Role of helical structure and dynamics in oligoadenylate synthetase 1 (OAS1) mismatch tolerance and activation by short dsRNAs

The 2’-5’-oligoadenylate synthetases (OAS) are innate immune sensors of cytosolic double-stranded RNA (dsRNA) that play a critical role in limiting viral infection. How these proteins are able to avoid aberrant activation by cellular RNAs is not fully understood, but adenosine-to-inosine (A-to-I) editing has been proposed to limit accumulation of endogenous RNAs that might otherwise cause stimulation of the OAS/RNase L pathway. Here, we aim to uncover whether and how such sequence modifications can restrict the ability of short, defined dsRNAs to activate the single-domain form of OAS, OAS1. Unexpectedly, we find that all tested inosine-containing dsRNAs have an increased capacity to activate OAS1, whether in a destabilizing (I•U) or standard Watson–Crick-like base pairing (I–C) context. Additional variants with strongly destabilizing A•C mismatches or stabilizing G–C pairs also exhibit increased capacity to activate OAS1, eliminating helical stability as a factor in the relative ability of the dsRNAs to activate OAS1. Using thermal difference spectra and molecular dynamics simulations, we identify both increased helical dynamics and specific local changes in helical structure as important factors in the capacity of short dsRNAs to activate OAS1. These helical features may facilitate more ready adoption of the distorted OAS1-bound conformation or stabilize important structures to predispose the dsRNA for optimal binding and activation of OAS1. These studies thus reveal the molecular basis for the greater capacity of some short dsRNAs to activate OAS1 in a sequence-independent manner.

Data analysis procedures for time-resolved x-ray photoelectron spectroscopy at a SASE free-electron-laser

The random nature of self-amplified spontaneous emission (SASE) is a well-known challenge for x-ray core level spectroscopy at SASE free-electron lasers (FELs). Especially in time-resolved experiments that require a combination of good temporal and spectral resolution the jitter and drifts in the spectral characteristics, relative arrival time as well as power fluctuations can smear out spectral-temporal features. We present a combination of methods for the analysis of time-resolved photoelectron spectra based on power and time corrections as well as self-referencing of a strong photoelectron line. Based on sulfur 2p photoelectron spectra of 2-thiouracil taken at the SASE FEL FLASH2, we show that it is possible to correct for some of the photon energy drift and jitter even when reliable shot-to-shot photon energy data is not available. The quality of pump-probe difference spectra improves as random jumps in energy between delay points reduce significantly. The data analysis allows to identify coherent oscillations of 1 eV shift on the mean photoelectron line of 4 eV width with an error of less than 0.1 eV.

Spin noise gradient echoes

Nuclear spin noise spectroscopy in the absence of radio frequency pulses was studied under the influence of pulsed field gradients (PFGs) on pure and mixed liquids. Under conditions where the radiation-damping-induced line broadening is smaller than the gradient-dependent inhomogeneous broadening, echo responses can be observed in difference spectra between experiments employing pulsed field gradient pairs of the same and opposite signs. These observed spin noise gradient echoes (SNGEs) were analyzed through a simple model to describe the effects of transient phenomena. Experiments performed on high-resolution nuclear magnetic resonance (NMR) probes demonstrate how refocused spin noise behaves and how it can be exploited to determine sample properties. In bulk liquids and their mixtures, transverse relaxation times and translational diffusion constants can be determined from SNGE spectra recorded following tailored sequences of magnetic field gradient pulses.

DeltaPCA: A Statistically Robust Method for Detecting Protein Analyte Binding to Aptamer-Functionalised Nanoparticles using Surface-Enhanced Raman Spectroscopy

In this work, we introduce a novel joint experimental design and computational analysis procedure to reliably and reproducibly quantify protein analyte binding to DNA aptamer-functionalised silver nanoparticles using slippery surface-enhanced Raman spectroscopy. We employ an indirect detection approach, based upon monitoring spectral changes in the covalent bond-stretching region as intermolecular bonds are formed between the surface-immobilized probe biomolecule and its target analyte. Sample variability is minimized by preparing aptamer-only and aptamer-plus-analyte samples under the same conditions, and then analysing difference spectra. To account for technical variability, multiple spectra are recorded from the same sample. Our new DeltaPCA analysis procedure takes into account technical variability within each spectral data set while also extracting statistically robust difference spectra between data sets. Proof of principle experiments using thiolated aptamers to detect CoV-SARS-2 spike protein reveal that analyte binding is mediated through the formation of N-H...X and C-H...X hydrogen bonds between the aptamer (H-bond donor) and protein (H-bond acceptor). Our computational analysis code can be freely downloaded from https://github.com/dlc62/DeltaPCA.

