The optimisation of synthetic and natural microbial communities has vast potential for emerging applications in medicine, agriculture and industry. Realising this goal is contingent on a close correlation between theory, experiments, and the real world. Although the temporal pattern of resource supply can play a major role in microbial community assembly, resource dynamics are commonly treated inconsistently in theoretical and experimental research. Here we explore how the composition of communities varies under continuous resource supply, typical of theoretical approaches, versus pulsed resource supply, typical of experiments. Using simulations of classical resource competition models, we show that community composition diverges rapidly between the two regimes, with almost zero overlap in composition once the pulsing interval stretches beyond just four hours. The implication for the rapidly growing field of microbial community optimisation is that the resource supply regime must be tailored to the community being optimised. As such, we argue that resource supply dynamics should be considered both a constraint in the design of novel microbial communities and as a tuning mechanism for the optimisation of pre-existing communities like those found in the human gut.

Non-mammalian model organisms have been essential for our understanding of the mechanisms that control development, disease, and physiology, but they are underutilized in pharmacological and toxicological phenotypic screening assays due to their low throughput in comparison with cell-based screens. To increase the utility of using Drosophila melanogaster in screening, we designed the Whole Animal Feeding FLat (WAFFL), a novel, flexible, and complete system for feeding, monitoring, and assaying flies in a high-throughput format. Our 3-D printed system is compatible with inexpensive and readily available, commercial 96-well plate consumables and equipment. Experimenters can change the diet at will during the experiment and video record for behavior analysis, enabling precise dosing, measurement of feeding, and analysis of behavior in 96-well plate format. Data was collected using the WAFFL and MUFFIN methods presented in the article. Data are provided that allow the main figures to be recapitulated, including the following: 1. Fly survival data 2. Fly food consumption data 3. A very large file of fly movements in the WAFFL-MUFFIN device 4. An accompanying movie of fly movements in the WAFFL-MUFFIN device. See the README.md file for specifics of the datasets. The file WAFFL-MUFFINoutput_smoothed_data.txt needs to be opened using a text editor or in the terminal. Any other software (i.e. excel, numbers, etc) will truncate the data to the software limits (~65,000 rows). Copyright: CC0 1.0 Universal (CC0 1.0) Public Domain Dedication

Non-mammalian model organisms have been essential for our understanding of the mechanisms that control development, disease, and physiology, but they are underutilized in pharmacological and toxicological phenotypic screening assays due to their low throughput in comparison with cell-based screens. To increase the utility of using Drosophila melanogaster in screening, we designed the Whole Animal Feeding FLat (WAFFL), a novel, flexible, and complete system for feeding, monitoring, and assaying flies in a high-throughput format. Our 3D printed system is compatible with inexpensive and readily available, commercial 96-well plate consumables and equipment. Experimenters can change the diet at will during the experiment and video record for behavior analysis, enabling precise dosing, measurement of feeding, and analysis of behavior in a 96-well plate format.

Identifying genetic variations or treatments that confer greater resistance to drought is paramount to ensuring sustainable crop productivity. Accurate and reproducible measurement of drought stress symptoms can be achieved via automated, image-based phenotyping. Many phenotyping platforms are either cost-prohibitive, require specific technical expertise, or are simply more complex than necessary to effectively evaluate drought resistance. Certain mutations, allelic variations, or treatments result in plants that constitutively use less water. To accurately identify genetic differences or treatments that confer a drought phenotype, plants from all experimental groups must be subjected to equal levels of drought stress. This can be easily achieved by growing and imaging plants that are grown in the same pot. Here, we provide a detailed protocol to configure a Raspberry Pi computer and camera module to image seedlings of multiple genotypes growing in shared pots and to transfer images and metadata via the cloud for downstream analyses. Also detailed is a method to calculate percent soil water content of pots while being imaged to allow for comparison of stress symptoms with water availability. This protocol was recently used to uncouple differential water usage from drought resistance in a dwarf Arabidopsis thaliana mutant chiquita1-1/cost1 compared to the wild-type control. It is cost effective, suitable for any plant species, customizable to various biological questions, and requires no prior experience with electronics or basic software programming.

The Earth's core formation mechanism determines the siderophile and light elements abundance in the Earth's mantle and core. Previous studies suggest that the sink of massive liquid metal through a solid silicate mantle resulted in an unequilibrated core and the lower mantle. Here, we show that percolation can be an effective core formation mechanism in a convective mantle and modify the compositions of the lower mantle and the core through partial equilibration between them. This grain-scale metal flow has a high velocity to meet the time constraint of core formation. The Earth's core could have been enriched with light elements, and the abundance of the moderately siderophile elements in the mantle could have been elevated to the current value during this process. The trapped core-forming melt in the mantle during the stress-induced percolation can also explain the highly siderophile element abundance in the Earth's mantle.

