Niche differentiation is spatially and temporally regulated in the rhizosphere.

The rhizosphere is a hotspot for microbial carbon transformations, and is the entry point for root polysaccharides and polymeric carbohydrates that are important precursors to soil organic matter (SOM). However, the ecological mechanisms that underpin rhizosphere carbohydrate depolymerization are poorly understood. Using Avena fatua, a common annual grass, we analyzed time-resolved metatranscriptomes to compare microbial functions in rhizosphere, detritusphere, and combined rhizosphere-detritusphere habitats. Transcripts were binned using a unique reference database generated from soil isolate genomes, single-cell amplified genomes, metagenomes, and stable isotope probing metagenomes. While soil habitat significantly affected both community composition and overall gene expression, the succession of microbial functions occurred at a faster time scale than compositional changes. Using hierarchical clustering of upregulated decomposition genes, we identified four distinct microbial guilds populated by taxa whose functional succession patterns suggest specialization for substrates provided by fresh growing roots, decaying root detritus, the combination of live and decaying root biomass, or aging root material. Carbohydrate depolymerization genes were consistently upregulated in the rhizosphere, and both taxonomic and functional diversity were highest in the combined rhizosphere-detritusphere, suggesting coexistence of rhizosphere guilds is facilitated by niche differentiation. Metatranscriptome-defined guilds provide a framework to model rhizosphere succession and its consequences for soil carbon cycling

Mixed mode data clustering: an approach based on tectrachoric correlations

In this paper we face the problem of clustering mixedmode data by assuming that the observed binary variables aregenerated from latent continuous variables. We perform a principalcomponents analysis on the matrix of tetrachoric correlations and wethen estimate the scores of each latent variable and construct adata matrix with continuous variables to be used in fully Guassianmixture models or in the k-means cluster analysis. The calculationof the expected a posteriori (EAP) estimates may proceed by simplyconsidering a limited number of quadrature points. Results on asimulation study and on a real data set are reported

Dual Routes from Social Identity to Collective Opposition against Criminal Organisations: Intracultural Appropriation Theory and the roles of Honour Codes and Social Change Beliefs

Italian criminal organisations (COs) are a serious global threat. Intracultural Appropriation Theory (ICAT) holds that such groups exploit cultural codes of masculinity and honour to legitimise and lower resistance to their actions. Such codes are an important feature of Southern Italian group membership. A large survey (N = 1173) investigated the role of two previously under-examined facets of honour cultures – personal concerns for reputation, and female honour ideology. In addition, drawing on social identity theory, and testing a dual route hypothesis, this research investigated the role of beliefs about the necessity of social change in the articulation between identification, honour, and collective action intentions. Consistent with ICAT, and with previous research, male-honour related values uniquely predicted collective action intentions against criminal organisations. In addition, consistent with the dual route hypothesis: a) regional identification positively predicted social change beliefs which in turn explained stronger intentions to oppose COs collectively, and, b) regional identification was also positively associated with masculine honour which in turn predicted weaker intentions to oppose COs. The evidence supports the idea that social identity can have opposing effects on collective action in the same context, depending on which beliefs are mobilised

Probing formation of cargo/importin-α transport complexes in plant cells using a pathogen effector

Importin-αs are essential adapter proteins that recruit cytoplasmic proteins destined for active nuclear import to the nuclear transport machinery. Cargo proteins interact with the importin-α armadillo repeat domain via nuclear localization sequences (NLSs), short amino acids motifs enriched in Lys and Arg residues. Plant genomes typically encode several importin-α paralogs that can have both specific and partially redundant functions. Although some cargos are preferentially imported by a distinct importin-α it remains unknown how this specificity is generated and to what extent cargos compete for binding to nuclear transport receptors. Here we report that the effector protein HaRxL106 from the oomycete pathogen Hyaloperonospora arabidopsidis co-opts the host cell's nuclear import machinery. We use HaRxL106 as a probe to determine redundant and specific functions of importin-α paralogs from Arabidopsis thaliana. A crystal structure of the importin-α3/MOS6 armadillo repeat domain suggests that five of the six Arabidopsis importin-αs expressed in rosette leaves have an almost identical NLS-binding site. Comparison of the importin-α binding affinities of HaRxL106 and other cargos in vitro and in plant cells suggests that relatively small affinity differences in vitro affect the rate of transport complex formation in vivo. Our results suggest that cargo affinity for importin-α, sequence variation at the importin-α NLS-binding sites and tissue-specific expression levels of importin-αs determine formation of cargo/importin-α transport complexes in plant cells

An ASKAP Search for a Radio Counterpart to the First High-significance Neutron Star-Black Hole Merger LIGO/Virgo S190814bv

We present results from a search for a radio transient associated with the LIGO/Virgo source S190814bv, a likely neutron star-black hole (NSBH) merger, with the Australian Square Kilometre Array Pathfinder. We imaged a 30 deg2 field at ΔT = 2, 9, and 33 days post-merger at a frequency of 944 MHz, comparing them to reference images from the Rapid ASKAP Continuum Survey observed 110 days prior to the event. Each epoch of our observations covers 89% of the LIGO/Virgo localization region. We conducted an untargeted search for radio transients in this field, resulting in 21 candidates. For one of these, AT2019osy, we performed multiwavelength follow-up and ultimately ruled out the association with S190814bv. All other candidates are likely unrelated variables, but we cannot conclusively rule them out. We discuss our results in the context of model predictions for radio emission from NSBH mergers and place constrains on the circum-merger density and inclination angle of the merger. This survey is simultaneously the first large-scale radio follow-up of an NSBH merger, and the most sensitive widefield radio transients search to-date

