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    Morphodynamics of an erodible channel under varying discharge
    Adams, DL (WILEY, 2021-09-30)
    Abstract Alluvial channels arise through the interaction between morphology, hydraulics, and sediment transport, known as the ‘fluvial trinity’. Over relatively short timescales where climate and geology are fixed but discharge and sediment supply may vary, this process facilitates adjustments towards steady state, where the system oscillates around a mean condition. The relationship between changes in conditions and geomorphic response may be highly complex and nonlinear, especially in systems with multiple modes of adjustment. This study examines the adjustment of an erodible channel with fixed banks and a widely graded sediment mixture to successive increases in discharge. With each increase in discharge, components of the fluvial trinity adjusted towards a steady state. Particularly at relatively low discharges, adjustments were controlled by intrinsic thresholds and highlighted important morphodynamic processes. Notably, there was a strong interplay between channel morphology and sediment transport, and an effect whereby larger‐than‐average grains controlled channel deformation. These two processes occurred at the bar scale and were highly spatialised, which has two important implications: (1) reach‐averaged representations of process provide only partial insight into morphodynamics; and (2) models of rivers that suppress these process feedbacks and size‐dependent transport may not replicate morphodynamics that typically occur in field conditions. The experiments provide quantitative evidence for conceptual models describing exponential approaches towards steady state and the potential for transiency if disturbance frequency exceeds the recovery time. They also highlight how in natural rivers, particularly those with greater degrees of freedom for adjustment (notably, lateral adjustment and meandering), continuous changes in discharge may lead to nonlinear rather than steady‐state behaviour. In these settings, more holistic analytical frameworks that embrace different aspects of the system are critical in understanding the direction, magnitude and timing of channel adjustments.
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    Separation and Paired Proteome Profiling of Plant Chloroplast and Cytoplasmic Ribosomes
    Firmino, AAP ; Gorka, M ; Graf, A ; Skirycz, A ; Martinez-Seidel, F ; Zander, K ; Kopka, J ; Beine-Golovchuk, O (MDPI, 2020-07)
    Conventional preparation methods of plant ribosomes fail to resolve non-translating chloroplast or cytoplasmic ribosome subunits from translating fractions. We established preparation of these ribosome complexes from Arabidopsis thaliana leaf, root, and seed tissues by optimized sucrose density gradient centrifugation of protease protected plant extracts. The method co-purified non-translating 30S and 40S ribosome subunits separated non-translating 50S from 60S subunits, and resolved assembled monosomes from low oligomeric polysomes. Combining ribosome fractionation with microfluidic rRNA analysis and proteomics, we characterized the rRNA and ribosomal protein (RP) composition. The identity of cytoplasmic and chloroplast ribosome complexes and the presence of ribosome biogenesis factors in the 60S-80S sedimentation interval were verified. In vivo cross-linking of leaf tissue stabilized ribosome biogenesis complexes, but induced polysome run-off. Omitting cross-linking, the established paired fractionation and proteome analysis monitored relative abundances of plant chloroplast and cytoplasmic ribosome fractions and enabled analysis of RP composition and ribosome associated proteins including transiently associated biogenesis factors.
