Exploring single-molecule interactions: heparin and FGF-1 proteins through solid-state nanopores.

Detection and characterization of protein-protein interactions are essential for many cellular processes, such as cell growth, tissue repair, drug delivery, and other physiological functions. In our research, we have utilized emerging solid-state nanopore sensing technology, which is highly sensitive to better understand heparin and fibroblast growth factor 1 (FGF-1) protein interactions at a single-molecule level without any modifications. Understanding the structure and behavior of heparin-FGF-1 complexes at the single-molecule level is very important. An abnormality in their formation can lead to life-threatening conditions like tumor growth, fibrosis, and neurological disorders. Using a controlled dielectric breakdown pore fabrication approach, we have characterized individual heparin and FGF-1 (one of the 22 known FGFs in humans) proteins through the fabrication of 17 ± 1 nm nanopores. Compared to heparin, the positively charged heparin-binding domains of some FGF-1 proteins translocationally react with the pore walls, giving rise to a distinguishable second peak with higher current blockade. Additionally, we have confirmed that the dynamic FGF-1 is stabilized upon binding with heparin-FGF-1 at the single-molecule level. The larger current blockades from the complexes relative to individual heparin and the FGF-1 recorded during the translocation ensure the binding of heparin-FGF-1 proteins, forming binding complexes with higher excluded volumes. Taken together, we demonstrate that solid-state nanopores can be employed to investigate the properties of individual proteins and their complex interactions, potentially paving the way for innovative medical therapies and advancements.

A non-FRET DNA reporter that changes fluorescence colour upon nuclease digestion.

Fluorescence resonance energy transfer (FRET) reporters are commonly used in the final stages of nucleic acid amplification tests to indicate the presence of nucleic acid targets, where fluorescence is restored by nucleases that cleave the FRET reporters. However, the need for dual labelling and purification during manufacturing contributes to the high cost of FRET reporters. Here we demonstrate a low-cost silver nanocluster reporter that does not rely on FRET as the on/off switching mechanism, but rather on a cluster transformation process that leads to fluorescence color change upon nuclease digestion. Notably, a 90 nm red shift in emission is observed upon reporter cleavage, a result unattainable by a simple donor-quencher FRET reporter. Electrospray ionization-mass spectrometry results suggest that the stoichiometric change of the silver nanoclusters from Ag13 (in the intact DNA host) to Ag10 (in the fragments) is probably responsible for the emission colour change observed after reporter digestion. Our results demonstrate that DNA-templated silver nanocluster probes can be versatile reporters for detecting nuclease activities and provide insights into the interactions between nucleases and metallo-DNA nanomaterials.

Real-time monitoring of Ti(IV) metal ion binding of transferrin using a solid-state nanopore.

Transferrin, a central player in iron transport, has been recognized not only for its role in binding iron but also for its interaction with other metals, including titanium. This study employs solid-state nanopores to investigate the binding of titanium ions [Ti(IV)] to transferrin in a single-molecule and label-free manner. We demonstrate the novel application of solid-state nanopores for single-molecule discrimination between apo-transferrin (metal-free) and Ti(IV)-transferrin. Despite their similar sizes, Ti(IV)-transferrin exhibits a reduced current drop, attributed to differences in translocation times and filter characteristics. Single-molecule analysis reveals Ti(IV)-transferrin's enhanced stability and faster translocations due to its distinct conformational flexibility compared to apo-transferrin. Furthermore, our study showcases solid-state nanopores as real-time monitors of biochemical reactions, tracking the gradual conversion of apo-transferrin to Ti(IV)-transferrin upon the addition of titanium citrate. This work offers insights into Ti(IV) binding to transferrin, promising applications for single-molecule analysis and expanding our comprehension of metal-protein interactions at the molecular level.

Cluster-Enhanced Nanopore Sensing of Ovarian Cancer Marker Peptides in Urine.

