The molecular interaction of six single-stranded DNA aptamers to cardiac troponin I revealed by docking and molecular dynamics simulation.

Cardiac troponin I (cTnI) is a cardiac biomarker for diagnosing ischemic heart disease and acute myocardial infarction. Current biochemical assays use antibodies (Abs) due to their high specificity and sensitivity. However, there are some limitations, such as the high-cost production of Abs due to complex instruments, reagents, and steps; the variability of Abs quality from batch to batch; the low stability at high temperatures; and the difficulty of chemical modification. Aptamer overcomes the limitations of antibodies, such as relatively lower cost, high reproducibility, high stability, and ease of being chemically modified. Aptamers are three-dimensional architectures of single-stranded RNA or DNA that bind to targets such as proteins. Six aptamers (Tro1-Tro6) with higher binding affinity than an antibody have been identified, but the molecular interaction has not been studied. In this study, six DNA aptamers were modeled and docked to cTnI protein. Molecular docking revealed that the interaction between all aptamer and cTnI happened in the similar cTnI region. The interaction between aptamer and cTnI involved hydrophobic interaction, hydrogen bonds, π-cation interactions, π-stack interactions, and salt-bridge formation. The calculated binding energy of all complexes was negative, which means that the complex formation was thermodynamically favorable. The electrostatic energy term was the main driving force of the interaction between all aptamer and cTnI. This study could be used to predict the behavior of further modified aptamer to improve aptamer performance.

A comprehensive study on transparent conducting oxides in compact microbial fuel cells: Integrated spectroscopic and electrochemical analyses for monitoring biofilm growth.

Microbial fuel cells (MFCs) are an emerging technology that holds promise for renewable energy production and the mitigation of environmental challenges. This research paper introduces a single-compartment MFC reactor that utilizes transparent conducting oxides (TCOs), such as fluorine-doped tin oxide (FTO) and indium tin oxides (ITO), as the working electrodes. The effectiveness of MFCs based on FTO and ITO was evaluated by characterizing the transparent electrode and examining its performance during biofilm cultivation. Additionally, the optical properties of the biofilm grown directly on these electrodes were investigated using LEDs as a light source. The impressive average current density of 200 µA cm-2 over 100 days demonstrates the efficiency of the see-through electrodes in bioenergy extraction. The correlation between spectroscopic and microscopic analyses substantiates the feasibility of employing transparent electrodes for accurate quantification of biofilm thickness, with an initial accuracy of ±10 µm in the initial cycle, ±22 µm in the subsequent cycle, and a maximum of ±31 µm after seven days of growth. This innovative approach holds great potential for advancing our understanding of MFCs and their application in environmentally friendly energy generation and optical-based monitoring.

Flower like-novel nanocomposite of Mg(Ti0.99Sn0.01)O3decorated on reduced graphene oxide (rGO) with high capacitive behavior as supercapacitor electrodes.

In this study, ceramic materials of Mg(Ti0.99Sn0.01)O3were synthesized and decorated on reduced graphene oxide, forming a nanocomposite of rGO/Mg(Ti0.99Sn0.01)O3(rGO/MTS001). The successful synthesis results were confirmed by XRD, UV-vis analysis, FT-IR, and SEM-EDS. The MTS001 has a flower-like morphology from scanning electron microscopy (SEM) analysis, and the nanocomposites of rGO/MTS001 showed MTS001 particles decorated on the rGO's surface. The electrochemical performance of rGO/MTS001 and MTS001 was investigated by determining the specific capacitance obtained in 1 M H2SO4solution by cyclic voltammetry, followed by galvanostatic charge-discharge analysis using a three-electrode setup. The rGO/MTS001 achieved a specific capacitance of 361.97 F g‒1, compared to MTS001 (194.90 F g‒1). The capacitance retention of rGO/MTS001 nanocomposite also depicted excellent cyclic stability of 95.72% after 5000 cycles at a current density of 0.1 A g‒1. The result showed that the nanocomposite of ceramics with graphene materials has a potential for high-performance supercapacitor electrodes.

