Biological Applications Research Articles

Assessing the Potential of Aconitum Laeve Extract for Biogenic Silver and Gold Nanoparticle Synthesis and Their Biological and Catalytic Applications.

The adoption of green chemistry protocols in nanoparticle (NP) synthesis has exhibited substantial potential and is presently a central focus in research for generating versatile NPs applicable across a broad spectrum of applications. In this scientific contribution, we, for the first time, examined the ability of Aconitum Laeve (A. Laeve) crude extract to synthesize silver and gold nanoparticles (AgNPs@AL; AuNP@AL) and explored their potential applications in biological activities and the catalytic degradation of environmental pollutants. The synthesized NPs exhibited a distinctive surface plasmon resonance pattern, a spherical morphology with approximate sizes of 5-10 nm (TEM imaging), a crystalline architecture (XRD analysis), and potential functional groups identified by FTIR spectroscopy. The antibacterial activity was demonstrated by inhibition zones that measured 16 and 14 mm for the AgNPs@AL and AuNP@AL at a concentration of 80 µg/mL against Staphylococcus aureus and 14 and 12 mm against Escherichia coli, respectively. The antioxidant potential of the synthesized NPs was evaluated using 2,2-diphenyl-1-picrylhydrazyl (DPPH), 2-Phenyl-4,4,5,5-tetramethylimidazoline-1-oxyl 3-Oxide (PTIO), and 3-ethylbenzothiazoline-6-sulfonic acid (ABTS) assays. Our findings suggest that the AuNP@AL effectively countered the tested radicals considerably, displaying IC50 values of 115.9, 103.54, and 180.85 µg/mL against DPPH, PTIO, and ABTS, respectively. In contrast, the AgNPs@AL showed IC50 values of 144.9, 116.36, and 95.39 µg/mL against the respective radicals. In addition, both the NPs presented significant effectiveness in the photocatalytic degradation of methylene blue and rhodamine B. The overall observations indicate that A. Laeve possesses a robust capability to synthesize spherical nanoparticles, exhibiting excellent dispersion and showcasing potential applications in both biological activities and environmental remediation.

His-Tagging: Exploring Precise Chemical Modification of Histidine-Containing Bioactive Peptide Sequences

AbstractThe modification of biomolecules, particularly peptides, has garnered considerable attention from researchers, effectively serving as a connection between chemistry and biology. The modification of peptides can facilitate, among others, the generation of peptide drugs, antibody–drug conjugates, and probes for molecular imaging. Herein, we have carefully curated reactions and chemical transformations of bioactive peptide sequences equipped with histidine amino acids that are conducive for biological applications. This Account also highlights strategies for the chemical modification of histidine that might capture the imagination of both peptide researchers and synthetic chemists.1 Introduction2 Histidine Modification in Bioactive Peptides and Proteins3 Remote Bioactive Peptides and Protein Modification Adjacent to Histidine4 Conclusions and Future Directions

Green Biosynthesis of TiO2 Nanoparticles Using Aqueous Extract of Brassica juncea (L.) Czern Seed: Characterization, Antimicrobial, Antioxidant and Anticancer Activities

AbstractPrimary objective of this research was to examine the biogenic production of TiO2 NPs using Brassica juncea (L.) Czern seed and investigate the prospective uses of thus synthesized nanoparticles in the area of biomedicine. The synthesized TiO2 NPs were subjected to characterization using several analytical methods namely TEM, UV‐vis, XRD, FE‐SEM, FTIR and EDAX. The average particle size (TEM) is found to be 38 nm, exhibiting irregular shapes. The FT‐IR spectra indicated that the extract contains functional groups, such as polyphenolic, hydroxyl and carboxylic groups, which are likely responsible for formation of nanoparticles. The cytotoxicity studies of the synthesized TiO2 NPs against breast cancer cells (MCF‐7) and lung cells (A549) are shown to be dosage dependent. The inhibitory doses (IC50) were determined to be 43.98 μg/mL and 74.50 μg/mL on MCF‐7 and A549 cells, respectively. Green synthesized TiO2 NPs were assessed for antioxidant activity inhibition rate (DPPH 89.42 %). TiO2 NPs exhibited a maximal zone of inhibition of Staphylococcus aureus 23±0.20 mm against and 20±0.30 against Klebsiella pneumoniae at a concentration of 100 μg/mL, indicating strong antibacterial activity. The findings suggest Brassica juncea (L.) Czern seed encapsulated TiO2 NPs possesses excellent biological applications which can be explored for its application in pharmaceutical field.