The development of novel methodologies that can detect biomarkers from cancer or other diseases is both a challenge and a need for clinical applications. This partly motivates efforts related to nanopore-based peptide sensing. Recent work has focused on the use of gold nanoparticles for selective detection of cysteine-containing peptides. Specifically, tiopronin-capped gold nanoparticles, trapped in the cis-side of a wild-type α-hemolysin nanopore, provide a suitable anchor for the attachment of cysteine-containing peptides. It was recently shown that the attachment of these peptides onto a nanoparticle yields unique current signatures that can be used to identify the peptide. In this article, we apply this technique to the detection of ovarian cancer marker peptides ranging in length from 8 to 23 amino acid residues. It is found that sequence variability complicates the detection of low-molecular-weight peptides (<10 amino acid residues), but higher-molecular-weight peptides yield complex, high-frequency current fluctuations. These fluctuations are characterized with chi-squared and autocorrelation analyses that yield significantly improved selectivity when compared to traditional open-pore analysis. We demonstrate that the technique is capable of detecting the only two cysteine-containing peptides from LRG-1, an emerging protein biomarker, that are uniquely present in the urine of ovarian cancer patients. We further demonstrate the detection of one of these LRG-1 peptides spiked into a sample of human female urine.

Serial estimations of serum albumin levels as a prognostic marker in critically ill patients admitted in ICU in tertiary center: An observational study.

Critical illness is a severe condition that poses a significant threat to multiple organ systems and can lead to substantial morbidity and mortality. Serum albumin concentration can serve as an independent predictor of mortality risk in critically ill patients. This study aimed to determine the role of serial monitoring of serum albumin (SA) levels as a prognostic marker of mortality and morbidity. This observational prospective study was conducted at a tertiary hospital over a period from January 1, 2020, to December 31, 2020, among critically ill patients admitted to the intensive care unit. Data collection was performed using a prestructured proforma. Statistical analysis was carried out using Statistical Package for the Social Sciences software version 23, employing appropriate tests. The P-value <.05 was considered statistically significant. The study included 78 patients with 59 (75.6%) were survivors, and 19 (24.4%) were non-survivors. Mean SA levels did not significantly differ between non-survivors (3.30 ±â€…0.40 g/dL) and survivors (3.42 ±â€…0.35 g/dL) on admission (day 1) (P = .234). However, on day 3, non-survivors had significantly lower levels (3.02 ±â€…0.46 g/dL) compared to survivors (3.31 ±â€…0.29 g/dL) (P = .001). This trend continued on day 5, with non-survivors having significantly lower levels (2.92 ±â€…0.30 g/dL) compared to survivors (3.31 ±â€…0.33 g/dL) (P = .003). The decline in SA levels from day 1 to day 3 and from day 1 to day 5 was statistically significant in non-survivors (P = .001). In survivors, a significant decline was observed from day 1 to day 3 (P = .019), while the decline from day 1 to day 5 was not statistically significant (P = .074). Serial estimation of SA levels in critically ill patients can serve as a valuable prognostic marker, aiding in the identification of individuals at a higher risk of mortality and morbidity.

Hole and Electron Doping Outcomes in Bi2YO4Cl.

Recognizing the deficiency in the hole and electron doping outcomes in layered bismuth-based oxyhalides intergrowths, the current study was addressed to the doping of Ca2+ and Zr4+ for Y3+ in Bi2YO4Cl. The samples were rapidly synthesized by a sol-gel auto combustion method and characterized extensively. Up to 30 mol % Y could be substituted with Ca in tetragonal symmetry and without the appearance of any additional phase. The unit cell parameters varied nonlinearly with the elongation of the Y-O bond. The Raman spectra supported the local site distortion. The calcium-substituted samples displayed selected area electron diffraction characteristics similar to those of Bi2YO4Cl. A blueshift of the absorption edge was noticed with increasing calcium content yielding optical band gap values in the 2.40-2.57 eV range. The creation of 10% Bi5+ in Bi2Y0.70Ca0.30O4Cl was established with the help of XPS measurements and redox titrations. The higher reactivity of Bi5+ in an aqueous solution has been demonstrated for the oxidation of As(III) to As(V). Electron doping through Zr4+ incorporation was possible up to 30 mol % in Bi2YO4Cl. The Y-O bonds are contracted, and the Bi-O bonds are elongated with increasing Zr4+ content. Zr4+'s incorporation induced a local distortion. The color of the sample changed from bright yellow to deep yellow with Zr inclusion, resulting in a progressive decrease in optical band gap values. The introduction of electrons caused the reduction of 13.6% of Bi(III) to Bi(0). These results have established the vulnerability of Bi2O2 chains to charge carriers in Bi2YO4Cl. Density functional theory (DFT) calculations were implemented to understand the electronic and optical properties of the pristine and doped compounds. From the band structure calculations, the chosen compounds were found to be indirect band gap semiconductors. The results of the DFT calculations were in good agreement with the experiment; however, for the doped cases, virtual crystal approximation has been used considering uniform doping at the Y-site.

