The activity of bacteriophages poses a major threat to bacterial survival. Upon infection, a temperate phage can either kill the host cell or be maintained as a prophage. In this state, the bacteria ...carrying the prophage is at risk of superinfection, where another phage injects its genetic material and competes for host cell resources. To avoid this, many phages have evolved mechanisms that alter the bacteria and make it resistant to phage superinfection. The mechanisms underlying these phentoypic conversions and the fitness consequences for the host are poorly understood, and systematic studies of superinfection exclusion mechanisms are lacking. In this study, we examined a wide range of Pseudomonas aeruginosa phages and found that they mediate superinfection exclusion through a variety of mechanisms, some of which affected the type IV pilus and O-antigen, and others that functioned inside the cell. The strongest resistance mechanism was a surface modification that we showed is cost-free for the bacterial host in a natural soil environment and in a Caenorhabditis. elegans infection model. This study represents the first systematic approach to address how a population of prophages influences phage resistance and bacterial behavior in P. aeruginosa.
Habitat loss and fragmentation has long been considered the primary cause for biodiversity loss and ecosystem degradation worldwide, and is a key research topic in landscape ecology.
RNA interference (RNAi) pathways have evolved as important modulators of gene expression that operate in the cytoplasm by degrading RNA target molecules through the activity of short (21-30 ...nucleotide) RNAs. RNAi components have been reported to have a role in the nucleus, as they are involved in epigenetic regulation and heterochromatin formation. However, although RNAi-mediated post-transcriptional gene silencing is well documented, the mechanisms of RNAi-mediated transcriptional gene silencing and, in particular, the role of RNAi components in chromatin dynamics, especially in animal multicellular organisms, are elusive. Here we show that the key RNAi components Dicer 2 (DCR2) and Argonaute 2 (AGO2) associate with chromatin (with a strong preference for euchromatic, transcriptionally active, loci) and interact with the core transcription machinery. Notably, loss of function of DCR2 or AGO2 showed that transcriptional defects are accompanied by the perturbation of RNA polymerase II positioning on promoters. Furthermore, after heat shock, both Dcr2 and Ago2 null mutations, as well as missense mutations that compromise the RNAi activity, impaired the global dynamics of RNA polymerase II. Finally, the deep sequencing of the AGO2-associated small RNAs (AGO2 RIP-seq) revealed that AGO2 is strongly enriched in small RNAs that encompass the promoter regions and other regions of heat-shock and other genetic loci on both the sense and antisense DNA strands, but with a strong bias for the antisense strand, particularly after heat shock. Taken together, our results show that DCR2 and AGO2 are globally associated with transcriptionally active loci and may have a pivotal role in shaping the transcriptome by controlling the processivity of RNA polymerase II.
Since amphibian declines were first proposed as a global phenomenon over a quarter century ago, the conservation community has made little progress in halting or reversing these trends. The early ...search for a "smoking gun" was replaced with the expectation that declines are caused by multiple drivers. While field observations and experiments have identified factors leading to increased local extinction risk, evidence for effects of these drivers is lacking at large spatial scales. Here, we use observations of 389 time-series of 83 species and complexes from 61 study areas across North America to test the effects of 4 of the major hypothesized drivers of declines. While we find that local amphibian populations are being lost from metapopulations at an average rate of 3.79% per year, these declines are not related to any particular threat at the continental scale; likewise the effect of each stressor is variable at regional scales. This result - that exposure to threats varies spatially, and populations vary in their response - provides little generality in the development of conservation strategies. Greater emphasis on local solutions to this globally shared phenomenon is needed.
The Data‐Intensive Farm Management (DIFM) project works with participating farmers, using precision technology to inexpensively design and run randomized agronomic field trials on whole commercial ...farm fields, to provide data‐based, site‐specific farm input management guidance, thus providing economic and environmental benefits. This article lays out a conceptual framework used by the multidisciplinary DIFM research team to facilitate collaboration and then presents details of DIFM's procedures for what it calls on‐farm precision experimentation (OFPE), which includes field trial design and implementation, data generation, processing, and management, and analysis. It is argued that DIFM's data and the agricultural “Big Data” currently being collected with remote and proximal sensors are complementary; that is, more of either increases the value of the other. In 2019, DIFM and affiliates conducted over 120 trials, ranging from 10 to 100 ha in size, on maize, wheat, soybeans, cotton, and barley in eight US states, Argentina, Brazil, and South Africa. The DIFM is developing cyberinfrastructure to “scale up” its activities, to permit researchers and crop consultants worldwide to work with farmers to conduct trials, then process and manage the data. In Addition, DIFM is in the early stages of developing a software system for semi‐automatic data analytics, and a cloud‐based farm management aid, the purpose of which is to facilitate conversations between agronomists and farmers about implementing data‐driven input management decisions. The proposed framework allows researchers, agronomists, and farmers to carry out on‐farm precision experimentation using novel digital tools.
Core Ideas
The Data‐Intensive Farm Management project's on‐farm trials can generate massive amounts varied managed input data.
The Data‐Intensive Farm Management project's data fill a gap in agricultural “Big Data,” to enable data‐intensive crop management.
The Data‐Intensive Farm Management project's protocols support trial design, data processing and analysis.
