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)

Combined pigment and metatranscriptomic analysis reveals highly synchronized diel patterns of phenotypic light response across domains in the open oligotrophic ocean

Sunlight is the most important environmental control on diel fluctuations in phytoplankton activity, and understanding diel microbial processes is essential to the study of oceanic biogeochemical cycles. Yet, little is known about the in situ temporal dynamics of phytoplankton metabolic activities and their coordination across different populations. We investigated diel orchestration of phytoplankton activity in photosynthesis, photoacclimation, and photoprotection by analyzing pigment and quinone distributions in combination with metatranscriptomes in surface waters of the North Pacific Subtropical Gyre (NPSG). We found diel cycles in pigment abundances resulting from the balance of their synthesis and consumption. These dynamics suggest that night represents a metabolic recovery phase, refilling cellular pigment stores, while photosystems are remodeled towards photoprotection during daytime. Transcript levels of genes involved in photosynthesis and pigment metabolism had synchronized diel expression patterns among all taxa, reflecting the driving force light imparts upon photosynthetic organisms in the ocean, while other environmental factors drive niche differentiation. For instance, observed decoupling of diel oscillations in transcripts and related pigments indicates that pigment abundances are modulated by environmental factors extending beyond gene expression/regulation reinforcing the need to combine metatranscriptomics with proteomics and metabolomics to fully understand the timing of these critical processes in situ

Infrared Optical Properties of Amorphous and Nanocrystalline Ta2O5 Thin Films

The optical constants of tantalum pentoxide (Ta 2O5) are determined in a broad spectral region from the visible to the far infrared. Ta 2O5 films of various thicknesses from approximately 170 to 1600 nm aredeposited using reactive magnetron sputtering on Si substrates. X-ray diffraction shows that the as-deposited films are amorphous, and annealing in air at 800 °C results in the formation of nanocrystallineTa 2O5. Ellipsometry is used to obtain the dispersion in the visible and near-infrared. Two Fourier-transform infrared spectrometers are used to measure the transmittance and reflectance at wavelengths from 1 to 1000 μm. The surface topography and microstructure of the samples are examined using atomic force microscopy, confocal microscopy, and scanning electron microscopy. Classical Lorentz oscillatorsare employed to model the absorption bands due to phonons and impurities. A simple model is introduced to account for light scattering in the annealed films, which contain micro-cracks. For the unannealed samples, an effective-medium approximation is used to take into account the adsorbed moisture in the film and a Drude free-electron term is also added to model the broad background absorption

Estudio experimental de las erosiones aguas abajo del modelo físico de la presa Los Molinos

En este trabajo se presentan los estudios experimentales realizados para evaluar las erosiones locales que se producirían aguas abajo de la de la presa Los Molinos para diferentes escenarios extremos.Fil: Eder, Matías. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas, Físicas y Naturales. Laboratorio de Hidráulica. Centro de Estudios y Tecnología del Agua; Argentina.Fil: Corral, Mariano. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas, Físicas y Naturales. Laboratorio de Hidráulica. Centro de Estudios y Tecnología del Agua; Argentina.Fil: Hillman, Gerardo. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas, Físicas y Naturales. Laboratorio de Hidráulica. Centro de Estudios y Tecnología del Agua; Argentina.Fil: Pagot, Mariana. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas, Físicas y Naturales. Laboratorio de Hidráulica. Centro de Estudios y Tecnología del Agua; Argentina.Fil: Bellino, Nicolás. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas, Físicas y Naturales. Laboratorio de Hidráulica. Centro de Estudios y Tecnología del Agua; Argentina.Fil: Gyssels, Paolo. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas, Físicas y Naturales. Laboratorio de Hidráulica. Centro de Estudios y Tecnología del Agua; Argentina.Fil: García, Carlos. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas, Físicas y Naturales. Laboratorio de Hidráulica. Centro de Estudios y Tecnología del Agua; Argentina.Fil: Rodríguez, Andrés. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas, Físicas y Naturales. Laboratorio de Hidráulica. Centro de Estudios y Tecnología del Agua; Argentina.Fil: Moya, Gonzalo. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas, Físicas y Naturales. Laboratorio de Hidráulica. Centro de Estudios y Tecnología del Agua; Argentina.Fil: Farías, Daniel. Universidad Nacional de Santiago del Estero; Argentina.Fil: Bachiega, Daniel. Instituto Nacional del Agua. Laboratorio de Hidráulica Aplicada; Argentina.Fil: Muratore, Hector. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas, Físicas y Naturales. Laboratorio de Hidráulica. Centro de Estudios y Tecnología del Agua; Argentina.Ingeniería Civi

Descripción del diseño y construcción de un modelo físico, de la presa Los Molinos (Jujuy)

