Biological Applications Research Articles

Comparative Analysis of 1,9-Dimethyl-Methylene Blue and Toluidine Blue Interactions with ct-DNA, G-Quadruplex DNA, and ssDNA

This study presents a comprehensive investigation into the interactions of two distinct synthetic dyes—1,9-Dimethyl-Methylene Blue and Toluidine Blue —with different DNA structures, namely calf thymus DNA (ct-DNA), G-quadruplex DNA, and single stranded DNA (ssDNA). The objective of this research is to elucidate the molecular affinities of these dyes for specific DNA structures and explore their potential applications in molecular biology and diagnostics. The experimental approach involved detailed UV-visible spectroscopic analyses, to probe the binding affinities of each dye with ct-DNA, G-quadruplex DNA, and ssDNA. The study aimed to assess the selectivity of these dyes towards the unique structural features of each DNA entity. The binding stoichiometry is defined from Job’s method. The selectivity of the dyes towards DNA also investigated with competitive dialysis experiments. The binding stoichiometry were 1:1 for 1,9-Dimethyl-Methylene Blue and Toluidine Blue and G-quadruplex DNA or ssDNA. Besides, results indicate that 1,9-Dimethyl-Methylene Blue and Toluidine Blue exhibit a pronounced affinity for G-quadruplex DNA, and ct-DNA. While single-stranded DNA is a fundamental component of DNA replication and transcription, our dyes exhibit lower affinity for this structure. The selectivity is advantageous, as it allows for the discrimination between single-stranded and structured DNA regions. The potential applications in studying DNA dynamics and unwinding processes are vast.

Synthesis of MPEG-b-PLLA Diblock Copolymers and Their Crystallization Performance with PDLA and PLLA Composite Films.

Methoxy poly(ethylene glycol)-block-poly(L-lactide) (MPEG-b-PLLA) has a wide range of applications in pharmaceuticals and biology, and its structure and morphology have been thoroughly studied. In the experiment, we synthesized MPEG-b-PLLA with different block lengths using the principle of ring-opening polymerization by controlling the amount of lactic acid added. The thermodynamic properties of copolymers and the crystallization properties of blends were studied separately. The crystallization kinetics of PDLA/MPEG-b-PLA and PLLA/MPEG-b-PLA composite films were studied using differential scanning calorimetry (DSC). The results indicate that the crystallization kinetics of composite films are closely related to the amount of block addition. The crystallinity of the sample first increases and then decreases with an increase in MPEG-b-PLLA content. These results were also confirmed in polarized optical microscope (POM) and wide-angle X-ray diffraction (WAXD) tests. When 3% MPEG-b-PLLA was added to the PDLA matrix, the blend exhibited the strongest crystallization performance.

Induced Mutagenesis using Gamma Rays: Biological Features and Applications in Crop Improvement

Induced mutagenesis has emerged as an essential field of plant breeding to address global food security challenges, offering tools to enhance crop productivity, resistance, and nutritional value. Among the mutation induction tools, the physical mutagen such as gamma rays holds promise for efficient mutation induction. Gamma rays, a type of high-energy electromagnetic radiation, possess unique characteristics that enable them to penetrate plant tissues and induce genetic mutations. The biological effects are influenced by various factors, including the source, type of radiation, dose rate, absorbed dose, and the sensitivity of the tissues and organs. Gamma rays have been successfully applied to various plant species, producing novel superior mutants for cultivation. This paper explores the different aspects of gamma irradiation, including the radiation facilities, the biological effects of gamma rays on plant species, and the potential applications to generate genetic diversity and unlock desirable trait improvement in crop plants. The paper also showcases successful examples of high-yielding mutants developed through gamma-ray mutagenesis and their impact on agriculture. The potential approach of plant mutagenesis offers to address challenges for plant improvement for sustainable and resilient food production.

Cerium Oxide Nanoparticles Synthesis Using Alhagi Maurorum Leaf Extract and Evaluation of Their Cytotoxic Effect on Breast Cancer Cell Lines and Antibacterial Effects.