The Data‐Intensive Farm Management project can be implemented by researchers, consultants, and farmers in diverse agronomic scenarios.
The potential habitability of known exoplanets is often categorized by a nominal equilibrium temperature assuming a Bond albedo of either ∼0.3, similar to Earth, or 0. As an indicator of ...habitability, this leaves much to be desired, because albedos of other planets can be very different, and because surface temperature exceeds equilibrium temperature due to the atmospheric greenhouse effect. We use an ensemble of general circulation model simulations to show that for a range of habitable planets, much of the variability of Bond albedo, equilibrium temperature and even surface temperature can be predicted with useful accuracy from incident stellar flux and stellar temperature, two known parameters for every confirmed exoplanet. Earth's Bond albedo is near the minimum possible for habitable planets orbiting G stars, because of increasing contributions from clouds and sea ice/snow at higher and lower instellations, respectively. For habitable M star planets, Bond albedo is usually lower than Earth's because of near-IR H2O absorption, except at high instellation where clouds are important. We apply relationships derived from this behavior to several known exoplanets to derive zeroth-order estimates of their potential habitability. More expansive multivariate statistical models that include currently non-observable parameters show that greenhouse gas variations produce significant variance in albedo and surface temperature, while increasing length of day and land fraction decrease surface temperature; insights for other parameters are limited by our sampling. We discuss how emerging information from global climate models might resolve some degeneracies and help focus scarce observing resources on the most promising planets.
The nearby exoplanet Proxima Centauri b will be a prime future target for characterization, despite questions about its retention of water. Climate models with static oceans suggest that Proxima b ...could harbor a small dayside surface ocean despite its weak instellation. We present the first climate simulations of Proxima b with a dynamic ocean. We find that an ocean-covered Proxima b could have a much broader area of surface liquid water but at much colder temperatures than previously suggested, due to ocean heat transport and/or depression of the freezing point by salinity. Elevated greenhouse gas concentrations do not necessarily produce more open ocean because of dynamical regime transitions between a state with an equatorial Rossby-Kelvin wave pattern and a state with a day-night circulation. For an evolutionary path leading to a highly saline ocean, Proxima b could be an inhabited, mostly open ocean planet with halophilic life. A freshwater ocean produces a smaller liquid region than does an Earth salinity ocean. An ocean planet in 3:2 spin-orbit resonance has a permanent tropical waterbelt for moderate eccentricity. A larger versus smaller area of surface liquid water for similar equilibrium temperature may be distinguishable by using the amplitude of the thermal phase curve. Simulations of Proxima Centauri b may be a model for the habitability of weakly irradiated planets orbiting slightly cooler or warmer stars, for example, in the TRAPPIST-1, LHS 1140, GJ 273, and GJ 3293 systems.
Management authorities seldom have the capacity to comprehensively address the full suite of anthropogenic stressors, particularly in the coastal zone where numerous threats can act simultaneously to ...impact reefs and other ecosystems. This situation requires tools to prioritise management interventions that result in optimum ecological outcomes under a set of constraints. Here we develop one such tool, introducing a Bayesian Belief Network to model the ecological condition of inshore coral reefs in Moreton Bay (Australia) under a range of management actions. Empirical field data was used to model a suite of possible ecological responses of coral reef assemblages to five key management actions both in the sea (e.g. expansion of reserves, mangrove & seagrass restoration, fishing restrictions) and on land (e.g. lower inputs of sediment and sewage from treatment plants). Models show that expanding marine reserves (a 'marine action') and reducing sediment inputs from the catchments (a 'land action') were the most effective investments to achieve a better status of reefs in the Bay, with both having been included in >58% of scenarios with positive outcomes, and >98% of the most effective (5th percentile) scenarios. Heightened fishing restrictions, restoring habitats, and reducing nutrient discharges from wastewater treatment plants have additional, albeit smaller effects. There was no evidence that combining individual management actions would consistently produce sizeable synergistic until after maximum investment on both marine reserves (i.e. increasing reserve extent from 31 to 62% of reefs) and sediments (i.e. rehabilitating 6350 km of waterways within catchments to reduce sediment loads by 50%) were implemented. The method presented here provides a useful tool to prioritize environmental actions in situations where multiple competing management interventions exist for coral reefs and in other systems subjected to multiple stressor from the land and the sea.
Transgenic plants have been widely adopted by growers to manage the western corn rootworm, Diabrotica virgifera virgifera LeConte, in field corn. Because of reduced efficacy in some Nebraska fields ...after repeated use of Cry3Bb1-expressing hybrids, single plant bioassays were conducted in 2012 and 2013 to characterize the susceptibility of western corn rootworm populations to the rootwormactive proteins Cry3Bb1, mCry3A, and Cry34/35Ab1. Results demonstrate that there are heritable differences in susceptibility of Nebraska western corn rootworm populations to rootworm-active Bt traits. Proportional survival and corrected survival data coupled with field histories collectively support the conclusion that a level of field resistance to Cry3Bb1 has evolved in some Nebraska populations in response to selection pressure and that cross-resistance exists between Cry3Bb1 and mCry3A. There was no apparent cross-resistance between Cry34/35Ab1 and either Cry3Bb1 or mCry3A. The potential implications of these results on current and future corn rootworm management strategies are discussed.
PDF
