RNA-sequencing exploration on SIR2 and SOD genes in Polyalthia longifolia leaf methanolic extracts (PLME) mediated anti-aging effects in Saccharomyces cerevisiae BY611 yeast cells.

Polyalthia longifolia is well-known for its abundance of polyphenol content and traditional medicinal uses. Previous research has demonstrated that the methanolic extract of P. longifolia leaves (PLME, 1 mg/mL) possesses anti-aging properties in Saccharomyces cerevisiae BY611 yeast cells. Building on these findings, this study delves deeper into the potential antiaging mechanism of PLME, by analyzing the transcriptional responses of BY611 cells treated with PLME using RNA-sequencing (RNA-seq) technology. The RNA-seq analysis results identified 1691 significantly (padj < 0.05) differentially expressed genes, with 947 upregulated and 744 downregulated genes. Notably, the expression of three important aging-related genes, SIR2, SOD1, and SOD2, showed a significant difference following PLME treatment. The subsequent integration of these targeted genes with GO and KEGG pathway analysis revealed the multifaceted nature of PLME's anti-aging effects in BY611 yeast cells. Enriched GO and KEGG analysis showed that PLME treatment promotes the upregulation of SIR2, SOD1, and SOD2 genes, leading to a boosted cellular antioxidant defense system, reduced oxidative stress, regulated cell metabolism, and maintain genome stability. These collectively increased longevities in PLME-treated BY611 yeast cells and indicate the potential anti-aging action of PLME through the modulation of SIR2 and SOD genes. The present study provided novel insights into the roles of SIR2, SOD1, and SOD2 genes in the anti-aging effects of PLME treatment, offering promising interventions for promoting healthy aging.

Cardiovascular biomarker troponin I biosensor: Aptamer-gold-antibody hybrid on a metal oxide surface.

Myocardial infarction (MI) is highly related to cardiac arrest leading to death and organ damage. Radiological techniques and electrocardiography have been used as preliminary tests to diagnose MI; however, these techniques are not sensitive enough for early-stage detection. A blood biomarker-based diagnosis is an immediate solution, and due to the high correlation of troponin with MI, it has been considered to be a gold-standard biomarker. In the present research, the cardiac biomarker troponin I (cTnI) was detected on an interdigitated electrode sensor with various surface interfaces. To detect cTnI, a capture aptamer-conjugated gold nanoparticle probe and detection antibody probe were utilized and compared through an alternating sandwich pattern. The surface metal oxide morphology of the developed sensor was proven by microscopic assessments. The limit of detection with the aptamer-gold-cTnI-antibody sandwich pattern was 100 aM, while it was 1 fM with antibody-gold-cTnI-aptamer, representing 10-fold differences. Further, the high performance of the sensor was confirmed by selective cTnI determination in serum, exhibiting superior nonfouling. These methods of determination provide options for generating novel assays for diagnosing MI.

Identification of Mycoplasma pneumoniae by DNA-modified gold nanomaterials in a colorimetric assay.

Mycoplasma pneumoniae is a highly infectious bacterium and the major cause of pneumonia especially in school-going children. Mycoplasma pneumoniae affects the respiratory tract, and 25% of patients experience health-related problems. It is important to have a suitable method to detect M. pneumoniae, and gold nanoparticle (GNP)-based colorimetric biosensing was used in this study to identify the specific target DNA for M. pneumoniae. The color of GNPs changes due to negatively charged GNPs in the presence of positively charged monovalent (Na+ ) ions from NaCl. This condition is reversed in the presence of a single-stranded oligonucleotide, as it attracts GNPs but not in the presence of double-stranded DNA. Single standard capture DNA was mixed with optimal target DNA that cannot be adsorbed by GNPs; under this condition, GNPs are not stabilized and aggregate at high ionic strength (from 100 mM). Without capture DNA, the GNPs that were stabilized by capture DNA (from 1 µM) became more stable under high ionic conditions and retaining their red color. The GNPs turned blue in the presence of target DNA at concentrations of 1 pM, and the GNPs retained a red color when there was no target in the solution. This method is useful for the simple, easy, and accurate identification of M. pneumoniae target DNA at higher discrimination and without involving sophisticated equipment, and this method provides a diagnostic for M. pneumoniae.

