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The members of the tribe Brassiceae share a whole-genome triplication (WGT), and one proposed model for its formation is a two-step pair of hybridizations producing hexaploid descendants. However, evidence for this model is incomplete, and the evolutionary and functional constraints that drove evolution after the hexaploidy are even less understood. Here, we report a new genome sequence of Crambe hispanica, a species sister to most sequenced Brassiceae. Using this new genome and three others that share the hexaploidy, we traced the history of gene loss after the WGT using the Polyploidy Orthology Inference Tool (POInT). We confirm the two-step formation model and infer that there was a significant temporal gap between those two allopolyploidizations, with about a third of the gene losses from the first two subgenomes occurring before the arrival of the third. We also, for the 90,000 individual genes in our study, make parental subgenome assignments, inferring, with measured uncertainty, from which of the progenitor genomes of the allohexaploidy each gene derives. We further show that each subgenome has a statistically distinguishable rate of homoeolog losses. There is little indication of functional distinction between the three subgenomes: the individual subgenomes show no patterns of functional enrichment, no excess of shared protein-protein or metabolic interactions between their members, and no biases in their likelihood of having experienced a recent selective sweep. We propose a "mix and match" model of allopolyploidy, in which subgenome origin drives homoeolog loss propensities but where genes from different subgenomes function together without difficulty.

Crab crossing scheme is an essential collision scheme to achieve high luminosity for the future colliders with large crossing angles. However, when bunch length of one or both colliding beams is comparable with the wavelength of the crab cavity voltage, the nonlinear dependence of the crabbing kick may present a challenge to the beam dynamics of the colliding beams and impact the beam quality and the luminosity lifetime. In this paper, the results of nonlinear dynamics in the crab crossing scheme are presented, using both analytical and numerical approaches. The result indicates that higher-order synchrobetatron resonances may be excited in the crab crossing scheme with large crossing angle, which causes the beam quality deterioration and luminosity degradation. The studies also reveal possible countermeasures to suppress the synchrobeta resonance, hence mitigate the degradation of beam quality and luminosity.

Abstract Background Carbon storage in deep saline reservoirs has the potential to lower the amount of CO2 emitted to the atmosphere and to mitigate global warming. Leakage back to the atmosphere through abandoned wells and along faults would reduce the efficiency of carbon storage, possibly leading to health and ecological hazards at the ground surface, and possibly impacting water quality of near-surface dilute aquifers. We use static equilibrium and reactive transport simulations to test the hypothesis that perturbations in water chemistry associated with a CO2 gas leak into dilute groundwater are important measures for the potential release of CO2 to the atmosphere. Simulation parameters are constrained by groundwater chemistry, flow, and lithology from the High Plains aquifer. The High Plains aquifer is used to represent a typical sedimentary aquifer overlying a deep CO2 storage reservoir. Specifically, we address the relationships between CO2 flux, groundwater flow, detection time and distance. The CO2 flux ranges from 103 to 2 × 106 t/yr (0.63 to 1250 t/m2/yr) to assess chemical perturbations resulting from relatively small leaks that may compromise long-term storage, water quality, and surface ecology, and larger leaks characteristic of short-term well failure. Results For the scenarios we studied, our simulations show pH and carbonate chemistry are good indicators for leakage of stored CO2 into an overlying aquifer because elevated CO2 yields a more acid pH than the ambient groundwater. CO2 leakage into a dilute groundwater creates a slightly acid plume that can be detected at some distance from the leak source due to groundwater flow and CO2 buoyancy. pH breakthrough curves demonstrate that CO2 leaks can be easily detected for CO2 flux ≥ 104 t/yr within a 15-month time period at a monitoring well screened within a permeable layer 500 m downstream from the vertical gas trace. At lower flux rates, the CO2 dissolves in the aqueous phase in the lower most permeable unit and does not reach the monitoring well. Sustained pumping in a developed aquifer mixes the CO2-affected water with the ambient water and enhances pH signal for small leaks (103 t/yr) and reduces pH signal for larger leaks (≥ 104t/yr). Conclusion The ability to detect CO2 leakage from a storage reservoir to overlying dilute groundwater is dependent on CO2 solubility, leak flux, CO2 buoyancy, and groundwater flow. Our simulations show that the most likely places to detect CO2 are at the base of the confining layer near the water table where CO2 gas accumulates and is transported laterally in all directions, and downstream of the vertical gas trace where groundwater flow is great enough to transport dissolved CO2 laterally. Our simulations show that CO2 may not rise high enough in the aquifer to be detected because aqueous solubility and lateral groundwater transport within the lower aquifer unit exceeds gas pressure build-up and buoyancy needed to drive the CO2 gas upwards.