Biological Applications Research Articles

Hydrolysis, Ligand Exchange, and Redox Properties of Vanadium Compounds: Implications of Solution Transformation on Biological, Therapeutic, and Environmental Applications

Hydrolysis, Ligand Exchange, and Redox Properties of Vanadium Compounds: Implications of Solution Transformation on Biological, Therapeutic, and Environmental Applications

Navigating the landscape of plant proteomics.

In plants, proteins are fundamental to virtually all biological processes, such as photosynthesis, signal transduction, metabolic regulation, and stress responses. Studying protein distribution, function, modifications, and interactions at the cellular and tissue levels is critical for unraveling the complexities of these biological pathways. Protein abundance and localization are highly dynamic and vary widely across the proteome, presenting a challenge for global protein quantification and analysis. Mass spectrometry-based proteomics approaches have proven to be powerful tools for addressing this complex issue. In this review, we summarize recent advancements in proteomics research and their applications in plant biology, with an emphasis on the current state and challenges of studying post-translational modifications, single-cell proteomics, and protein-protein interactions. Additionally, we discuss future prospects for plant proteomics, highlighting potential opportunities that proteomics technologies offer in advancing plant biology research.

Structural Basis of High-Precision Protein Ligation and Its Application.

Enzyme-catalyzed protein modifications have become invaluable in diverse applications, outperforming chemical methods in terms of precision, conjugation efficiency, and biological compatibility. Despite significant advances in ligases, such as sortase A and OaAEP1, their use in heterogeneous biological environments remains constrained by limited target sequence specificity. In 2021, Lupas' group introduced Connectase, a family of repurposed archaeal proteases for protein ligations, but its low processivity and lack of structural information have impeded further engineering for practical biological and biophysical applications. Here, we present the X-ray crystallographic structures of MmConnectase (Methanococcus maripaludis, MmCET) in both apo and substrate-bound forms. Comparative analysis with its inactive paralogue, MjCET (Methanococcus janaschi), reveals the structural basis of MmCET's high-precision ligation activity. We propose modifications to the N-terminal substrate recognition motifs to suppress MmCET's reversible protease activity, enabling high-precision protein ligations in complex biological environments, such as serum-containing cell cultures. To further demonstrate the enhanced processivity and precision, single-molecule protein unfolding experiments showed that our optimized Connectase, in conjunction with OaAEP1(C247A), can perform stepwise tandem ligations of protein leading to a well-defined protein polymer.

Characterisation of C‐β‐Cyclodextrin‐Thymol Inclusion Complexes as Delivery Systems for Antibacterial and Antioxidant Applications

ABSTRACTThymol (THY) is a natural antioxidant and antimicrobial; however, its biological activity and application in the food and pharmaceutical fields are limited due to its low water solubility and volatility. In this study, inclusion complexes of cationic‐β‐cyclodextrin‐THY (C‐β‐CD‐THY) were prepared by using the aqueous stirring method. Then UV–Vis spectra, FT‐IR, NMR, DSC, XRD and SEM data were collected to characterise the structure and morphology of the inclusion complexes. Phase solubility experiments showed a better solubilisation effect of C‐β‐CD‐THY than HP‐β‐CD‐THY. At a concentration of 0.64 mmol/L for THY, the DPPH scavenging rate was 60.99% and 61.31% for HP‐β‐CD‐THY and C‐β‐CD‐THY, respectively, whereas that of THY in 10% ethanol was only 43.47%. The bacteriostatic activity was verified using a circle of inhibition and the live/dead bacterial double stain. C‐β‐CD‐THY exhibited better antimicrobial activities against Escherichia coli and Staphylococcus aureus than HP‐β‐CD‐THY. In conclusion, the C‐β‐CD‐THY inclusion complexes have the potential to be applied as an effective bacteriostatic agent for food and pharmaceutical applications.

Constructing Activatable Photosensitizers Using Covalently Modified Mesoporous Silica.