CoTe2 : A Quantum Critical Dirac Metal with Strong Spin Fluctuations.

Quantum critical points separating weak ferromagnetic and paramagnetic phases trigger many novel phenomena. Dynamical spin fluctuations not only suppress the long-range order, but can also lead to unusual transport and even superconductivity. Combining quantum criticality with topological electronic properties presents a rare and unique opportunity. Here, by means of ab initio calculations and magnetic, thermal, and transport measurements, it is shown that the orthorhombic CoTe2 is close to ferromagnetism, which appears suppressed by spin fluctuations. Calculations and transport measurements reveal nodal Dirac lines, making it a rare combination of proximity to quantum criticality and Dirac topology.

Identification of potential human pancreatic α-amylase inhibitors from natural products by molecular docking, MM/GBSA calculations, MD simulations, and ADMET analysis.

Human pancreatic α-amylase (HPA), which works as a catalyst for carbohydrate hydrolysis, is one of the viable targets to control type 2 diabetes. The inhibition of α-amylase lowers blood glucose levels and helps to alleviate hyperglycemia complications. Herein, we systematically screened the potential HPA inhibitors from a library of natural products by molecular modeling. The modeling encompasses molecular docking, MM/GBSA binding energy calculations, MD simulations, and ADMET analysis. This research identified newboulaside B, newboulaside A, quercetin-3-O-ß-glucoside, and sasastilboside A as the top four potential HPA inhibitors from the library of natural products, whose Glide docking scores and MM/GBSA binding energies range from -9.191 to -11.366 kcal/mol and -19.38 to -77.95 kcal/mol, respectively. Based on the simulation, among them, newboulaside B was found as the best HPA inhibitor. Throughout the simulation, with the deviation of 3Å (acarbose = 3Å), it interacted with ASP356, ASP300, ASP197, THR163, ARG161, ASP147, ALA106, and GLN63 via hydrogen bonding. Additionally, the comprehensive ADMET analysis revealed that it has good pharmacokinetic properties having not acutely toxic, moderately bioavailable, and non-inhibitor nature toward cytochrome P450. All the results suggest that newboulaside B might be a promising candidate for drug discovery against type 2 diabetes.

Engineering of Hydrogenated (6,0) Single-Walled Carbon Nanotube under Applied Uniaxial Stress: A DFT-1/2 and Molecular Dynamics Study.

Herein, we systematically studied the electronic, optical, and mechanical properties of a hydrogenated (6,0) single-walled carbon nanotube [(6,0) h-SWCNT] under applied uniaxial stress from first-principles density functional theory (DFT) and molecular dynamics (MD) simulation. We have applied the uniaxial stress range from -18 to 22 GPa on the (6,0) h-SWCNT (- sign indicates compressive and + indicates tensile stress) along the tube axes. Our system was found to be an indirect semiconductor (Γ-Δ), with a band gap value of ∼0.77 eV within the linear combination of atomic orbitals (LCAO) method using a GGA-1/2 exchange-correlation approximation. The band gap for (6,0) h-SWCNT significantly varies with the application of stress. The indirect to direct band gap transition was observed under compressive stress (-14 GPa). The strained (6,0) h-SWCNT showed a strong optical absorption in the infrared region. Application of external stress enhanced the optically active region from infrared to Vis with maximum intensity within the Vis-IR region, making it a promising candidate for optoelectronic devices. Ab initio molecular dynamics (AIMD) simulation has been used to study the elastic properties of the (6,0) h-SWCNT which has a strong influence under applied stress.

A Comparison of the Spot Urine Protein-Creatinine Ratio with 24-h Urinary Protein for Quantification of Proteinuria: A Hospital-based Cross-sectional Study.

