Statistical Removal of Background Signals from High-throughput 1H NMR Line-broadening Ligand-affinity Screens

NMR ligand-affinity screens are vital to drug discovery, are routinely used to screen fragment-based libraries, and used to verify chemical leads from high-throughput assays and virtual screens. NMR ligand-affinity screens are also a highly informative first step towards identifying functional epitopes of unknown proteins, as well as elucidating the biochemical functions of protein-ligand interaction at their binding interfaces. While simple one-dimensional (1D) 1H NMR experiments are capable of indicating binding through a change in ligand line shape, they are plagued by broad, ill-defined background signals from protein 1H resonances. We present an uncomplicated method for subtraction of protein background in high-throughput ligand-based affinity screens, and show that its performance is maximized when phase-scatter correction (PSC) is applied prior to subtraction

Investigating the relationship between multi-scale perfusion and white matter microstructural integrity in patients with relapsing-remitting MS

Background: Multiple sclerosis is characterized by the formation of central nervous system demyelinating lesions with microvasculature inflammation. Objective: Evaluate how lesion cerebral perfusion relates to white matter microstructural integrity in patients with RRMS using perfusion MRI and myelin-related T1-weighted to T2-weighted (T1w/T2w) ratios. Methods: Forty-eight patients with RRMS were imaged with dynamic susceptibility contrast imaging using SAGE (spin- and gradient-echo) to calculate global and capillary-sized perfusion parameters, including cerebral blood flow (CBF), volume (CBV), and mean transit time (MTT). T1w/T2w ratios were used to indirectly assess white matter microstructural integrity. Results: For global perfusion metrics, CBF was reduced 28.4% in lesion regions of interest (ROIs) compared to normal appearing white matter (NAWM), CBV was reduced 25.9% in lesion ROIs compared to NAWM, and MTT increased 12.9%. For capillary perfusion metrics (via spin-echo (SE)), CBF-SE was reduced 35.7% in lesion ROIs compared to NAWM, CBV-SE was reduced 35.2% in lesion ROIs compared to NAWM, and MTT-SE increased 9.1%. Capillary-level CBF was correlated (ρ = 0.34, p = 0.024) with white matter microstructural integrity in lesion ROIs. Conclusion: This study demonstrates that lesion perfusion is reduced at both the global and capillary level and capillary-associated hypoperfusion is associated with reduced white matter microstructural integrity in RRMS

Rapid parameter estimation for selective inversion recovery myelin imaging using an open-source Julia toolkit

BACKGROUND: Magnetic resonance imaging (MRI) is used extensively to quantify myelin content, however computational bottlenecks remain challenging for advanced imaging techniques in clinical settings. We present a fast, open-source toolkit for processing quantitative magnetization transfer derived from selective inversion recovery (SIR) acquisitions that allows parameter map estimation, including the myelin-sensitive macromolecular pool size ratio (). Significant progress has been made in reducing SIR acquisition times to improve clinically feasibility. However, parameter map estimation from the resulting data remains computationally expensive. To overcome this computational limitation, we developed a computationally efficient, open-source toolkit implemented in the Julia language. METHODS: To test the accuracy of this toolkit, we simulated SIR images with varying and spin-lattice relaxation time of the free water pool ( ) over a physiologically meaningful scale from 5% to 20% and 0.5 to 1.5 s, respectively. Rician noise was then added, and the parameter maps were estimated using our Julia toolkit. Probability density histogram plots and Lin\u27s concordance correlation coefficients (LCCC) were used to assess accuracy and precision of the fits to our known simulation data. To further mimic biological tissue, we generated five cross-linked bovine serum albumin (BSA) phantoms with concentrations that ranged from 1.25% to 20%. The phantoms were imaged at 3T using SIR, and data were fit to estimate and . Similarly, a healthy volunteer was imaged at 3T, and SIR parameter maps were estimated to demonstrate the reduced computational time for a real-world clinical example. RESULTS: Estimated SIR parameter maps from our Julia toolkit agreed with simulated values (LCCC \u3e 0.98). This toolkit was further validated using BSA phantoms and a whole brain scan at 3T. In both cases, SIR parameter estimates were consistent with published values using MATLAB. However, compared to earlier work using MATLAB, our Julia toolkit provided an approximate 20-fold reduction in computational time. CONCLUSIONS: Presented here, we developed a fast, open-source, toolkit for rapid and accurate SIR MRI using Julia. The reduction in computational cost should allow SIR parameters to be accessible in clinical settings

PIRT the TRP Channel Regulating Protein Binds Calmodulin and Cholesterol-Like Ligands

