Search Results (102)

Rhamnose is a natural sugar found in glycoproteins and structural polysaccharides of plants, fungi, and bacteria. Its incorporation into glycoconjugates is mediated by rhamnosyltransferases (RHTs), key enzymes for biomolecular stability and function. While rhamnose biosynthesis has been studied in certain fungal genera, the evolutionary history and distribution of RHTs across the fungal kingdom remain largely unknown. In this study, 351 fungal species were found to encode putative RHTs. Phylogenetic and structural analyses revealed conserved patterns and similarities with previously characterized RHTs. Molecular docking predicted a high affinity of these proteins for UDP-L-rhamnose, and in silico mutagenesis identified key residues potentially involved in substrate binding. Carbohydrate profiling confirmed the presence of rhamnose in the cell walls of multiple fungi, including Aspergillus, Madurella, Metarhizium, and Trichoderma species. Enzymatic assays further supported rhamnose transfer activity. These findings provide the first comprehensive in silico characterization of fungal RHTs, uncovering conserved sequence motifs despite overall diversity, which may be linked to functional adaptation in different fungal lineages. Full article

We synthesized QM-AgNPs (Dianthus superbus L.-AgNPs, Qu Mai-AgNPs) by an economical and environmentally friendly method using Dianthus superbus L. extract as a reducing and stabilizing agent. The resulting QM-AgNPs were comprehensively characterized and evaluated for their antioxidant, cytotoxic, and antibacterial activities. Herein, TEM analysis revealed that the QM-AgNPs were predominantly spherical, polydisperse, and exhibited a core particle size ranging from 11 to 18 nm. In contrast, DLS analysis showed a larger hydrodynamic diameter (primarily 60–87 nm), reflecting the hydrated shell and surface biomolecular corona. The crystalline nature of QM-AgNPs was confirmed by XRD and SAED spectra while FTIR spectroscopy indicated the presence of functional groups from the plant extract that may contribute to nanoparticle stabilization. Functional assessments demonstrated that QM-AgNPs exhibited strong antioxidant activity, with efficient DPPH radical scavenging, and selective cytotoxicity against A549 cancer cells while sparing normal cells. Moreover, QM-AgNPs showed significant antibacterial activity against both Staphylococcus aureus (Gram-positive) and Escherichia coli (Gram-negative), likely due to membrane disruption and the leakage of intracellular contents. To explore practical applications, we developed a GEL@AgNPs coating system for the postharvest preservation of grapes. As a result, the reduced weight loss and decay rate suggest a potential role for QM-AgNPs in extending fruit freshness. Comprehensive shelf-life studies are planned to further substantiate the potential of QM-AgNPs as an effective material for active food packaging applications. Full article

The continued effective control of retroviral infections will no doubt require the development of new clinical interventions targeting underexploited areas of retroviral biology such as genome selection and virion assembly. In our previous work, we demonstrated that both the Gag-psi (Ψ) interaction and genomic RNA (gRNA) dimerization each uniquely contribute to the formation, morphology, and stability of Rous sarcoma virus (RSV) Gag-viral RNA (vRNA) biomolecular condensates (BMCs). The present work builds upon those observations, utilizing atomic force microscopy (AFM) and fluorescence correlation spectroscopy (FCS) to elucidate the nanoscale morphology, resistance to mechanical deformation, and constituent diffusivity of RSV Gag-vRNA BMCs. These approaches revealed a novel role for gRNA dimerization in nanoscale condensate architecture and mechanical stability that aids in our understanding of why gRNA dimerization is critical for efficient packaging of the retroviral genome. Further biophysical characterization of RSV Gag-gRNA BMCs therefore possesses great potential to reveal novel avenues for therapeutic intervention. Full article

Background/Objectives: Drug-coated balloons (DCBs) are emerging as a promising treatment for peripheral artery disease; however, current technologies lack flexibility in customizing drug release profiles and composition, limiting their therapeutic potential. This study aims to develop a Gelatin (Gel) and Sodium Alginate (Alg) bioink loaded with apolipoprotein A-I (apoA-I) for controlled drug delivery by using additive manufacturing technologies. Methods: We developed and printed via rapid freeze prototyping (RFP) a Gel and Alg bioink loaded with different concentrations of apoA-I. Mechanical properties related to compressional and tensile forces have been studied, as well as the structural stability and active release from the 3D structure of apoA-I (cholesterol efflux assays). The biological behavior of HUVEC cells with and without ApoA-I was assessed by proliferation assay, metabolic activity analysis, and fluorescence imaging. Results: The 3D structures presented breakpoint stress values consistent with the mechanical requirements for integration within a DCB, and the ability to effectively promote cholesterol transport in J774 cells. Moreover, in vitro studies on HUVECs revealed that the scaffolds exhibited no cytotoxic effects, leading to increased ATP levels and enhanced metabolic activity over time, confirming the possibility to obtain RFP-printed Alg/Gel scaffolds able to provide a stable structure capable of controlled apoA-I release. Conclusions: These findings support the potential of Alg/Gel+apoA-I scaffolds as biocompatible drug delivery systems for vascular applications. Their ability to maintain structural integrity while enabling controlled biomolecular release positions them as promising candidates for personalized cardiovascular therapy, facilitating the rapid customization of bioprinted therapeutic platforms. Full article