Quantifying the amount of proteinuria is mandatory in various disease conditions. The aim of this study was to study whether the spot urine protein-creatinine ratio (P-CR) correlates well with 24-h urinary total protein (UTP). The research hypothesis was that spot urine P-CR would correlate well with 24-h UTP. This was a cross-sectional, single-center study conducted in a tertiary care hospital. The spot urinary P-CR and 24-h urinary protein were determined from 70 patients with persistent glomerular proteinuria. This study included Nepalese patients aged 2-83 years, with a mean age of 36.56 years (standard deviation: 20.78). The number of males was slightly higher than females, and the male-female ratio was 1.26:1. Hypertension was present in 44.3% of patients, diabetes was present in 20% of patients, 74.3% of patients were suffering from acute glomerulonephritis with various causes, and 12.9% of patients had chronic kidney disease. A linear relationship existed between the spot urine P-CR and the 24-h UTP, with a correlation coefficient of 0.877 (P <0.01). The correlation was suboptimal at higher levels of protein excretion (>3.5 g/day). Random spot urine P-CR correlated well with the 24-h UTP, particularly at lower levels of protein excretion.

Selective Detection and Characterization of Small Cysteine-Containing Peptides with Cluster-Modified Nanopore Sensing.

It was recently demonstrated that one can monitor ligand-induced structure fluctuations of individual thiolate-capped gold nanoclusters using resistive-pulse nanopore sensing. The magnitude of the fluctuations scales with the size of the capping ligand, and it was later shown one can observe ligand exchange in this nanopore setup. We expand on these results by exploring the different types of current fluctuations associated with peptide ligands attaching to tiopronin-capped gold nanoclusters. We show here that the fluctuations can be used to identify the attaching peptide through either the magnitude of the peptide-induced current jumps or the onset of high-frequency current fluctuations. Importantly, the peptide attachment process requires that the peptide contains a cysteine residue. This suggests that nanopore-based monitoring of peptide attachments with thiolate-capped clusters could provide a means for selective detection of cysteine-containing peptides. Finally, we demonstrate the cluster-based protocol with various peptide mixtures to show that one can identify more than one cysteine-containing peptide in a mixture.

Structural stability, electronic, optical, and thermoelectric properties of layered perovskite Bi2LaO4I.

Layered perovskites are an interesting class of materials due to their possible applications in microelectronics and optoelectronics. Here, by means of density functional theory calculations, we investigated the structural, elastic, electronic, optical, and thermoelectric properties of the layered perovskite Bi2LaO4I within the parametrization of the standard generalized gradient approximation (GGA). The transport coefficients were evaluated by adopting Boltzmann semi-classical theory and a collision time approach. The calculated elastic constants were found to satisfy the Born criteria, indicating that Bi2LaO4I is mechanically stable. Taking into account spin-orbit coupling (SOC), the material was found to be a non-magnetic insulator, with an energy bandgap of 0.82 eV (within GGA+SOC), and 1.85 eV (within GGA+mBJ+SOC). The optical-property calculations showed this material to be optically active in the visible and ultraviolet regions, and that it may be a candidate for use in optoelectronic devices. Furthermore, this material is predicted to be a potential candidate for use in thermoelectric devices due to its large value of power factor, ranging from 2811 to 7326 µW m-1 K-2, corresponding to a temperature range of 300 K to 800 K.

Rhodium-based half-Heusler alloys as thermoelectric materials.

Thermoelectric phenomena provide an alternative for power generation and refrigeration, which could be the best solution to the energy crisis by utilizing waste heat energy in the near future. In this study, we have investigated the structural, elastic, electronic, and thermoelectric properties of 18-valence electron count rhodium-based half-Heusler alloys focusing on RhTiP, RhTiAs, RhTiSb, and RhTiBi. The non-existence of imaginary frequencies in the phonon dispersion curve for these systems verifies that they are structurally stable. RhTiP is ductile, while others are brittle. The alloys are semiconducting with indirect band gaps ranging from 0.94 to 1.01 eV. While considering thermoelectricity, we discovered that p-type doping is more favorable in improving the thermoelectric properties. The calculated power factor values with p-type doping are comparable to some of the reported half-Heusler materials. The optimum figure of merit ZT is ∼1 for RhTiBi, and in between ∼(0.38-0.67) for RhTiP, RhTiAs, and RhTiSb. The low thermal conductivities and sufficiently large value of power factor of these alloys suggest that they are promising thermoelectric materials for use in thermoelectric applications.