Revealing Propolis Potential Activity on Inhibiting Estrogen Receptor and Heat Shock Protein 90 Overexpressed in Breast Cancer by Bioinformatics Approaches.

Breast cancer is the most commonly diagnosed cancer globally, with the highest incidence of breast cancer occurring in Asian countries including Indonesia. Among the types of breast cancer, the estrogen receptor (ER)-positive subtype which is prominent with estrogen receptor alpha (ERα) and heat shock protein 90 (HSP90) overexpression genes becomes the most prevalent than the others, approximately 75% of all breast cancer cases. ERα and HSP90 play a role in breast cancer activities including breast tumor growth, invasion, and metastasis mechanism. Propolis, a natural bee product, has been explored for its anticancer activity. However, there is lack of studies that evaluated the potential inhibitor from propolis compounds to the ERα and HSP90 proteins. Therefore, this article focuses on examining the correlation between ERα and HSP90's role in breast cancer and investigating the potential of 93 unique propolis compositions in inhibiting these genes in breast cancer using in silico approaches. This study revealed the positive correlation between ERα and HSP90 genes in breast cancer disease development. Furthermore, we also found novel potential bioactive compounds of propolis against breast cancer through binding with ERα and HSP90; they were 3',4',7-trihydroxyisoflavone and baicalein-7-O-ß-D glucopyranoside, respectively. Further research on these compounds is needed to elucidate deeper mechanisms and activity in the real biological system to develop new breast cancer drug treatments.

Durable nonenzymatic electrochemical sensing using silver decorated multi-walled carbon nanotubes for uric acid detection.

In this study, we demonstrate a facile, durable, and inexpensive technique of producing silver nanoparticles-decorated multi-walled carbon nanotubes (MWCNT/AgNP) on the easy-to-use screen-printed carbon electrodes (SPCE) for non-enzymatic detection of uric acid (UA) in an electrochemical sensor. The developed sensors show great durability for three months in storage, and high specificity performance for preclinical study using spiked UA in a synthetic urine sample. A simple route for this hybrid nanocomposite was proposed through an oxidation-reduction with reflux (ORR) process. A significant increase in the electroactive surface area of SPCE was achieved by modifying it with MWCNT/AgNP. Scanning electron microscopy (SEM), transmission electron microscopy (TEM), energy-dispersive X-ray spectroscopy (EDX), Fourier-transform infrared (FT-IR) spectroscopy, Raman spectroscopy, and X-ray diffraction (XRD) analysis confirmed this synthesis. The nanocomposite nanostructure electrodes achieved an outstanding UA detection with a sensitivity of 0.1021 µA/µM and a wide dynamic range of 10-1000 µM. In PBS, the measurements achieved a detection limit of 84.04 nM while in pure synthetic urine; it was 6.074 µM. The constructed sensor exhibits excellent stability and durability for several months, and great specificity against interfering compounds, including dopamine (DA), urea, and glucose. Overall, the present outcomes denote the potential of MWCNT/AgNP-decorated SPCE for early uric acid diagnostics tools in health monitoring.

Fabric-Based Electrochemical Glucose Sensor with Integrated Millifluidic Path from a Hydrophobic Batik Wax.

In recent years, measuring and monitoring analyte concentrations continuously, frequently, and periodically has been a vital necessity for certain individuals. We developed a cotton-based millifluidic fabric-based electrochemical device (mFED) to monitor glucose continuously and evaluate the effects of mechanical deformation on the device's electrochemical performance. The mFED was fabricated using stencil printing (thick film method) for patterning the electrodes and wax-patterning to make the reaction zone. The analytical performance of the device was carried out using the chronoamperometry method at a detection potential of -0.2 V. The mFED has a linear working range of 0-20 mM of glucose, with LOD and LOQ of 0.98 mM and 3.26 mM. The 3D mFED shows the potential to be integrated as a wearable sensor that can continuously measure glucose under mechanical deformation.

The assessment of molecular dynamics results of three-dimensional RNA aptamer structure prediction.