An Adaptive Interacting Wang-Landau Algorithm for Automatic Density Exploration

While statisticians are well-accustomed to performing exploratory analysis in the modeling stage of an analysis, the notion of conducting preliminary general-purpose exploratory analysis in the Monte Carlo stage (or more generally, the model-fitting stage) of an analysis is an area which we feel deserves much further attention. Towards this aim, this paper proposes a general-purpose algorithm for automatic density exploration. The proposed exploration algorithm combines and expands upon components from various adaptive Markov chain Monte Carlo methods, with the Wang-Landau algorithm at its heart. Additionally, the algorithm is run on interacting parallel chains -- a feature which both decreases computational cost as well as stabilizes the algorithm, improving its ability to explore the density. Performance is studied in several applications. Through a Bayesian variable selection example, the authors demonstrate the convergence gains obtained with interacting chains. The ability of the algorithm's adaptive proposal to induce mode-jumping is illustrated through a trimodal density and a Bayesian mixture modeling application. Lastly, through a 2D Ising model, the authors demonstrate the ability of the algorithm to overcome the high correlations encountered in spatial models.Comment: 33 pages, 20 figures (the supplementary materials are included as appendices

A Vision for Ice Giant Exploration

From Voyager to a Vision for 2050: NASA and ESA have just completed a study of candidate missionsto Uranus and Neptune, the so-called ice giant planets. It is a Pre-Decadal Survey Study, meant to inform the next Planetary Science Decadal Survey about opportunities for missions launching in the 2020's and early 2030's. There have been no space flight missions to the ice giants since the Voyager 2 flybys of Uranus in 1986 and Neptune in 1989. This paper presents some conclusions of that study (hereafter referred to as The Study), and how the results feed into a vision for where planetary science can be in 2050. Reaching that vision will require investments in technology andground-based science in the 2020's, flight during the 2030's along with continued technological development of both ground- and space-based capabilities, and data analysis and additional flights in the 2040's. We first discuss why exploring the ice giants is important. We then summarize the science objectives identified by The Study, and our vision of the science goals for 2050. We then review some of the technologies needed to make this vision a reality

Broadband polarimetry with the square kilometre array: A unique astrophysical probe

Faraday rotation of polarised background sources is a unique probe of astrophysical magnetic fields in a diverse range of foreground objects. However, to understand the properties of the polarised sources themselves and of depolarising phenomena along the line of sight, we need to complement Faraday rotation data with polarisation observations over very broad bandwidths. Just as it is impossible to properly image a complex source with limited u-v coverage, we can only meaningfully understand the magneto-ionic properties of polarised sources if we have excellent coverage in l2-space. We here propose a set of broadband polarisation surveys with both SKA1 and SKA2, which will provide a singular set of scientific insights on the ways in which galaxies and their environments have evolved over cosmic time

Clades of huge phages from across Earth's ecosystems.

Bacteriophages typically have small genomes1 and depend on their bacterial hosts for replication2. Here we sequenced DNA from diverse ecosystems and found hundreds of phage genomes with lengths of more than 200 kilobases (kb), including a genome of 735 kb, which is-to our knowledge-the largest phage genome to be described to date. Thirty-five genomes were manually curated to completion (circular and no gaps). Expanded genetic repertoires include diverse and previously undescribed CRISPR-Cas systems, transfer RNAs (tRNAs), tRNA synthetases, tRNA-modification enzymes, translation-initiation and elongation factors, and ribosomal proteins. The CRISPR-Cas systems of phages have the capacity to silence host transcription factors and translational genes, potentially as part of a larger interaction network that intercepts translation to redirect biosynthesis to phage-encoded functions. In addition, some phages may repurpose bacterial CRISPR-Cas systems to eliminate competing phages. We phylogenetically define the major clades of huge phages from human and other animal microbiomes, as well as from oceans, lakes, sediments, soils and the built environment. We conclude that the large gene inventories of huge phages reflect a conserved biological strategy, and that the phages are distributed across a broad bacterial host range and across Earth's ecosystems

Perception of structurally distinct effectors by the integrated WRKY domain of a plant immune receptor

Plants use intracellular nucleotide-binding domain (NBD) and leucine-rich repeat (LRR)–containing immune receptors (NLRs) to detect pathogen-derived effector proteins. The Arabidopsis NLR pair RRS1-R/RPS4 confers disease resistance to different bacterial pathogens by perceiving the structurally distinct effectors AvrRps4 from Pseudomonas syringae pv. pisi and PopP2 from Ralstonia solanacearum via an integrated WRKY domain in RRS1-R. How the WRKY domain of RRS1 (RRS1WRKY) perceives distinct classes of effector to initiate an immune response is unknown. Here, we report the crystal structure of the in planta processed C-terminal domain of AvrRps4 (AvrRps4C) in complex with RRS1WRKY. Perception of AvrRps4C by RRS1WRKY is mediated by the β2-β3 segment of RRS1WRKY that binds an electronegative patch on the surface of AvrRps4C. Structure-based mutations that disrupt AvrRps4C–RRS1WRKY interactions in vitro compromise RRS1/RPS4-dependent immune responses. We also show that AvrRps4C can associate with the WRKY domain of the related but distinct RRS1B/RPS4B NLR pair, and the DNA-binding domain of AtWRKY41, with similar binding affinities and how effector binding interferes with WRKY–W-box DNA interactions. This work demonstrates how integrated domains in plant NLRs can directly bind structurally distinct effectors to initiate immunity