Nanopore Analysis as a Tool for Studying Rapid Holliday Junction Dynamics and Analyte Binding.

Holliday junctions (HJs) are an important class of nucleic acid structure utilized in DNA break repair processes. As such, these structures have great importance as therapeutic targets and for understanding the onset and development of various diseases. Single-molecule fluorescence resonance energy transfer (smFRET) has been used to study HJ structure-fluctuation kinetics, but given the rapid time scales associated with these kinetics (approximately sub-milliseconds) and the limited bandwidth of smFRET, these studies typically require one to slow down the structure fluctuations using divalent ions (e.g., Mg2+). This modification limits the ability to understand and model the underlying kinetics associated with HJ fluctuations. We address this here by utilizing nanopore sensing in a gating configuration to monitor DNA structure fluctuations without divalent ions. A nanopore analysis shows that HJ fluctuations occur on the order of 0.1-10 ms and that the HJ remains locked in a single conformation with short-lived transitions to a second conformation. It is not clear what role the nanopore plays in affecting these kinetics, but the time scales observed indicate that HJs are capable of undergoing rapid transitions that are not detectable with lower bandwidth measurement techniques. In addition to monitoring rapid HJ fluctuations, we also report on the use of nanopore sensing to develop a highly selective sensor capable of clear and rapid detection of short oligo DNA strands that bind to various HJ targets.

Determination of Cleavage Energy and Efficient Nanostructuring of Layered Materials by Atomic Force Microscopy.

A method is presented to use atomic force microscopy to measure the cleavage energy of van der Waals materials and similar quasi-two-dimensional materials. The cleavage energy of graphite is measured to be 0.36 J/m2, in good agreement with literature data. The same method yields a cleavage energy of 0.6 J/m2 for MoS2 as a representative of the dichalcogenides. In the case of the weak topological insulator Bi14Rh3I9 no cleavage energy is obtained, although cleavage is successful with an adapted approach. The cleavage energies of these materials are evaluated by means of density-functional calculations and literature data. This further validates the presented method and sets an upper limit of about 0.7 J/m2 to the cleavage energy that can be measured by the present setup. In addition, this method can be used as a tool for manipulating exfoliated flakes, prior to or after contacting, which may open a new route for the fabrication of nanostructures.

Evaluation of SARS-CoV-2 main protease and inhibitor interactions using dihedral angle distributions and radial distribution function.

In order to evaluate the interactions between a potential drug candidate like inhibitor N3 and the residues in substrate binding site of SARS-CoV-2 main protease ( M pro ), we used molecular docking and dynamics simulations. The structural features describing the degrees of folding states of M pro formed by beta-barrels and alpha-helices were analyzed by means of root mean square deviation, root mean square fluctuation, radius of gyration, residue velocity, H-bonding, dihedral angle distributions and radial distribution function. All of the residues forming ligand binding domain (LBD) of M pro lie within the allowed region of the dihedral angle distributions as observed from the equilibrating best pose of M pro -N3 system. Sharp peaks of radial distribution function (RDF) for H-bonding atom pairs (about 2 Å radial distance apart) describe the strong interactions between inhibitor and SARS-CoV-2 M pro . During MD simulations, HSE163 has the lowest residue speed offering a sharp RDF peak whereas GLN192 has the highest residue speed resulting a flat RDF peak for the H-bonding atom pairs of M pro -N3 system. Along with negative values of coulombic and Lenard-Jones energies, MM/PBSA free energy of binding contributed by the non-covalent interactions between M pro and N3 has been obtained to be -19.45 ± 3.6 kcal/mol. These physical parameters demonstrate the binding nature of an inhibitor in M pro -LBD. This study will be helpful in evaluating the drug candidates which are expected to inhibit the SARS-CoV-2 structural proteins.

Prevalence of Newly Diagnosed End-Stage Renal Disease Patients in a Tertiary Hospital of Central Nepal, Chitwan: A Descriptive Cross-sectional Study.

