Ferredoxin containing bacteriocins suggest a novel mechanism of iron uptake in <i>Pectobacterium spp</i>

In order to kill competing strains of the same or closely related bacterial species, many bacteria produce potent narrow-spectrum protein antibiotics known as bacteriocins. Two sequenced strains of the phytopathogenic bacterium &lt;i&gt;Pectobacterium carotovorum&lt;/i&gt; carry genes encoding putative bacteriocins which have seemingly evolved through a recombination event to encode proteins containing an N-terminal domain with extensive similarity to a [2Fe-2S] plant ferredoxin and a C-terminal colicin M-like catalytic domain. In this work, we show that these genes encode active bacteriocins, pectocin M1 and M2, which target strains of &lt;i&gt;Pectobacterium carotovorum&lt;/i&gt; and &lt;i&gt;Pectobacterium atrosepticum&lt;/i&gt; with increased potency under iron limiting conditions. The activity of pectocin M1 and M2 can be inhibited by the addition of spinach ferredoxin, indicating that the ferredoxin domain of these proteins acts as a receptor binding domain. This effect is not observed with the mammalian ferredoxin protein adrenodoxin, indicating that &lt;i&gt;Pectobacterium spp.&lt;/i&gt; carries a specific receptor for plant ferredoxins and that these plant pathogens may acquire iron from the host through the uptake of ferredoxin. In further support of this hypothesis we show that the growth of strains of &lt;i&gt;Pectobacterium carotovorum&lt;/i&gt; and &lt;i&gt;atrosepticum&lt;/i&gt; that are not sensitive to the cytotoxic effects of pectocin M1 is enhanced in the presence of pectocin M1 and M2 under iron limiting conditions. A similar growth enhancement under iron limiting conditions is observed with spinach ferrodoxin, but not with adrenodoxin. Our data indicate that pectocin M1 and M2 have evolved to parasitise an existing iron uptake pathway by using a ferredoxin-containing receptor binding domain as a Trojan horse to gain entry into susceptible cells

Manifold Elastic Net: A Unified Framework for Sparse Dimension Reduction

It is difficult to find the optimal sparse solution of a manifold learning based dimensionality reduction algorithm. The lasso or the elastic net penalized manifold learning based dimensionality reduction is not directly a lasso penalized least square problem and thus the least angle regression (LARS) (Efron et al. \cite{LARS}), one of the most popular algorithms in sparse learning, cannot be applied. Therefore, most current approaches take indirect ways or have strict settings, which can be inconvenient for applications. In this paper, we proposed the manifold elastic net or MEN for short. MEN incorporates the merits of both the manifold learning based dimensionality reduction and the sparse learning based dimensionality reduction. By using a series of equivalent transformations, we show MEN is equivalent to the lasso penalized least square problem and thus LARS is adopted to obtain the optimal sparse solution of MEN. In particular, MEN has the following advantages for subsequent classification: 1) the local geometry of samples is well preserved for low dimensional data representation, 2) both the margin maximization and the classification error minimization are considered for sparse projection calculation, 3) the projection matrix of MEN improves the parsimony in computation, 4) the elastic net penalty reduces the over-fitting problem, and 5) the projection matrix of MEN can be interpreted psychologically and physiologically. Experimental evidence on face recognition over various popular datasets suggests that MEN is superior to top level dimensionality reduction algorithms.Comment: 33 pages, 12 figure

A 'Performative' Social Movement: The Emergence of Collective Contentions within Collaborative Governance

The enmeshment of urban movements in networks of collaborative governance has been characterised as a process of co-option in which previously disruptive contentions are absorbed by regimes and reproduced in ways that do not threaten the stability of power relations. Applying a theoretical framework drawn from feminist philosopher Judith Butler this paper directs attention to the development of collective oppositional identities that remain embedded in conventional political processes. In a case study of the English tenants' movement, it investigates the potential of regulatory discourses that draw on market theories of performative voice to offer the collectivising narratives and belief in change that can generate the emotional identification of a social movement. The paper originates the concept of the ‘performative social movement’ to denote the contentious claims that continue to emerge from urban movements that otherwise appear quiescent

