174 research outputs found
A trans-splicing group I intron and tRNA-hyperediting in the mitochondrial genome of the lycophyte Isoetes engelmannii
No full textGrewe F, Viehöver P, Weisshaar B, Knoop V. A trans-splicing group I intron and tRNA-hyperediting in the mitochondrial genome of the lycophyte Isoetes engelmannii. Nucleic Acids Research. 2009;37(15):5093-5104
Complete plastid genomes from Ophioglossum californicum, Psilotum nudum, and Equisetum hyemale reveal an ancestral land plant genome structure and resolve the position of Equisetales among monilophytes
No full textFelix Grewe, Wenhu Guo, Emily A. Gubbels, and Jeffrey P. Mower are with the Center for Plant Science Innovation, University of Nebraska, Lincoln, NE, USA -- Felix Grewe and Jeffrey P. Mower are with the Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, USA -- Wenhu Guo, Emily A. Gubbels, and A. Katie Hansen are with the School of Biological Sciences, University of Nebraska, Lincoln, NE, USA – A. Katie Hansen is with College of Natural Sciences, The University of Texas at Austin, Austin, TX, USABackground: Plastid genome structure and content is remarkably conserved in land plants. This widespread conservation has facilitated taxon-rich phylogenetic analyses that have resolved organismal relationships among many land plant groups. However, the relationships among major fern lineages, especially the placement of Equisetales, remain enigmatic.
Results: In order to understand the evolution of plastid genomes and to establish phylogenetic relationships among ferns, we sequenced the plastid genomes from three early diverging species: Equisetum hyemale (Equisetales), Ophioglossum californicum (Ophioglossales), and Psilotum nudum (Psilotales). A comparison of fern plastid genomes showed that some lineages have retained inverted repeat (IR) boundaries originating from the common ancestor of land plants, while other lineages have experienced multiple IR changes including expansions and inversions. Genome content has remained stable throughout ferns, except for a few lineage-specific losses of genes and introns. Notably, the losses of the rps16 gene and the rps12i346 intron are shared among Psilotales, Ophioglossales, and Equisetales, while the gain of a mitochondrial atp1 intron is shared between Marattiales and Polypodiopsida. These genomic structural changes support the placement of Equisetales as sister to Ophioglossales + Psilotales and Marattiales as sister to Polypodiopsida. This result is augmented by some molecular phylogenetic analyses that recover the same relationships, whereas others suggest a relationship between Equisetales and Polypodiopsida.
Conclusions: Although molecular analyses were inconsistent with respect to the position of Marattiales and Equisetales, several genomic structural changes have for the first time provided a clear placement of these lineages within the ferns. These results further demonstrate the power of using rare genomic structural changes in cases where molecular data fail to provide strong phylogenetic resolution.Integrative [email protected]
Resolving evolutionary relationships in lichen-forming fungi using diverse phylogenomic datasets and analytical approa.