Analysis of Gas Nanoclusters in Water Using All-Atom Molecular Dynamics.

The Young-Laplace equation suggests that nanosized gas clusters would dissolve under the effects of perturbation. The fact that nanobubbles are observed raises questions as to the mechanism underlying their stability. In the current study, we used all-atom molecular dynamics simulations to investigate the gas-water interfacial properties of gas clusters. We employed the instantaneous coarse-graining method to define the fluctuating boundaries and analyze the deformation of gas clusters. Fourier transform analysis of the cluster morphology revealed that the radius and morphology deformation variations exhibit power law relationships with the vibrational frequency, indicating that the surface energy dissipated through morphology variations. Increasing pressure in the liquid region was found to alter the network of water molecules at the interface, whereas increasing pressure in the gas region did not exhibit this effect. The overall gas concentration was oversaturated and proportional to the gas density inside the clusters. However, the result of comparison with Henry's law reveals that the gas pressure at the interface reduced by the interfacial effects is much lower than that inside the gas region, thus reducing the demanding degree of oversaturation. Originating from the interfacial charge allocation, the magnitude of the electrostatic stress is greater than that of the gas pressure inside the cluster. However, the magnitude of the reversed tension induced by electrostatic stress is far below the value of interfacial tension. The potential of mean force (PMF) profiles revealed that a barrier potential at the interface hindered gas particles from escaping the cluster. Several effects contribute to stabilizing the gas clusters in water, including high-frequency morphological deformation, electrostatic stress, reduced interfacial tension, and gas oversaturation conditions. Our results suggest that gas clusters can exist in water under gas oversaturation conditions in the absence of hydrophobic contaminants or pinning charges at interfaces.

Nanosensing colon cancer biomarker on zeolite-modified gap-fingered dielectrodes.

Nanomaterial on the sensing area elevates the biomolecular immobilization by its right orientation with a proper alignment, and zeolite is one of the suitable materials. In this research, the zeolite nanoparticles were synthesized using rice hush ash as the basic source and the prepared zeolite by the addition of sodium silicate was utilized to attach antibody as a probe on a gap-fingered dielectrode surface to identify the colon cancer biomarker, "colon cancer-secreted protein-2" (CCSP-2). Field Emission Scanning Electron Microscopy and Field Emission Transmission Electron Microscopy images confirmed the size of the nanoparticle to be ∼15 nm and the occurrence of silica and alumina. Zeolite was modified on the electrode surface through the amine linker, and then anti-CCSP-2 was attached by an aldehyde linker. On this surface, CCSP-2 was detected and attained the detection limit to be 3 nM on the linear regression curve with 3-5 nM of CCSP-2. Estimated by the determination coefficient of y = 2.3952x - 4.4869 and R2 = 9041 with 3δ (n = 3). In addition, control proteins did not produce the notable current response representing the specific sensing of CCSP-2. This research is suitable to identify CCSP-2 at a lower level in the bloodstream under the physiological condition of a colon cancer patient.

Diversity-Oriented Synthesis of a Molecular Library of Immunomodulatory α-Galactosylceramides with Fluorous-Tag-Assisted Purification and Evaluation of Their Bioactivities in Regard to IL-2 Secretion.

Structural variants of α-galactosylceramide (α-GalCer) that stimulate invariant natural killer T (iNKT) cells constitute an emerging class of immunomodulatory agents in development for numerous biological applications. Variations in lipid chain length and/or fatty acids in these glycoceramides selectively trigger specific pro-inflammatory responses. Studies that would link a specific function to a structurally distinct α-GalCer rely heavily on the availability of homogeneous and pure materials. To address this need, we report herein a general route to the diversification of the ceramide portion of α-GalCer glycolipids. Our convergent synthesis commences from common building blocks and relies on the Julia-Kocienski olefination as a key step. A cleavable fluorous tag is introduced at the non-reducing end of the sugar that facilitates quick purification of products by standard fluorous solid-phase extraction. The strategy enabled the rapid generation of a focused library of 61 α-GalCer analogs by efficiently assembling various lipids and fatty acids. Furthermore, when compared against parent α-GalCer in murine cells, many of these glycolipid variants were found to have iNKT cell stimulating activity similar to or greater than KRN7000. ELISA assaying indicated that glycolipids carrying short fatty N-acyl chains (1fc and 1ga), an unsubstituted (1fh and 1fi) or CF3-substituted phenyl ring at the lipid tail, and a flexible, shorter fatty acyl chain with an aromatic ring (1ge, 1gf, and 1gg) strongly affected the activation of iNKT cells by the glycolipid-loaded antigen-presenting molecule, CD1d. This indicates that the method may benefit the design of structural modifications to potent iNKT cell-binding glycolipids.

