Deciphering the genome structure and paleohistory of _Theobroma cacao_

We sequenced and assembled the genome of _Theobroma cacao_, an economically important tropical fruit tree crop that is the source of chocolate. The assembly corresponds to 76% of the estimated genome size and contains almost all previously described genes, with 82% of them anchored on the 10 _T. cacao_ chromosomes. Analysis of this sequence information highlighted specific expansion of some gene families during evolution, for example flavonoid-related genes. It also provides a major source of candidate genes for _T. cacao_ disease resistance and quality improvement. Based on the inferred paleohistory of the T. cacao genome, we propose an evolutionary scenario whereby the ten _T. cacao_ chromosomes were shaped from an ancestor through eleven chromosome fusions. The _T. cacao_ genome can be considered as a simple living relic of higher plant evolution

Exploring the stellar surface phenomena of WASP-52 and HAT-P-30 with ESPRESSO

We analyse spectroscopic and photometric transits of the hot Jupiters WASP-52b and HAT-P30b obtained with ESPRESSO, Eulercam and NGTS for both targets, and additional TESS data for HAT-P-30. Our goal is to update the system parameters and refine our knowledge of the host star surfaces. For WASP-52, the companion planet has occulted starspots in the past, and as such our aim was to use the reloaded Rossiter-McLaughlin technique to directly probe its starspot properties. Unfortunately, we find no evidence for starspot occultations in the datasets herein. Additionally, we searched for stellar surface differential rotation (DR) and any centre-to-limb variation (CLV) due to convection, but return a null detection of both. This is unsurprising for WASP-52, given its relatively cool temperature, high magnetic activity (which leads to lower CLV), and projected obliquity near 0 degrees (meaning the transit chord is less likely to cross several stellar latitudes). For HAT-P-30, this result was more surprising given its hotter effective temperature, lower magnetic field, and high projected obliquity (near 70 degrees). To explore the reasons behind the null DR and CLV detection for HAT-P-30, we simulated a variety of scenarios. We find that either the CLV present on HAT-P-30 is below the solar level or the presence of DR prevents a CLV detection given the precision of the data herein. A careful treatment of both DR and CLV is required, especially for systems with high impact factors, due to potential degeneracies between the two. Future observations and/or a sophisticated treatment of the red noise present in the data (likely due to granulation) is required to refine the DR and CLV for these particular systems; such observations would also present another opportunity to try to examine starspots on WASP-52.Comment: 11 pages main text, 8 figures; accepted for publication in A&

Exploring the stellar surface phenomena of WASP-52 and HAT-P-30 with ESPRESSO

We analyse spectroscopic and photometric transits of the hot Jupiters WASP-52 b and HAT-P30 b obtained with ESPRESSO, Eulercam and NGTS for both targets, and additional TESS data for HAT-P-30. Our goal is to update the system parameters and refine our knowledge of the host star surfaces. For WASP-52, the companion planet has occulted starspots in the past, and as such our aim was to use the reloaded Rossiter-McLaughlin technique to directly probe its starspot properties. Unfortunately, we find no evidence for starspot occultations in the datasets herein. Additionally, we searched for stellar surface differential rotation (DR) and any centre-to-limb variation (CLV) due to convection, but return a null detection of both. This is unsurprising for WASP-52, given its relatively cool temperature, high magnetic activity (which leads to lower CLV), and projected obliquity near 0° (meaning the transit chord is less likely to cross several stellar latitudes). For HAT-P-30, this result was more surprising given its hotter effective temperature, lower magnetic field, and high projected obliquity (near 70°). To explore the reasons behind the null DR and CLV detection for HAT-P-30, we simulated a variety of scenarios. We find that either the CLV present on HAT-P-30 is below the solar level or the presence of DR prevents a CLV detection given the precision of the data herein. A careful treatment of both DR and CLV is required, especially for systems with high impact factors, due to potential degeneracies between the two. Future observations and/or a sophisticated treatment of the red noise present in the data (likely due to granulation) is required to refine the DR and CLV for these particular systems; such observations would also present another opportunity to try to examine starspots on WASP-52

Agent based modelling helps in understanding the rules by which fibroblasts support keratinocyte colony formation

Background: Autologous keratincoytes are routinely expanded using irradiated mouse fibroblasts and bovine serum for clinical use. With growing concerns about the safety of these xenobiotic materials, it is desirable to culture keratinocytes in media without animal derived products. An improved understanding of epithelial/mesenchymal interactions could assist in this. Methodology/Principal Findings: A keratincyte/fibroblast o-culture model was developed by extending an agent-based keratinocyte colony formation model to include the response of keratinocytes to both fibroblasts and serum. The model was validated by comparison of the in virtuo and in vitro multicellular behaviour of keratinocytes and fibroblasts in single and co-culture in Greens medium. To test the robustness of the model, several properties of the fibroblasts were changed to investigate their influence on the multicellular morphogenesis of keratinocyes and fibroblasts. The model was then used to generate hypotheses to explore the interactions of both proliferative and growth arrested fibroblasts with keratinocytes. The key predictions arising from the model which were confirmed by in vitro experiments were that 1) the ratio of fibroblasts to keratinocytes would critically influence keratinocyte colony expansion, 2) this ratio needed to be optimum at the beginning of the co-culture, 3) proliferative fibroblasts would be more effective than irradiated cells in expanding keratinocytes and 4) in the presence of an adequate number of fibroblasts, keratinocyte expansion would be independent of serum. Conclusions: A closely associated computational and biological approach is a powerful tool for understanding complex biological systems such as the interactions between keratinocytes and fibroblasts. The key outcome of this study is the finding that the early addition of a critical ratio of proliferative fibroblasts can give rapid keratinocyte expansion without the use of irradiated mouse fibroblasts and bovine serum

The hot Neptune WASP-166 b with ESPRESSO – I. Refining the planetary architecture and stellar variability

In this paper, we present high-resolution spectroscopic transit observations from ESPRESSO of the super-Neptune WASP-166 b. In addition to spectroscopic ESPRESSO data, we analyse photometric data from TESS of six WASP-166 b transits along with simultaneous NGTS observations of the ESPRESSO runs. These observations were used to fit for the planetary parameters as well as assessing the level of stellar activity (e.g. spot crossings, flares) present during the ESPRESSO observations. We utilize the reloaded Rossiter McLaughlin (RRM) technique to spatially resolve the stellar surface, characterizing the centre-to-limb convection-induced variations, and to refine the star–planet obliquity. We find WASP-166 b has a projected obliquity of λ=−15.52+2.85−2.76∘ and vsin (i) = 4.97 ± 0.09 km s−1 which is consistent with the literature. We were able to characterize centre-to-limb convective variations as a result of granulation on the surface of the star on the order of a few km s−1 for the first time. We modelled the centre-to-limb convective variations using a linear, quadratic, and cubic model with the cubic being preferred. In addition, by modelling the differential rotation and centre-to-limb convective variations simultaneously, we were able to retrieve a potential antisolar differential rotational shear (α ∼ −0.5) and stellar inclination (i* either 42.03+9.13−9.60∘ or 133.64+8.42−7.98∘ if the star is pointing towards or away from us). Finally, we investigate how the shape of the cross-correlation functions change as a function of limb angle and compare our results to magnetohydrodynamic simulations