Green synthesis offers a fast, simple, and economical method for producing metallic nanoparticles.The basis of this method is to obtain nanoparticles using natural materials, such as plants, fungi, and bacteria, instead of harmful and expensive chemical-reducing agents. In this study, CeO2NPs were produced using Alhagi maurorum extract, and their anticancer and antibacterial activities were evaluated. Alhagi maurorum extract was prepared according to a previously described protocol, and CeO2NPs were synthesized from the salt of this extract. The resulting nanoparticles were characterized using Transmission electron microscopy (TEM), scanning electron microscope (SEM), and X-ray diffraction (XRD) techniques. The antibacterial and cytotoxic effects of the nanoparticles were measured by MIC, MBC, and MTT assays, respectively. The results were analyzed using one-way analysis of variance (ANOVA) using Prism software. The MTT assay on breast cancer cell lines showed that the cytotoxic effect of CeO2NPs on cell lines was concentration-dependent. In addition, this nanoparticle was more effective against Gram-positive bacteria. These nanoparticles can be used as cancer drug delivery systems with specific targeting at low concentrations in addition to anticancer treatments. It can also have biological and medicinal applications, such as natural food preservation and wound dressing.

Numerical investigation of planar microcoils integrated in microfluidic devices for biological applications

Numerical investigation of planar microcoils integrated in microfluidic devices for biological applications

Recent advancement in nanocellulose synthesis, characterization and application: A review

Cellulose Nanocrystal, known as CNCs, is a form of material that can be produced by synthesizing carbon from naturally occurring substances, such as plants. Due to the unique properties it possesses, including a large surface area, impressive mechanical strength, and the ability to biodegrade, it draws significant attractions to the researchers nowadays. Several methods are available to prepare CNC, such as acid hydrolysis, enzymatic hydrolysis, and mechanical procedures. Characterization of CNC includes X-ray diffraction, transmission electron microscopy, and dynamic light scattering, etc. In this article, recent development of CNC preparation and their characterizations are thoroughly discussed. Significant breakthroughs are listed accordingly. Furthermore, a variety of CNC applications such as paper and packaging, biological applications, and energy storage, etc. are illustrated. This study demonstrates the insights of using of CNC as the potential environmentally friendly materials with remarkable properties.

Advancing 2D imaging of ammonium for biological application: Planar and nanoparticle-based ion-selective optodes

This study investigates the development and optimization of ammonium-selective chromoionophore-based optodes for two-dimensional (2D) imaging with conventional cameras. Ammonium, vital in various fields like agriculture, ecology, and health, requires accurate measurement. Traditional methods have limitations, leading to the exploration of optical sensors, or optodes, for direct imaging of ammonium gradients. The research covers planar and nanoparticle designs, exploring absorbance and fluorescence readouts with commercial cameras. The study extends to repeatability, response time, and selectivity of the optodes. Planar optodes, utilizing chromoionophores under different background colors, demonstrate improved characteristics with the addition of TiO2. The impact of plasticizer choice on response characteristics, including hysteresis, is explored. Nanoparticle designs using PVC and F127 are compared, with autoclaving identified as the superior sterilization method. The work effectively demonstrates 2D real-time NH4+ visualization using optode nanoparticles in agar gels. Finally, a proof-of-concept was performed to showcase a biological application for identifying urease-producing pathogens (Bacillus subtilis) without relying on pH changes. Overall, this study provides a comprehensive exploration of ammonium-selective optodes with promising applications in environmental monitoring and biological studies.