Identification of potential glycoprotein biomarkers in oral squamous cell carcinoma using sweet strategies.

The prevalence of oral squamous cell carcinoma (OSCC) is high in South and Southeast Asia regions. Most OSCC patients are detected at advanced stages low 5-year survival rates. Aberrant expression of glycosylated proteins was found to be associated with malignant transformation and cancer progression. Hence, identification of cancer-associated glycoproteins could be used as potential biomarkers that are beneficial for diagnosis or clinical management of patients. This study aims to identify the differentially expressed glycoproteins using lectin-based glycoproteomics approaches. Serum samples of 40 patients with OSCC, 10 patients with oral potentially malignant disorder (OPMD), and 10 healthy individuals as control group were subjected to two-dimensional gel electrophoresis (2-DE) coupled with lectin Concanavalin A and Jacalin that specifically bind to N- and O-glycosylated proteins, respectively. Five differentially expressed N- and O-glycoproteins with various potential glycosylation sites were identified, namely N-glycosylated α1-antitrypsin (AAT), α2-HS-glycoprotein (AHSG), apolipoprotein A-I (APOA1), and haptoglobin (HP); as well as O-glycosylated AHSG and clusterin (CLU). Among them, AAT and APOA1 were further validated using enzyme-linked immunosorbent assay (ELISA) (n = 120). It was found that AAT and APOA1 are significantly upregulated in OSCC and these glycoproteins are independent risk factors of OSCC. The clinical utility of AAT and APOA1 as potential biomarkers of OSCC is needed for further evaluation.

Effects of Gas Adsorption and Surface Conditions on Interfacial Nanobubbles.

Gas aggregation and formation of interfacial nanobubbles (INBs) provide challenges and opportunities in the operation of micro-/nanofluidic devices. In the current study, we used molecular dynamics(MD) simulations to investigate the effects of hydrophobicity and various homogeneous surface conditions on gas aggregation and INB stability with a series of 3D argon-water-solid and water-solid systems. Among various signatures of surface hydrophobicity, the potential of mean force (PMF) minima exhibited the strongest correlation with the water molecular orientation at the liquid-solid interface, compared to the depletion layer width and the droplet contact angle. Our results indicated that argon aggregation on the substrate was a function of hydrophobicity as well as competition between gas-solid and water-solid PMFs. Thus, one precondition for gas aggregation on a surface is that the free energy minima of gas induced by the surface be much lower than that induced by water. We found that although the presence of gas molecules had little effect on the measures of wettability, it enhanced density fluctuations near liquid-solid interfaces. The PMF of gas along the surface tangential plane exhibited a small energy barrier between the epitaxial gas layer (EGL) in the bubble and the gas enrichment layer (GEL) in the liquid, which may benefit nanobubble stability. Much lower PMF in the EGL compared to that in the GEL indicated that gas molecules could migrate from the GEL to the nanobubble basement. However, density fluctuations enhanced by the GEL could reduce the energy barrier, thus reducing the stability of INBs.

Aptamer-17ß-estradiol-antibody sandwich ELISA for determination of gynecological endocrine function.