Ligand density-optimized peroxidase-like activity of gold nanoclusters for colorimetric sensing of biothiols and acetylcholinesterase

Nanozymes are emerging as an attractive alternative to natural enzymes for a wide range of biological applications, but the effect of surface ligands’ density on the catalytic activity of nanozymes remains largely unclear. Herein, taken gold nanoclusters (AuNCs) as a model nanozyme, glutathione-protected AuNCs (GSH-AuNCs) with three different ligand densities: low (l-AuNCs), medium (m-AuNCs), and high (h-AuNCs) were synthesized and the role of ligand density on the catalytic activity of GSH-AuNCs was systematically investigated. It was disclosed that a relatively lower ligand density is favorable for the peroxidase-like catalytic activity due to weaker steric hindrance effects. Consequently, colorimetric detection of biothiols (e.g., cysteine) and acetylcholinesterase activity was successfully achieved based on the peroxidase property of ligand density-optimized AuNCs, which exhibit a detection limit of 0.08 μM and 0.005 mU/mL, respectively. Moreover, application of the present system for detection of acetylcholinesterase activity in human serum samples was successfully demonstrated. This study provides new avenues for designing robust nanozymes with enhanced catalytic performances for application in biocatalysis as well as biosensing.

An upgraded Myxococcus xanthus chassis with enhanced growth characteristics for efficient genetic manipulation

Myxobacteria are well known for multicellular social behaviors and valued for biosynthesis of natural products. Myxobacteria social behaviors such as clumping growth severely hamper strain cultivation and genetic manipulation. Using Myxococcus xanthus DK1622, we engineered Hu04, which is deficient in multicellular behavior and pigmentation. Hu04, while maintaining nutritional growth and a similar metabolic background, exhibits improved dispersed growth, streamlining operational procedures. It achieves high cell densities in culture and is promising for synthetic biology applications.

Substrate-based synthetic strategies and biological activities of 1,3,4-oxadiazole: A review.

The five-membered 1,3,4-oxadiazole heterocyclic ring has received considerable attention because of its unique bio-isosteric properties and an unusually wide spectrum of biological activities. After a century since 1,3,4-oxadiazole was discovered, its uncommon potential attracted medicinal chemist's attention, leading to the discovery of a few presently accessible drugs containing 1,3,4-oxadiazole units, and a large number of patents have been granted on research related to 1,3,4-oxadiazole. It is worth noting that interest in 1,3,4-oxadiazoles' biological applications has doubled in the last few years. Herein, this review presents a comprehensive overview of the recent achievements in the synthesis of 1,3,4-oxadiazole-based compounds and highlights the major advances in their biological applications in the last 10 years, as well as brief remarks on prospects for further development. We hope that researchers across the scientific streams will benefit from the presented review articles for designing their work related to 1,3,4-oxadiazoles.

The use of phages for the biosynthesis of metal nanoparticles and their biological applications: A review.

Nowadays, the use of biological methods of synthesis of nanoparticles as substitutes for methods that use high energy and consumption of expensive and dangerous materials is of interest to researchers all over the world. Biological methods of synthesising metal nanoparticles are very important because they are easy, affordable, safe, environmentally friendly and able to control the size and shape of nanoparticles. One of the methods that is of interest today is the use of bacteriophages as the most abundant organisms in nature in the synthesis of metal nanoparticles. Nanomaterials biosynthesized from phages have shown various clinical applications, including antimicrobial activities, biomedical sensors, drug and gene delivery systems, cancer treatment and tissue regeneration. Therefore, the purpose of this review is to investigate the biosynthesis of metal nanoparticles with phages and their biomedical applications.

Development of an miRFP680-Based Fluorescent Calcium Ion Biosensor Using End-Optimized Transposons.

The development of new or improved single fluorescent protein (FP)-based biosensors (SFPBs), particularly those with excitation and emission at near-infrared wavelengths, is important for the continued advancement of biological imaging applications. In an effort to accelerate the development of new SFPBs, we report modified transposons for the transposase-based creation of libraries of FPs randomly inserted into analyte binding domains, or vice versa. These modified transposons feature ends that are optimized to minimize the length of the linkers that connect the FP to the analyte binding domain. We rationalized that shorter linkers between the domains should result in more effective allosteric coupling between the analyte binding-dependent conformational change in the binding domain and the fluorescence modulation of the chromophore of the FP domain. As a proof of concept, we employed end-modified Mu transposons for the discovery of SFPB prototypes based on the insertion of two circularly permuted red FPs (mApple and FusionRed) into binding proteins for l-lactate and spermidine. Using an analogous approach, we discovered calcium ion (Ca2+)-specific SFPBs by random insertion of calmodulin (CaM)-RS20 into miRFP680, a particularly bright near-infrared (NIR) FP based on a biliverdin (BV)-binding fluorescent protein. Starting from an miRFP680-based Ca2+ biosensor prototype, we performed extensive directed evolution, including under BV-deficient conditions, to create highly optimized biosensors designated the NIR-GECO3 series. We have extensively characterized the NIR-GECO3 series and explored their utility for biological Ca2+ imaging. The methods described in this work will serve to accelerate SFPB development and open avenues for further exploration and optimization of SFPBs across a spectrum of biological applications.

