Real-time analysis of the biomolecular interaction between gelsolin and Aß1-42 monomer and its implication for Alzheimer's disease.

Biomolecular interaction acts a pivotal part in understanding the mechanisms underlying the development of Alzheimer's disease (AD). Herein, we built a biosensing platform to explore the interaction between gelsolin (GSN) and different ß-amyloid protein 1-42 (Aß1-42) species, including Aß1-42 monomer (m-Aß), Aß1-42 oligomers with both low and high levels of aggregation (LLo-Aß and HLo-Aß) via dual polarization interferometry (DPI). Real-time molecular interaction process and kinetic analysis showed that m-Aß had the strongest affinity and specificity with GSN compared with LLo-Aß and HLo-Aß. The impact of GSN on inhibiting aggregation of Aß1-42 and solubilizing Aß1-42 aggregates was evaluated by circular dichroism (CD) spectroscopy. The maintenance of random coil structure of m-Aß and the reversal of ß-sheet structure in HLo-Aß were observed, demonstrating the beneficial effects of GSN on preventing Aß from aggregation. In addition, the structure of m-Aß/GSN complex was analyzed in detail by molecular dynamics (MD) simulation and molecular docking. The specific binding sites and crucial intermolecular forces were identified, which are believed to stabilize m-Aß in its soluble state and to inhibit the fibrilization of Aß1-42. Combined theoretical simulations and experiment results, we speculate that the success of GSN sequestration mechanism and the balance of GSN levels in cerebrospinal fluid and plasma of AD subjects may contribute to a delay in AD progression. This research not only unveils the molecular basis of the interaction between GSN and Aß1-42, but also provides clues to understanding the crucial functions of GSN in AD and drives the development of AD drugs and therapeutic approaches.

Expansivity of Fused Quartz Glass Measured Within 6 × 10-10 K-1.

A method is described to measure the thermal expansion coefficient of fused quartz glass. The measurement principle is to monitor the change in resonance frequency of a Fabry-Perot cavity as its temperature changes; the Fabry-Perot cavity is made from fused quartz glass. The standard uncertainty in the measurement was less than 0.6 (nm·m-1)·K-1, or 0.15 %. The limit on performance is arguably uncertainty in the reflection phase-shift temperature dependence, because neither thermooptic nor thermal expansion coefficients of thin-film coatings are reliably known. However, several other uncertainty contributors are at the same level of magnitude, and so any improvement in performance would entail significant effort. Furthermore, measurements of three different samples revealed that material inhomogeneity leads to differences in the effective thermal expansion coefficient of fused quartz; inhomogeneity in thermal expansion among samples is 24 times larger than the measurement uncertainty in a single sample.

A spectroscopic study on the Amyloid-ß interaction with clicked peptide-porphyrin conjugates: a vision toward the detection of Aß peptides in aqueous solution.

Alzheimer's disease (AD) is a multifactorial form of dementia mainly affecting people in the elderly, but no effective cure is available. According to the amyloid hypothesis the aggregation of Amyloid-ß (Aß) into oligomeric toxic species is believed to concur with the onset and progression of the disease heavily. By using a click chemistry approach, we conjugated a suitable designed peptide sequence to a metalloporphyrin moiety to obtain three hybrid peptide systems to be studied for their interact ion with Amyloid-ß peptides. The aim is to get new tools for the diagnosis and therapy in AD. The results described in this study, which were obtained through spectroscopic techniques (UV-Vis, CD, Bis-Ans and intrinsic porphyrin Fluorescence), Microfluidics (GCI) and cell biology (MTT, Live cell imaging and flow cytometry), reveal interesting features about the structure-activity relationships connecting these conjugates with the interaction with Aß, as well as on their potential use as sensing systems. In our opinion the data reported in this paper make the porphyrin-peptide conjugates highly compelling for further exploration as spectroscopic probes to detect Aß biomarkers in biological fluids.