The combination of photosensitizers (PSs) and nanomaterials is a widely used strategy to enhance PS efficacy and broaden their applicability. However, the current nanocarrier-based delivery strategies focus on conventional PSs, neglecting the critical issue of PS phototoxicity. In this study, DHUOCl-25, an activatable PS (aPS) activated by hypochlorous acid, is synthesized by combining a silicon source structure and an activation unit. DHUOCl-25 functions as a silica source for synthesizing activatable mesoporous silica nanostrctures (MSNs) using a standardized protocol, enabling the synthesis of aPS-covalently modified MSNs for a variety of biologic therapeutic applications. On one hand, the resulting nano-aPS maintains aPS functionality for antibacterial application by achieving synergistic antibacterial action via MB PDT and retained cetyltrimethylammonium bromide (CTAB) (antibacterial agent) (DHU-MSNs-2). On the other hand, the nano-aPS exhibits MSN properties for drug loading, facilitating the synergistic integration of photodynamic therapy with chemotherapy (DHU-MSNs-6) of tumors and demonstrating efficacy against the spinal metastases of lung cancer. These results validate this strategy for developing novel aPSs and expanding the application of aPSs and MSNs.

Effect of surface-engineered AuNPs on gene expression, bacterial interaction, protein denaturation, and toxicology assay: an in vitro and in vivo model.

We investigated the in vitro and in vivo uses of pamoic acid functionalized gold nanoparticles (PA@AuNPs), with a focus on determining their safety and potential toxicity in living beings. To test this theory, the bacterial interaction of PA@AuNPs was studied using Escherichia coli, Staphylococcus aureus, and Pseudomonas aeruginosa cultures, as well as the inhibition of the bovine serum albumin (BSA) protein. The real-time polymerase chain reaction (RT-PCR) is used to measure the expression of target genes. PA@AuNPs caused dose-dependent cell death in MDA-MB-231, a triple-negative breast cancer (BC) cell line, with an LC50 of -42.23 μL mL-1. It also caused apoptosis in BC cells. The results indicated that in the early weeks, inflammatory cells (mostly neutrophils and macrophages) penetrated the connective tissue, but in the latter weeks, a substantial number of fibroblasts and fibrocytes were identified. Changes in vascular channels, extravasated red blood cells (RBCs), and necrosis are all indicators of growing tissue pathology. These data could point to a dynamic process including an anti-inflammatory response followed by tissue remodeling or repair. These findings show that PA@AuNPs were not hazardous to the tested Sprague Dawley rats, are highly biocompatible, and can be used in a variety of biological applications.

Polycarbonate-Based Polymersome Photosensitizers with Cell-Penetrating Properties for Improved Killing of Cancer Cells.

Polymer-based photosensitizers have found various applications in photodynamic therapy (PDT). However, the absence of targeting ability commonly results in a substantial reduction in photosensitizer accumulation at the tumor site, significantly limiting the therapeutic efficacy of the system. In addition, the development of biodegradable polymeric photosensitizers is of critical importance for biological applications. In this work, we present the development of guanidine-functionalized biodegradable photosensitizers based on poly(trimethylene carbonate) (PTMC) block copolymers, which can self-assemble into polymersomes. The presence of guanidine groups on the surface of polymersomes can significantly enhance the cellular uptake efficiency of photosensitizers, thereby improving the intracellular production of reactive oxygen species (ROS). The in vitro study demonstrates that the guanidinylated polymersome photosensitizers can promote the killing of cancer cells compared to unfunctionalized polymersomes in the presence of light irradiation. The guanidine-functionalized PTMC-based polymersome photosensitizers, with the integration of cell-targeting ability and biodegradability, are anticipated to provide a novel strategy for developing advanced biomedical polymer systems for PDT.