A new water−soluble naphthalene diimide as a highly selective fluorescent chemosensor for Cu(II) ion: Synthesis, DFT calculations, photophysical and electrochemical properties

The highly selective, sensitive, and water-soluble fluorescent sensors are desideratum for optoelectronic, environmental, biological, and biomedical applications. An innovative fluorescence chemosensor, naphthalene diimide (3) with metal binding sites, was designed, synthesized and characterized. The chemosensor's optical, electrochemical, spectroelectrochemical, and morphological properties were investigated, and then the density functional theory (DFT) simulations were conducted. The selectivity of 3 for the metals Cu(II), Ag(I), Hg(II), Mg(II), Fe(III), Ca(II), Co(II), Zn(II), Pb(II) and Cd(II) were investigated through UV–visible and fluorescence spectroscopy techniques. 3 was highly selective and sensitive toward Cu(II) metal ions. The chemosensor can detect Cu(II) in water with a detection limit of 1.11 μM, which is lower than the WHO standard and has good repeatability. Further investigations through the IR, DPV, AFM, UV–visible and fluorescence spectroscopies, SEM, EDX and TEM techniques confirmed the binding capabilities of the 3 with Cu(II).

Sarcopenia as a Risk Factor for Alzheimer’s Disease: Genetic and Epigenetic Perspectives

Sarcopenia, defined as the age-associated loss of muscle mass and increased fragility with age, is increasing worldwide. The condition often precedes the development of Alzheimer’s disease, thereby decreasing the levels of mobility and physical activity in those affected. Indeed, the loss of muscle mass has, in some studies, been associated with an increased risk of Alzheimer’s disease and other dementias. However, a detailed understanding of the interplay between both conditions is not available and needs to be thoroughly addressed. In the following review, we focus on several genes, specifically APOE, BDNF, ACE, FTO, and FNDC5, that have been associated with both conditions. We also discuss the epigenetic regulation of each of these genes along with non-coding RNAs (ncRNAs) that may have a role in the development of both the sarcopenic and Alzheimer’s disease phenotypes. Finally, we assert that the application of systems biology will unravel the relationship between sarcopenia and Alzheimer’s disease and believe that the prevention of muscle loss in older age will reduce the incidence of debilitating cognitive decline.

IM-Seeker: a webserver for DNA i-motifs prediction and scoring via automated machine learning.

DNA, beyond its canonical B-form double helix, adopts various alternative conformations, among which the i-motif, emerging in cytosine-rich sequences under acidic conditions, holds significant biological implications in transcription modulation and telomere biology. Despite recognizing the crucial role of i-motifs, predictive software for i-motif forming sequences has been limited. Addressing this gap, we introduce 'iM-Seeker', an innovative computational platform designed for the prediction and evaluation of i-motifs. iM-Seeker exhibits the capability to identify potential i-motifs within DNA segments or entire genomes, calculating stability scores for each predicted i-motif based on parameters such as the cytosine tracts number, loop lengths, and sequence composition. Furthermore, the webserver leverages automated machine learning (AutoML) to effortlessly fine-tune the optimal i-motif scoring model, incorporating user-supplied experimental data and customised features. As an advanced, versatile approach, 'iM-Seeker' promises to advance genomic research, highlighting the potential of i-motifs in cell biology and therapeutic applications. The webserver is freely available at https://im-seeker.org.

Sustainable production of sophorolipid biosurfactants using renewable cellulose‐derived feedstocks

AbstractGlycolipids produced and secreted by oleaginous yeasts are renewable compounds with important physico‐chemical properties, and multiple biological and industrial applications. The large‐scale production of these compounds has been limited by high production costs and low yields. The sophorolipid‐producing yeast Pseudohyphozyma bogoriensis may possess the ability to grow in fermentation systems using carbon substrates deriving from inexpensive lignocellulosic biomass, while simultaneously secreting high value biomaterials. In this study, comparative analyses between different cellulose‐derived carbon sources including glucose, cellobiose, and sodium carboxymethyl cellulose confirmed the ability of P. bogoriensis to grow and accumulate glycolipids using these substrates. On a dry weight basis, the highest yields of about 4% (wt/wt) glycolipids were obtained when cellobiose was supplemented at 10 g/L in shake‐flask fermentations. When the unconventional carbon substrate sodium carboxymethyl cellulose was supplemented, cultures exhibited a lower glycolipid yield of 0.3% (wt/wt), but the dry weight was higher compared to other substrates. Analytical analyses using various chromatography methods confirmed the chemical profiles, whereas both monoacetylated and diacetylated sophorolipid forms with 22 carbon long‐chain hydroxy fatty acid were identified in all glycolipid extracts. Surface tension (ST) and critical micelle concentration (CMC) measurements showed that glycolipids produced on cellulose‐derived substrates exhibited similar or even superior physical properties compared with glucose. Furthermore, availability of the yeast genome sequences facilitated the identification of putative genes that may be involved in cellulose hydrolysis (e.g., cellulase‐like). Information on genomic and metabolic pathways is a prerequisite for trait improvement toward increasing the production of high value biomaterials.

