Search bioRxiv⌕ Search

bioRxiv · 10.1101/2024.02.27.582276

Quantification of NAD+ T1 and T2 relaxation times using downfield 1H MRS at 7 T in human brain in vivo

Abstract

IntroductionThe purpose of this study was to use a single-slice spectrally-selective sequence to measure T1 and T2 relaxation times of NAD+ proton resonances in the downfield 1H MRS spectrum in human brain at 7 T in vivo and assess the propagation of relaxation time uncertainty in NAD+ quantification. MethodsDownfield spectra from 7 healthy volunteers were acquired at multiple echo times in all subjects to measure T2 relaxation, and saturation recovery data were to measure T1 relaxation. The downfield acquisition used a spectrally-selective 90{degrees} sinc pulse for excitation centered at 9.1 ppm with a bandwidth of 2 ppm, followed by a 180{degrees} spatially-selective Shinnar-Le Roux refocusing pulse for localization. For the multiple echo experiment, spectra were collected with echo times ranging from 13 to 33 ms. For the saturation recovery experiment, saturation was performed prior to excitation using the same spectrally-selective sinc pulse as was used for excitation. Saturation delay times (TS) ranged from 100 to 600 ms. Uncertainty propagation analysis was performed analytically and with Monte Carlo simulation. ResultsThe mean {+/-} standard deviation of T1 relaxation times of the H2, H6, and H4 protons were 152.7 {+/-} 16.6, 163.6 {+/-} 22.3, and 169.9 {+/-} 11.2 ms, respectively. The mean {+/-} standard deviation of T2 relaxation times of the H2, H6, and H4 protons were 32.5 {+/-} 7.0, 27.4 {+/-} 5.2, and 38.1 {+/-} 11.7 ms, respectively. The mean R2 of the H2 and H6 T1 fits were 0.98. The mean R2 of the H4 proton T1 fit was 0.96. The mean R2 of the T2 fits of the H2 and H4 proton resonances were 0.98, while the mean R2 of the T2 fits of the H4 proton was 0.93. The relative uncertainty in NAD+ concentration due to relaxation time uncertainty was 8.5%-11%. ConclusionUsing downfield spectrally-selective spectroscopy with single-slice localization, we found NAD+ T1 and T2 relaxation times to be approximately 162 ms and 32 ms respectively in the human brain in vivo at 7 T.

Explore related subjects

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Swago, S., Wilson, N. E., Elliott, M. A., Nanga, R. P. R., Reddy, R., Witschey, W. R.. 2024-03-01. Quantification of NAD+ T1 and T2 relaxation times using downfield 1H MRS at 7 T in human brain in vivo. https://doi.org/10.1101/2024.02.27.582276

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

RNASeek: A Cross-Phyla Generative Foundation Model for Multipurpose RNA Modeling and Reinforcement Learning-Based Design

RNA plays central roles in regulating information flow and provides a versatile substrate for engineering biological functions. While large language models (LLMs) have transformed natural language processing and protein design, a general framework connecting RNA foundation models to functional sequence design remains limited. Here, we present RNASeek, a 1.6-billion-parameter generative foundation model built on a DeepSeek architecture and trained on a cross-phyla transcriptomic corpus for RNA sequence representation and generation. Natural-language tokens enable flexible conditional prediction and sequence design using a unified backbone. RNASeek captures species-specific transcript features and intron-exon boundaries in a zero-shot setting. We then fine-tune RNASeek to predict ribozyme self-cleavage activity and viral mRNA stability, revealing interpretable sequence features associated with function, including ribozyme loop flexibility and stem stability, as well as AU-rich motifs associated with mRNA stability. We use these functional predictors as reward models and apply Group Relative Policy Optimization (GRPO) to update the generation policy of RNASeek toward sequences with desired properties. GRPO-guided generation produces faster-cleaving ribozymes and stability-enhancing 3' UTRs while satisfying user-specified IUPAC constraints. Experimentally validated RNASeek-generated ribozymes achieve wild-type levels of activity, while RNASeek-generated 3' UTR sequences exceed the performance of the training data and benchmarked AI-generated 3' UTRs. Together, RNASeek establishes a unified pretrain-predict-optimize framework that connects learned RNA function to controllable de novo sequence design and provides a general strategy for engineering regulatory RNAs with desired properties.

