The Xp10 bacteriophage protein P7 inhibits transcription by the major and major variant forms of the host RNA polymerase via a common mechanism

The σ factor is a functionally obligatory subunit of the bacterial transcription machinery, the RNA polymerase. Bacteriophage-encoded small proteins that either modulate or inhibit the bacterial RNAP to allow the temporal regulation of bacteriophage gene expression often target the activity of the major bacterial σ factor, σ70. Previously, we showed that during Xanthomonas oryzae phage Xp10 infection, the phage protein P7 inhibits the host RNAP by preventing the productive engagement with the promoter and simultaneously displaces the σ70 factor from the RNAP. In this study, we demonstrate that P7 also inhibits the productive engagement of the bacterial RNAP containing the major variant bacterial σ factor, σ54, with its cognate promoter. The results suggest for the first time that the major variant form of the host RNAP can also be targeted by bacteriophage-encoded transcription regulatory proteins. Since the major and major variant σ factor interacting surfaces in the RNAP substantially overlap, but different regions of σ70 and σ54 are used for binding to the RNAP, our results further underscore the importance of the σ–RNAP interface in bacterial RNAP function and regulation and potentially for intervention by antibacterials

Next-generation microbiology : from comparative genomics to gene function

Microbiology is at a turning point in its 120-year history. Widespread next-generation sequencing has revealed genetic complexity among bacteria that could hardly have been imagined by pioneers such as Pasteur, Escherich and Koch. This data cascade brings enormous potential to improve our understanding of individual bacterial cells and the genetic basis of phenotype variation. However, this revolution in data science cannot replace established microbiology practices, presenting the challenge of how to integrate these new techniques. Contrasting comparative and functional genomic approaches, we evoke molecular microbiology theory and established practice to present a conceptual framework and practical roadmap for next-generation microbiology

Three-dimensional magnetic resonance imaging of the phakic crystalline lens during accommodation

To quantify changes in crystalline lens curvature, thickness, equatorial diameter, surface area, and volume during accommodation using a novel two-dimensional magnetic resonance imaging (MRI) paradigm to generate a complete three-dimensional crystalline lens surface model

Loss of Pde1 function acts as an evolutionary gateway to penicillin resistance in Streptococcus pneumoniae

Streptococcus pneumoniae is a major human pathogen and rising resistance to β-lactam antibiotics, such as penicillin, is a significant threat to global public health. Mutations occurring in the penicillin-binding proteins (PBPs) can confer high-level penicillin resistance but other poorly understood genetic factors are also important. Here, we combined strictly controlled laboratory experiments and population analyses to identify a new penicillin resistance pathway that is independent of PBP modification. Initial laboratory selection experiments identified high-frequency pde1 mutations conferring S. pneumoniae penicillin resistance. The importance of variation at the pde1 locus was confirmed in natural and clinical populations in an analysis of >7,200 S. pneumoniae genomes. The pde1 mutations identified by these approaches reduce the hydrolytic activity of the Pde1 enzyme in bacterial cells and thereby elevate levels of cyclic-di-adenosine monophosphate and penicillin resistance. Our results reveal rapid de novo loss of function mutations in pde1 as an evolutionary gateway conferring low-level penicillin resistance. This relatively simple genomic change allows cells to persist in populations on an adaptive evolutionary pathway to acquire further genetic changes and high-level penicillin resistance

Stable Coexistence of an Invasive Plant and Biocontrol Agent: A Parameterized Coupled Plant-Herbivore Model

1. Coupled plant-herbivore models, allowing feedback from plant to herbivore populations and vice versa, enable us to predict the impact of biocontrol agents on their target weed populations; however, they are rarely used in biocontrol studies. We describe the population biology of the invasive plant Echium plantagineum and the weevil Mogulones larvatus, a biocontrol agent, in Australia. In order to understand the dynamics of this plant-herbivore system, a series of coupled models of increasing complexity was developed. 2. A simple model was extended to include a seed bank, density-dependent plant fecundity, competition between weevil larvae and plant tolerance of herbivory, where below a threshold plants could compensate for larval feeding. Parameters and functional forms were estimated from experimental and field data. 3. The plant model, in the absence of the weevil, exhibited stable dynamics and provided a good quantitative description of field densities before the weevil was introduced. 4. In the coupled plant-herbivore model, density dependence in both plant fecundity and weevil larval competition stabilized the dynamics. Without larval competition the model was unstable, and plant tolerance of herbivory exacerbated this instability. This was a result of a time delay in plant response to herbivore densities. 5. Synthesis and applications. The coupled plant-herbivore model allowed us to predict whether stable coexistence of target plant and biocontrol agents was achievable at an acceptable level. We found this to be the case for the Echium-Mogulones system and believe that similar models would be of use when assessing new agents in this and other invasive plant biocontrol systems. Density dependence in new biocontrol agents should be assessed in order to determine whether it is likely to result in the aims of classical biocontrol: low, stable and sustainable populations of plant and herbivore. Further work should be done to characterize the strength of density dependence according to the niche occupied by the biocontrol agent, for example the strength and functional form of density dependence in stem borers may be quite different to that of defoliators