INTRODUCTION: End-stage renal disease patients are in rising trend globally, and they have been found to occur predominantly in developing countries. Many studies have been published before, within and across the countries, to know the clinicodemographic profile of end-stage renal disease patients. However, no such studies were done in Chitwan, Nepal. This study's main objective was to find the prevalence of newly diagnosed end-stage renal disease patients. METHODS: A hospital-based descriptive cross-sectional study was carried out in the Department of Nephrology from May 2016 to April 2019. Convenient sampling was done, and all the consecutive new end-stage renal disease patients were included in the study. The ethical approval was taken from the Institutional Review Committee (reference number. 2016/COMSTH/IRC/042). The prevalence and demographic profile of new end-stage renal disease patients were studied. The data were analyzed with appropriate statistical tools. RESULTS: A total of 250 new end-stage renal disease patients were found among 2200 admitted patients. The prevalence of new end-stage renal disease was found to be 250 (11.36%). Out of 250 patients, males were 156 (62.4%), and females were 94 (37.6%). The mean age was 49.6±15.5 years. The commonest cause of the incident end-stage renal disease was Type 2 Diabetes mellitus 89 (35.6%). CONCLUSIONS: The prevalence of new end-stage renal disease was found to be quite high. The commonest cause of the incident end-stage renal disease was Type 2 Diabetes Mellitus.

Evidence of two-dimensional flat band at the surface of antiferromagnetic kagome metal FeSn.

The kagome lattice has long been regarded as a theoretical framework that connects lattice geometry to unusual singularities in electronic structure. Transition metal kagome compounds have been recently identified as a promising material platform to investigate the long-sought electronic flat band. Here we report the signature of a two-dimensional flat band at the surface of antiferromagnetic kagome metal FeSn by means of planar tunneling spectroscopy. Employing a Schottky heterointerface of FeSn and an n-type semiconductor Nb-doped SrTiO3, we observe an anomalous enhancement in tunneling conductance within a finite energy range of FeSn. Our first-principles calculations show this is consistent with a spin-polarized flat band localized at the ferromagnetic kagome layer at the Schottky interface. The spectroscopic capability to characterize the electronic structure of a kagome compound at a thin film heterointerface will provide a unique opportunity to probe flat band induced phenomena in an energy-resolved fashion with simultaneous electrical tuning of its properties. Furthermore, the exotic surface state discussed herein is expected to manifest as peculiar spin-orbit torque signals in heterostructure-based spintronic devices.

Nanopore sensing: A physical-chemical approach.

Protein nanopores have emerged as an important class of sensors for the understanding of biophysical processes, such as molecular transport across membranes, and for the detection and characterization of biopolymers. Here, we trace the development of these sensors from the Coulter counter and squid axon studies to the modern applications including exquisite detection of small volume changes and molecular reactions at the single molecule (or reactant) scale. This review focuses on the chemistry of biological pores, and how that influences the physical chemistry of molecular detection.

Spin reorientation in antiferromagnetic Dy2FeCoO6 double perovskite.

We explored the electronic and magnetic properties of the lanthanide double perovskite Dy2FeCoO6 by combining magnetization, Raman and Mössbauer spectroscopy and neutron diffraction along with density functional theory (DFT) calculations. Our magnetization measurements revealed two magnetic phase transitions in Dy2FeCoO6. First, a paramagnetic to antiferromagnetic transition at T N = 248 K and subsequently, a spin reorientation transition at T SR = 86 K. In addition, a field-induced magnetic phase transition with a critical field of H c ≈ 20 kOe is seen at 2 K. Neutron diffraction data suggested cation-disordered orthorhombic structure for Dy2FeCoO6 in Pnma space group which is supported by Raman scattering results. The magnetic structures ascertained through representational analysis indicate that at T N, a paramagnetic state is transformed to Γ5(Cx, Fy, Az) antiferromagnetic structure while, at T SR, Fe/Co moments undergo a spin reorientation to Γ3(Gx, Ay, Fz). The refined magnetic moment of (Fe/Co) is 1.47(4) µ B at 7 K. The antiferromagnetic structure found experimentally is supported through the DFT calculations which predict an insulating electronic state in Dy2FeCoO6.