There is growing interest in developing methods to deduce the geographic origin of diamonds. Most approaches have focused on trace elements within diamonds, which can be sensitive recorders of geological conditions during the growth of minerals. Gem-quality diamonds have ultra-low concentrations of trace elements, making them extremely challenging to analyze quantitatively. Nonetheless, high-quality trace element data from multiple studies reveal complex and variable patterns, but with striking similarities and overlap between worldwide deposits. Diamond properties such as trace element or isotopic characteristics vary as a function of geological conditions that are not necessarily distinct and resolvable between diamonds of different geographic origin. We conclude that there has been no study by any method demonstrating unique and measurable characteristics that would allow for independent provenance determination of a random individual diamond. For now and the foreseeable future, the only definitive method to establish diamond origin depends on preserving and retaining origin information from the time of mining.

The mutualistic cnidarian-dinoflagellate symbiosis underpins the evolutionary success of stony corals and the persistence of coral reefs. However, a molecular understanding of the signalling events that lead to the successful establishment and maintenance of this symbiosis remains unresolved. For example, the phosphatidylinositol (PI) signalling pathway has been implicated during the establishment of multiple mutualistic and parasitic interactions across the kingdoms of life, yet its role within the cnidarian-dinoflagellate symbiosis remains unexplored. Here, we aimed to confirm the presence and assess the specific enzymatic composition of the PI signalling pathway across cnidaria and dinoflagellates by compiling 21 symbiotic anthozoan (corals and sea anemones) and 28 symbiotic dinoflagellate (Symbiodiniaceae) transcriptomic and genomic datasets and querying genes related to this pathway. Presence or absence of PI-kinase and PI-phosphatase orthologs were also compared between a broad sampling of taxonomically related symbiotic and non-symbiotic species. Across the symbiotic anthozoans analysed, there was a complete and highly conserved PI pathway, analogous to the pathway found in model eukaryotes. The Symbiodiniaceae pathway showed similarities to its sister taxon, the Apicomplexa, with the absence of PI 4-phosphatases. However, conversely to Apicomplexa, there was also an expansion of homologs present in the PI5-phosphatase and PI5-kinase groups, with unique Symbiodiniaceae proteins identified that are unknown from non-symbiotic unicellular organisms. Additionally, we aimed to unravel the putative functionalities of the PI signalling pathway in this symbiosis by analysing phosphoinositide (PIP)-binding proteins. Analysis of phosphoinositide (PIP)-binding proteins showed that, on average, 2.23 and 1.29% of the total assemblies of anthozoan and Symbiodiniaceae, respectively, have the potential to bind to PIPs. Enrichment of Gene Ontology (GO) terms associated with predicted PIP-binding proteins within each taxon revealed a broad range of functions, including compelling links to processes putatively involved in symbiosis regulation. This analysis establishes a baseline for current understanding of the PI pathway across anthozoans and Symbiodiniaceae, and thus a framework to target future research.

Understanding evolutionary genomic and population processes within a species range is key to anticipating the extinction of plant species before it is too late. However, most models of biodiversity risk under global change do not account for the genetic variation and local adaptation of different populations. Population diversity is critical to understanding extinction because different populations may be more or less susceptible to global change and, if lost, would reduce the total diversity within a species. Two new modeling frameworks advance our understanding of extinction from a population and evolutionary angle: Rapid climate change-driven disruptions in population adaptation are predicted from associations between genomes and local climates. Furthermore, losses of population diversity from global land-use transformations are estimated by scaling relationships of species' genomic diversity with habitat area. Overall, these global eco-evolutionary methods advance the predictability - and possibly the preventability - of the ongoing extinction of plant species.

Brillouin spectroscopy at room temperature and pressures up to 40 GPa documents nearly identical elasticity and refractive index of amorphous CaSiO3 created by two different methods: temperature-quenching the melt at ambient pressure and pressure-amorphizing crystalline wollastonite at room temperature. We find reproducible hysteresis of 0 to 8% on pressure cycling that is small relative to the 30 to 60% changes in shear and longitudinal wave velocities over this pressure range. Together with observed changes in refractive index and previous results from Raman spectroscopy, these measurements reveal a continuous and reversible change in atomic packing induced by pressure. Unlike many other silicate glasses, amorphous CaSiO3 exhibits highly reproducible properties, behaving smoothly and reversibly under pressure cycling and possessing similar structure and elasticity regardless of synthesis paths for the starting material, which suggests that the amorphous solid may mimic the liquid over the pressure range investigated.