Double-layer optical fiber interferometer with bio-layer-modified reflector for label-free biosensing of inflammatory proteins.

This work discusses label-free biosensing application of a double-layer optical fiber interferometer where the second layer tailors the reflection conditions at the external plain and supports changes in reflected optical spectrum when a bio-layer binds to it. The double-layer nanostructure consists of precisely tailored thin films, i.e., titanium (TiO2) and hafnium oxides (HfO2) deposited on single-mode fiber end-face by magnetron sputtering. It has been shown numerically and experimentally that the approach besides well spectrally defined interference pattern distinguishes refractive index (RI) changes taking place in a volume and on the sensor surface. These are of interest when label-free biosensing applications are considered. The case of myeloperoxidase (MPO) detection-a protein, which concentration rises during inflammation-is reported as an example of application. The response of the sensor to MPO in a concentration range of 1 × 10-11-5 × 10-6 g/mL was tested. An increase in the MPO concentration was followed by a redshift of the interference pattern and a decrease in reflected power. The negative control performed using ferritin proved specificity of the sensor. The results reported in this work indicate capability of the approach for diagnostic label-free biosensing, possibly also at in vivo conditions.

Characterization of PARP1 binding to c-KIT1 G-quadruplex DNA: Insights into domain-specific interactions.

Poly(ADP-ribose) polymerase 1 (PARP1) is a nuclear enzyme involved in catalyzing Poly-(ADP-ribosyl)ation. PARP1 binds to different forms of DNA and DNA breaks and thus plays important roles in several cellular processes, including DNA damage repair, cell cycle regulation, chromatin remodeling, and maintaining genomic stability. In this study, we conducted biochemical and biophysical characterization of PARP1 binding to G-quadruplex DNA (G4-DNA). Our investigation identified ZnF1, ZnF3, and WGR as the critical domains to mediate PARP1 binding to G4-c-KIT1. Also, our results show that these domains together show cooperativity for G4-c-KIT1 recognition. Further, we establish that the presence of an oxidized (5-carboxylcytosine) base in the loop region of G4-c-KIT1 (G4-5caC-cKIT1) does not affect its recognition by PARP1. Both G4-c-KIT1 and G4-5caC-cKIT1 are potent stimulators of PARP1's catalytic activity. Our study advances the understanding of PARP1's versatile DNA binding capabilities for G4-c-KIT1 DNA irrespective of the oxidation/ modification in the DNA base. These insights into PARP1's domain-specific contributions to G4-c-KIT1 DNA recognition and catalysis expand our knowledge of its multifaceted roles in DNA repair and genome maintenance.

Precursor-film-driven ultra-early depinning of the three-phase contact line.

HYPOTHESIS: Despite its importance in colloid and interface science, contact line pinning remains poorly understood, especially in the presence of a precursor film. We hypothesized that this is due to a lack of an experimental method capable of directly observing their physics at the nanoscale. METHODS: Using coherence scanning interferometry, we visualized the three-dimensional behavior of contact lines with a precursor film near a nanogroove structure composed of flat terrace surfaces and steps with an inclination angle of 30° while achieving nanoscale vertical resolution. FINDINGS: We found that even when the contact line is pinned at the edge of the step, the precursor film is not and advances beyond the edge. Furthermore, we discovered that the precursor film has two distinct effects on contact line motion. Specifically, the precursor film facilitates depinning when the contact line descends the step - a contact angle change was 0.9°, only 3.0% of the value predicted by a classical theory of contact angle at a solid edge. This ultra-early depinning is attributed to the formation of a new liquid film past the edge, driven by the progression of the precursor film that overcomes the pinning effect. In contrast, when the contact line ascends the step, the precursor film acts as a resistance to movement due to steric interaction.

Systematic design and evaluation of aptamers for VEGF and PlGF biomarkers of Preeclampsia.