Tissue preservation plays an essential role in biomedical research and histopathological applications. Traditional methods, despite their efficiency, are associated with compromised long-term tissue integrity and probable ecotoxicities. This study explores the application of silver nanoparticles (AgNPs), known for their antimicrobial properties, as a potential tissue preservative. In this work, AgNPs were synthesized via a chemical reduction method. Heart, liver, and kidney tissues were obtained from BALB/c mice and preserved using 10% neutral buffered formalin (NBF) and AgNPs solution for 72 h. Preservation efficiency was assessed by quantifying and measuring DNA and RNA integrity, evaluating protein stability, and conducting histopathological examinations. This study aimed to compare the performance of AgNPs against 10% NBF across these parameters to determine their suitability as an alternative fixative. Our results showed that AgNPs solution maintained consistent DNA, RNA, and protein concentrations/quality across all tissues over 72 h, whereas formalin treatment led to degradation over time. Conversely, 10% NBF demonstrated better preservation of tissue morphology. These results highlighted the differential strengths of each fixative, with AgNPs excelling in molecular preservation and NBF in structural integrity. Overall, AgNPs exhibited superior qualitative and quantitative preservation of nucleic acids and intracellular proteins, indicating their potential as an alternative to formalin for molecular testing. Despite their demonstrated efficacy in biomolecular preservation, further studies are needed to optimize tissue morphology preservation. Full article

The coordination chemistry, structural characterization, and biomolecular interactions of europium(III) and iron(III) complexes with the pyridoxal-semicarbazone (PLSC) ligand were thoroughly examined using experimental and computational approaches. Single-crystal X-ray diffraction revealed that the europium complex exhibits a nine-coordinate geometry with one protonated and one deprotonated PLSC ligand and nitrato and aqua ligands. In contrast, the iron complex adopts a six-coordinate structure featuring a monoprotonated PLSC, two chlorido, and an aqua ligand. Hirshfeld surface analysis confirmed the significance of intermolecular contacts in stabilizing the crystal lattice. Theoretical geometry optimizations using DFT methods demonstrated excellent agreement with experimental bond lengths and angles, thereby validating the reliability of the chosen computational levels for subsequent quantum chemical analyses. Quantum Theory of Atoms in Molecules (QTAIM) analysis was employed to investigate the nature of metal–ligand interactions, with variations based on the identity of the donor atom and the ligand’s protonation state. The biological potential of the complexes was evaluated through spectrofluorimetric titration and molecular docking. Eu-PLSC displayed stronger binding to human serum albumin (HSA), while Fe-PLSC showed higher affinity for calf thymus DNA (CT-DNA), driven by intercalation. Thermodynamic data confirmed spontaneous and enthalpy-driven interactions. These findings support using PLSC-based metal complexes as promising candidates for future biomedical applications, particularly in drug delivery and DNA targeting. Full article

Surface plasmon resonance (SPR) sensing technology has been widely utilized in fields such as biomedicine, food safety, and drug screening for real-time, rapid, and label-free detection of biomolecular interactions. However, conventional SPR sensing methods find it difficult to provide the necessary sensitivity and stability when detection applications go toward ultra-low concentrations and tiny molecular weight analytes. Here, we present a high-sensitivity Goos–Hänchen shift sensing based on SPR and beam displacement amplification technology (BDAT). The incorporation of BDAT significantly amplifies the magnitude of GH shift with remarkable stability, enhancing the sensing sensitivity by an order of magnitude. The sensor achieves a sensitivity of 3.62 × 10⁴ μm/RIU and a minimum detection limit of 3.10 × 10⁻⁵ RIU. Furthermore, both theoretical and experimental results demonstrate that GH shift sensing offers superior performance compared with traditional intensity-based SPR, particularly for low-concentration solutions. The BDAT approach amplifies GH shifts by at least 12 times, significantly improving sensitivity. With the use of SPR and BDAT, we are able to generate a large GH shift, which makes it easier to detect low concentrations and offers a wide range of possible uses in clinical diagnostics and biomedicine. Full article