Tandem mass spectrometry imaging to assess illudin S distributions in Omphalotus illudens mushrooms

Poisoning metabolites within mushrooms typically exert varying physiological and biological effects; however, their distributions within mushrooms are seldom investigated. This study focused on imaging illudin S, a representative poisoning metabolite within Omphalotus illudens mushroom, using desorption electrospray ionization–tandem mass spectrometry (DESI–MS/MS) coupled with liquid chromatography–electrospray ionization–tandem mass spectrometry (LC–ESI–MS/MS). Initially, LC–ESI–MS/MS conditions were established for the selective detection of illudin S (m/z 247→159, positive mode) from extracted mushroom. Based on this MS/MS condition, each mushroom was divided into nine sections, and each section was subjected to specific DESI–MS/MS mode imaging (pixel size: 200 × 200 μm). The results revealed high concentrations of illudin S in the stalks of the mushrooms growing on trees. Further, re-evaluations using the LC–MS/MS assay revealed a seven-fold difference in the illudin S between the stalk and other regions. This study marks the first attempt at assessing toxic metabolite distributions within poisonous mushrooms, thus offering valuable insights including the efficient utilization of illudin analogs in biological applications.

Accurate, scalable, and fully automated inference of species trees from raw genome assemblies using ROADIES.

Inference of species trees plays a crucial role in advancing our understanding of evolutionary relationships and has immense significance for diverse biological and medical applications. Extensive genome sequencing efforts are currently in progress across a broad spectrum of life forms, holding the potential to unravel the intricate branching patterns within the tree of life. However, estimating species trees starting from raw genome sequences is quite challenging, and the current cutting-edge methodologies require a series of error-prone steps that are neither entirely automated nor standardized. In this paper, we present ROADIES, a novel pipeline for species tree inference from raw genome assemblies that is fully automated, easy to use, scalable, free from reference bias, and provides flexibility to adjust the tradeoff between accuracy and runtime. The ROADIES pipeline eliminates the need to align whole genomes, choose a single reference species, or pre-select loci such as functional genes found using cumbersome annotation steps. Moreover, it leverages recent advances in phylogenetic inference to allow multi-copy genes, eliminating the need to detect orthology. Using the genomic datasets released from large-scale sequencing consortia across three diverse life forms (placental mammals, pomace flies, and birds), we show that ROADIES infers species trees that are comparable in quality with the state-of-the-art approaches but in a fraction of the time. By incorporating optimal approaches and automating all steps from assembled genomes to species and gene trees, ROADIES is poised to improve the accuracy, scalability, and reproducibility of phylogenomic analyses.

Photocatalytic C3-H acylmethylation of quinoxalinone with sulfoxonium ylides for the synthesis of 3-(γ-dicarbonyl)-quinoxalin-2(1H)-ones

We have developed a method for the acylmethylation of quinoxalin-2(1H)-ones under visible light utilizing sulfoxonium ylides for the first time. This method proves effective not only for 1-methylquinoxalin-2(1H)-ones but also for quinoxalin-2(1H)-ones, yielding a series of novel dual acylmethylation products, namely 3-(γ-dicarbonyl)-quinoxalinones, at room temperature. These target products exhibit potential for further transformation into furan derivatives, thereby enhancing the versatility and applicability of this strategy. Mechanistic studies suggest that this reaction may proceed via two mechanisms: single-electron transfer and energy transfer. This method offers a practical and efficient approach for the acylmethylation of quinoxalin-2(1H)-ones, yielding valuable 3-(γ-dicarbonyl)-quinoxalin-2(1H)-ones under mild reaction conditions, thus expanding the toolbox of synthetic strategies for the functionalization of quinoxalin-2(1H)-ones. The findings hold implications for drug development, organic synthesis, and materials science, providing a versatile platform for the synthesis of structurally diverse compounds with potential biological and material applications.

Antifungal Properties of Streptomyces bacillaris S8 for Biological Control Applications.