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    Systematic Review of Plant Ribosome Heterogeneity and Specialization
    Martinez-Seidel, F ; Beine-Golovchuk, O ; Hsieh, Y-C ; Kopka, J (FRONTIERS MEDIA SA, 2020-06-25)
    Plants dedicate a high amount of energy and resources to the production of ribosomes. Historically, these multi-protein ribosome complexes have been considered static protein synthesis machines that are not subject to extensive regulation but only read mRNA and produce polypeptides accordingly. New and increasing evidence across various model organisms demonstrated the heterogeneous nature of ribosomes. This heterogeneity can constitute specialized ribosomes that regulate mRNA translation and control protein synthesis. A prominent example of ribosome heterogeneity is seen in the model plant, Arabidopsis thaliana, which, due to genome duplications, has multiple paralogs of each ribosomal protein (RP) gene. We support the notion of plant evolution directing high RP paralog divergence toward functional heterogeneity, underpinned in part by a vast resource of ribosome mutants that suggest specialization extends beyond the pleiotropic effects of single structural RPs or RP paralogs. Thus, Arabidopsis is a highly suitable model to study this phenomenon. Arabidopsis enables reverse genetics approaches that could provide evidence of ribosome specialization. In this review, we critically assess evidence of plant ribosome specialization and highlight steps along ribosome biogenesis in which heterogeneity may arise, filling the knowledge gaps in plant science by providing advanced insights from the human or yeast fields. We propose a data analysis pipeline that infers the heterogeneity of ribosome complexes and deviations from canonical structural compositions linked to stress events. This analysis pipeline can be extrapolated and enhanced by combination with other high-throughput methodologies, such as proteomics. Technologies, such as kinetic mass spectrometry and ribosome profiling, will be necessary to resolve the temporal and spatial aspects of translational regulation while the functional features of ribosomal subpopulations will become clear with the combination of reverse genetics and systems biology approaches.
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    COSNeti: ComplexOme-Structural Network Interpreter used to study spatial enrichment in metazoan ribosomes
    Martinez-Seidel, F ; Hsieh, Y-C ; Walther, D ; Kopka, J ; Firmino, AAP (BMC, 2021-12-20)
    BACKGROUND: Upon environmental stimuli, ribosomes are surmised to undergo compositional rearrangements due to abundance changes among proteins assembled into the complex, leading to modulated structural and functional characteristics. Here, we present the ComplexOme-Structural Network Interpreter ([Formula: see text]), a computational method to allow testing whether ribosomal proteins (rProteins) that exhibit abundance changes under specific conditions are spatially confined to particular regions within the large ribosomal complex. RESULTS: [Formula: see text] translates experimentally determined structures into graphs, with nodes representing proteins and edges the spatial proximity between them. In its first implementation, [Formula: see text] considers rProteins and ignores rRNA and other objects. Spatial regions are defined using a random walk with restart methodology, followed by a procedure to obtain a minimum set of regions that cover all proteins in the complex. Structural coherence is achieved by applying weights to the edges reflecting the physical proximity between purportedly contacting proteins. The weighting probabilistically guides the random-walk path trajectory. Parameter tuning during region selection provides the option to tailor the method to specific biological questions by yielding regions of different sizes with minimum overlaps. In addition, other graph community detection algorithms may be used for the [Formula: see text] workflow, considering that they yield different sized, non-overlapping regions. All tested algorithms result in the same node kernels under equivalent regions. Based on the defined regions, available abundance change information of proteins is mapped onto the graph and subsequently tested for enrichment in any of the defined spatial regions. We applied [Formula: see text] to the cytosolic ribosome structures of Saccharomyces cerevisiae, Oryctolagus cuniculus, and Triticum aestivum using datasets with available quantitative protein abundance change information. We found that in yeast, substoichiometric rProteins depleted from translating polysomes are significantly constrained to a ribosomal region close to the tRNA entry and exit sites. CONCLUSIONS: [Formula: see text] offers a computational method to partition multi-protein complexes into structural regions and a statistical approach to test for spatial enrichments of any given subsets of proteins. [Formula: see text] is applicable to any multi-protein complex given appropriate structural and abundance-change data. [Formula: see text] is publicly available as a GitHub repository https://github.com/MSeidelFed/COSNet_i and can be installed using the python installer pip.
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    Insights into the Vertical Stratification of Microbial Ecological Roles across the Deepest Seawater Column on Earth.