Preeclampsia is a potentially life-threatening condition for both mother and baby, characterized by hypertension and potential organ damage. Early diagnosis is crucial to mitigate its adverse health effects. Traditional diagnostic methods, which focus on late-manifesting symptoms like hypertension and proteinuria, underscore the need for molecular diagnostic approaches for timely detection. This study successfully designs and evaluates novel aptamers with high specificity and affinity for Vascular Endothelial Growth Factor (VEGF) and Placental Growth Factor (PlGF), biomarkers closely associated with preeclampsia. Using molecular docking, molecular dynamics simulations, and BioLayer Interferometry (BLI), we identified aptamers that demonstrated strong binding affinities, comparable or superior to traditional antibodies. Our findings suggest that these aptamers have the potential to be integrated into cost-effective, point-of-care diagnostic tools, significantly improving early detection and intervention strategies for preeclampsia. The robust performance of these aptamers marks a pivotal step toward the development of more reliable and accessible diagnostic solutions, with implications for better maternal and fetal health outcomes.

Development of Biolayer Interferometry (BLI)-Based Double-Stranded RNA Detection Method with Application in mRNA-Based Therapeutics and Vaccines.

Background: In vitro-transcribed (IVT) mRNA has been established as a promising platform for therapeutics and vaccine development. Double-stranded RNA (dsRNA) is a major impurity of IVT mRNA and can trigger unfavored immune responses, potentially causing adverse events in patients. Existing dsRNA detection and quantitation methods, such as gel electrophoresis, ELISA, or homogeneous time-resolved fluorescence (HTRF), have low sensitivity or are time-consuming. A recently published lateral flow immunoassay (LFSA) was shown to be fast, but it lacks the sensitivity for dsRNA with uridine modifications. Methods: In this study, we provided a possible explanation for the reduced sensitivity of existing quantitation methods for dsRNA with modified uridines by characterizing the binding affinities of commonly used anti-dsRNA antibodies. Then, a rapid and sensitive biolayer interferometry (BLI) dsRNA detection assay utilizing Flock House Virus (FHV) B2 protein was developed to overcome the challenges in dsRNA detection and the reduced sensitivity. Results: This assay allows the detection of dsRNA with different uridine modifications (ψ, m1ψ, 5 moU) with similar sensitivity as dsRNA without modification. Furthermore, we demonstrated this method can be used to quantify both short and long dsRNA, as well as hairpin-structured dsRNA, providing a more comprehensive detection for dsRNA impurities. Moreover, we applied this assay to monitor dsRNA removal through a purification process. Conclusions: Taken together, this BLI method could enable real-time monitoring of impurities in IVT mRNA production to prevent immunogenicity stemming from dsRNA.

Biolayer interferometry for adeno-associated virus capsid titer measurement and applications to upstream and downstream process development.

Faster and more accurate analytical methods are needed to support the advancement of recombinant adeno-associated virus (rAAV) production systems. Recently, biolayer interferometry (BLI) has been developed for high-throughput AAV capsid titer measurement by functionalizing the AAVX ligand onto biosensor probes (AAVX-BLI). In this work, an AAVX-BLI method was evaluated using Octet AAVX biosensors across four rAAV serotypes (rAAV2, -5, -8, and -9) and applied in an upstream and downstream processing context. AAVX-BLI measured the capsid titer across a wide concentration range (1 × 1010-1 × 1012 capsids/mL) for different rAAV serotypes and sample backgrounds with reduced measurement variance and error compared to an enzyme-linked immunosorbent assay (ELISA) method. Biosensors were regenerated for repeated use, with lysate samples showing reduced regeneration capacity compared to purified and supernatant samples. The AAVX-BLI method was applied in a transfection optimization study where direct capsid titer measurement of culture supernatants generated a representative response surface for the total vector genome (VG) titer. For rAAV purification, AAVX-BLI was used to measure dynamic binding capacity with POROS CaptureSelect AAVX affinity chromatography, showing resin breakthrough dependence on the operating flow rate. Measurement accuracy, serotype and sample background flexibility, and high sample throughput make AAVX-BLI an attractive alternative to other capsid titer measurement techniques.