No full textEvolutionary histories are now being inferred from unprecedented, genome-scale datasets for a broad range of organismal groups. While phylogenomic data has helped in resolving a number of difficult, long-standing questions, constructing appropriate datasets from genomes is not straightforward, particularly in non-model groups. Here we explore the utility of phylogenomic data to infer robust phylogenies for a lineage of closely related lichen-forming fungal species. We assembled multiple, distinct nuclear phylogenomic datasets, ranging from ca. 25 Kb to 16.8 Mb and inferred topologies using both concatenated gene tree approaches and species tree methods based on the multispecies coalescent model. In spite of evidence for rampant incongruence among individual loci, these genome-scale datasets provide a consistent, well-supported phylogenetic hypothesis using both concatenation and multispecies coalescent approaches (ASTRAL-II and SVDquartets). However, the popular full hierarchical coalescent approach implemented in *BEAST provided inconsistent inferences, both in terms of nodal support and topology, with smaller subsets of the phylogenomic data. While comparable, well-supported topologies can be accurately inferred with only a small fraction of the overall genome, consistent results across a variety of datasets and methodological approaches provide reassurance that phylogenomic data can effectively be used to provide robust phylogenies for closely related lichen-forming fungal lineages
Le Conseil de Securité et le contrôle du juge
No full textThis article makes a comparison between the case law of international courts (already examined by the author in another contribution published in the "European Journal of International Law", 2009), and the case law of domestic courts concerning UN and EU targeted sanctions, adopted in the framework of the fight against terrorism. It argues that the said courts have adopted different theoretical approaches, as far as art. 103 of the United Nations Charter is concerned. These approaches are investigated in depth in paragraphs III and IV. In paragraph V, section A, some observations are submitted, aimed at explaining the (legal) reasons behind such different approaches. Some critical reflections focussed particularly on the general approach chosen by the domestic Courts are developed in the folloving section. Finally, the author argues that the theoretical model of the "Balancing of values", adopted by the European Court of Justice in the Kadi Judgment, could be followed also by domestic Courts (by having recourse to domestic constitutional values), in order to counterbalance the legal effects of anti-terrorism measures. Some domestic judgments going this way are examined in the (final) “Addendum”
The epochs of international law
No full textA theoretical overview and detailed analysis of the history of international law from the Middle Ages through to the end of the twentieth century (updated from the 1984 German language edition). Wilhelm Grewe's "Epochen der Völkerrechtsgeschichte" is widely regarded as one of the classic twentieth century works of international law. This revised translation by Michael Byers of Oxford University makes this important book available to non-German readers for the first time. "The Epochs of International Law" provides a theoretical overview and detailed analysis of the history of international law from the Middle Ages, to the Age of Discovery and the Thirty Years War, from Napoleon Bonaparte to the Treaty of Versailles and the Age of the Single Superpower, and does so in a way that reflects Grewe's own experience as one of Germany's leading diplomats and professors of international law. A new chapter, written by Wilhelm Grewe and Michael Byers, updates the book to 1998, making the revised translation of interest to German international lawyers, international relations scholars and historians as well. The author was one of Germany's leading diplomats, serving as West German ambassador to Washington, Tokyo and NATO and was a member of the International Court of Arbitration in The Hague. Subsequently professor of International Law at the University of Freiburg, he remains one of Germany's most famous academic lawyers
Green Flight Trajectories: A REACT4C data analysis
No full textREACT4C is a project that received European funding to investigate whether air traffic across the North Atlantic Ocean can be rerouted such that the resulting climate impact is reduced. The project considered 400 daily flights in each direction. Eight frequently occurring weather situations were identified, based on the strength and location of the jet stream between North America and Europe. It was found that the climate impact could be reduced to a large extent, although the impact reduction potential heavily depends on the direction of flight, the weather pattern under consideration, the climate metric used to quantify climate impact, and the relative importance of climate impact and economic cost during the optimization. The way in which climate-optimal trajectories compare to their cost-optimal counterparts, is still largely unknown. This research examines how the routes are affected by the climate optimization. Two kinds of studies are performed. The first one is a case study, in which the trajectories of one