Protein engineering using circular permutation - structure, function, stability, and applications.

Protein engineering is important for creating novel variants from natural proteins, enabling a wide range of applications. Approaches such as rational design and directed evolution are routinely used to make new protein variants. Computational tools like de novo design can introduce new protein folds. Expanding the amino acid repertoire to include unnatural amino acids with non-canonical side chains in vitro by native chemical ligation and in vivo via codon expansion methods broadens sequence and structural possibilities. Circular permutation (CP) is an invaluable approach to redesigning a protein by rearranging the amino acid sequence, where the connectivity of the secondary structural elements is altered without changing the overall structure of the protein. Artificial CP proteins (CPs) are employed in various applications such as biocatalysis, sensing of small molecules by fluorescence, genome editing, ligand-binding protein switches, and optogenetic engineering. Many studies have shown that CP can lead to either reduced or enhanced stability or catalytic efficiency. The effects of CP on a protein's energy landscape cannot be predicted a priori. Thus, it is important to understand how CP can affect the thermodynamic and kinetic stability of a protein. In this review, we discuss the discovery and advancement of techniques to create protein CP, and existing reviews on CP. We delve into the plethora of biological applications for designed CP proteins. We subsequently discuss the experimental and computational reports on the effects of CP on the thermodynamic and kinetic stabilities of proteins of various topologies. An understanding of the various aspects of CP will allow the reader to design robust CP proteins for their specific purposes.

The hinge-engineered IgG1-IgG3 hybrid subclass IgGh47 potently enhances Fc-mediated function of anti-streptococcal and SARS-CoV-2 antibodies

Streptococcus pyogenes can cause invasive disease with high mortality despite adequate antibiotic treatments. To address this unmet need, we have previously generated an opsonic IgG1 monoclonal antibody, Ab25, targeting the bacterial M protein. Here, we engineer the IgG2-4 subclasses of Ab25. Despite having reduced binding, the IgG3 version promotes stronger phagocytosis of bacteria. Using atomic simulations, we show that IgG3’s Fc tail has extensive movement in 3D space due to its extended hinge region, possibly facilitating interactions with immune cells. We replaced the hinge of IgG1 with four different IgG3-hinge segment subclasses, IgGhxx. Hinge-engineering does not diminish binding as with IgG3 but enhances opsonic function, where a 47 amino acid hinge is comparable to IgG3 in function. IgGh47 shows improved protection against S. pyogenes in a systemic infection mouse model, suggesting that IgGh47 has promise as a preclinical therapeutic candidate. Importantly, the enhanced opsonic function of IgGh47 is generalizable to diverse S. pyogenes strains from clinical isolates. We generated IgGh47 versions of anti-SARS-CoV-2 mAbs to broaden the biological applicability, and these also exhibit strongly enhanced opsonic function compared to the IgG1 subclass. The improved function of the IgGh47 subclass in two distant biological systems provides new insights into antibody function.

Research Progress on Liposome Pulmonary Delivery of Mycobacterium tuberculosis Nucleic Acid Vaccine and Its Mechanism of Action.