Theoretical and Experimental Study of an Electrokinetic Micromanipulator for Biological Applications

The ability to control and manipulate biological fluids within microchannels is a fundamental challenge in biological diagnosis and pharmaceutical analyses, particularly when buffers with very high ionic strength are used. In this study, we investigate the numerical and experimental study of fluidic biochips driven by ac electrothermal flow for controlling and manipulating biological samples inside a microchannel, e.g., for fluid-driven and manipulation purposes such as concentrating and mixing. By appropriately switching the voltage on the electrode structures and inducing AC electrothermal forces within the channel, a fluidic network with pumping and manipulation capabilities can be achieved, enabling the control of fluid velocity/direction and also fluid rotation. By using finite element analysis, coupled physics of electrical, thermal, fluidic fields, and molecular diffusion transport were solved. AC electrothermal flow was studied for pumping and mixing applications, and the optimal model was extracted. The microfluidic chip was fabricated using two processes: electrode structure development on the chip and silicon mold fabrication in a cleanroom. PDMS was prepared as the microchannel material and bonded to the electrode structure. After implementing the chip holder and excitation circuit, a biological buffer with varying ionic strengths (0.2, 0.4, and 0.6 [S/m]) was prepared, mixed with fluorescent particles, and loaded into the microfluidic chip. Experimental results demonstrated the efficiency of the proposed chip for biological applications, showing that stronger flows were generated with increasing fluid conductivity and excitation voltage. The system behavior was characterized using an impedance analyzer. Frequency response analysis revealed that for a solution with an electrical conductivity of 0.6 [S/m], the fluid velocity remained almost constant within a frequency range of 100 kHz to 10 MHz. Overall, the experimental results showed good agreement with the simulation outcomes.

Genetically Encoded Nucleic Acid Nanostructures for Biological Applications.

Nucleic acid, as a carrier of genetic information, has been widely employed as a building block for the construction of versatile nanostructures with pre-designed sizes and shapes through complementary base pairing. With excellent programmability, addressability, and biocompatibility, nucleic acid nanostructures are extensively applied in biomedical researches, such as bio-imaging, bio-sensing, and drug delivery. Notably, the original gene-encoding capability of the nucleic acids themselves has been utilized in these structurally well-defined nanostructures. In this review, we will summarize the recent progress in the design of double-stranded DNA and mRNA-encoded nanostructures for various biological applications, such as gene regulation, gene expression, and mRNA transcription. Furthermore, the challenges and future opportunities of genetically encoded nucleic acid nanostructures in biomedical applications will be discussed.

Green Ferrites: Eco‐Friendly Synthesis to Applications in Environmental Remediation, Antimicrobial Activity, and Catalysis—A Comprehensive Review

ABSTRACTFerrite magnetic materials have emerged as capable materials in engineering, research, and medicine because of their exclusive and fascinating properties obtained from a variety of synthesis techniques. These ferrites are significant in commercial products, research, and biomedical applications. Green synthesis methods for ferrite nanocomposites and nanoparticles are becoming increasingly popular due to their usefulness in a range of industries, engineering, environmental, and medicinal remediation. Ferrite nanoparticles and nanocomposites (MFe2O4, where M = Ni, Cu, Mg, Co, Zn, and Mn) have recently gained popularity due to their many uses in biological, environmental, and chemical interactions. This review covers the most recent investigations over the last few years on green‐synthesized ferrite nanoparticles, ferrites containing nanocomposites, and more elements, with a focus on microorganism‐mediated and plant‐based synthesis processes. The surface features of ferrite nanoparticles synthesized from green materials are discussed, as is their potential for sensors, energy, water treatment, antibacterial activity, biological, and heavy metal removal applications. This article presents an inclusive overview of green‐synthesized ferrites, including the most recent research advances and findings. To fully realize the promise of nanoferrites in several fields, a thorough understanding of green manufacturing, properties, and applications is essential. Green‐synthesized ferrites are chosen due to their potential for improved control over particle size and shape, lower cost, decreased toxicity, and environmental friendliness, all of which preserve magnetic properties that are better than those of conventionally synthesized ferrites, making them a more sustainable choice for a range of applications.

Antimicrobial Potential of Secalonic Acids from Arctic-Derived Penicillium chrysogenum INA 01369

In this study, two compounds have been isolated from the Arctic-derived fungus Penicillium chrysogenum INA 13460. Structural elucidation, performed using 2D NMR and HR-ESIMS data, has identified the compounds as stereoisomers of secalonic acids, dimeric tetrahydroxanthones. The absolute configurations of these stereoisomers have been determined through conformational NMR analysis and circular dichroism spectroscopy. The antimicrobial activity of secalonic acids D and F has been evaluated against a diverse range of microorganisms, including Gram-positive multidrug-resistant Staphylococcus aureus, Gram-negative Escherichia coli ATCC 25922, Pseudomonas aeruginosa ATCC 27853, the phytopathogen Pectobacterium carotovorum VKM-B1247, and the fungi Fusarium oxysporum VKPM F 890, Aspergillus fumigatus VKM F-37, and A. niger ATCC 16404. Genomic and chemical analyses further support P. chrysogenum INA 13460 as a promising natural source for antimicrobial drug discovery and biological control applications.