Soybean (Glycine max), a crucial global crop, experiences yearly yield reduction due to diseases such as anthracnose (Colletotrichum truncatum) and root rot (Fusarium spp.). The use of fungicides, which have traditionally been employed to control these phytopathogens, is now facing challenges due to the emergence of fungicide-resistant strains. Streptomyces bacillaris S8 strain S8 is previously known to produce valinomycin t through a nonribosomal peptide synthetase (NRPS) pathway. The objective of this study was to evaluate the antifungal activity of S. bacillaris S8 against C. truncatum and Fusarium sp., assessing its efficacy against soybean pathogens. The results indicate that strain S8 effectively controlled both above-ground and underground soybean diseases, using the NRPS and NRPS-related compound, suggesting its potential as a biological control in plant-microbe interactions. These findings underscore the pivotal role of the stain S8 in fostering healthy soybean microbial communities and emphasize the significance of microbiota structure studies in unveiling potent biocontrol agents.

Triazole-linked Nucleic Acids: Synthesis, Therapeutics and Synthetic Biology Applications.

This article covers the triazole-linked nucleic acids where the triazole linkage (TL) replaces the natural phosphate backbone. The replacement is done at either a few selected linkages or all the phosphate linkages. Two triazole linkages, the four-atom TL1 and the six-atom TL2, have been discussed in detail. These triazole-modified oligonucleotides have found a wide range of applications, from therapeutics to synthetic biology. For example, the triazole-linked oligonucleotides have been used in the antisense oligonucleotide (ASO), small interfering RNA (siRNA) and clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 technology as therapeutic agents. Due to the ease of the synthesis and a wide range of biocompatibility, the triazole linkage TL2 has been used to assemble a functional 300-mer DNA from alkyne- and azide-functionalized 100-mer oligonucleotides as well as an epigenetically modified variant of a 335 base-pair gene from ten short oligonucleotides. These outcomes highlight the potential of triazole-linked nucleic acids and open the doors for other TL designs and artificial backbones to fully exploit the vast potential of artificial nucleic acids in therapeutics, synthetic biology and biotechnology.

Decoding characteristics of key physical properties in silver nanoparticles by attaining centroids for cytotoxicity prediction through data cleansing

This research underscores the profound impact of data cleansing, ensuring dataset integrity and providing a structured foundation for unraveling convoluted connections between diverse physical properties and cytotoxicity. As the scientific community delves deeper into this interplay, it becomes clear that precise data purification is a fundamental aspect of investigating parameters within datasets. The study presents the need for data filtration in the background of machine learning (ML) that has widened its horizon into the field of biological application through the amalgamation of predictive systems and algorithms that delve into the intricate characteristics of cytotoxicity of nanoparticles. The reliability and accuracy of models in the ML landscape hinge on the quality of input data, making data cleansing a critical component of the pre-processing pipeline. The main encounter faced here is the lengthy, broad and complex datasets that have to be toned down for further studies. Through a thorough data cleansing process, this study addresses the complexities arising from diverse sources, resulting in a refined dataset. The filtration process employs K-means clustering to derive centroids, revealing the correlation between the physical properties of nanoparticles, viz, concentration, zeta potential, hydrodynamic diameter, morphology, and absorbance wavelength, and cytotoxicity outcomes measured in terms of cell viability. The cell lines considered for determining the centroid values that predicts the cytotoxicity of silver nanoparticles are human and animal cell lines which were categorized as normal and carcinoma type. The objective of the study is to simplify the high-dimensional data for accurate analysis of the parameters that affect the cytotoxicity of silver NPs through centroids.

Synthesis and Biological Applications of Coumarinyl-Chalcones

Abstract: This survey provides information on the synthesis and biological applications of coumarinyl-chalcones. Chalcones are unsaturated ketones involving the reactive ketoethylenic group (CO-CH=CH). Chalcones are naturally abundant in many medical plants, including vegetables, fruits, and foods. Natural and synthetic chalcone compounds exhibit a broad spectrum of biological properties like anticancer, anti-inflammatory, anti-HIV, antioxidant, antimalarial, and antimicrobial. Some conventional, microwave, and grinding techniques have been utilized for the synthesis of chalcones. Noteworthy, the Claisen- Schmidt condensation reaction remains the most popular and effective method for synthesis. It summarizes information about its synthetic methods as building blocks in some reactions like cyclization reactions and medical applications. This review article presents an overview of approaches and biological data for chalcones bearing a coumarin scaffold.

Introduction of the Capsules environment to support further growth of the SBGrid structural biology software collection.

