Visualization of pseudogenes in intracellular bacteria reveals the different tracks to gene destruction

Variably present genes and pseudogenes in Rickettsia species tend to have been acquired more recently and to be more divergent from the genes conserved across all specie

Alkali interactions with a calcium manganite oxygen carrier used in chemical looping combustion

Chemical-Looping Combustion (CLC) of biofuels is a promising technology for cost-efficient CO2 separation and can lead to negative CO2 emissions when combined with carbon capture and storage. A potential challenge in developing CLC technology is the effects of alkali metal-containing compounds released during fuel conversion. This study investigates the interactions between alkali and an oxygen carrier (OC), CaMn0.775Ti0.125Mg0.1O3-δ, to better understand the fate of alkali in CLC. A laboratory-scale fluidized bed reactor is operated at 800–900 \ub0C in oxidizing, reducing and inert atmospheres to mimic CLC conditions. Alkali is fed to the reactor as aerosol KCl particles, and alkali in the exhaust is measured online with a surface ionization detector. The alkali concentration changes with gas environment, temperature, and alkali loading, and the concentration profile has excellent reproducibility over repeated redox cycles. Alkali-OC interactions are dominated by alkali uptake under most conditions, except for a release during OC reduction. Uptake is significant during stable reducing conditions, and is limited under oxidizing conditions. The total uptake during a redox cycle is favored by a high alkali loading, while the influence of temperature is weak. The implications for the understanding of alkali behavior in CLC and further development are discussed

Alkali-wall interactions in a laboratory-scale reactor for chemical looping combustion studies

Alkali metal-containing compounds are readily released during thermal conversion of solid fuels, and may have both detrimental and beneficial effects on chemical looping combustion. Here, we characterize alkali interactions with the inner walls of a laboratory-scale reactor under oxidizing, reducing and inert conditions at temperatures up to 900 \ub0C. KCl aerosol particles are continuously introduced to the stainless steel reactor and the alkali concentration is measured on-line with a surface ionization detector. Aerosol particles evaporate at temperatures above 500 \ub0C and KCl molecules rapidly diffuse to the reactor wall. Up to 92% of the alkali reaching the wall below 700 \ub0C remains adsorbed, while re-evaporation is important at higher temperatures, where up to 74% remains adsorbed. Transient changes in alkali concentration are observed during repeated redox cycles, which are associated with changes in chemical composition of the wall material. Metal oxides on the reactor wall are partially depleted under reducing conditions, which allow for the formation of a new potassium-rich phase that is stable in a reducing atmosphere, but not under inert conditions. The observed wall effects are concluded to be extensive and include major transient effects depending on gas composition, and the implications for laboratory studies and improved experimental methodology are discussed

Influence of reed beds (Phragmites australis) and submerged vegetation on pike (Esox lucius)

Eutrophication and reduced grazing have led to an expansion of the common reed (Phragmites australis) in ar-chipelago areas in the Baltic Sea, while at the same time the composition of submerged vegetation has changed. Although reed is important as nursery habitat for many fish species, extensive emergent vegetation may reduce biodiversity and abundance of predatory fish. Pike (Esox lucius) is a predatory fish whose larvae and young-of -the-year find both food and shelter in reed but use different micro-habitats during different life-stages. Here we investigate the influence of reed and submerged vegetation on abundance and body size of adult pike during the spawning season. We predicted that coastal bays with extensive but heterogeneous reed beds with higher cover of submerged vegetation would have more and larger pike than bays with smaller, homogenous reed belts or with less submerged vegetation. To test these predictions, we estimated abundance and size-structure of adult pike from catches in angling fishing among 22 bays in the Stockholm archipelago at the Swedish Baltic Sea coast. Our analyses show that catches of adult pike were positively associated with both extensive reed beds and cover of rooted submerged vegetation. However, pike size was not correlated with any vegetation variable, but instead increased with wave exposure and bay area. Our study suggests that reed beds and submerged vegetation are important for adult pike during the spawning season, and even the most extensive reed beds had no evident negative effect on pike populations. We could not see any clear relationship between emergent reed habitat and cover of submerged vegetation among the studied bays, and conclude that to maintain pike population during the spawning season it is important that coastal bays have sufficient amounts of both reed beds and rooted submerged vegetation