combination of direction, climate metric, weather type and level of climate optimization are compared with the cost- optimal routes. The influence of each of these four case differentiators on the flights is examined as well, using a one-factor-at-a-time approach. A tool is made that can be used to analyze the trajectories of any combination of flight direction, climate metric, weather pattern and level of climate optimization. The second study is a general analysis of the REACT4C routes, taking into account all combinations of the four case differentiators. This study is conducted to unravel general trends in the way direction, metric, weather and level of climate optimization influence the way in which flights are rerouted. The following characteristics are used to quantify how routes are altered. First, the percentage of affected flights is determined. Then, the flight duration and flight distance increments with respect to the cost-optimized flights are computed. Furthermore, the shift in latitude and altitude is also considered. Finally, frequently occurring rerouting schemes are identified, and the percentage of flights belonging to each scheme is determined. It was found in both the case study and the general analysis that the way in which climate-optimized routes compare to their cost-optimized counterparts, highly depends on the direction of flight, the weather pattern and the relative importance of economic cost and climate impact during the optimization. However, the choice of climate metric proved to have hardly any influence on the rerouting strategies. Because of the substantial cross-case differences, the preferred strategy to investigate rerouting characteristics is by making use of the case analysis tool that was created. Nonetheless, the general study unravelled some general trends. The trajectories in general are altered such that the flight duration and flight distance are increased, and the cruise altitude is lowered. Furthermore, generally there are more shifts towards the south than there are towards the north. Increasing the level of climate optimization is shown to result into more extreme route alterations. Flights towards Europe are in general more often north of the original routes than in westbound direction. The climate metric used during the optimization has little to no influence on the way the routes are changed. Finally, no trends in trajectory alterations are distinguishable between the eight weather patterns.Aerospace EngineeringControl & OperationsAircraft Noise & Climate Effects (ANCE
Analysis of driving parameters for green flight trajectories
No full textClimate change is an important problem nowadays. There are several industries causing this problem. One of them is the air transport industry. In order to reduce its induced climate impact there are different approaches: design of new aircrafts or engines, use of alternative fuels, more efficient air traffic management, or re-routing. All of them except re-routing aim on reducing carbon dioxide emissions. Re-routing, on the other hand, aims on reducing the climate impact of non-CO2 emissions (that considerably alter their climate impact depending on the region of the atmosphere where they are released) by increasing slightly the carbon dioxide emissions. This study focuses on this last approach. It establishes an analysis of the results obtained within the REACT4C project (Reducing Emissions from Aviation by Changing Trajectories for the benefit of Climate). The project aims to reduce aircraft induced climate impact in the North Atlantic flight corridor by changes in flight trajectories and considers fleets of around 400 aircraft. Moreover, this project considers eight different weather patterns (three for summer and five for winter), two flight directions (westbound and eastbound), and three climate metrics. Therefore, a total of 48 configurations have to be studied. Moreover it considers six different climate parameters causing the total climate impact. The climate parameters are carbon dioxide, water vapor, contrails, and NOx. The NOx climate impact is obtained as the summation of ozone, methane, and primary mode ozone climate impacts. The results that are analyzed are the climate impact caused by each of the climate parameters and how this climate impact changes when applying gradual changes on the aircraft trajectories. The analysis shows that water vapor has a negligible effect on climate impact. Carbon dioxide climate impact is more relevant when considering long term time horizons. Also, it increases when more trajectories are modified since the fuel consumption increases. Contrails are the main driver of the optimization for seven out of eight weather patterns. Their climate impact goes down during the optimization. Moreover, they are more important when considering short term time horizons and westbound flights. NOx is driving the optimization for only one weather pattern. Its contribution to reduce the total climate impact during the optimization is higher in the long term due to the enhanced net-cooling effect caused by methane depletion. Moreover, it is more important for eastbound flights. However, for winter weather patterns, NOx is controlled mainly by methane and primary mode ozone during most part of the optimization. Ozone is only important in the first and last