En este trabajo se describen las etapas de diseño y construcción del modelo físico de la presa Los Molinos, Jujuy, cuyos objetivos específicos son: a) Verificar el comportamiento hidráulico de las estructuras proyectadas en las obras de re funcionalización, b) Analizar y cuantificar las erosiones locales aguas abajo de las estructuras de descarga y disipación, c) Verificar y optimizar las consignas de operación de las compuertas del Dique Móvil y Canal Moderador a los fines de regular los procesos hidrosedimentológicos para permitir el paso de los sedimentos a través de estas estructuras.Fil: Eder, Matías. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas, Físicas y Naturales. Laboratorio de Hidráulica y Centro de Estudios y Tecnología del Agua; Argentina.Fil: Moya, Gonzalo. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas, Físicas y Naturales. Laboratorio de Hidráulica y Centro de Estudios y Tecnología del Agua; Argentina.Fil: Hillman, Gerardo. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas, Físicas y Naturales. Laboratorio de Hidráulica y Centro de Estudios y Tecnología del Agua; Argentina.Fil: Bacchiega, Daniel. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas, Físicas y Naturales. Laboratorio de Hidráulica y Centro de Estudios y Tecnología del Agua; Argentina.Fil: Gyssel, Paolo. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas, Físicas y Naturales. Laboratorio de Hidráulica y Centro de Estudios y Tecnología del Agua; Argentina.Fil: Díaz Lozada, José Manuel. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas, Físicas y Naturales. Laboratorio de Hidráulica y Centro de Estudios y Tecnología del Agua; Argentina.Fil: Quiroga Crespo, Lucas. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas, Físicas y Naturales. Laboratorio de Hidráulica y Centro de Estudios y Tecnología del Agua; Argentina.Fil: Muratore, Héctor. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas, Físicas y Naturales. Laboratorio de Hidráulica y Centro de Estudios y Tecnología del Agua; Argentina.Fil: Pagot, Mariana. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas, Físicas y Naturales. Laboratorio de Hidráulica y Centro de Estudios y Tecnología del Agua; Argentina.Fil: Corral, Mariano. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas, Físicas y Naturales. Laboratorio de Hidráulica y Centro de Estudios y Tecnología del Agua; Argentina.Fil: Rodriguez, Andrés. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas, Físicas y Naturales. Laboratorio de Hidráulica y Centro de Estudios y Tecnología del Agua; Argentina.Fil: García, Carlos. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas, Físicas y Naturales. Laboratorio de Hidráulica y Centro de Estudios y Tecnología del Agua; Argentina.Ingeniería Civi

Nutrition and the ageing brain: moving towards clinical applications

The global increases in life expectancy and population have resulted in a growing ageing population and with it a growing number of people living with age-related neurodegenerative conditions and dementia, shifting focus towards methods of prevention, with lifestyle approaches such as nutrition representing a promising avenue for further development. This overview summarises the main themes discussed during the 3 Symposium on "Nutrition for the Ageing Brain: Moving Towards Clinical Applications" held in Madrid in August 2018, enlarged with the current state of knowledge on how nutrition influences healthy ageing and gives recommendations regarding how the critical field of nutrition and neurodegeneration research should move forward into the future. Specific nutrients are discussed as well as the impact of multi-nutrient and whole diet approaches, showing particular promise to combatting the growing burden of age-related cognitive decline. The emergence of new avenues for exploring the role of diet in healthy ageing, such as the impact of the gut microbiome and development of new techniques (imaging measures of brain metabolism, metabolomics, biomarkers) are enabling researchers to approach finding answers to these questions. But the translation of these findings into clinical and public health contexts remains an obstacle due to significant shortcomings in nutrition research or pressure on the scientific community to communicate recommendations to the general public in a convincing and accessible way. Some promising programs exist but further investigation to improve our understanding of the mechanisms by which nutrition can improve brain health across the human lifespan is still required

Multi-messenger observations of a binary neutron star merger

On 2017 August 17 a binary neutron star coalescence candidate (later designated GW170817) with merger time 12:41:04 UTC was observed through gravitational waves by the Advanced LIGO and Advanced Virgo detectors. The Fermi Gamma-ray Burst Monitor independently detected a gamma-ray burst (GRB 170817A) with a time delay of ~1.7 s with respect to the merger time. From the gravitational-wave signal, the source was initially localized to a sky region of 31 deg2 at a luminosity distance of 40+8-8 Mpc and with component masses consistent with neutron stars. The component masses were later measured to be in the range 0.86 to 2.26 Mo. An extensive observing campaign was launched across the electromagnetic spectrum leading to the discovery of a bright optical transient (SSS17a, now with the IAU identification of AT 2017gfo) in NGC 4993 (at ~40 Mpc) less than 11 hours after the merger by the One- Meter, Two Hemisphere (1M2H) team using the 1 m Swope Telescope. The optical transient was independently detected by multiple teams within an hour. Subsequent observations targeted the object and its environment. Early ultraviolet observations revealed a blue transient that faded within 48 hours. Optical and infrared observations showed a redward evolution over ~10 days. Following early non-detections, X-ray and radio emission were discovered at the transient’s position ~9 and ~16 days, respectively, after the merger. Both the X-ray and radio emission likely arise from a physical process that is distinct from the one that generates the UV/optical/near-infrared emission. No ultra-high-energy gamma-rays and no neutrino candidates consistent with the source were found in follow-up searches. These observations support the hypothesis that GW170817 was produced by the merger of two neutron stars in NGC4993 followed by a short gamma-ray burst (GRB 170817A) and a kilonova/macronova powered by the radioactive decay of r-process nuclei synthesized in the ejecta