Free water molecules and hydrogen bonding form the basis of variation in homeopathic potencies as revealed by vibrational spectroscopy

Objective: Using Fourier Transform Infrared spectroscopy (FTIR) we have demonstrated that homeopathic potencies of Natrum mur, Cantharis, Nux vomica and Sulphur show differences with respect to the number of free water molecules and strength of hydrogen bonding. The purpose of the present study is to confirm this phenomenon in three potencies of two more drugs Calcarea carb and Silicea. Design: The potencies used for each of the two drugs were 30cH, 200cH and 1000cH. The control was 90% ethanol as also the potentized drugs. The control, as well as the potencies, were diluted with distilled water to reduce the level of ethanol to 0.03 molar fraction in each of them. FTIR spectra of all the potentized drugs, control and sterile distilled water (reference water) were taken in the wave number region of 4000-2800 cm-1. The full width at half maximum (fwhm) of OH band was measured for each spectrum. The width was divided into two in the middle. The difference spectrum (absorbance of drug solution - absorbance of reference water) for each potency and the control was obtained after normalization of the spectrum at 3410 cm-1. One difference spectrum so obtained for a potency was subtracted from another to find out if there is a difference between two different potencies. Results: The half width half maximum (hwhm) in both the high and low-frequency sides of the OH band is far less narrow in potencies than in the control as compared to that in water. The difference spectra for different potencies show different levels of fall in intensity at the wave number region of dip at 3630 cm-1. The level of dip at 3630 cm-1 and subsequent rise in intensity in the lower frequency region represent the quantity of free water molecules and strong alcoholic OH bond around 3250 cm-1, respectively. The results of subtraction between two different potencies are not zero but have marked positive or negative values. Conclusion (i) Potencies have stronger intermolecular interactions and a higher number of chemical environments than the control, as revealed by the data on hwhm. (ii) The three potencies of each of the two drugs show distinct variation in the number of free water molecules and strength of hydrogen bonding. (iii) There exists both inter-drug and inter-potency variation as revealed by the difference spectra and results of subtraction between two difference spectra.

Multidimensional four-wave mixing signals detected by quantum squeezed light

Four-wave mixing (FWM) of optical fields has been extensively used in quantum information processing, sensing, and memories. It also forms a basis for nonlinear spectroscopies such as transient grating, stimulated Raman, and photon echo where phase matching is used to select desired components of the third-order response of matter. Here we report an experimental study of the two-dimensional quantum noise intensity difference spectra of a pair of squeezed beams generated by FWM in hot Rb vapor. The measurement reveals details of the χ(3) susceptibility dressed by the strong pump field which induces an AC Stark shift, with higher spectral resolution compared to classical measurements of probe and conjugate beam intensities. We demonstrate how quantum correlations of squeezed light can be utilized as a spectroscopic tool which unlike their classical counterparts are robust to external noise.

Diagnosing COVID-19 in human serum using Raman spectroscopy: a preliminary study

This preliminary study proposed the diagnosis of COVID-19 by means of Raman spectroscopy. Samples of blood serum from 10 patients positive and 10 patients negative for COVID-19 by RT-PCR RNA and ELISA tests were analyzed. Raman spectra were obtained with a dispersive Raman spectrometer (830 nm, 350 mW) in triplicate, being submitted to exploratory analysis with principal component analysis (PCA) to identify the spectral differences and discriminant analysis with PCA (PCA-DA) and partial least squares (PLS-DA) for classification of the blood serum spectra into Control and COVID-19. The spectra of both groups positive and negative for COVID-19 showed peaks referred to the basal constitution of the serum (mainly albumin). The difference spectra showed decrease in the peaks referred to proteins and amino acids for the group positive. PCA variables showed more detailed spectral differences related to the biochemical alterations due to the COVID-19 such as increase in lipids, nitrogen compounds (urea and amines/amides) and nucleic acids, and decrease of proteins and amino acids (tryptophan) in the COVID-19 group. The discriminant analysis applied to the principal component loadings (PC 2, PC 4, PC 5 and PC 6) could classify spectra with 87% sensitivity and 100% specificity compared to 95% sensitivity and 100% specificity indicated in the RT-PCR kit leaflet, demonstrating the possibilities of a rapid, label-free and costless technique for diagnosing COVID-19 infection.