Transient receptor potential (TRP) ion channels are polymodal receptors that have been implicated in a variety of pathophysiologies, including pain, obesity, and cancer. The capsaicin and heat sensor TRPV1, and the menthol and cold sensor TRPM8, have been shown to be modulated by the membrane protein PIRT (Phosphoinositide-interacting regulator of TRP). The emerging mechanism of PIRT-dependent TRPM8 regulation involves a competitive interaction between PIRT and TRPM8 for the activating phosphatidylinositol 4,5-bisphosphate (PIP2) lipid. As many PIP2 modulated ion channels also interact with calmodulin, we investigated the possible interaction between PIRT and calmodulin. Using microscale thermophoresis (MST), we show that calmodulin binds to the PIRT C-terminal α-helix, which we corroborate with a pull-down experiment, nuclear magnetic resonance-detected binding study, and Rosetta-based computational studies. Furthermore, we identify a cholesterol-recognition amino acid consensus (CRAC) domain in the outer leaflet of the first transmembrane helix of PIRT, and with MST, show that PIRT specifically binds to a number of cholesterol-derivatives. Additional studies identified that PIRT binds to cholecalciferol and oxytocin, which has mechanistic implications for the role of PIRT regulation of additional ion channels. This is the first study to show that PIRT specifically binds to a variety of ligands beyond TRP channels and PIP2

Rapid whole-brain myelin imaging with selective inversion recovery and compressed SENSE

PURPOSE: Quantitative magnetization transfer (QMT) using selective inversion recovery (SIR) can quantify the macromolecular-to-free proton pool size ratio (PSR), which has been shown to relate closely with myelin content. Currently clinical applications of SIR have been hampered by long scan times. In this work, the acceleration of SIR-QMT using CS-SENSE (compressed sensing SENSE) was systematically studied. THEORY AND METHODS: Phantoms of varied concentrations of bovine serum albumin and human scans were first conducted to evaluate the SNR, precision of SIR-QMT parameters, and scan time. Based on these results, an optimized CS-SENSE factor of 8 was determined and the test-retest repeatability was further investigated. RESULTS: A whole-brain SIR imaging of 6 min can be achieved. Bland-Altman analyses indicated excellent agreement between the test and retest sessions with a difference in mean PSR of 0.06% (and a difference in mean R of -0.001 s ). In addition, the assessment of the intraclass correlation coefficient (ICC) revealed high reliability in nearly all the white matter and gray matter regions. In white matter regions, the ICC was 0.93 (95% confidence interval [CI]: 0.88-0.96, p \u3c 0.001) for PSR, and 0.90 (95% CI: 0.83-0.94, p \u3c 0.001) for R . In gray matter, ICC was 0.84 (95% CI: 0.66-0.93, p \u3c 0.001) in PSR, and 0.98 (95% CI: 0.95-0.99, p \u3c 0.001) for R . The method also showed excellent capability to detect focal lesions in multiple sclerosis. CONCLUSION: Rapid, reliable, and sensitive whole-brain SIR imaging can be achieved using CS-SENSE, which is expected to significantly promote widespread clinical translation

Sex Differences in Alzheimer\u27s Disease Revealed by Free-Water Diffusion Tensor Imaging and Voxel-Based Morphometry

Background: Imaging biomarkers are increasingly used in Alzheimer\u27s disease (AD), and the identification of sex differences using neuroimaging may provide insight into disease heterogeneity, progression, and therapeutic targets. Objective: The purpose of this study was to investigate differences in grey matter (GM) volume and white matter (WM) microstructural disorganization between males and females with AD using voxel-based morphometry (VBM) and free-water-corrected diffusion tensor imaging (FW-DTI). Methods: Data were downloaded from the OASIS-3 database, including 158 healthy control (HC; 86 females) and 46 mild AD subjects (24 females). VBM and FW-DTI metrics (fractional anisotropy (FA), axial and radial diffusivities (AxD and RD, respectively), and FW index) were compared using effect size for the main effects of group, sex, and their interaction. Results: Significant group and sex differences were observed, with no significant interaction. Post-hoc comparisons showed that AD is associated with reduced GM volume, reduced FW-FA, and higher FW-RD/FW-index, consistent with neurodegeneration. Females in both groups exhibited higher GM volume than males, while FW-DTI metrics showed sex differences only in the AD group. Lower FW, lower FW-FA and higher FW-RD were observed in females relative to males in the AD group. Conclusion: The combination of VBM and DTI may reveal complementary sex-specific changes in GM and WM associated with AD and aging. Sex differences in GM volume were observed for both groups, while FW-DTI metrics only showed significant sex differences in the AD group, suggesting that WM tract disorganization may play a differential role in AD pathophysiology between females and males

Evidence that the TRPV1 S1-S4 membrane domain contributes to thermosensing

The TRPV1 ion channel is a heat-sensing receptor that is also activated by vanilloid compounds, but the molecular underpinnings of thermosensing have remained elusive. Here authors use in solution NMR on the isolated human TRPV1 S1-S4 domain and show that this domain undergoes a non-denaturing temperature-dependent transition with a high thermosensitivity