17ß-Estradiol-E2 (17ß-E2) is a steroid hormone that plays a major role in the reproductive endocrine system and is involved in various processes, such as pregnancy, fertility, and menopause. In this study, the performance of an enzyme-linked immunosorbent assay (ELISA) for 17ß-E2 quantification was enhanced by using a gold nanoparticle (GNP)-conjugated aptamer. An anti-17ß-E2-aptamer-GNP antibody was immobilized on an amine-modified ELISA surface. Then, 17ß-E2 was allowed to interact with and be sandwiched by antibodies. Aptamer-GNP conjugation was confirmed by colorimetric assays via the naked eye and UV-visible light spectroscopy. The detection limit based on a signal-to-noise ratio (S/N) of 3 was estimated to be 1.5 nM (400 pg/mL), and the linear range was 1.5-50 nM. Control experiments (without 17ß-E2/with a complementary aptamer sequence/with a nonimmune antibody) confirmed the specific detection of 17ß-E2. Moreover, 17ß-E2 spiking of human serum did not interrupt the interaction between 17ß-E2 and its antibody and aptamer. Thus, the developed ELISA can be used as an alternate assay for quantification of 17ß-E2 and assessment of endocrine-related gynecological problems.

Rich phase transitions in strongly confined polymer-nanoparticle mixtures: Nematic ordering, crystallization, and liquid-liquid phase separation.

We investigate the rich phase behavior of strongly confined semi-flexible (SFC) polymer-nanoparticle (NP) systems using the graphics processing unit accelerated Langevin dynamics simulation. Hard nanoparticles (HNP) that repel each other and ideal nanoparticles (INP) that do not interact with the same species are used as model additives to a strongly confined semiflexible polymer fluid. Both types of NPs exclude the monomer beads in the same way, but they have qualitatively different effects on the SFC isotropic-nematic (I-N) transition. For the total volume fraction ϕtot < 0.16, adding a low volume fraction of HNPs (ϕp) disrupts the long range nematic order of the polymers, whereas adding HNPs in a moderately packed system (0.16 < ϕtot < 0.32) facilitates polymer alignment due to the restricted polymer orientational degree of freedom. For dense packing (ϕtot > 0.32), polymers and NPs separate into layers along the slit height and the NPs form crystalline microdomains. In contrast, INP additives always promote inter-polymer alignment for low to moderate monomer volume fractions (ϕm). Furthermore, we found that INPs form a droplet-like fluid domain in dense nematic polymer systems.

Clusters of circulating tumor cells traverse capillary-sized vessels.

Multicellular aggregates of circulating tumor cells (CTC clusters) are potent initiators of distant organ metastasis. However, it is currently assumed that CTC clusters are too large to pass through narrow vessels to reach these organs. Here, we present evidence that challenges this assumption through the use of microfluidic devices designed to mimic human capillary constrictions and CTC clusters obtained from patient and cancer cell origins. Over 90% of clusters containing up to 20 cells successfully traversed 5- to 10-µm constrictions even in whole blood. Clusters rapidly and reversibly reorganized into single-file chain-like geometries that substantially reduced their hydrodynamic resistances. Xenotransplantation of human CTC clusters into zebrafish showed similar reorganization and transit through capillary-sized vessels in vivo. Preliminary experiments demonstrated that clusters could be disrupted during transit using drugs that affected cellular interaction energies. These findings suggest that CTC clusters may contribute a greater role to tumor dissemination than previously believed and may point to strategies for combating CTC cluster-initiated metastasis.

Electrofluidic Circuit-Based Microfluidic Viscometer for Analysis of Newtonian and Non-Newtonian Liquids under Different Temperatures.

This paper reports a microfluidic viscometer with an integrated pressure sensor based on electrofluidic circuits, which are electrical circuits constructed by ionic liquid-filled microfluidic channels. The electrofluidic circuit provides a pressure-sensing scheme with great long-term and thermal stability. The viscosity of the tested fluidic sample is estimated by its flow resistance, which is a function of pressure drop, flow rate, and the geometry of the microfluidic channel. The viscometer can be exploited to measure viscosity of either Newtonian or non-Newtonian power-law fluid under various shear rates (3-500 1/s) and temperatures (4-70 °C) with small sample volume (less than 400 µL). The developed sensor-integrated microfluidic viscometer is made of poly(dimethylsiloxane) (PDMS) with transparent electrofluidic circuit, which makes it feasible to simultaneously image samples under tests. In addition, the entire device is disposable to prevent cross-contamination between samples, which is desired for various chemical and biomedical applications. In the experiments, viscosities of Newtonian fluids, glycerol water solutions with different concentrations and a mixture of pyrogallol and sodium hydroxide (NaOH), and non-Newtonian fluids, xanthan gum solutions and human blood samples, have been characterized. The results demonstrate that the developed microfluidic viscometer provides a convenient and useful platform for practical viscosity characterization of fluidic samples for a wide variety of applications.