The Kuiper Belt and Other Debris Disks

We discuss the current knowledge of the Solar system, focusing on bodies in the outer regions, on the information they provide concerning Solar system formation, and on the possible relationships that may exist between our system and the debris disks of other stars. Beyond the domains of the Terrestrial and giant planets, the comets in the Kuiper belt and the Oort cloud preserve some of our most pristine materials. The Kuiper belt, in particular, is a collisional dust source and a scientific bridge to the dusty "debris disks" observed around many nearby main-sequence stars. Study of the Solar system provides a level of detail that we cannot discern in the distant disks while observations of the disks may help to set the Solar system in proper context.Comment: 50 pages, 25 Figures. To appear in conference proceedings book "Astrophysics in the Next Decade

On the reliability of a simple method for scoring phenotypes to estimate heritability: A case study with pupal color in Heliconius erato phyllis, Fabricius 1775 (Lepidoptera, Nymphalidae)

In this paper, two methods for assessing the degree of melanization of pupal exuviae from the butterfly Heliconius erato phyllis, Fabricius 1775 (Lepidoptera, Nymphalidae, Heliconiini) are compared. In the first method, which was qualitative, the exuviae were classified by scoring the degree of melanization, whereas in the second method, which was quantitative, the exuviae were classified by optical density followed by analysis with appropriate software. The heritability (h2) of the degree of melanization was estimated by regression and analysis of variance. The estimates of h 2 were similar with both methods, indicating that the qualitative method could be particularly suitable for field work. The low estimates obtained for heritability may have resulted from the small sample size (n = 7-18 broods, including the parents) or from the allocation-priority hypothesis in which pupal color would be a lower priority trait compared to morphological traits and adequate larval development

What Drives Fitness Apps Usage? An Empirical Evaluation

Part 3: Creating Value through ApplicationsInternational audienceThe increased health problems associated with lack of physical activity is of great concern around the world. Mobile phone based fitness applications appear to be a cost effective promising solution for this problem. The aim of this study is to develop a research model that can broaden understanding of the factors that influence the user acceptance of mobile fitness apps. Drawing from Unified Theory of Acceptance and Use of Technology (UTAUT) and Elaboration Likelihood Model (ELM), we conceptualize the antecedents and moderating factors of fitness app use. We validate our model using field survey. Implications for research and practice are discussed

The geology and geophysics of Kuiper Belt object (486958) Arrokoth

The Cold Classical Kuiper Belt, a class of small bodies in undisturbed orbits beyond Neptune, are primitive objects preserving information about Solar System formation. The New Horizons spacecraft flew past one of these objects, the 36 km long contact binary (486958) Arrokoth (2014 MU69), in January 2019. Images from the flyby show that Arrokoth has no detectable rings, and no satellites (larger than 180 meters diameter) within a radius of 8000 km, and has a lightly-cratered smooth surface with complex geological features, unlike those on previously visited Solar System bodies. The density of impact craters indicates the surface dates from the formation of the Solar System. The two lobes of the contact binary have closely aligned poles and equators, constraining their accretion mechanism

TRY plant trait database – enhanced coverage and open access

Plant traits—the morphological, anatomical, physiological, biochemical and phenological characteristics of plants—determine how plants respond to environmental factors, affect other trophic levels, and influence ecosystem properties and their benefits and detriments to people. Plant trait data thus represent the basis for a vast area of research spanning from evolutionary biology, community and functional ecology, to biodiversity conservation, ecosystem and landscape management, restoration, biogeography and earth system modelling. Since its foundation in 2007, the TRY database of plant traits has grown continuously. It now provides unprecedented data coverage under an open access data policy and is the main plant trait database used by the research community worldwide. Increasingly, the TRY database also supports new frontiers of trait‐based plant research, including the identification of data gaps and the subsequent mobilization or measurement of new data. To support this development, in this article we evaluate the extent of the trait data compiled in TRY and analyse emerging patterns of data coverage and representativeness. Best species coverage is achieved for categorical traits—almost complete coverage for ‘plant growth form’. However, most traits relevant for ecology and vegetation modelling are characterized by continuous intraspecific variation and trait–environmental relationships. These traits have to be measured on individual plants in their respective environment. Despite unprecedented data coverage, we observe a humbling lack of completeness and representativeness of these continuous traits in many aspects. We, therefore, conclude that reducing data gaps and biases in the TRY database remains a key challenge and requires a coordinated approach to data mobilization and trait measurements. This can only be achieved in collaboration with other initiatives