segments. In addition, ozone presents the highest values of climate impact and has more contribution in the short term; while methane has always a negative climate impact or net-cooling effect due to its depletion, and is more important in the long term. The climate impact reduction is caused in the first part of the optimization by a small number of flights that reduce considerably their climate impact. Their trajectories change to go through regions of the atmosphere where their climate impact is smaller. As the optimization progresses, there are more flights modifying their routes. However, their climate impact reduction is not as noticeable as in the first cases. This happens because the regions of the atmosphere where the emissions have a lower climate impact are busier with the prior flights. Therefore the latter flights changing their trajectories have less potential to reduce their climate impact. This leads to a small part of the fleet causing an important climate impact reduction while the vast majority of flights slightly reduce their climate impact.Aerospace EngineeringControl & OperationsAircraft Noise and Climate Effects (ANCE
Using target enrichment sequencing to study the higher-level phylogeny of the largest lichen-forming fungi family: Parmeliaceae (Ascomycota)
No full textAbstract Parmeliaceae is the largest family of lichen-forming fungi with a worldwide distribution. We used a target enrichment data set and a qualitative selection method for 250 out of 350 genes to infer the phylogeny of the major clades in this family including 81 taxa, with both subfamilies and all seven major clades previously recognized in the subfamily Parmelioideae. The reduced genome-scale data set was analyzed using concatenated-based Bayesian inference and two different Maximum Likelihood analyses, and a coalescent-based species tree method. The resulting topology was strongly supported with the majority of nodes being fully supported in all three concatenated-based analyses. The two subfamilies and each of the seven major clades in Parmelioideae were strongly supported as monophyletic. In addition, most backbone relationships in the topology were recovered with high nodal support. The genus Parmotrema was found to be polyphyletic and consequently, it is suggested to accept the genus Crespoa to accommodate the species previously placed in Parmotrema subgen. Crespoa. This study demonstrates the power of reduced genome-scale data sets to resolve phylogenetic relationships with high support. Due to lower costs, target enrichment methods provide a promising avenue for phylogenetic studies including larger taxonomic/specimen sampling than whole genome data would allow
Aviation H2O and NOx climate cost functions based on local weather
No full textAviation contributes significantly to anthropogenic global warming, and one promising possibility for mitigation is climate-optimised routing. For the REACT4C project a novel approach was used to simulate the variation of aviation water vapour and NOx emission climate impact with location and weather patterns, but this is too computationally expensive to apply beyond initial research. Results showed about 10% climate impact reduction from a 1% cost increase. For implementation of climate-optimised routing, algorithms are needed which will allow climate impact to be estimated in real-time from weather predictions. This research focuses on formulating algorithmic approximations of aviation water vapour and NOx emission climate impact based on local weather data by systematically examining correlations between climate impact data and weather data at the time of emission in the REACT4C dataset. The methods and models used for generating the REACT4C data are assessed in detail down to their first publications and potential errors and omissions are identified. The analysis is split into direct water vapour, short-lived ozone from NOx, and methane from NOx climate impact. Long-lived ozone and stratospheric water vapour from methane effects are neglected. The water vapour and NOx ozone and methane Climate Cost Function (CCF) results from REACT4C are reverse-engineered to the original grid they were emitted from to prevent inflation of statistical power. Weather and chemistry data at the time of emission are interpolated to the same grid for regression analysis. Literature reviews are used to identify causal predictors and derived variables. A variety of statistical tools are applied to assess variability of the CCFs and search for the best predictors. Four algorithms are developed for each species, using zero-dimensional instantaneous regression analysis. A tailored trade-off framework is applied to choose the best algorithm for application. The chosen algorithmic CCF for water vapour emissions is linear with potential vorticity and has an adjusted R2 of 0.59. Both the mean and the variance of the water vapour climate impact appear strongly determined by the altitude of an emission relative to the tropopause. The relationship between water vapour CCF results and emission altitude is investigated to critically reflect and expand on results from a previous publication. The chosen algorithmic CCF for ozone is bilinear with geopotential and temperature plus their interaction and has an adjusted R2 of 0.42. Ozone climate impact appears moderately determined