Emerging Roles of Air Gases in Lipid Bilayers.

Recent studies indicate that changing the physical properties of lipid bilayers may profoundly change the function of membrane proteins. Here, the effects of dissolved nitrogen and oxygen molecules on the mechanical properties and stability of lipid bilayers are investigated using differential confocal microscopy, atomic force microscopy, and molecular dynamics simulations. All experiments evidence the presence of dissolved air gas in lipid bilayers prepared without gas control. The lipid bilayers in degassed solutions are softer and less stable than those in ambient solutions. High concentrations of nitrogen increase the bending moduli and stability of the lipid bilayers and impede phase separation in ternary lipid bilayers. The effect of oxygen is less prominent. Molecular dynamics simulations indicate that higher nitrogen affinity accounts for increased rigidity. These findings have fundamental and wide implications for phenomena related to lipid bilayers and cell membranes, including the origin of life.

Investigating Interfacial Effects on Surface Nanobubbles without Pinning Using Molecular Dynamics Simulation.

We investigated how the stability of aqueous argon surface nanobubbles on hydrophobic surfaces depends on gas adsorption, solid-gas interaction energy, and the bulk gas concentration using molecular dynamics simulation with the SPC/E water solvent. We observed stable surface nanobubbles without surface pinning sites for longer than 160 ns, contrary to previous findings using monoatomic Lennard-Jones solvent. In addition, the hydrophobicity of a substrate has an effect to reduce the requirement degree of oversaturation on water bulk. We found that the gas enrichment layer, gas adsorption monolayer on the hydrophobic substrate, and water hydrogen bonding near the interface are likely necessary conditions for nanobubble stability. We concluded that gas nanobubble stability does not necessarily require three-phase pinning sites.

Investigation of nematic to smectic phase transition and dynamical properties of strongly confined semiflexible polymers using Langevin dynamics.

We investigated the nematic to smectic phase transition for strongly confined semiflexible polymer solutions in slit-like confinements using GPU-accelerated Langevin dynamics. We characterized the phase transitions from the nematic to smectic phases for semi-flexible polymer solutions as the polymer density increased. The dependence for the lyotropic nematic to smectic transition can be collapsed by scaling exponents between 0.2 and 0.3. The smectic C phase is found for all the cases with the polymer orientation director tilted with respect to smectic layer lateral alignment. As the chain rigidity increases, the transition density decreases for systems in which the polymer persistence length (P) to slit height (H) ratios are 1.25, 2.5, 3.75, 5 and 25. We also characterized the polymer dynamics for the isotropic-nematic-smectic transitions. The overall polymer diffusivity decreased steadily as the polymer density increased. We observed anomalous polymer diffusion along the nematic director near the isotropic-nematic transition, similar to previously reported behavior for nematic-forming ellipsoids. Polymer diffusivity decreased sharply by two orders of magnitude upon the nematic-smectic transition.

Functional Analysis of Circular RNAs.

Circular RNAs characterize a class of widespread and diverse endogenous RNAs which are non-coding RNAs that are made by back-splicing events and have covalently closed loops with no polyadenylated tails. Various indications specify that circular RNAs (circRNAs) are plentiful in the human transcriptome. However, their participation in biological processes remains mostly undescribed. To date thousands of circRNAs have been revealed in organisms ranging from Drosophila melanogaster to Homo sapiens. Functional studies specify that these transcripts control expression of protein-coding linear transcripts and thus encompass a key component of gene expression regulation. This chapter provide a comprehensive overview on functional validation of circRNAs. Furthermore, we discuss the recent modern methodologies for the functional validation of circRNAs such as RNA interference (RNAi) gene silencing assay, luciferase reporter assays, circRNA gain-of-function investigation via overexpression of circular transcript assay, RT-q-PCR quantification, and other latest applicable assays. The methods described in this chapter are demonstrated on the cellular model.