    Xue, C-X ; Liu, J ; Lea-Smith, DJ ; Rowley, G ; Lin, H ; Zheng, Y ; Zhu, X-Y ; Liang, J ; Ahmad, W ; Todd, JD ; Zhang, X-H (MDPI AG, 2020-08-27)
    The Earth's oceans are a huge body of water with physicochemical properties and microbial community profiles that change with depth, which in turn influences their biogeochemical cycling potential. The differences between microbial communities and their functional potential in surface to hadopelagic water samples are only beginning to be explored. Here, we used metagenomics to investigate the microbial communities and their potential to drive biogeochemical cycling in seven different water layers down the vertical profile of the Challenger Deep (0-10,500 m) in the Mariana Trench, the deepest natural point in the Earth's oceans. We recovered 726 metagenome-assembled genomes (MAGs) affiliated to 27 phyla. Overall, biodiversity increased in line with increased depth. In addition, the genome size of MAGs at ≥4000 m layers was slightly larger compared to those at 0-2000 m. As expected, surface waters were the main source of primary production, predominantly from Cyanobacteria. Intriguingly, microbes conducting an unusual form of nitrogen metabolism were identified in the deepest waters (>10,000 m), as demonstrated by an enrichment of genes encoding proteins involved in dissimilatory nitrate to ammonia conversion (DNRA), nitrogen fixation and urea transport. These likely facilitate the survival of ammonia-oxidizing archaea α lineage, which are typically present in environments with a high ammonia concentration. In addition, the microbial potential for oxidative phosphorylation and the glyoxylate shunt was enhanced in >10,000 m waters. This study provides novel insights into how microbial communities and their genetic potential for biogeochemical cycling differs through the Challenger deep water column, and into the unique adaptive lifestyle of microbes in the Earth's deepest seawater.
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    DiTing: A Pipeline to Infer and Compare Biogeochemical Pathways From Metagenomic and Metatranscriptomic Data
    Xue, C-X ; Lin, H ; Zhu, X-Y ; Liu, J ; Zhang, Y ; Rowley, G ; Todd, JD ; Li, M ; Zhang, X-H (FRONTIERS MEDIA SA, 2021-08-02)
    Metagenomics and metatranscriptomics are powerful methods to uncover key micro-organisms and processes driving biogeochemical cycling in natural ecosystems. Databases dedicated to depicting biogeochemical pathways (for example, metabolism of dimethylsulfoniopropionate (DMSP), which is an abundant organosulfur compound) from metagenomic/metatranscriptomic data are rarely seen. Additionally, a recognized normalization model to estimate the relative abundance and environmental importance of pathways from metagenomic and metatranscriptomic data has not been organized to date. These limitations impact the ability to accurately relate key microbial-driven biogeochemical processes to differences in environmental conditions. Thus, an easy-to-use, specialized tool that infers and visually compares the potential for biogeochemical processes, including DMSP cycling, is urgently required. To solve these issues, we developed DiTing, a tool wrapper to infer and compare biogeochemical pathways among a set of given metagenomic or metatranscriptomic reads in one step, based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) and a manually created DMSP cycling gene database. Accurate and specific formulae for over 100 pathways were developed to calculate their relative abundance. Output reports detail the relative abundance of biogeochemical pathways in both text and graphical format. DiTing was applied to simulated metagenomic data and resulted in consistent genetic features of simulated benchmark genomic data. Subsequently, when applied to natural metagenomic and metatranscriptomic data from hydrothermal vents and the Tara Ocean project, the functional profiles predicted by DiTing were correlated with environmental condition changes. DiTing can now be confidently applied to wider metagenomic and metatranscriptomic datasets, and it is available at https://github.com/xuechunxu/DiTing.