Aptamers are single-stranded DNA or RNA that bind to specific targets such as proteins, thus having similar characteristics to antibodies. It can be synthesized at a lower cost, with no batch-to-batch variations, and is easier to modify chemically than antibodies, thus potentially being used as therapeutic and biosensing agents. The current method for RNA aptamer identification in vitro uses the SELEX method, which is considered inefficient due to its complex process. Computational models of aptamers have been used to predict and study the molecular interaction of modified aptamers to improve affinity. In this study, we generated three-dimensional models of five RNA aptamers from their sequence using mFold, RNAComposer web server, and molecular dynamics simulation. The model structures were then evaluated and compared with the experimentally determined structures. This study showed that the combination of mFold, RNAComposer, and molecular dynamics simulation could generate 14-16, 28, or 29 nucleotides length of 3D RNA aptamer with similar geometry and topology to the experimentally determined structures. The non-canonical basepair structure of the aptamer loop was formed through the MD simulation, which also improved the three-dimensional RNA aptamers model. Clustering analysis was recommended to choose the more representative model.

The revelation of glucose adsorption mechanisms on hierarchical metal-organic frameworks using a surface plasmon resonance sensor.

The gold layer on the surface plasmon resonance (SPR) sensor chip cannot detect small molecules, such as glucose without the use of specific receptors. Metal-organic frameworks (MOFs) are useful in biosensing technologies for capturing and co-localizing enzymes and receptors with the target biomolecule. In many previous studies, the properties of the MOFs were often ignored, with these studies focusing on the selection of appropriate receptors. To take advantage of the unique properties of MOFs in biosensors, one must also consider the technique and transducer used because these aspects will strongly influence the detection mechanism. In this work, we have investigated for the first time, the applications of hierarchical metal-BDC (M-BDC) MOFs for glucose detection using the SPR technique without the use of specific receptors. The underlying interactions and adsorption mechanisms were analyzed using adsorption isotherm and kinetic models. The sensing measurements show that the SPR chips functionalized with M-BDC MOFs exhibit higher sensitivity and lower limit of detection (LOD). Specifically, the sensitivity follows the order of Zr-BDC > Cu-BDC > Mn-BDC > Ni-BDC > bare Au SPR chips with the LOD in the order of Zr-BDC < Mn-BDC < Ni-BDC < Cu-BDC < bare Au SPR chips. The selectivity test results reveal that Zr-BDC exhibits a decent selectivity to glucose in the presence of other interfering compounds, such as ascorbic acid, uric acid, maltose, and urea. These results demonstrate the promising potential of MOFs for SPR biosensing.

Immunoinformatics Study: Multi-Epitope Based Vaccine Design from SARS-CoV-2 Spike Glycoprotein.

The coronavirus disease 2019 outbreak has become a huge challenge in the human sector for the past two years. The coronavirus is capable of mutating at a higher rate than other viruses. Thus, an approach for creating an effective vaccine is still needed to induce antibodies against multiple variants with lower side effects. Currently, there is a lack of research on designing a multiepitope of the COVID-19 spike protein for the Indonesian population with comprehensive immunoinformatic analysis. Therefore, this study aimed to design a multiepitope-based vaccine for the Indonesian population using an immunoinformatic approach. This study was conducted using the SARS-CoV-2 spike glycoprotein sequences from Indonesia that were retrieved from the GISAID database. Three SARS-CoV-2 sequences, with IDs of EIJK-61453, UGM0002, and B.1.1.7 were selected. The CD8+ cytotoxic T-cell lymphocyte (CTL) epitope, CD4+ helper T lymphocyte (HTL) epitope, B-cell epitope, and IFN-γ production were predicted. After modeling the vaccines, molecular docking, molecular dynamics, in silico immune simulations, and plasmid vector design were performed. The designed vaccine is antigenic, non-allergenic, non-toxic, capable of inducing IFN-γ with a population reach of 86.29% in Indonesia, and has good stability during molecular dynamics and immune simulation. Hence, this vaccine model is recommended to be investigated for further study.

CeO2@NH2 functionalized electrodes for the rapid detection of SARS-CoV-2 spike receptor binding domain.