Retroviral genome selection and virion assembly remain promising targets for novel therapeutic intervention. Recent studies have demonstrated that the Gag proteins of Rous sarcoma virus (RSV) and human immunodeficiency virus type-1 (HIV-1) undergo nuclear trafficking, colocalize with nascent genomic viral RNA (gRNA) at transcription sites, may interact with host transcription factors, and display biophysical properties characteristic of biomolecular condensates. In the present work, we utilized a controlled in vitro condensate assay and advanced imaging approaches to investigate the effects of interactions between RSV Gag condensates and viral and nonviral RNAs on condensate abundance and organization. We observed that the psi (Ψ) packaging signal and the dimerization initiation sequence (DIS) had stabilizing effects on RSV Gag condensates, while RNAs lacking these features promoted or antagonized condensation, depending on local protein concentration and condensate architecture. An RNA containing Ψ, DIS, and the dimerization linkage structure (DLS) that is capable of stable dimer formation was observed to act as a bridge between RSV Gag condensates. These observations suggest additional, condensate-related roles for Gag-Ψ binding, gRNA dimerization, and Gag dimerization/multimerization in gRNA selection and packaging, representing a significant step forward in our understanding of how these interactions collectively facilitate efficient genome packaging. Full article

Introduction/Objectives: Since the biological activities and toxicities of ‘foreign’ and/or excess levels of metal ions are predominantly determined by their precise molecular nature, here we have employed high-resolution ¹H NMR analysis to explore the ‘speciation’ of paramagnetic Ni(II) ions in human saliva, a potentially rich source of biomolecular Ni(II)-complexants/chelators. These studies are of relevance to the in vivo corrosion of nickel-containing metal alloy dental prostheses (NiC-MADPs) in addition to the dietary or adverse toxicological intake of Ni(II) ions by humans. Methods: Unstimulated whole-mouth human saliva samples were obtained from n = 12 pre-fasted (≥8 h) healthy participants, and clear whole-mouth salivary supernatants (WMSSs) were obtained from these via centrifugation. Microlitre aliquots of stock aqueous Ni(II) solutions were sequentially titrated into WMSS samples via micropipette. Any possible added concentration-dependent Ni(II)-mediated pH changes therein were experimentally controlled. ¹H NMR spectra were acquired on a JEOL JNM-ECZ600R/S1 spectrometer. Results: Univariate and multivariate (MV) metabolomics and MV clustering analyses were conducted in a sequential stepwise manner in order to follow the differential effects of increasing concentrations of added Ni(II). The results acquired showed that important Ni(II)-responsive biomolecules could be clustered into distinguishable patterns on the basis of added concentration-dependent responses of their resonance intensities and line widths. At low added concentrations (71 µmol/L), low-WMSS-level N-donor amino acids (especially histidine) and amines with relatively high stability constants for this paramagnetic metal ion were the most responsive (severe resonance broadenings were observed). However, at higher Ni(II) concentrations (140–670 µmol/L), weaker carboxylate O-donor ligands such as lactate, formate, succinate, and acetate were featured as major Ni(II) ligands, a consequence of their much higher WMSS concentrations, which were sufficient for them to compete for these higher Ni(II) availabilities. From these experiments, the metabolites most affected were found to be histidine ≈ methylamines > taurine ≈ lactate ≈ succinate > formate > acetate ≈ ethanol ≈ glycine ≈ N-acetylneuraminate, although they predominantly comprised carboxylato oxygen donor ligands/chelators at the higher added Ni(II) levels. Removal of the interfering effects arising from the differential biomolecular compositions of the WMSS samples collected from different participants and those from the effects exerted by a first-order interaction effect substantially enhanced the statistical significance of the differences observed between the added Ni(II) levels. The addition of EDTA to Ni(II)-treated WMSS samples successfully reversed these resonance modifications, an observation confirming the transfer of Ni(II) from the above endogenous complexants to this exogenous chelator to form the highly stable diamagnetic octahedral [Ni(II)-EDTA] complex (K_stab = 1.0 × 10¹⁹ M⁻¹). Conclusions: The results acquired demonstrated the value of linking advanced experimental design and multivariate metabolomics/statistical analysis techniques to ¹H NMR analysis for such speciation studies. These provided valuable molecular information regarding the identities of Ni(II) complexes in human saliva, which is relevant to trace metal ion speciation and toxicology, the in vivo corrosion of NiC-MADPs, and the molecular fate of ingested Ni(II) ions in this biofluid. The carcinogenic potential of these low-molecular-mass Ni(II) complexes is discussed. Full article