Spin-Noise Gradient Echoes

Nuclear spin-noise spectroscopy in absence of radio frequency pulses was studied under the influence of pulsed field gradients (PFGs) on pure and mixed liquids. Under conditions, where the radiation-damping induced line broadening is smaller than the gradient dependent inhomogeneous broadening, echo responses can be observed in difference spectra between experiments employing pulsed field gradient pairs of same and opposite signs. These observed “spin-noise gradient echoes” (SNGEs) were analyzed through a simple model to describe the effects of transient phenomena. Experiments performed on high resolution NMR probes demonstrate how “refocused spin noise” behaves and how it can be exploited to determine sample properties. In bulk liquids and their mixtures transverse relaxation times as well as translational diffusion constants can be determined from SNGE spectra recorded following tailored sequences of magnetic field gradient pulses.

Methacrylate peak determination and selection recommendations using ATR-FTIR to investigate polymerisation of dental methacrylate mixtures

Investigation of polymerisation kinetics using ATR-FTIR systems is common in many dental studies. However, peak selection methods to calculate monomer-polymer conversion can vary, consequently affecting final results. Thus, the aim of this study is to experimentally confirm which method is less prone to systematic errors. Three commercial restorative materials were tested–Vertise Flow (VF), Constic and Activa Bioactive Restorative Kids. Firstly, Attenuated Total Reflectance Fourier Transform Infra-Red (ATR-FTIR) (Spectrum One, Perkin-Elmer, UK) spectra of monomers were acquired—10-methacryloyloxy decyl dihydrogen phosphate (10-MDP), bisphenol-A glycidyl dimethacrylate (Bis-GMA), 2-hydroxyethyl methacrylate (HEMA), triethyelene glycol dimethacrylate (TEGDMA) and urethane dimethacrylate (UDMA) to investigate proportionality of methacrylate peak heights versus concentration. Spectral changes upon light exposure of 2 mm discs of the restorative materials (irradiated for 20 s, LED curing unit 1100–1330 mW/cm2) were assessed to study polymerisation kinetics (n = 3), with continuous acquisition of spectra, before, during and after light exposure. Peak differences and degrees of conversion (DC %) were calculated using 1320/1336, 1320/1350 and 1636/1648 cm-1 as reaction/reference peaks. Inferential statistics included a MANOVA and within-subjects repeated measures ANOVA design (5% significance level). Proportionality of methacrylate peak height to concentration was confirmed, with the 1320/1352 cm-1 peak combination showing the lowest coefficient of variation (8%). Difference spectra of the polymerisation reaction showed noise interference around the 1500–1800 cm-1 region. Across the different materials, DC % results are highly dependent upon peak selection (p<0.001), with higher variability associated to the 1636 cm-1. Significant differences in the materials were only detected when the 1320 cm-1 peak was used (p<0.05). Within the same materials, methods were significantly different for Constic and Activa (p<0.05). It is possible to conclude that the 1320 cm-1 peak is more adequate to assess polymerisation of methacrylates and is therefore recommended.

Evaluation of BOLD effects in the rat cortex

Purpose: This study aimed to characterize Blood oxygen level-dependent (BOLD) effects in 1H- MR spectra obtained during optogenetic activation of the rat forelimb cortex for the correction and estimation of accurate metabolite concentration changes. Methods : T2*-induced effects were characterized by linewidth changes and amplitude changes of water, NAA and tCr spectral peaks during the stimulation paradigm. Spectral linewidth-matching procedures were used to correct for the line-narrowing effect induced by BOLD. For an increased understanding of spectroscopic BOLD effects and the optimized way to correct them, a 1 Hz line-narrowing effect was also simulated on mouseproton MR spectrum1H-fMRS data acquired using STEAM acquisitions at 9.4T in rats (n=8) upon optogenetic stimulation of the primary somatosensory cortex were used. Data were analyzed with MATLAB routines and LCModel. Uncorrected and corrected 1H-MR spectra of simulated and in-vivo data were quantified and compared. BOLD-corrected difference spectra were also calculated and analyzed. Results: Significant mean increases in water and NAA peak heights (+ 1.1% and +4.5%, respectively) were found accompanied by decreased linewidths (-0.5 Hz and -2.8%) upon optogenetic stimulation. These estimates were used for further definition of an accurate line-broadening factor (lb). Usage of an erroneous lb introduced false-positive errors in metabolite concentration change estimates thereby altering the specificity of findings. Using different water scalings within LCModel, the water and metabolite BOLD contributions were separated. Conclusion : The linewidth-matching procedure using a precise lb factor remains the most performant approach for the accurate quantification of small (0.3 micromol/g) metabolic changes in 1H-fMRS studies. A simple and preliminary compartmentation of BOLD effects was proposed, which will require validation.