by altitude and temperature of the emission location. The relationship between ozone CCF results, background NOx concentration and latitude during emission is investigated to critically reflect and expand on results from a previous publication. The chosen algorithmic CCF for methane is bilinear with geopotential and the solar incidence, and has an adjusted R2 of 0.17. Methane climate impact has low variability and is relatively independent of weather at the time and location of emission. The relationship between methane CCF results and background NOx concentrations during emission is investigated to critically reflect and expand on results from a previous publication. Methane climate impact can be more accurately predicted by using simulated ozone climate impact, but the variance left unexplained by the ozone algorithm would lead to worse results in application. The correlation between methane and ozone is weaker than in previous studies. Chemical concentrations, lightning frequency, and lightning NOx production at the time and location of emission do not predict aviation NOx climate impact beyond the extent of basic meteorology unless a large amount of predictors are included in the regression. The chain of models and assumptions from basic climate science to algorithmic CCFs is assessed to identify relative effects on uncertainty of the results. Several steps are identified that should be revisited and several opportunities for future data analyses to increase understanding and certainty of algorithmic CCFs. Future steps for research into and application of algorithmic CCFs depend on upcoming verification activities for the results presented here.Aerospace EngineeringControl & Operations / Aircraft Noise and Climate Effects (ANCE)Aerospace Engineerin
Assessing the appropriateness of different climate modelling approaches for the estimation of aviation NOx climate effects
No full textAviation’s contribution to anthropogenic global warming is estimated to be between 3 – 5% [1]. This assessment comprises two contributions: the well understood atmospheric impact of carbon dioxide (CO2) and the more uncertain non-CO2 effects. The latter pertain to persistent contrails and pollutants like nitrogen oxides (NOx), water vapor (H2O), sulfur oxides (SOx) and soot particles. NOx emissions are involved in non-linear processes that result in the short-term production of ozone (O3) and longer-term destruction of methane (CH4), stratospheric water vapor (SWV), and primary mode ozone (PMO). The aviation-attributable impacts arising from this short-term increase in O3 can vary by more than a factor of 1.5 depending on the selected modelling approach. This O3 increase is associated with the second largest warming effect across aviation’s main climate forcers [1]. We therefore quantify this figure using three modelling approaches (an Eulerian and a Lagrangian tagging scheme as well as a perturbation approach) at three potential aircraft cruise altitudes (200, 250 and 300 hPa) at which NOx pulse emissions are introduced in the Americas, Africa, Eurasia and Australasia. In general, the tagging method computes the contribution by an emission source to the concentration of a chemical species while a perturbation approach consists in calculating the total impact of an emission to the concentration of a species by means of subtracting two simulations: one with all emissions and a second without the specific source’s emissions. We compare results from Eulerian and Lagrangian simulations using the same climate-chemistry code: the ECHAM5/MESSy Atmospheric Chemistry (EMAC) model. With the Eulerian setup, we are able to capture non-linear processes and feedback effects, but not track the transport of emitted species in detail. The Lagrangian setup [2], on the other hand, allows for the accompaniment of thousands of air parcel trajectories, but at the cost of assuming a simplified linear chemistry mechanism. We find that the Lagrangian tagging approach provides the largest estimates for O3 production and radiative forcing (RF), followed by the Eulerian tagging scheme and lastly by the perturbation method. We therefore investigate the appropriateness of each of these in quantifying aviation’s total and marginal climate effects by addressing the following research questions: 1) By how much are the estimates for the short-term NOx-induced O3 perturbation and consequent RF varying across the three modelling approaches and why? 2) How does this RF vary with emission altitude within the upper Troposphere/lower Stratosphere (UTLS)?[1] Lee, D.S., Fahey, D.W., Skowron, A., Allen, M.R., Burkhardt, U., Chen, Q., Doherty, S.J., Freeman, S., Forster, P.M., Fuglestvedt, J., Gettelman, A., De León, R.R., Lim, L.L., Lund, M.T., Millar, R.J., Owen, B., Penner, J.E., Pitari, G., Prather, M.J., Sausen, R., and Wilcox, L.J.: The contribution of global aviation to anthropogenic climate forcing for 2000 to 2018, Atmos. Environ., 244, 117834, https://doi.org/10.1016/j.atmosenv.2020.117834, 2021.[2] Maruhashi, J., Grewe, V., Frömming, C., Jöckel, P., and Dedoussi, I. C.: Transport patterns of global aviation NOx and their short-term O3 radiative forcing – a machine learning approach, Atmos. Chem. Phys., 22, 14253–14282, https://doi.org/10.5194/acp-22-14253-2022, 2022
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