Tractable non-local correlation density functionals for flat surfaces and slabs

A systematic approach for the construction of a density functional for van der Waals interactions that also accounts for saturation effects is described, i.e. one that is applicable at short distances. A very efficient method to calculate the resulting expressions in the case of flat surfaces, a method leading to an order reduction in computational complexity, is presented. Results for the interaction of two parallel jellium slabs are shown to agree with those of a recent RPA calculation (J.F. Dobson and J. Wang, Phys. Rev. Lett. 82, 2123 1999). The method is easy to use; its input consists of the electron density of the system, and we show that it can be successfully approximated by the electron densities of the interacting fragments. Results for the surface correlation energy of jellium compare very well with those of other studies. The correlation-interaction energy between two parallel jellia is calculated for all separations d, and substantial saturation effects are predicted.Comment: 10 pages, 6 figure

Effects of seasonal spawning closures on pike (<i>Esox lucius</i> L.) and perch (<i>Perca fluviatilis</i> L.) catches and coastal food webs in the western Baltic Sea

Marine protected areas have become one of the main tools in the battle to curb marine biodiversity loss and habitat degradation. Yet, implementation of permanent fishery closures has often generated resource user conflicts that ultimately undermine conservation goals. Here we assessed the influence of an alternative and often more accepted measure – seasonal fish spawning closures – on large predatory fish and coastal food webs in the western Baltic Sea (Sweden). In spring 2017, we conducted a multivariable field survey in 11 seasonal closures and 11 paired references areas open to fishing. In each area, pike was sampled through angling, and perch and mesopredators through gillnet surveys. To assess trophic cascades, we measured zooplankton abundance and loss of tethered gammarids from predation. Catches per unit effort of northern pike (Esox lucius) – the main target species in recreational fisheries – were ca. 2.5 times higher per unit effort in closures than reference areas; an effect that may be caused by higher abundance and/or higher catchability of pike in the absence of fishing. Catch and weight per unit effort of the more common predator European perch (Perca fluviatilus), and the mesopredators roach (Rutilus rutilus) and three-spined stickleback (Gasterosteus aculeatus) in survey nets were, however, unaffected by closures. Moreover, a previously hypothesized trophic cascade from perch to zooplankton via three-spined stickleback was supported by the analyses, but appeared independent of closures. Yet, predation risk for tethered gammarid amphipods (a prey of stickleback and an important grazer on macroalgae) was three times higher in fished areas than in closures; a cascading closure effect that may potentially be caused by small predatory fish being less active in protected areas to avoid pike predation. Overall, our results suggest that spawning closures impact pike abundance and/or behavior and could help limit the effects of fishing, but that more research is needed to disentangle i) what mechanism(s) that underlie the protection effect on pike catches, ii) the apparently weaker closure impacts on other fish species, as well as iii) the potential for cascading effects on lower trophic levels. Therefore, new seasonal spawning closures should be implemented in addition to (and not instead of) much-needed permanent closures, which have well-known effects on the wider ecosystem.</p

Effects of seasonal spawning closures on pike (Esox lucius L.) and perch (Percafluviatilis L.) catches and coastal food webs in the western Baltic Sea

Marine protected areas have become one of the main tools in the battle to curb marine biodiversity loss and habitat degradation. Yet, implementation of permanent fishery closures has often generated resource user conflicts that ultimately undermine conservation goals. Here we assessed the influence of an alternative and often more accepted measure - seasonal fish spawning closures - on large predatory fish and coastal food webs in the western Baltic Sea (Sweden). In spring 2017, we conducted a multivariable field survey in 11 seasonal closures and 11 paired references areas open to fishing. In each area, pike was sampled through angling, and perch and mesopredators through gillnet surveys. To assess trophic cascades, we measured zooplankton abun-dance and loss of tethered gammarids from predation. Catches per unit effort of northern pike (Esox lucius) - the main target species in recreational fisheries - were ca. 2.5 times higher per unit effort in closures than reference areas; an effect that may be caused by higher abundance and/or higher catchability of pike in the absence of fishing. Catch and weight per unit effort of the more common predator European perch (Perca fluviatilus), and the mesopredators roach (Rutilus rutilus) and three-spined stickleback (Gasterosteus aculeatus) in survey nets were, however, unaffected by closures. Moreover, a previously hypothesized trophic cascade from perch to zooplankton via three-spined stickleback was supported by the analyses, but appeared independent of closures. Yet, predation risk for tethered gammarid amphipods (a prey of stickleback and an important grazer on mac-roalgae) was three times higher in fished areas than in closures; a cascading closure effect that may potentially be caused by small predatory fish being less active in protected areas to avoid pike predation. Overall, our results suggest that spawning closures impact pike abundance and/or behavior and could help limit the effects of fishing, but that more research is needed to disentangle i) what mechanism(s) that underlie the protection effect on pike catches, ii) the apparently weaker closure impacts on other fish species, as well as iii) the potential for cascading effects on lower trophic levels. Therefore, new seasonal spawning closures should be implemented in addition to (and not instead of) much-needed permanent closures, which have well-known effects on the wider ecosystem

