated benchmark concentrations (BMCs) revealed the sensitivity of histone-modifying enzyme activities to these chemicals. Our findings suggest that the 'disturbance of HMT and HDM' can serve as the molecular initiating event (MIE) leading to reproductive toxicity in the epigenetic AOP for TCS and TBBPA. The study extended the biological applicability of these enzymes by identifying model species with analogous protein sequences and functions. This combined approach enhances the essentiality, empirical support, and taxonomic domain of applicability (tDOA), which are crucial considerations for ecotoxicological AOPs. Given the widespread use and environmental distribution of chemicals in consumer products, this study proposes histone-modifying enzyme activity as an effective screening tool for reproductive toxicants and emphasizes the integration of epigenetic mechanisms into a prospective ERA.

Entropically and enthalpically driven self-assembly of a naphthalimide-based luminescent organic π-amphiphile in water.

The self-assembly of π conjugated systems in water has emerged as an efficient method for the development of functional materials for biological applications. But the process is more difficult to understand and to control in water compared to organic solvents due to hydrophobic effects. For π-conjugated molecules, self-assembly in solution generally occurs due to either an enthalpic or entropic gain, but designing π systems that undergo self-assembly via both an entropically and enthalpically favorable process is challenging. Herein, we elucidate in detail the self-assembly of a luminescent naphthalene monoamide-based dipolar π-bolaamphiphile appended with a primary amine and triethylene glycol monomethyl ether (NMI-W) side chain into a vesicular nanostructure. By utilizing a detailed isothermal titration calorimetry (ITC) experiment, we have calculated the thermodynamic parameters associated with the self-assembly of NMI-W in water. Interestingly, the NMI-W shows both entropically and enthalpically favorable robust self-assembly into a vesicular structure, which can encapsulate both hydrophilic and hydrophobic guest molecules. The synergistic effect of dipole-dipole, π-π stacking and hydrophobic interactions of the NMI chromophore is found to be very crucial in driving self-assembly in an aqueous medium as revealed by various experiments and molecular dynamics.