The truth and beauty of chemical potentials

This essay in honour of Mike Brown addresses aspects of chemical equilibrium and equilibration in rocks, with a focus on the role that chemical potentials play. Chemical equilibrium is achieved by diffusive attening of chemical potential gradients. The idea of equilibration volume is developed, and the way equilibration volumes may evolve along a pressure-temperature path is discussed. The effect of the environment of an equilibration volume is key to understanding the evolution of the equilibration volume with changing conditions. The likely behaviour of equilibration volumes is used to suggest why preservation of equilibrium mineral assemblages and mineral compositions from metamorphism tends to occur. This line of logic then provides the conceptual support to conventional equilibrium thermodynamic approaches to studying rocks, using, for example, thermobarometry and pseudosections.PostprintPeer reviewe

Europe's lost forests: a pollen-based synthesis for the last 11,000 years

8000 years ago, prior to Neolithic agriculture, Europe was mostly a wooded continent. Since then, its forest cover has been progressively fragmented, so that today it covers less than half of Europe’s land area, in many cases having been cleared to make way for fields and pasture-land. Establishing the origin of Europe’s current, more open land-cover mosaic requires a long-term perspective, for which pollen analysis offers a key tool. In this study we utilise and compare three numerical approaches to transforming pollen data into past forest cover, drawing on >1000 14C-dated site records. All reconstructions highlight the different histories of the mixed temperate and the northern boreal forests, with the former declining progressively since ~6000 years ago, linked to forest clearance for agriculture in later prehistory (especially in northwest Europe) and early historic times (e.g. in north central Europe). In contrast, extensive human impact on the needle-leaf forests of northern Europe only becomes detectable in the last two millennia and has left a larger area of forest in place. Forest loss has been a dominant feature of Europe’s landscape ecology in the second half of the current interglacial, with consequences for carbon cycling, ecosystem functioning and biodiversity

The Polar Amplification Model Intercomparison Project (PAMIP) contribution to CMIP6: Investigating the causes and consequences of polar amplification

This is the final version. Available on open access from the European Geosciences Union via the DOI in this recordPolar amplification-the phenomenon where external radiative forcing produces a larger change in surface temperature at high latitudes than the global average-is a key aspect of anthropogenic climate change, but its causes and consequences are not fully understood. The Polar Amplification Model Intercomparison Project (PAMIP) contribution to the sixth Coupled Model Intercomparison Project (CMIP6; Eyring et al., 2016) seeks to improve our understanding of this phenomenon through a coordinated set of numerical model experiments documented here. In particular, PAMIP will address the following primary questions: (1) what are the relative roles of local sea ice and remote sea surface temperature changes in driving polar amplification? (2) How does the global climate system respond to changes in Arctic and Antarctic sea ice? These issues will be addressed with multi-model simulations that are forced with different combinations of sea ice and/or sea surface temperatures representing present-day, pre-industrial and future conditions. The use of three time periods allows the signals of interest to be diagnosed in multiple ways. Lower-priority tier experiments are proposed to investigate additional aspects and provide further understanding of the physical processes. These experiments will address the following specific questions: what role does ocean-atmosphere coupling play in the response to sea ice? How and why does the atmospheric response to Arctic sea ice depend on the pattern of sea ice page1140 forcing? How and why does the atmospheric response to Arctic sea ice depend on the model background state? What have been the roles of local sea ice and remote sea surface temperature in polar amplification, and the response to sea ice, over the recent period since 1979? How does the response to sea ice evolve on decadal and longer timescales? A key goal of PAMIP is to determine the real-world situation using imperfect climate models. Although the experiments proposed here form a coordinated set, we anticipate a large spread across models. However, this spread will be exploited by seeking "emergent constraints" in which model uncertainty may be reduced by using an observable quantity that physically explains the intermodel spread. In summary, PAMIP will improve our understanding of the physical processes that drive polar amplification and its global climate impacts, thereby reducing the uncertainties in future projections and predictions of climate change and variability.DECC/Defra Met Office Hadley Centre Climate ProgrammeEuropean Union Horizon 2020Natural Environment Research Council (NERC)National Science Foundation (NSF)Korean Polar Research InstituteBMBFArCSInderDe

The inflammatory microenvironment in colorectal neoplasia

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