Anticancer Activity and Molecular Mechanism of Polyphenol Rich Calophyllum inophyllum Fruit Extract in MCF-7 Breast Cancer Cells.

This study was conducted to investigate the anticancer effects and mechanism of Calophyllum inophyllum fruit extract against MCF-7 cells. C. inophyllum fruit extract was found to have markedly cytotoxic effect against MCF-7 cells in a dose-dependent manner with the IC50 for 24 h of 23.59 µg/mL. Flow cytometry analysis revealed that C. inophyllum fruit extract mediated cell cycle at G0/G1 and G2/M phases, and MCF-7 cells entered the early phase of apoptosis. The expression of anti-apoptotic proteins Bcl-2 was decreased whereas the expression of the pro-apoptotic protein Bax, cytochrome C and p53 were increased after treatment. C. inophyllum fruit extract led to apoptosis in MCF-7 cells via the mitochondrial pathway in a dose dependent manner. This is evidenced by the elevation of intracellular ROS, the loss of mitochondria membrane potential (Δψm), and activation of caspase-3. Meanwhile, dose-dependent genomic DNA fragmentation was observed after C. inophyllum fruits extract treatment by comet assay. This study shows that C. inophyllum fruits extract-induced apoptosis is primarily p53 dependent and mediated through the activation of caspase-3. C. inophyllum fruit extract could be an excellent source of chemopreventive agent in the treatment of breast cancer and has potential to be explored as green anticancer agent.

Confinement, curvature, and attractive interaction effects on polymer surface adsorption.

We investigate the conformation and dynamics of a semi-flexible polymer near an attractive plane or a cylindrical post using Langevin dynamics. We characterize the transition from the desorbed to absorbed state and quantify how absorption depends on the attraction interaction, polymer molecular weight, polymer flexibility, intra-polymer interaction, and micro-confinement. We find that the critical point of adsorption for ideal flexible polymers only weakly depends on confinement. However, the critical point of adsorption increases significantly for self-avoiding flexible polymers and under confinement, deviating from scaling theory predictions. These findings provide insights into DNA surface adsorption in nanoslits and nanochannels.

Abnormal polymer transport in crowded attractive micropost arrays.

We investigate polymer diffusion in a quasi-two-dimensional environment decorated with attractive cylindrical posts using Langevin dynamics simulation. We find that the polymer diffusivity has non-monotonic dependence on the post array density. This diffusive behavior strongly depends on the adsorption-desorption transition and the critical adsorption strength εc. For ε < εc, the polymer undergoes normal diffusion and the diffusivity decreases as the post density increases due to the reduction of the void volume. For ε > εc, polymer dynamics is strongly mediated by post adsorption, and we observe a regime where the polymer diffusivity increases as the post density increases. The polymer diffusivity reaches a maximum, which can be attributed to cross-post translation enabled by large polymer conformation fluctuations. We find both cross-post transport and polymer conformation fluctuations strongly depend on the post absorption strength and the chain length.

Cell-targeting aptamers act as intracellular delivery vehicles.

Aptamers are single-stranded nucleic acids or peptides identified from a randomized combinatorial library through specific interaction with the target of interest. Targets can be of any size, from small molecules to whole cells, attesting to the versatility of aptamers for binding a wide range of targets. Aptamers show drug properties that are analogous to antibodies, with high specificity and affinity to their target molecules. Aptamers can penetrate disease-causing microbial and mammalian cells. Generated aptamers that target surface biomarkers act as cell-targeting agents and intracellular delivery vehicles. Within this context, the "cell-internalizing aptamers" are widely investigated via the process of cell uptake with selective binding during in vivo systematic evolution of ligands by exponential enrichment (SELEX) or by cell-internalization SELEX, which targets cell surface antigens to be receptors. These internalizing aptamers are highly preferable for the localization and functional analyses of multiple targets. In this overview, we discuss the ways by which internalizing aptamers are generated and their successful applications. Furthermore, theranostic approaches featuring cell-internalized aptamers are discussed with the purpose of analyzing and diagnosing disease-causing pathogens.