Editorial: Seismic microzonation and risk reduction

Editorial on the Research Topic Seismic microzonation and risk reductio

Exponentially Modified Protein Abundance Index (emPAI) for Estimation of Absolute Protein Amount in Proteomics by the Number of Sequenced Peptides per Protein

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Seismic characterisation of the subsoil under a historic building: Cathedral Church of Saint Mary in Murcia case study

This research focuses on the Cathedral Church of Saint Mary in Murcia, Spain, which is located in a moderate-to-high seismic risk zone in the Spanish context. The study uses geophysical techniques and geotechnical investigation to characterise seismic ground models at the building's scale, aiming to understand the real amplification of the ground under seismic effect in historic buildings. Three soil layers (silt, sand with gravel, and gravel) were identified through core borings. Multichannel Analysis of Surface Waves (MASW) profiles and Mini-array profiles revealed Vs values of 305 ± 32 m/s, 296 ± 62 m/s, and 440 ± 38.5 m/s, respectively, for these materials. Seismic Refraction Tomography (SRT) showed Vp values of 586 ± 73 m/s, 700 m/s, and 1466 ± 489 m/s for the corresponding layers. The horizontal-to-vertical spectral ratio (HVSR) approach identified a ground predominant period ranging from 0.37 to 0.38 s. Another significant peak at 2.3 s is observed, probably associated to the Triassic basement. Three seismic events with magnitudes Mw between 4.9 and 5.1 were used as inputs to determine the amplification factor (AF). The results indicate a PGA amplification factor between 1.7 and 2.1. These results contribute to the conservation and mitigation of seismic risk of this cultural heritage generating input data that enables precise computation of the soil-structure interaction

Synaptic activity prompts γ-secretase–mediated cleavage of EphA4 and dendritic spine formation

Alzheimer's disease is an age-dependent neurodegenerative disorder that is characterized by a progressive decline in cognitive function. γ-secretase dysfunction is evident in many cases of early onset familial Alzheimer's disease. However, the mechanism by which γ-secretase dysfunction results in memory loss and neurodegeneration is not fully understood. Here, we demonstrate that γ-secretase is localized at synapses and regulates spine formation. We identify EphA4, one of the Ephrin receptor family members, as a substrate of γ-secretase, and find that EphA4 processing is enhanced by synaptic activity. Moreover, overexpression of EphA4 intracellular domain increases the number of dendritic spines by activating the Rac signaling pathway. These findings reveal a function for EphA4-mediated intracellular signaling in the morphogenesis of dendritic spines and suggest that the processing of EphA4 by γ-secretase affects the pathogenesis of Alzheimer's disease

TRACES: A Lightweight Browser for Liquid Chromatography–Multiple Reaction Monitoring–Mass Spectrometry Chromatograms

In targeted metabolomic analysis using liquid chromatography–multiple reaction monitoring–mass spectrometry (LC-MRM-MS), hundreds of MRMs are performed in a single run, yielding a large dataset containing thousands of chromatographic peaks. Automation tools for processing large MRM datasets have been reported, but a visual review of chromatograms is still critical, as real samples with biological matrices often cause complex chromatographic patterns owing to non-specific, insufficiently separated, isomeric, and isotopic components. Herein, we report the development of new software, TRACES, a lightweight chromatogram browser for MRM-based targeted LC-MS analysis. TRACES provides rapid access to all MRM chromatograms in a dataset, allowing users to start ad hoc data browsing without preparations such as loading compound libraries. As a special function of the software, we implemented a chromatogram-level deisotoping function that facilitates the identification of regions potentially affected by isotopic signals. Using MRM libraries containing precursor and product formulae, the algorithm reveals all possible isotopic interferences in the dataset and generates deisotoped chromatograms. To validate the deisotoping function in real applications, we analyzed mouse tissue phospholipids in which isotopic interference by molecules with different fatty-acyl unsaturation levels is known. TRACES successfully removed isotopic signals within the MRM chromatograms, helping users avoid inappropriate regions for integration

Isobaric mass tagging and triple quadrupole mass spectrometry to determine lipid biomarker candidates for Alzheimer's disease.

The isobaric tagging method widely used in proteomic and lipidomic fields, with the multiple reaction monitoring (MRM) approach using a triple quadrupole mass spectrometer, was applied to identify biomarker candidates from plasma samples for Alzheimer's disease (AD). We focused on the following phospholipids that have amino groups as the functional group: phosphatidylethanolamine (PE), Lyso-PE, phosphatidylserine, and Lyso-phosphatidylserine. We also investigated fatty acids that have a carboxy group. A sixplex tandem mass tag (TMT) was used for the isobaric tagging method in this study. The TMT reaction had high reproducibility in human plasma. A total of 196 human plasma samples from three AD cohorts were used for the study, and compared to pooled plasma quality control (QC) samples. The described method required only 40 MRM measurements, including the pooled QC samples, for a full comparison of the data. We found that the content of free fatty acids increased in AD samples in all the three cohorts, alkenyl PEs (ePEs) decreased over a one-year interval in AD patients, and ePEs weakly correlated with amyloid peptide (a-beta) 1-42 in cerebrospinal fluid. In conclusion, total free fatty acids in plasma are a risk factor for AD, and ePEs monitor candidates for AD. Therefore, TMT-lipidomics is a powerful approach for the determination of plasma biomarkers because of the high sample throughput