Photonic Dipstick Immunosensor to Detect Adulteration of Ewe, Goat, and Donkey Milk with Cow Milk through Bovine κ-Casein Detection.

The quality and authenticity of milk are of paramount importance. Cow milk is more allergenic and less nutritious than ewe, goat, or donkey milk, which are often adulterated with cow milk due to their seasonal availability and higher prices. In this work, a silicon photonic dipstick sensor accommodating two U-shaped Mach-Zehnder Interferometers (MZIs) was employed for the label-free detection of the adulteration of ewe, goat, and donkey milk with cow milk. One of the two MZIs of the chip was modified with bovine κ-casein, while the other was modified with bovine serum albumin to serve as a blank. All assay steps were performed by immersion of the chip side where the MZIs are positioned into the reagent solutions, leading to a photonic dipstick immunosensor. Thus, the chip was first immersed in a mixture of milk with anti-bovine κ-casein antibody and then in a secondary antibody solution for signal enhancement. A limit of detection of 0.05% v/v cow milk in ewe, goat, or donkey milk was achieved in 12 min using a 50-times diluted sample. This fast, sensitive, and simple assay, without the need for sample pre-processing, microfluidics, or pumps, makes the developed sensor ideal for the detection of milk adulteration at the point of need.

A Reflected-Light-Mode Multiwavelength Interferometer for Measurement of Step Height Standards.

The article is dedicated to measuring the thickness of step height standards using the author's version of the variable wavelength interferometer (VAWI) in the reflected-light mode, where the interference pattern is created by the combination of two Wollaston prisms. The element of novelty consists in replacing the traditional search for the coincidence of fringes in the object and background with a continuous measurement of their periods and phases relative to the zero-order fringe. The resulting system of sinusoids is then analyzed using two methods: the classical one and the second utilizing the criterion of uniform thickness. The theory is followed by simulation and experimental parts, providing insight to the metrological potential of the VAWI technology.

Comparison of Eye Axial Length Measurements Taken Using Partial Coherence Interferometry and OCT Biometry.

This study evaluates the inter-device measurement properties of partial coherence interferometry (PCI) and spectral domain optical coherence tomography (SD-OCT) in measuring axial length, particularly for myopia management. We recruited 82 eyes from 41 adult participants with a mean age of 31.0 ± 17.6 years and a mean spherical equivalent of -2.20 ± 2.28 D. Axial length was measured using SD-OCT and PCI for both the right and left eyes. Agreement between the two measurements was assessed using Bland-Altman analysis, and graphs and values were compared with linear mixed models. The results show a near-to-zero and non-significant bias between measurements. The 95% limits of agreement showed a value of 0.06 mm. Both devices can accurately measure the axial length. OCT biometry performed with SD-OCT can be successfully interchanged with partial coherence interferometry, but they should be cautiously interchanged when performing longitudinal comparisons.

The surface deformation of permafrost and active layer thickness in the upper reaches of the Black River basin, revealed by InSAR observations and independent component analysis.

The Heihe River Basin, located in the northeastern part of the Qinghai-Tibetan Plateau, is part of the perennial permafrost belt of the Qilian Mountains. Recent observations indicate ongoing permafrost degradation in this region. This study utilizes data from 255 observations provided by Sentinel-1 satellites, MODIS Land Surface Temperature, SMAP-L4 soil moisture data, GNSS measurements, and in situ measurement. We introduced Variational Bayesian independent Component Analysis (VB-ICA) in multi-temporal Interferometric Synthetic Aperture Radar (MT-InSAR) processing to investigate the spatial-temporal characteristics of surface deformation and permafrost active layer thickness (ALT) variations. The analysis demonstrates strong agreement with borehole data and offers improvements over traditional methodologies. The maximum value of ALT in the basin is found to be 5.7 m. VB-ICA effectively delineates seasonal deformations related to the freeze-thaw cycles, with a peak seasonal deformation amplitude of 60 mm. Moreover, the seasonal permafrost's lower boundary reaches an elevation of 3700 m, revealing that permafrost is experiencing widespread degradation and associated soil erosion in the high elevation region of The Heihe River Basin. The paper also explores the efficacy of reference point selection and baseline network establishment for employing the InSAR method in monitoring freeze-thaw deformations. The study underscores the InSAR method's adaptability and its importance for interpreting permafrost deformation and related parameters.

