A primer for microbiome time-series analysis

© The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Coenen, A. R., Hu, S. K., Luo, E., Muratore, D., & Weitz, J. S. A primer for microbiome time-series analysis. Frontiers in Genetics, 11, (2020): 310, doi:10.3389/fgene.2020.00310.Time-series can provide critical insights into the structure and function of microbial communities. The analysis of temporal data warrants statistical considerations, distinct from comparative microbiome studies, to address ecological questions. This primer identifies unique challenges and approaches for analyzing microbiome time-series. In doing so, we focus on (1) identifying compositionally similar samples, (2) inferring putative interactions among populations, and (3) detecting periodic signals. We connect theory, code and data via a series of hands-on modules with a motivating biological question centered on marine microbial ecology. The topics of the modules include characterizing shifts in community structure and activity, identifying expression levels with a diel periodic signal, and identifying putative interactions within a complex community. Modules are presented as self-contained, open-access, interactive tutorials in R and Matlab. Throughout, we highlight statistical considerations for dealing with autocorrelated and compositional data, with an eye to improving the robustness of inferences from microbiome time-series. In doing so, we hope that this primer helps to broaden the use of time-series analytic methods within the microbial ecology research community.This work was supported by the Simons Foundation (SCOPE award ID 329108) and the National Science Foundation (NSF Bio Oc 1829636)

Stokes−Einstein−Debye failure in molecular orientational diffusion: exception or rule?

The Stokes–Einstein–Debye (SED) expression is used routinely to relate orientational molecular diffusivity quantitatively to viscosity. However, it is well-known that Einstein’s equations are derived from hydrodynamic theory for the diffusion of a Brownian particle in a homogeneous fluid and examples of SED breakdown and failure for molecular diffusion are not unusual. Here, using optical Kerr-effect spectroscopy to measure orientational diffusion for solutions of guanidine hydrochloride in water and mixtures of carbon disulfide with hexadecane, we show that these two contrasting systems each show pronounced exception to the SED relation and ask if it is reasonable to expect molecular diffusion to be a simple function of viscosity

Biochemical assessment of nanostructures in human trabecular bone: Proposal of a Raman microspectroscopy based measurements protocol

Background: Improvements to the understating of the compositional contributions of bone mineral and organic components to the competence of trabecular bone are crucial. The purpose of this study was to propose a protocol to study biochemical composition of trabecular bone, based on two combined Raman analysis methodologies. Material and Methods: Both cluster and single point Raman mappings were obtained, in order to assess bone degeneration associated with aging, disease, or injury, and to help in the evaluation and development of successful therapies. In this study, human trabecular bone has been analysed throughout a) Raman cluster analysis: bone mineral content, carbonate-to-phosphate ratio (both from the mineral components), the crosslinking and nature/secondary structure of collagen (both from the organic components); and b) Single point Raman spectra, where Raman points related to the minerals and organic components were also obtained, both techniques were employed in spectra attained at 400 to 1700 cm- 1. Results: Multivariate analysis confirmed: 1) the different spectral composition, 2) the existence of centroids grouped by chemical affinity of the various components of the trabecular bone, and 3) the several traces of centroids and distribution of chemical compositional clusters. Conclusions: This study is important, because it delivers a study protocol that provides molecular variations information in both mineral and collagen structure of trabecular bone tissue. This will enable clinicians to benefit knowing the microstructural differences in the bone subjected to degeneration of their patients.Project MAT2017-85999-P supported by the Ministry of Economy and Competitiveness (MINECO) of Spanish Government and European Regional Development Fund (ERDF)