Traditional vaccines have played an important role in the prevention and treatment of infectious diseases, but they still have problems such as low immunogenicity, poor stability, and difficulty in inducing lasting immune responses. In recent years, the nucleic acid vaccine has emerged as a relatively cheap and safe new vaccine. Compared with traditional vaccines, nucleic acid vaccine has some unique advantages, such as easy production and storage, scalability, and consistency between batches. However, the direct administration of naked nucleic acid vaccine is not ideal, and safer and more effective vaccine delivery systems are needed. With the rapid development of nanocarrier technology, the combination of gene therapy and nanodelivery systems has broadened the therapeutic application of molecular biology and the medical application of biological nanomaterials. Nanoparticles can be used as potential drug-delivery vehicles for the treatment of hereditary and infectious diseases. In addition, due to the advantages of lung immunity, such as rapid onset of action, good efficacy, and reduced adverse reactions, pulmonary delivery of nucleic acid vaccine has become a hot spot in the field of research. In recent years, lipid nanocarriers have become safe, efficient, and ideal materials for vaccine delivery due to their unique physical and chemical properties, which can effectively reduce the toxic side effects of drugs and achieve the effect of slow release and controlled release, and there have been a large number of studies using lipid nanocarriers to efficiently deliver target components into the body. Based on the delivery of tuberculosis (TB) nucleic acid vaccine by lipid carrier, this article systematically reviews the advantages and mechanism of liposomes as a nucleic acid vaccine delivery carrier, so as to lay a solid foundation for the faster and more effective development of new anti-TB vaccine delivery systems in the future.

Beyond Luminescence: How Science and Technology are being Revolutionized by Quantum Dots

A brief review of quantum dots (QDs), a new class of nanomaterials with profound implications for cutting edge technological developments and research, is provided in this work. The notion of quantum dots is presented, explaining their special characteristics and operation, which originate from several quantum events in these remarkable spherical crystals. Because of their exceptional optical and electrical characteristics, QDs have great promise for a variety of uses. This paper also showcases some of the most widely used QD-based applications in biology and electronics, highlighting their adaptability and potential influence in several domains.

Synthesis of zinc oxide nanoparticles via biomass of Hypnea pannosa as a green mediator and their biological applications

The biological manufacturing of zinc oxide nanoparticles (ZnO-NPs) using renewable sources is safe, harmless, and compatible with the environment. The capacity of Hypnea pannosa to synthesize ZnO-NPs was investigated in this work. Ultraviolet visible (UV-Vis) spectroscopy, transmission electron microscopy (TEM), Fourier transform infrared (FTIR) spectroscopy, dynamic light scattering (DLS), X-ray diffraction (XRD), and zeta potential analysis were employed to characterize the ZnO-NPs. The created ZnO-NPs showed antimicrobial activity against Staphylococcus aureus, Enterococcus faecalis, Klebsiella pneumoniae, Acinetobacter baumannii, Candida albicans, and Candida auris. ZnO-NPs showed an MIC of 12.5 µg/mL against S. aureus, E. faecalis, K. pneumoniae, C. albicans, and C. auris, but it had a 25 µg/mL against Acinetobacter baumannii. ZnO-NPs’ ability to scavenge free radicals was assessed using the 1,1-diphenyl-2-picryl hydrazyl (DPPH) technique with IC50 of 36.2 µg/mL. Anti-inflammatory activity of ZnO-NPs compared to indomethacin at 1000 µg/mL was investigated, where the membrane’s maximum stabilizer was 93.3%. ZnO-NPs demonstrated anticancer activity against PC3 and Caco2 cell lines with IC50 of 174.3 μg/mL and 83.3 μg/mL, respectively. Furthermore, ZnO-NPs demonstrated a range of anti-biofilm activities against Pseudomonas aeruginosa and Staphylococcus aureus. Furthermore, ZnO-NPs showed encouraging antiviral effect versus COX B4 as well as HSV1 with antiviral activities of 54.8% and 61.1%, respectively.

Synthesis and Medicinal Applications of N-Heterocyclic Carbene Complexes based on Caffeine and other Xanthines.

Xanthines are purine derivatives predominantly found in plants. These include compounds such as caffeine, theophylline, and theobromine and exhibit a variety of pharmacological properties, demonstrating efficacy in treating neurodegenerative disorders, respiratory dysfunctions, and also in cancer. The versatile attributes of these materials render them privileged scaffolds for the development of compounds for various biological applications. Xanthines are N-heterocyclic carbene precursors that combine a pyrimidine and an imidazole ring. Owing to their biological relevance, xanthines have been employed as N-heterocyclic carbenes in the development of metallodrugs for anticancer and antimicrobial purposes. In this conceptual review, we examine key examples of N-heterocyclic carbene complexes derived from caffeine and other xanthines, elucidating their synthetic methods and describing their pertinent medicinal applications.