Background: Pembrolizumab has recently emerged as a PD-1 blockade immunotherapy treatment for lung cancer. It is critical that such treatment strategies for lung cancer should be chosen not only on the basis of histopathological features and the expression of targetable cell surface proteins (such as PD-1), but should rather be selected based on other determinants of treatment success or risk factors for poor prognosis. One method to forecast cancer trajectory is the identification of biomolecular signatures such as microRNAs (miRNAs), non-protein-coding RNA molecules that play a regulatory role in gene expression by modulating the translation or stability of messenger RNA. Methods: To find out which miRNAs have an important influence on anti-PD-1 treatment outcomes, we evaluated miRNA levels in sera from 38 lung cancer patients undergoing 3 months of pembrolizumab treatment. We selected a panel of miRNAs previously shown to be involved in lung cancer or PD-1 signaling and performed qPCR analysis. Results: Overall, we observed a significant decrease in the levels of miR126-5p (4-fold), let-7a (5-fold), miR133a-3p (4-fold), miR3615 (2-fold), miR4516 (3-fold), miR16 (3-fold), miR34c-5p (2-fold), miR20b-5p (5-fold), miR106b-5p (5-fold), miR146a-5p (3-fold) and miR181b-5p (3-fold) in response to treatment indicating effectiveness of immunotherapy. Within our selected panel of miRNAs, we identified two markers relevant to cancer prognosis: miR-217, which is negatively associated with patient survival, and let-7a, which is positively associated with patient survival. Conclusions: Our findings suggest that circulating miRNAs can be used for future treatment evaluation and lung cancer prognosis, with potential as therapeutic targets. Full article

Biological phenomena are chemical reactions, which are inherently non-stopping or “flowing” in nature. Molecular dynamics (MD) is used to analyze the dynamics and energetics of interacting atoms, but it cannot handle chemical reactions involving bond formation and breaking. Quantum mechanics/molecular mechanics (QM/MM) umbrella sampling MD simulations gives us a significant clue about transition states of chemical reactions and their energy levels, which are the pivotal points in understanding the nature of life. To demonstrate the importance of this method, we present here the results of our application of it to the elucidation of the mechanism of chiral-selective aminoacylation of an RNA minihelix considered to be a primitive form of tRNA. The QM/MM MD simulation, for the first time, elucidated the “flowing” atomistic mechanisms of the reaction and indicated that the L-Ala moiety stabilizes the transition state more than D-Ala, resulting in L-Ala preference in the aminoacylation reaction in the RNA. The QM/MM method not only provides important clues to the elucidation of the origin of homochirality of biological systems, but also is expected to become an important tool that will play a critical role in the analysis of biomolecular reactions, combined with the development of artificial intelligence. Full article

Micro- and nanorobots (MNRs) have attracted significant interest owing to their promising applications in various fields, including environmental monitoring, biomedicine, and microengineering. This review explores advances in the synthetic routes used for the preparation of MNRs, focusing on both top-down and bottom-up approaches. Although the top-down approach dominates the field because of its versatility in design and functionality, bottom-up strategies that utilize template-assisted electrochemical deposition and bioconjugation present unique advantages in terms of biocompatibility. This review investigates the diverse propulsion mechanisms employed in MNRs, including magnetic, electric, light, and biological forces, which enable efficient navigation in various fluidic environments. The interplay between the synthesis and propulsion mechanisms of MNRs in the development of colorimetric and fluorescence detection platforms is emphasized. Additionally, we summarize the recent advancements in MNRs as sensing and biosensing platforms, particularly focusing on colorimetric and fluorescence-based detection systems. By utilizing the controlled motion of MNRs, dynamic changes in the fluorescent signals and colorimetric responses can be achieved, thereby enhancing the sensitivity and selectivity of biomolecular detection. This review highlights the transformative potential of MNRs in sensing applications and emphasizes their role in advancing diagnostic technologies through innovative motion-driven signal transduction mechanisms. Subsequently, we provide an overview of the primary challenges currently faced in MNR research, along with our perspective on the future applications of MNR-assisted colorimetric and fluorescence biosensing in chemical and biological sensing. Moreover, issues related to enhanced stability, biocompatibility, and integration with existing detection systems are discussed. Full article