bioengineering↗

Joint Vector Flow Mapping and Segmentation: Ill-Posedness,Differentiable Bayesian Inference, and Synthetic Vortex-FlowBenchmarks

Vector flow mapping (VFM) reconstructs left-ventricular (LV) blood velocity from color-Doppler echocardiography by combining the measured beamwise component with physical and regularizing constraints. Analysis of the discrete VFM formulation shows that the inverse problem is intrinsically ill posed: the occurrence of singular modes can be predicted from the geometry of the segmented blood-pool domain, the imposed boundary conditions, and the degree of smoothing. These modes can propagate uncertainty along entire transverse bands of the reconstructed velocity field, yet conventional VFM neither quantifies this uncertainty nor allows for correcting the blood-pool segmentation. We introduce Bayesian VFM (B--VFM), a hierarchical framework that jointly infers radial and transverse velocities, a probabilistic blood-pool mask, their spatially resolved uncertainties, and hyperparameters weighting Doppler and segmentation fidelity, mass conservation, boundary conditions, and smoothness. The discretized posterior admits a closed-form gradient and exact Hessian, enabling computationally efficient, gradient-based MAP estimation, sampling, and direct analysis of ill-posed modes. Posterior inference combines Gibbs sampling of conjugate Gamma-distributed hyperparameters with conditional maximum-a-posteriori estimation and a Laplace approximation for the high-dimensional velocity and mask fields. To accommodate systematic departures from planar mass conservation, B-VFM can learn the covariance of the planar divergence residual from an ensemble of flows and incorporate it as a structured model-discrepancy prior. Independent chains converged reproducibly, while covariance priors learned from flow ensembles illustrated how model discrepancies can be incorporated into the inference. B--VFM was evaluated using Lamb-Chaplygin dipoles under ideal conditions and with Doppler corruption, Doppler voids, and segmentation defects, and using the Hicks-Moffatt family of spherical vortices to assess violations of planar mass conservation. The method produced smooth reconstructions, localized uncertainty near unreliable measurements and regions of model inconsistency, and used flow information to correct segmentation errors. Within the tested vortex family, the data-informed planar divergence prior reduced velocity bias and mask distortion. B--VFM thus provides an uncertainty-aware reconstruction method and a flexible foundation for future VFM formulations incorporating additional priors, observations, and physical models. Future work will evaluate the method using clinical data and more complex three-dimensional benchmark flows.

bioengineering↗

Computational design of a versatile, zero-radius proximity labeling enzyme

The ability to map protein interactomes and organelle proteomes is foundational for achieving a molecular understanding of living cells. Proximity labeling (PL) provides a powerful strategy for this, but existing enzymes and photocatalysts are limited by their spatial resolution, reliance on biotin, and/or in vivo compatibility. Here we report FlexID, an engineered promiscuous ligase that catalyzes the rapid attachment of diverse small-molecule probes to proximal endogenous proteins. Critically, FlexID operates through a zero-radius, direct-contact mechanism, offering superior spatial precision compared to existing PL tools. We engineered FlexID by combining the strengths of sequence- and structure-trained computational models to enhance its catalytic activity and structural stability. Biophysical analysis revealed that specific conformational changes in FlexID improve its ability to recognize diverse target proteins while simultaneously preventing the premature release of the reactive intermediate. We demonstrate FlexID's versatility through in vivo proximity labeling, comprehensive organelle proteome mapping, and a high-throughput, fluorescence-based screen for molecular glues. Our work shows that computational methods can be harnessed to create mechanistically distinct PL enzymes and establishes FlexID as a flexible, high-resolution tool for mapping protein interactions and proteomes in living cells.

bioengineering↗