Erratum to: Contouring Multifaceted Biological Activities and Applications of Trichoderma spp. for Managing Plant Health

Erratum to: Contouring Multifaceted Biological Activities and Applications of Trichoderma spp. for Managing Plant Health

NNO donor Schiff base metal complexes: Enzyme mimicking, DNA binding and biological insights

The present work focuses on the microwave-assisted synthesis, characterization and biological applications of a novel tridentate NNO donor Schiff base ligand derived from the condensation of 4-(Diethylamino)salicylaldehyde and 4,5-Dimethyl-1,2-phenylenediamine, along with its transition metal complexes of Cu(II) and Co(II) in 1:1 and 1:2 ratios each respectively. A theoretical basis for comprehending the electronic framework and characteristics of the complexes has been studied through the use of a computational approach. Further, the distorted octahedral geometry of the Schiff base metal complexes is confirmed by using analytical methods such as elemental analysis, molar conductance, ESI-MS, UV–Vis, FTIR, TGA and NMR spectra, which confirmed that NNO donor site of the ligand is coordinated with the metal ions. The complexes have been screened for their potential application as a catalyst for the catalytic conversion of 3,5-di‑tert‑butyl‑catechol (3,5-DTBC) to 3,5-di‑tert-butylquinone (3,5-DTBQ) and the turnover numbers (Kcat) have been found in the range 36.46–43.05 h−1 in methanol. Absorption spectroscopic technique has been employed to examine the possible modalities of interactions with the synthesized complexes using CT-DNA and the related binding constants exhibited in the range 2.58 × 104 M−1 to 1.98 × 105 M−1 thus depicting appreciable binding affinity. To evaluate the bioactivities, in-vitro assays for anti-oxidant and anti-inflammatory activity have also been implemented. The Cu(II) complex (CuL) has significant anti-oxidant activity and the Co(II) complex (CoL) has superior anti-inflammatory activity compared to all other complexes with IC50 values of 238.78 µM and 140.25 µM respectively. To better understand the molecular-level interactions and identify probable binding energies of inhibitors, molecular docking simulations have been performed.

Biocompatible aggregation-induced emission active polyphosphate-manganese nanosheets with glutamine synthetase-like activity in excitotoxic nerve cells

Glutamine synthetase (GS) is vital in maintaining ammonia and glutamate (Glu) homeostasis in living organisms. However, the natural enzyme relies on adenosine triphosphate (ATP) to activate Glu, resulting in impaired GS function during ATP-deficient neurotoxic events. To date, no reports demonstrate using artificial nanostructures to mimic GS function. In this study, we synthesize aggregation-induced emission active polyP-Mn nanosheets (STPE-PMNSs) based on end-labeled polyphosphate (polyP), exhibiting remarkable GS-like activity independent of ATP presence. Further investigation reveals polyP in STPE-PMNSs serves as phosphate source to activate Glu at low ATP levels. This self-feeding mechanism offers a significant advantage in regulating Glu homeostasis at reduced ATP levels in nerve cells during excitotoxic conditions. STPE-PMNSs can effectively promote the conversion of Glu to glutamine (Gln) in excitatory neurotoxic human neuroblastoma cells (SH-SY5Y) and alleviate Glu-induced neurotoxicity. Additionally, the fluorescence signal of nanosheets enables precise monitoring of the subcellular distribution of STPE-PMNSs. More importantly, the intracellular fluorescence signal is enhanced in a conversion-responsive manner, allowing real-time tracking of reaction progression. This study presents a self-sustaining strategy to address GS functional impairment caused by ATP deficiency in nerve cells during neurotoxic events. Furthermore, it offers a fresh perspective on the potential biological applications of polyP-based nanostructures.