Unified Treatment of Asymptotic van der Waals Forces

In a framework for long-range density-functional theory we present a unified full-field treatment of the asymptotic van der Waals interaction for atoms, molecules, surfaces, and other objects. The only input needed consists of the electron densities of the interacting fragments and the static polarizability or the static image plane, which can be easily evaluated in a ground-state density-functional calculation for each fragment. Results for separated atoms, molecules, and for atoms/molecules outside surfaces are in agreement with those of other, more elaborate, calculations.Comment: 6 pages, 5 figure

The global build-up to intrinsic edge localized mode bursts seen in divertor full flux loops in JET

A global signature of the build-up to an intrinsic edge localized mode (ELM) is found in the temporal analytic phase of signals measured in full flux azimuthal loops in the divertor region of JET. Toroidally integrating, full flux loop signals provide a global measurement proportional to the voltage induced by changes in poloidal magnetic flux; they are electromagnetically induced by the dynamics of spatially integrated current density. We perform direct time-domain analysis of the high time-resolution full flux loop signals VLD2 and VLD3. We analyze plasmas where a steady H-mode is sustained over several seconds during which all the observed ELMs are intrinsic; there is no deliberate intent to pace the ELMing process by external means. ELM occurrence times are determined from the Be II emission at the divertor. We previously [Chapman et al., Phys. Plasmas 21, 062302 (2014); Chapman et al., in 41st EPS Conference on Plasma Physics, Europhysics Conference Abstracts (European Physical Society, 2014), Vol. 38F, ISBN 2-914771-90-8] found that the occurrence times of intrinsic ELMs correlate with specific temporal analytic phases of the VLD2 and VLD3 signals. Here, we investigate how the VLD2 and VLD3 temporal analytic phases vary with time in advance of the ELM occurrence time. We identify a build-up to the ELM in which the VLD2 and VLD3 signals progressively align to the temporal analytic phase at which ELMs preferentially occur, on a ∼2−5ms timescale. At the same time, the VLD2 and VLD3 signals become temporally phase synchronized with each other, consistent with the emergence of coherent global dynamics in the integrated current density. In a plasma that remains close to a global magnetic equilibrium, this can reflect bulk displacement or motion of the plasma. This build-up signature to an intrinsic ELM can be extracted from a time interval of data that does not extend beyond the ELM occurrence time, so that these full flux loop signals could assist in ELM prediction or mitigation

The Rose-comb Mutation in Chickens Constitutes a Structural Rearrangement Causing Both Altered Comb Morphology and Defective Sperm Motility

Rose-comb, a classical monogenic trait of chickens, is characterized by a drastically altered comb morphology compared to the single-combed wild-type. Here we show that Rose-comb is caused by a 7.4 Mb inversion on chromosome 7 and that a second Rose-comb allele arose by unequal crossing over between a Rose-comb and wild-type chromosome. The comb phenotype is caused by the relocalization of the MNR2 homeodomain protein gene leading to transient ectopic expression of MNR2 during comb development. We also provide a molecular explanation for the first example of epistatic interaction reported by Bateson and Punnett 104 years ago, namely that walnut-comb is caused by the combined effects of the Rose-comb and Pea-comb alleles. Transient ectopic expression of MNR2 and SOX5 (causing the Pea-comb phenotype) occurs in the same population of mesenchymal cells and with at least partially overlapping expression in individual cells in the comb primordium. Rose-comb has pleiotropic effects, as homozygosity in males has been associated with poor sperm motility. We postulate that this is caused by the disruption of the CCDC108 gene located at one of the inversion breakpoints. CCDC108 is a poorly characterized protein, but it contains a MSP (major sperm protein) domain and is expressed in testis. The study illustrates several characteristic features of the genetic diversity present in domestic animals, including the evolution of alleles by two or more consecutive mutations and the fact that structural changes have contributed to fast phenotypic evolution