The Evolution of Nucleic Acid Nanotechnology: From DNA Assembly to DNA-Encoded Library.

Deoxyribonucleic acid (DNA), a fundamental biomacromolecule in living organisms, serves as the carrier of genetic information. Beyond its role in encoding biological functions, DNA's inherent ability to hybridize through base pairing has opened new avenues for its application in biological sciences. This review introduces DNA nanotechnology and DNA-encoded library (DEL), and highlights their shared design principles related to DNA assembly. First, a foundational overview of structural DNA nanotechnology, including its design strategies and historical development is provided. Subsequently, various approaches are examined to dynamic DNA nanotechnology, from strand displacement reactions to DNA-templated polymer synthesis. Second, how the principle of DNA assembly has facilitated the development of diverse formats of self-assembly-based DEL synthesis, DNA-template reactions (DTS), and DNA template-mediated proximity induction effects are examined. These advancements are all underpinned by the unique property of DNA assembly. Finally, this review summarizes the common principles shared by DNA nanotechnology and DEL in terms of methodology and design. Additionally, the potential synergies are explored between these two technologies, envisioning future applications where they can be combined to create more versatile and exquisite functionalities.

MoS2–Plasmonic Hybrid Platforms: Next-Generation Tools for Biological Applications

The combination of molybdenum disulfide (MoS2) with plasmonic nanomaterials has opened up new possibilities in biological applications by combining MoS2’s biocompatibility and high surface area with the optical sensitivity of plasmonic metals. These MoS2–plasmonic hybrid systems hold great promise in areas such as biosensing, bioimaging, and phototherapy, where their complementary properties facilitate improved detection, real-time visualization, and targeted therapeutic interventions. MoS2’s adjustable optical features, combined with the plasmon resonance of noble metals such as gold and silver, enhance signal amplification, enabling detailed imaging and selective photothermal or photodynamic therapies while minimizing effects on healthy tissue. This review explores various synthesis strategies for MoS2–plasmonic hybrids, including seed-mediated growth, in situ deposition, and heterojunction formation, which enable tailored configurations optimized for specific biological applications. The primary focus areas include highly sensitive biosensors for detecting cancer and infectious disease biomarkers, high-resolution imaging of cellular dynamics, and the development of phototherapy methods that allow for accurate tumor ablation through light-induced thermal and reactive oxygen species generation. Despite the promising advancements of MoS2–plasmonic hybrids, translating these platforms into clinical practice requires overcoming considerable challenges, such as synthesis reproducibility, toxicity, stability in physiological conditions, targeted delivery, and scalable manufacturing. Addressing these challenges is essential for realizing their potential as next-generation tools in diagnostics and targeted therapies.

Nucleoside Derivatives: An Assessment of Its Synthesis and Application

Purpose: This review advances the synthesis methodologies, biological roles, and therapeutic applications of nucleoside derivatives, emphasizing their pivotal role in the development of biomedical sciences. Methodology: There are several methods for synthesizing nucleosides, including fusion reactions, metal salt procedures, and the Hilbert-Johnson method, each of which offers distinct advantages and challenges. These synthetic approaches take advantage of the interaction of sugars and nitrogenous bases, allowing for tailored modifications for specific applications. Findings: Nucleoside derivatives, essential molecules that are the building blocks of nucleic acids such as DNA and RNA, exhibit diverse structural and functional properties. Their biological synthesis, through novel pathways or rescue mechanisms, ensures the availability of the primary genetic material. Synthetic nucleoside derivatives have found significant roles in medicinal chemistry, particularly in antiviral, anticancer and antibacterial therapies. Modifications of sugars or basic components have led to the emergence of pioneering drugs such as acyclovir, zidovudine and remdesivir. Unique Contribution to Theory, Practice and Policy: Nucleoside derivatives have great therapeutic potential. They act as antiviral agents by disrupting viral replication and as chemotherapeutics targeting rapidly dividing cells in cancers. However, their efficacy faces challenges such as toxicity and development of resistance. Ongoing research aims to enhance their safety and expand their applications in molecular biology, diagnostics and nanotechnology.

