T2* weighted Deconvolution of NMR Spectra: Application to 2D Homonuclear MAS Solid-State NMR of Membrane Proteins

Cellular Prion Protein Attenuates OGD/R-Induced Damage by Skewing Microglia toward an Anti-inflammatory State via Enhanced and Prolonged Activation of Autophagy

Modulation of microglial pro/anti-inflammatory states and autophagy are promising new therapies for ischemic stroke, but the underlying mechanisms remain largely unexplored. The objective of the study is to determine the intrinsic role of PrP^C (cellular prion protein) in the regulation of microglial inflammatory states and autophagy in ischemic stroke. PrP^C was expressed in murine microglia, and an in vitro oxygen-glucose deprivation/reperfusion (OGD/R) model was established in microglia of different PRNP genotypes. During reperfusion following OGD, wild-type (WT) microglia had significantly increased pro/anti-inflammatory microglial percentages and related cytokine [interleukin [IL]-6, IL-10, IL-4, tumor necrosis factor, and interferon-gamma] release at reperfusion after 48 or 72 h. WT microglia also showed greater accumulation of the autophagy markers LC3B-II/I (microtubule-associated protein B-light chain 3), but not of p62 or LAMP1 (lysosome-associated membrane protein) at reperfusion after 24 h and 48 h. Inhibition of autophagy using 3-methyladenine or bafilomycin A1 aggravated the OGD/R-induced pro-inflammatory state, and the effect of 3-methyladenine was significantly stronger than that of bafilomycin A1. Concomitantly, PRNP knockout shortened the accumulation of LC3B-II/I, suppressed microglial anti-inflammatory states, and further aggravated the pro-inflammatory states. Conversely, PRNP overexpression had the opposite effects. Bafilomycin A1 reversed the effect of PrP^C on microglial inflammatory state transformation. Moreover, microglia with PRNP overexpression exhibited higher levels of LAMP1 expression in the control and OGD/R groups and delayed the OGD/R-induced decrease of LAMP1 to reperfusion after 48 h. PrP^C attenuates OGD/R-induced damage by skewing microglia toward an anti-inflammatory state via enhanced and prolonged activation of autophagy.

Cross-seeding between the functional amyloidogenic CRES and CRES3 family members and their regulation of Aβ assembly

Accumulating evidence shows that amyloids perform biological roles. We previously showed that an amyloid matrix composed of four members of the CRES subgroup of reproductive family 2 cystatins is a normal component of the mouse epididymal lumen. The cellular mechanisms that control the assembly of these and other functional amyloid structures, however, remain unclear. We speculated that cross-seeding between CRES members could be a mechanism to control the assembly of the endogenous functional amyloid. Herein we used thioflavin T assays and negative stain transmission electron microscopy to explore this possibility. We show that CRES3 rapidly formed large networks of beaded chains that possessed the characteristic cross-β reflections of amyloid when examined by X-ray diffraction. The beaded amyloids accelerated the amyloidogenesis of CRES, a less amyloidogenic family member, in seeding assays during which beads transitioned into films and fibrils. Similarly, CRES seeds expedited CRES3 amyloidogenesis, although less efficiently than the CRES3 seeding of CRES. These studies suggest that CRES and CRES3 hetero-oligomerize and that CRES3 beaded amyloids may function as stable preassembled seeds. The CRES3 beaded amyloids also facilitated assembly of the unrelated amyloidogenic precursor Aβ by providing a surface for polymerization though, intriguingly, CRES3 (and CRES) monomer/early oligomer profoundly inhibited Aβ assembly. The cross-seeding between the CRES subgroup members is similar to that which occurs between bacterial curli proteins suggesting that it may be an evolutionarily conserved mechanism to control the assembly of some functional amyloids. Further, interactions between unrelated amyloidogenic precursors may also be a means to regulate functional amyloid assembly.

Signal Deconvolution and Noise Factor Analysis Based on a Combination of Time-Frequency Analysis and Probabilistic Sparse Matrix Factorization

Nuclear magnetic resonance (NMR) spectroscopy is commonly used to characterize molecular complexity because it produces informative atomic-resolution data on the chemical structure and molecular mobility of samples non-invasively by means of various acquisition parameters and pulse programs. However, analyzing the accumulated NMR data of mixtures is challenging due to noise and signal overlap. Therefore, data-cleansing steps, such as quality checking, noise reduction, and signal deconvolution, are important processes before spectrum analysis. Here, we have developed an NMR measurement informatics tool for data cleansing that combines short-time Fourier transform (STFT; a time-frequency analytical method) and probabilistic sparse matrix factorization (PSMF) for signal deconvolution and noise factor analysis. Our tool can be applied to the original free induction decay (FID) signals of a one-dimensional NMR spectrum. We show that the signal deconvolution method reduces the noise of FID signals, increasing the signal-to-noise ratio (SNR) about tenfold, and its application to diffusion-edited spectra allows signals of macromolecules and unsuppressed small molecules to be separated by the length of the T₂* relaxation time. Noise factor analysis of NMR datasets identified correlations between SNR and acquisition parameters, identifying major experimental factors that can lower SNR.