A detection method based on an electrochemical aptasensor has been developed as an alternative fast, portable, simple, inexpensive, and high-accuracy detection method for detecting the SARS-CoV-2 Spike Receptor Binding Domain (spike RBD). The CeO2@NH2 functionalized Screen Printed Carbon Electrode (SPCE) was used to immobilize an aminated aptamer of spike RBD protein via glutaraldehyde as a linker. The aptamer's interaction with the SARS-CoV-2 Spike RBD was measured via the [Fe(CN)6]4-/3- redox system signal. Experimental conditions were optimized using a Box-Behnken experimental design and showed that the optimal conditions of the SARS-CoV-2 aptasensor were 1.5 ng mL-1 of aptamer, immobilization of aptamer for 60 minutes, and Spike RBD incubation for 10 minutes. The developed aptasensor was able to detect the standard SARS-CoV-2 Spike RBD with a detection limit of 0.017 ng mL-1 in the range of 0.001-100 ng mL-1. This aptasensor was used to detect salivary and oropharyngeal swab samples of normal individuals with the addition of Spike RBD, and the recoveries were 92.96% and 96.52%, respectively. The testing on nasopharyngeal swab samples of COVID-19 patients showed that the aptasensor results were comparable with the qRT-PCR results. Thus, the developed aptasensor has the potential to be applied as a SARS-CoV-2 rapid test method for clinical samples.

Development of a Single-Chain Variable Fragment of CR3022 for a Plasmonic-Based Biosensor Targeting the SARS-CoV-2 Spike Protein.

Two years after SARS-CoV-2 caused the first case of COVID-19, we are now in the "new normal" period, where people's activity has bounced back, followed by the easing of travel policy restrictions. The lesson learned is that the wide availability of accurate and rapid testing procedures is crucial to overcome possible outbreaks in the future. Therefore, many laboratories worldwide have been racing to develop a new point-of-care diagnostic test. To aid continuous innovation, we developed a plasmonic-based biosensor designed explicitly for portable Surface Plasmon Resonance (SPR). In this study, we designed a single chain variable fragment (scFv) from the CR3022 antibody with a particular linker that inserted a cysteine residue at the second position. It caused the linker to have a strong affinity to the gold surface through thiol-coupling and possibly become a ready-to-use bioreceptor toward a portable SPR gold chip without purification steps. The theoretical affinity of this scFv on spike protein was -64.7 kcal/mol, computed using the Molecular Mechanics Generalized Born Surface Area (MM/GBSA) method from the 100 ns molecular dynamics trajectory. Furthermore, the scFv was produced in Escherichia coli BL21 (DE3) as a soluble protein. The binding activity toward Spike Receptor Binding Domain (RBD) SARS-CoV-2 was confirmed with a spot-test, and the experimental binding free energy of -10.82 kcal/mol was determined using portable SPR spectroscopy. We hope this study will be useful in designing specific and low-cost bioreceptors, particularly early in an outbreak when the information on antibody capture is still limited.

Simulation of Laser-Heating and Energetic Plasma Plume Expansion in Pulsed Laser Deposition of Y3Fe5O12.

In the present study, numerically iterative models are employed to study two processes involved in the pulsed laser deposition of an Y3Fe5O12 target. The 1D conduction heat model is used to evaluate the temperature of the target irradiated by a nano-second pulse laser, taking into account the plasma shielding effect. Further, the gas dynamics model is employed to simulate the kinetic of plasma plume expansion. The results may be important in obtaining high-quality Y3Fe5O12 thin films.

Facile and controllable synthesis of monodisperse gold nanoparticle bipyramid for electrochemical dopamine sensor.

