ALBERT

Description: As genes originate at different evolutionary times, they harbor distinctive genomic signatures of evolutionary ages. Although previous studies have investigated different gene age-related signatures, what signatures dominantly associate with gene age remains unresolved. Here we address this question via a combined approach of comprehensive assignment of gene ages, gene family identification, and multivariate analyses. We first provide a comprehensive and improved gene age assignment by combining homolog clustering with phylogeny inference and categorize human genes into 26 age classes spanning the whole tree of life. We then explore the dominant age-related signatures based on a collection of 10 potential signatures (including gene composition, gene length, selection pressure, expression level, connectivity in protein–protein interaction network and DNA methylation). Our results show that GC content and connectivity in protein–protein interaction network (PPIN) associate dominantly with gene age. Furthermore, we investigate the heterogeneity of dominant signatures in duplicates and singletons. We find that GC content is a consistent primary factor of gene age in duplicates and singletons, whereas PPIN is more strongly associated with gene age in singletons than in duplicates. Taken together, GC content and PPIN are two dominant signatures in close association with gene age, exhibiting heterogeneity in duplicates and singletons and presumably reflecting complex differential interplays between natural selection and mutation.

Description: Differential acoustic resonance spectroscopy (DARS) was developed to examine changes in the resonant frequencies of a cavity perturbed by the introduction of a centimetre-sized sample. Resonant frequency shifts, measured at different resonance modes and between empty and sample-loaded cavities, were used to infer the acoustic properties of the loaded samples in the low frequency range (0.5–2 kHz). To some extent, this laboratory-based measurement technique fills an experimental gap between the low-frequency stress–strain method (quasi-static to several kHz) and the ultrasonic transmission technique (hundreds of kHz to MHz). By means of an effective perturbation model against the DARS system, this study presents a Green's function-based theoretical derivation of an amended DARS perturbation formula under a general impedance boundary condition. Numerical and experimental results show that the amended DARS perturbation is able to reflect the DARS operation mechanism more accurately and more precisely than past efforts. In addition, inversion was performed by fitting the resonance frequencies, measured at various locations inside the DARS resonance cavity, in a least-square sense to estimate the acoustic properties of a test sample. Inversion implementation at different resonance modes makes it possible to perform direct dispersion analysis on reservoir rocks at different low-frequency bands. The results of this study show that the DARS laboratory device, in conjunction with the amended perturbation formula and the proposed inversion strategy, are useful tools for estimating the acoustic properties of centimetre-sized rock samples in the low frequency range.