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    sandpyper: A Python package for UAV-SfM beach volumetric and behavioural analysis
    Pucino, N ; Kennedy, D ; Ierodiaconou, D (The Open Journal, 2021-10-13)
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    Do-It-Together: Collective action in and against the Anthropocene
    Singer, H ; Dunn, A ; Laird, T ; Lavau, S ; Verlie, B (Feral Feminisms Publishing, 2021)
    This special issue features creative-critical responses to the theme, “Hacking the Anthropocene: Do-It-Together (DIT).” The “Anthropocene” is a term that has gained significant cultural and academic cache, even though it is wildly out of touch with the analyses and calls of such movements as Black Lives Matter, #MeToo, youth climate strikers and land defender activists. Building on the work of critical feminists Astrida Neimanis and Jennifer Hamilton (and collaborators), in this editorial we explore hacking as a multivalent method for resisting, ejecting, adapting and disrupting the anthropocentric “settler atmospherics” (Simmons 2017) of our times. Considering how we might hack the Anthropocene together, the works in this special issue negotiate a series of co-constitutive tensions, between inclusion/exclusion, good/bad relations, and holding on/letting go. They not only question who or what the “we” in the “together” is, they also trouble the “it,” and ask what it means to “do,” or even be, together.
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    Pelage variation in dingoes across southeastern Australia: implications for conservation and management
    Cairns, KM ; Newman, KD ; Crowther, MS ; Letnic, M (WILEY, 2021-06)
    Abstract How to manage hybridization and introgression in wild animals is controversial. Wildlife managers and researchers may often rely upon phenotypic variables such as coat colour to inform on ground management decisions. In Australia, dingoes are typically believed to be ginger in colour, and unusual coat colours such as brindle or sable are widely posited to be evidence of contemporary domestic dog hybridization. We carried out microsatellite‐based genotyping on 1325 wild canids from southeastern Australia of known coat colour to estimate the extent of domestic dog introgression. A key aim of our study was to examine the relationship between coat colour and ancestry in wild dingoes. We observed that 27.4% of our samples were dingoes with no evidence of domestic dog ancestry whilst 72.6% were dingoes with some domestic dog ancestry. Our data confirm that feral dogs, domestic dogs with no dingo ancestry, are rare in the wild, representing less than 1.5% of the population. There was no coat colour that could distinguish dingoes with or without dog ancestry from each other. Contrary to popular belief, colours such as brindle and patchy were positively associated with dingoes with no dog ancestry and were less common in dingoes of mixed ancestry. A key finding of this work is that coat colour should not be used to assess ancestry in dingoes. Further research is needed to uncover the antiquity, origin and potential adaptive value of these genomic regions. It is possible that this is a similar example of adaptive introgression as has been observed in North American wolves with black coat colour. These data add perspective to global debates about how to manage and conserve enigmatic animal populations in the presence of modern or historical introgression.
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    Rapidly assessing cobenefits to advance threat-management alliances.
    Rees, MW ; Carwardine, J ; Reeson, A ; Firn, J (Wiley, 2020-08)
    Conservation strategies aimed at reducing threats to biodiversity can have significant implications for multiple sectors in a socioeconomic system, but these cobenefits are often poorly understood. For example, many of the threats to native species also impede agricultural production, yet agriculture is typically perceived as in competition with conservation objectives. Although a comprehensive, multiobjective decision analysis is usually beyond the scope and capacity of conservation decision makers, failing to incorporate key socioeconomic costs and benefits into conservation decision-making processes can result in missed opportunities for diversifying outcomes and creating cost-sharing multisectoral partnerships. We devised a straightforward and readily interpretable approach to incorporate cobenefits into a threat-management prioritization approach. We used it to analyze the agricultural cobenefits of implementing 9 invasive animal management strategies designed to ensure the persistence of 148 threatened species across Australia's Lake Eyre Basin over 50 years. A structured elicitation process with 24 participants (scientists, land managers, agriculturalists, and other stakeholders) was used to collect information on each strategy, including costs, technical and social feasibility, benefits to native threatened species, and cobenefits to agricultural production systems. The costs of targeted invasive animal management to save threatened species across the basin (AU$33 million/year) outweighed the overall benefits to the agricultural industry (estimated AU$226 million/year). The return on investment for these management strategies varied substantially when agricultural cobenefits were considered alongside threatened species benefits and showed synergies and challenges. Our approach demonstrates the value of incorporating cobenefits of conservation actions into cost-effectiveness analyses to guide potential investment and partnerships and to diversify implementation pathways.