We demonstrated potential features of gold nanoparticle bipyramid (AuNB) for an electrochemical biosensor. The facile synthesis method and controllable shape and size of the AuNB are achieved through the optimization of cetyltrimethylammonium chloride (CTAC) surfactant over citric acid (CA) ratio determining the control of typically spherical Au seed size and its transition into a penta-twinned crystal structure. We observe that the optimized ratio of CTAC and CA facilitates flocculation control in which Au seeds with size as tiny as ∼14.8 nm could be attained and finally transformed into AuNB structures with an average length of ∼55 nm with high reproducibility. To improve the electrochemical sensing performance of a screen-printed carbon electrode, surface modification with AuNB via distinctive linking procedures effectively enhanced the electroactive surface area by 40%. Carried out for the detection of dopamine, a neurotransmitter frequently linked to the risk of Parkinson's, Alzheimer's, and Huntington's diseases, the AuNB decorated-carbon electrode shows outstanding electrocatalytic activity that improves sensing performance, including high sensitivity, low detection limit, wide dynamic range, high selectivity against different analytes, such as ascorbic acid, uric acid and urea, and excellent reproducibility.

Versatile and Low-Cost Fabrication of Modular Lock-and-Key Microfluidics for Integrated Connector Mixer Using a Stereolithography 3D Printing.

We present a low-cost and simple method to fabricate a novel lock-and-key mixer microfluidics using an economic stereolithography (SLA) three-dimensional (3D) printer, which costs less than USD 400 for the investment. The proposed study is promising for a high throughput fabrication module, typically limited by conventional microfluidics fabrications, such as photolithography and polymer-casting methods. We demonstrate the novel modular lock-and-key mixer for the connector and its chamber modules with optimized parameters, such as exposure condition and printing orientation. In addition, the optimization of post-processing was performed to investigate the reliability of the fabricated hollow structures, which are fundamental to creating a fluidic channel or chamber. We found out that by using an inexpensive 3D printer, the fabricated resolution can be pushed down to 850 µm and 550 µm size for squared- and circled-shapes, respectively, by the gradual hollow structure, applying vertical printing orientation. These strategies opened up the possibility of developing straightforward microfluidics platforms that could replace conventional microfluidics mold fabrication methods, such as photolithography and milling, which are costly and time consuming. Considerably cheap commercial resin and its tiny volume employed for a single printing procedure significantly cut down the estimated fabrication cost to less than 50 cents USD/module. The simulation study unravels the prominent properties of the fabricated devices for biological fluid mixers, such as PBS, urine and plasma blood. This study is eminently prospective toward microfluidics application in clinical biosensing, where disposable, low-cost, high-throughput, and reproducible chips are highly required.

Metal-Organic-Framework FeBDC-Derived Fe3O4 for Non-Enzymatic Electrochemical Detection of Glucose.

Present-day science indicates that developing sensors with excellent sensitivity and selectivity for detecting early signs of diseases is highly desirable. Electrochemical sensors offer a method for detecting diseases that are simpler, faster, and more accurate than conventional laboratory analysis methods. Primarily, exploiting non-noble-metal nanomaterials with excellent conductivity and large surface area is still an area of active research due to its highly sensitive and selective catalysts for electrochemical detection in enzyme-free sensors. In this research, we successfully fabricate Metal-Organic Framework (MOF) FeBDC-derived Fe3O4 for non-enzymatic electrochemical detection of glucose. FeBDC synthesis was carried out using the solvothermal method. FeCl2.4H2O and Benzene-1,4-dicarboxylic acid (H2BDC) are used as precursors to form FeBDC. The materials were further characterized utilizing X-ray Powder Diffraction (XRD), Scanning Electron Microscopy (SEM), and Fourier-Transform Infrared Spectroscopy (FTIR). The resulting MOF yields good crystallinity and micro-rod like morphology. Electrochemical properties were tested using Cyclic Voltammetry (CV) and Differential Pulse Voltammetry (DPV) with a 0.1 M of Phosphate Buffer Saline (PBS pH 7.4) solution as the supporting electrolyte. The measurement results show the reduction and oxidation peaks in the CV curve of FeBDC, as well as Fe3O4. Pyrolysis of FeBDC to Fe3O4 increases the peak of oxidation and reduction currents. The Fe3O4 sample obtained has a sensitivity of 4.67 µA mM-1.cm-2, a linear range between 0.0 to 9.0 mM, and a glucose detection limit of 15.70 µM.