An Integrated Photonic Biosensing Platform for Pathogen Detection in Aquaculture.

Aquaculture is expected to play a vital role in solving the challenge of sustainably providing the growing world population with healthy and nutritious food. Pathogen outbreaks are a major risk for the sector, so early detection and a timely response are crucial. This can be enabled by monitoring the pathogen levels in aquaculture facilities. This paper describes a photonic biosensing platform based on silicon nitride waveguide technology with integrated active components, which could be used for such applications. Compared to the state of the art, the current system presents improvements in terms of miniaturization of the Photonic Integrated Circuit (PIC) and the development of wafer-level processes for hybrid integration of active components and for material-selective chemical and biological surface modification. Furthermore, scalable processes for integrating the PIC in a microfluidic cartridge were developed, as well as a prototype desktop readout instrument. Three bacterial aquaculture pathogens (Aeromonas salmonicida, Vagococcus salmoninarum, and Yersinia ruckeri) were selected for assay development. DNA biomarkers were identified, corresponding primer-probe sets designed, and qPCR assays developed. The biomarker for Aeromonas was also detected using the hybrid PIC platform. This is the first successful demonstration of biosensing on the hybrid PIC platform.

Methods for monitoring protein-membrane binding. Comparison based on the interactions between amyloidogenic protein human cystatin C and phospholipid liposomes.

A cell membrane is an essential cellular component providing protection against the outer environment. It is also a host for proteins and carbohydrates responsible for, e.g. transporter, receptor, or enzymatic functions. In parallel, the membrane may also be implicated in pathological processes leading, e.g. to the oligomerization of amyloid-forming proteins, a hallmark of i.a. Alzheimer's disease. The increasing need for detailed information on mechanisms driving the amyloid formation and the potential role of cell membranes in the process proves the research on protein-membrane interactions biologically relevant. Considering the potential and limitations of the relatively well established and newly developed methods, this study focused on selecting methods that allow a broad and comprehensive description of interactions between amyloidogenic protein human cystatin C and lipid bilayers. In the first step, dot-blot and ELISA tests were selected as techniques allowing fast screening for protein-ligand interactions. Next, surface plasmon resonance, spectral shift, biolayer interferometry, and switchSENSE® technology were used to determine kinetic parameters and binding constants for interactions between human cystatin C and the selected lipid bilayers. Based on the obtained results we have proposed the most promising candidates for monitoring of interactions and determining affinity between amyloidogenic proteins and membrane mimetics.

Real-time monitoring of peptic and tryptic digestions of immunoglobulin G and the impact of dietary hydrocolloids on digestion.

Immunoglobulin G (IgG) exhibits potent antiviral, antibacterial, and immunological activities. The digestion process and bioavailability of IgG are often a concern. Dietary hydrocolloids are crucial for regulating healthy digestion and the bioavailability of protein as functional components. Understanding the effects of dietary hydrocolloids on the digestive kinetics of IgG is requisite. Herein, the pepsin and trypsin digestion of IgG was investigated using ordered porous layer interferometry (OPLI). The real-time variation in the interference spectral shift reflected by OPLI can be converted into changes in the optical thickness (OT) to obtain a degradation kinetics curve. The impact of dietary hydrocolloids, including alginic acid sodium salt (ALG), polydextrose (PD), and konjac glucomannan (KG), on IgG degradation was evaluated using OPLI. The results demonstrated that ALG significantly inhibited the degradation of IgG by pepsin under acidic conditions, whereas the addition of PD increased the Michaelis-Menten constant for IgG degradation by trypsin. Notably, this dependence is not based on the hydrocolloid viscosity, but relies more on the electrical properties. The study enhances our understanding of how hydrocolloids affect IgG digestion and could provide valuable insights into preserving IgG activity and facilitating the development of oral drugs or health products related to IgG.