The cell cycle, essential for growth, reproduction, and genetic stability, is regulated by a complex network of cyclins, Cyclin-Dependent Kinases (CDKs), phosphatases, and checkpoints that ensure accurate cell division. CDKs and phosphatases are crucial for controlling cell cycle progression, with CDKs promoting it and phosphatases counteracting their activity to maintain balance. The nucleolus, as a biomolecular condensate, plays a key regulatory role by serving as a hub for ribosome biogenesis and the sequestration and release of various cell cycle regulators. This phase separation characteristic of the nucleolus is vital for the specific and timely release of Cdc14, required for most essential functions of phosphatase in the cell cycle. While mitosis distributes chromosomes to daughter cells, meiosis is a specialized division process that produces gametes and introduces genetic diversity. Central to meiosis is meiotic recombination, which enhances genetic diversity by generating crossover and non-crossover products. This process begins with the introduction of double-strand breaks, which are then processed by numerous repair enzymes. Meiotic recombination and progression are regulated by proteins and feedback mechanisms. CDKs and polo-like kinase Cdc5 drive recombination through positive feedback, while phosphatases like Cdc14 are crucial for activating Yen1, a Holliday junction resolvase involved in repairing unresolved recombination intermediates in both mitosis and meiosis. Cdc14 is released from the nucleolus in a regulated manner, especially during the transition between meiosis I and II, where it helps inactivate CDK activity and promote proper chromosome segregation. This review integrates current knowledge, providing a synthesis of these interconnected processes and an overview of the mechanisms governing cell cycle regulation and meiotic recombination. Full article

Fused in sarcoma (FUS) is involved in the formation of nuclear biomolecular condensates associated with poly(ADP-ribose) [PAR] synthesis catalyzed by a DNA damage sensor such as PARP1. Here, we studied FUS microphase separation induced by poly(ADP-ribosyl)ated PARP1^WT [PAR-PARP1^WT] or its catalytic variants PARP1^Y986S and PARP1^Y986H, respectively, synthesizing (short PAR)-PARP1^Y986S or (short hyperbranched PAR)-PARP1^Y986H using dynamic light scattering, fluorescence microscopy, turbidity assays, and atomic force microscopy. We observed that biologically relevant cations such as Mg²⁺, Ca²⁺, or Mn²⁺ or polyamines (spermine⁴⁺ or spermidine³⁺) were essential for the assembly of FUS with PAR-PARP1^WT and FUS with PAR-PARP1^Y986S in vitro. We estimated the range of the FUS-to-PAR-PARP1 molar ratio and the cation concentration that are favorable for the stability of the protein’s microphase-separated state. We also found that FUS microphase separation induced by PAR-PARP1^Y986H (i.e., a PARP1 variant attaching short hyperbranched PAR to itself) can occur in the absence of cations. The dependence of PAR-PARP1-induced FUS microphase separation on cations and on the branching of the PAR structure points to a potential role of the latter in the regulation of the formation of FUS-related biological condensates and requires further investigation. Full article

Background: The concept of radiotheranostics relies on the overexpression of a biomolecular target on malignant cells to direct diagnostic/therapeutic radionuclide-carriers specifically to cancer lesions. The concomitant expression of more than one target in pathological lesions may be elegantly exploited to improve diagnostic sensitivity and therapeutic efficacy. Toward this goal, we explored a first example of a combined application of [^99mTc]Tc-DT11 (DT11, N₄-Lys(MPBA-PEG4)-Arg-Arg-Pro-Tyr-Ile-Leu-OH; NTS₁R-specific) and [^99mTc]Tc-DB7(DB7, N₄-PEG2-DPhe-Gln-Trp-Ala-Val-Gly-His-Leu-NHEt; GRPR-specific) in prostate cancer models. Methods: Accordingly, the behavior of [^99mTc]Tc-DT11 was compared with that of the [^99mTc]Tc-DT11+[^99mTc]Tc-DB7 mixture in prostate adenocarcinoma PC-3 cells and xenografts in mice. The impact of stabilizing both radiotracers by Entresto^®, as a source of the potent neprilysin inhibitor sacubitrilat, was also investigated. Results: The PC-3 cell binding of the [^99mTc]Tc-DT11+[^99mTc]Tc-DB7 mixture surpassed that of [^99mTc]Tc-DT11. Likewise, the PC-3 tumor uptake of the [^99mTc]Tc-DT11+[^99mTc]Tc-DB7 mixture at 4 h post-injection was superior (7.70 ± 0.89%IA/g) compared with [^99mTc]Tc-DT11 (4.23 ± 0.58%IA/g; p < 0.0001). Treatment with Entresto^® led to further enhancement of the tumor uptake (to 11.57 ± 1.92%IA/g; p < 0.0001). Conclusions: In conclusion, this first preclinical study on prostate cancer models revealed clear advantages of dual NTS₁R/GRPR targeting, justifying further assessment of this promising concept in other cancer models. Full article