The expansive scientific software ecosystem, characterized by millions of titles across various platforms and formats, poses significant challenges in maintaining reproducibility and provenance in scientific research. The diversity of independently developed applications, evolving versions and heterogeneous components highlights the need for rigorous methodologies to navigate these complexities. In response to these challenges, the SBGrid team builds, installs and configures over 530 specialized software applications for use in the on-premises and cloud-based computing environments of SBGrid Consortium members. To address the intricacies of supporting this diverse application collection, the team has developed the Capsule Software Execution Environment, generally referred to as Capsules. Capsules rely on a collection of programmatically generated bash scripts that work together to isolate the runtime environment of one application from all other applications, thereby providing a transparent cross-platform solution without requiring specialized tools or elevated account privileges for researchers. Capsules facilitate modular, secure software distribution while maintaining a centralized, conflict-free environment. The SBGrid platform, which combines Capsules with the SBGrid collection of structural biology applications, aligns with FAIR goals by enhancing the findability, accessibility, interoperability and reusability of scientific software, ensuring seamless functionality across diverse computing environments. Its adaptability enables application beyond structural biology into other scientific fields.

Biological Applications of Thiourea Derivatives: Detailed Review

Thiourea and its derivatives have become a significant focal point within the organic synthesis field, garnering attention for their diverse biological applications, including antibacterial, antioxidant, anticancer, anti-inflammatory, anti-Alzheimer, antituberculosis and antimalarial properties. My objective is to present a comprehensive and easily understandable analysis of recent advancements in the organic synthesis of thiourea derivatives. My focus is on the structure and activity of these derivatives over the past five years, highlighting the significant progress made in the field of organic synthesis. Additionally, I evaluate the current state of research in this area and provide an overview of the latest trends and future prospects. This review will prove to be beneficial for researchers, academics and industry professionals involved in drug development and organic synthesis.

DeClUt: Decluttering differentially expressed genes through clustering of their expression profiles

Background and Objective:differential expression analysis is one of the most popular activities in transcriptomic studies based on next-generation sequencing technologies. In fact, differentially expressed genes (DEGs) between two conditions represent ideal prognostic and diagnostic candidate biomarkers for many pathologies. As a result, several algorithms, such as DESeq2 and edgeR, have been developed to identify DEGs. Despite their widespread use, there is no consensus on which model performs best for different types of data, and many existing methods suffer from high False Discovery Rates (FDR). Methods:we present a new algorithm, DeClUt, based on the intuition that the expression profile of differentially expressed genes should form two reasonably compact and well-separated clusters. This, in turn, implies that the bipartition induced by the two conditions being compared should overlap with the clustering. The clustering algorithm underlying DeClUt was designed to be robust to outliers typical of RNA-seq data. In particular, we used the average silhouette function to enforce membership assignment of samples to the most appropriate condition. Results:DeClUt was tested on real RNA-seq datasets and benchmarked against four of the most widely used methods (edgeR, DESeq2, NOISeq, and SAMseq). Experiments showed a higher self-consistency of results than the competitors as well as a significantly lower False Positive Rate (FPR). Moreover, tested on a real prostate cancer RNA-seq dataset, DeClUt has highlighted 8 DE genes, linked to neoplastic process according to DisGeNET database, that none of the other methods had identified. Conclusions:our work presents a novel algorithm that builds upon basic concepts of data clustering and exhibits greater consistency and significantly lower False Positive Rate than state-of-the-art methods. Additionally, DeClUt is able to highlight relevant differentially expressed genes not otherwise identified by other tools contributing to improve efficacy of differential expression analyses in various biological applications.

Diastereoselective Synthesis of Pyridone ribo‐C‐Nucleosides via Heck Reaction and Oxidation

Nucleosides find applications in medicinal chemistry, chemical biology and diagnostics. Among the nucleosides, C‑nucleosides have attracted particular attention because their carbon‐carbon bond between nucleobase and ribose provides stability against degradation. While several well‐established methods exist for the synthesis of 2'‐deoxy‐C‐nucleosides, the preparation of their ribofuranosyl counterparts is more challenging. Established methods for their synthesis give mixtures of anomers and require harsh reagents or conditions. Here we report a diastereoselective glycosylation method involving a Heck reaction between a glycal and an aryl iodide, followed by oxidation of the silyl enol ether with methyl(trifluoromethyl)dioxirane (TFDO). The resulting ketone is then diastereoselectively reduced to the ribonucleoside. The new route has been applied to pyridones and is expected to also yield other ribo‐C‑nucleosides in diastereoselective fashion.

Systems biology: from the fundamentals of complexity to applications in plant biology

Systems biology: from the fundamentals of complexity to applications in plant biology