Unravelling the aromatic symphony: redirecting bifunctional mushroom synthases towards linalool monofunctionality

Enzymes are the cornerstone of biocatalysis, biosynthesis and synthetic biology. However, their applicability is often limited by low substrate selectivity. A prime example is the bifunctional linalool/nerolidol synthase (LNS) that can use both geranyl diphosphate (GPP) and farnesyl diphosphate (FPP) to produce linalool and nerolidol, respectively. This bifunctionality can lead to undesired byproducts in synthetic biology applications. To enhance enzyme specificity and create monofunctional linalool synthases, we modified amino acids in the loop between helices C and D of four bifunctional mushroom LNSs. Through these modifications, we successfully shifted the substrate preference of two LNSs (ApLNS from Agrocybe pediades and HsLNS from Hypholoma sublateritium) from FPP towards GPP. Although complete monofunctionality was not achieved, we significantly increased linalool yield by 13 times while minimizing nerolidol production to 1% of the wildtype HsLNS. Docking simulations revealed a substantial reduction in the FPP binding score compared to that of the wildtype. Molecular dynamics simulations suggested that Tyr300 in the apo HsLNS mutant has a greater tendency to adopt an inward orientation. Together with Met77, the inward-facing Tyr300 creates a steric barrier that prevents the longer FPP molecule from entering the substrate binding pocket, thereby greatly reducing its activity towards FPP. This study demonstrates the potential of enzyme engineering to design substrate-specific terpene synthases, which is a challenging task and few successful examples are available. The insights gained can inform future enzyme design efforts, including the development of artificial intelligence models.

Bi24Al2O39:Mn5+-phosphor-based single-emission ratiometric thermometer

Both excitation and single emission of Bi24Al2O39:Mn5+ phosphors are possible in the near-infrared (NIR) region, which can be simultaneously detected. Monitoring the excitation radiation allows us to prevent its fluctuations from affecting the luminescence. Single emission is a technique that involves the luminescence intensity ratio, so fluctuations in the intensity of the excitation radiation do not affect the result. This technique has the advantage of involving conventional methods and is not affected by optical dispersion, so it provides reliable results suitable for practical applications. Using this method, we investigate the temperature-sensing characteristics of Bi24Al2O39:0.5%Mn5+ phosphors from 300 to 380 K. Under 970 nm excitation, the maximal relative sensitivity is 3.54% K−1 in the physiological temperature range (300–330 K) and reaches 3.98% K−1 at 351 K. The excellent temperature sensing and NIR excitation and emission suggest that this NIR thermometer can be used for biological applications.

Temperature-Directed Morphology Transformation Method for Precision-Engineered Polymer Nanostructures.

With polymer nanoparticles now playing an influential role in biological applications, the synthesis of nanoparticles with precise control over size, shape, and chemical functionality, along with a responsive ability to environmental changes, remains a significant challenge. To address this challenge, innovative polymerization methods must be developed that can incorporate diverse functional groups and stimuli-responsive moieties into polymer nanostructures, which can then be tailored for specific biological applications. By combining the advantages of emulsion polymerization in an environmentally friendly reaction medium, high polymerization rates due to the compartmentalization effect, chemical functionality, and scalability, with the precise control over polymer chain growth achieved through reversible-deactivation radical polymerization, our group developed the temperature-directed morphology transformation (TDMT) method to produce polymer nanoparticles. This method utilized temperature or pH responsive nanoreactors for controlled particle growth and with the added advantages of controlled surface chemical functionality and the ability to produce well-defined asymmetric structures (e.g., tadpoles and kettlebells). This review summarizes the fundamental thermodynamic and kinetic principles that govern particle formation and control using the TDMT method, allowing precision-engineered polymer nanoparticles, offering a versatile and an efficient means to produce 3D nanostructures directly in water with diverse morphologies, high purity, high solids content, and controlled surface and internal functionality. With such control over the nanoparticle features, the TDMT-generated nanostructures could be designed for a wide variety of biological applications, including antiviral coatings effective against SARS-CoV-2 and other pathogens, reversible scaffolds for stem cell expansion and release, and vaccine and drug delivery systems.