Application of bio-layer interferometry for the analysis of ribosome-protein interactions.

The ribosome, a ribonucleoprotein complex, performs the function of protein translation. While ribosomal RNA catalyzes polypeptide formation, several proteins assist the ribosome throughout the translation process. Studying the biochemical and kinetic properties of these proteins interacting with the ribosome is vital for elucidating their roles. Various techniques, such as zonal centrifugation, pull-down assays, dynamic light scattering (DLS), fluorescence polarization, and surface plasmon resonance (SPR) are employed for this purpose, each presenting unique advantages and limitations. We add to the repertoire of techniques by using Bio-Layer Interferometry (BLI) to examine interactions between the ribosome and translation factors. Our findings demonstrate that BLI can detect interactions of Escherichia coli ribosomes with two proteins: E. coli initiation factor 2 (IF2) and P. falciparum translation enhancing factor (PTEF). A protein (Green Fluorescent Protein; GFP) known not to bind to E. coli ribosomes, shows no binding in the BLI assay. We show that BLI could be used to study the ribosome-protein interactions as it has key advantages like label-free procedures, ease of assay performance, and ribosome sample reuse. Our results highlight the comprehensive use of BLI in studying the ribosome-protein interactions, in addition to studying protein-protein and protein-ligand interactions.

Impact of temperature and relative humidity variations on coda waves in concrete.

The microstructure of concrete can be affected by many factors, from non-destructive environmental factors through to destructive damage induced by transient stresses. Coda wave interferometry is a technique that is sensitive enough to detect weak changes within concrete by evaluating the ultrasonic signal perturbation compared to a reference state. As concrete microstructure is sensitive to many factors, it is important to separate their contributions to the observables. In this study, we characterize the relationships between the concrete elastic and inelastic properties, and temperature and relative humidity. We confirm previous theoretical studies that found a linear relationship between temperature changes and velocity variation of the ultrasonic waves for a given concrete mix, and provide scaling factors per Kelvin for multiple settings. We also confirm an anti-correlation with relative humidity using long-term conditioning. Furthermore, we explore beyond the existing studies to establish the relationship linking humidity and temperature changes to ultrasonic wave attenuation.

Intra- and interobserver reliability of ocular surface analyzer LacryDiag®.

AIM: To invastigate intra- and interobserver reliability of interferometry, tear meniscus height (TMH) measurement and meibography (MBG) of an ocular surface analyzer, LacryDiag (Quantel Medical, France). METHODS: Five consecutive measurements and subsequent analysis of interferometry, TMH, and MBG were recorded by two examiners using the LacryDiag. To assess intra- and interobserver reliability, we used Cohen's kappa for categorical variables (interferometry), or intraclass correlation coefficient for continuous variables (TMH, MBG). RESULTS: Thirty eyes of 30 examinees were included. For both observers, there was excellent intraobserver reliability for MBG (0.955 and 0.970 for observer 1 and 2, respectively). Intraobserver reliability for observer 1 was substantial for interferometry (0.799), and excellent for TMH (0.863). Reliability for observer 2 was moderate for interferometry (0.535) and fair to good for TMH (0.431). Interobserver reliability was poor for interferometry (0.074) and fair to good for TMH (0.680) and MBG (0.414). CONCLUSION: LacryDiag ocular surface analyzer in our study proves to be a reliable noninvasive tool for the evaluation of TMH and MBG. As for interferometry, poor interobserver reliability, fair to good intraobserver reliability for observer 1, and moderate for observer 2, leave room for improvement.