Conditional Split Inteins: Adaptable Tools for Programming Protein Functions

Split inteins are biological mechanisms for the operation of the spatiotemporal control of protein activities. They function through protein trans-splicing, in which their N- and C-terminal fragments are expressed contiguously with two protein halves. The subsequent self-excision upon recognition of the complimentary fragment yields a mature, complete, and functional protein. The conditional regulation of protein splicing through environmental factors or the attachment of regulatory modules can be used to determine when and where a protein will operate, providing potential novel approaches for engineering biology applications. This review will discuss current split intein applications and the mechanistic basis for novel species classification. These considerations can provide guidance in intein and extein engineering through activation strategies, in the design of spatial arrangements, and in taking advantage of unique reaction environments. This can pave the way for the future implementation of novel split intein discoveries and the selection of appropriate intein species and aid in designing novel protein engineering strategies.

Precise Sizing and Collision Detection of Functional Nanoparticles by Deep Learning Empowered Plasmonic Microscopy.

Single nanoparticle analysis is crucial for various applications in biology, materials, and energy. However, precisely profiling and monitoring weakly scattering nanoparticles remains challenging. Here, it is demonstrated that deep learning-empowered plasmonic microscopy (Deep-SM) enables precise sizing and collision detection of functional chemical and biological nanoparticles. Image sequences are recorded by the state-of-the-art plasmonic microscopy during single nanoparticle collision onto the sensor surface. Deep-SM can enhance signal detection and suppresses noise by leveraging spatio-temporal correlations of the unique signal and noise characteristics in plasmonic microscopy image sequences. Deep-SM can provide significant scattering signal enhancement and noise reduction in dynamic imaging of biological nanoparticles as small as 10nm, as well as the collision detection of metallic nanoparticle electrochemistry and quantum coupling with plasmonic microscopy. The high sensitivity and simplicity make this approach promising for routine use in nanoparticle analysis across diverse scientific fields.

Scalable Manufacturing Method for Model Protein-Loaded PLGA Nanoparticles: Biocompatibility, Trafficking and Release Properties

Background and Objectives: Drug delivery systems (DDSs) offer efficient treatment solutions to challenging diseases such as central nervous system (CNS) diseases by bypassing biological barriers such as the blood–brain barrier (BBB). Among DDSs, polymeric nanoparticles (NPs), particularly poly(lactic-co-glycolic acid) (PLGA) NPs, hold an outstanding position due to their biocompatible and biodegradable qualities. Despite their potential, the translation of PLGA NPs from laboratory-scale production to clinical applications remains a significant challenge. This study aims to address these limitations by developing scalable PLGA NPs and evaluating their potential biological applications. Methods: We prepared blank and model-protein-loaded (albumin–FITC and wheat germ agglutinin-488 (WGA-488)) fluorescent PLGA NPs using the traditional double-emulsion method combined with the micro-spray-reactor system, a novel approach that enables fine particle production enabling scale-up applications. We tested the biocompatibility of the NPs in living RPMI 2650 and neuroblastoma cell lines, as well as their trafficking and uptake. Release kinetics of the encapsulated proteins were investigated through confocal microscopy and in vitro release studies, providing insights into the stability and functionality of the released proteins. Results: The formulation demonstrated sustained and prolonged protein release profiles. Importantly, cellular uptake studies revealed that the NPs were not internalized. Furthermore, encapsulated WGA-488 protein retained its functional activity after release, validating the integrity of the encapsulation and release processes. Conclusions: The proof-of-concept study on NP manufacturing and an innovative drug trafficking and release approach can bring new perspectives on scalable preparations of PLGA NPs and their biological applications.