Computational Stem Cell Biology: Open Questions and Guiding Principles

Computational biology is enabling an explosive growth in our understanding of stem cells and our ability to use them for disease modeling, regenerative medicine, and drug discovery. We discuss four topics that exemplify applications of computation to stem cell biology: cell typing, lineage tracing, trajectory inference, and regulatory networks. We use these examples to articulate principles that have guided computational biology broadly and call for renewed attention to these principles as computation becomes increasingly important in stem cell biology. We also discuss important challenges for this field with the hope that it will inspire more to join this exciting area

The discovery of ash dieback in the UK: the making of a focusing event

Why did the identification of ‘Ash Dieback’ (Chalara Fraxinea) in 2012 in the UK catch the national media, public and political zeitgeist, and lead to policy changes, in a way that no other contemporary tree pest or pathogen outbreak has?The identification of Ash Dieback in the UK is conceptualised as a successful ‘focusing event’ and the ways in which it was socially constructed by the media, stakeholders and the government are analysed. National newspaper coverage contributed to the way that the disease was understood and was significant in driving the political response. Ash Dieback’s focal power derived from the perceived scale and nature of its impact; the initial attribution of blame on government; the ‘war-like’ response from the government; and Ash’s status as a threatened ‘native’ tree. The Ash Dieback focusing event has increased the salience of plant health issues amongst policymakers, the public and conservation organisations in the UK

Stronger diversity effects with increased environmental stress : a study of multitrophic interactions between oak, powdery mildew and ladybirds

Recent research has suggested that increasing neighbourhood tree species diversity may mitigate the impact of pests or pathogens by supporting the activities of their natural enemies and/or reducing the density of available hosts. In this study, we attempted to assess these mechanisms in a multitrophic study system of young oak (Quercus), oak powdery mildew (PM, caused by Erysiphe spp.) and a mycophagous ladybird (Psyllobora vigintiduo-punctata). We assessed ladybird mycophagy on oak PM in function of different neighbourhood tree species compositions. We also evaluated whether these species interactions were modulated by environmental conditions as suggested by the Stress Gradient Hypothesis. We adopted a complementary approach of a field experiment where we monitored oak saplings subjected to a reduced rainfall gradient in a young planted forest consisting of different tree species mixtures, as well as a lab experiment where we independently evaluated the effect of different watering treatments on PM infections and ladybird mycophagy. In the field experiment, we found effects of neighbourhood tree species richness on ladybird mycophagy becoming more positive as the target trees received less water. This effect was only found as weather conditions grew drier. In the lab experiment, we found a preference of ladybirds to graze on infected leaves from trees that received less water. We discuss potential mechanisms that might explain this preference, such as emissions of volatile leaf chemicals. Our results are in line with the expectations of the Natural Enemies Hypothesis and support the hypothesis that biodiversity effects become stronger with increased environmental stress

The effects of stand characteristics on the understory vegetation in Quercus petraea and Q. cerris dominated forests

The shelterwood system used in Hungary has many effects on the composition and structure of the herb layer. The aim of our study was to identify the main variables that affect the occurence of herbs and seedlings in Turkey oak-sessile oak (Quercus cerris and Q. petraea) stands. The study was carried out in the Bükk mountains, Hungary. 122 sampling plots were established in 50-150 year old oak forests, where we studied the species composition and structure of the understorey and overstorey. The occurence of herbs was affected by canopy closure, the heterogenity and patchiness of the stand, the slope and the east-west component of the aspect. The composition of saplings was significantly explained by the ratio of the two major oak species in the stand and the proximity of the adult plants. An important result for forest management was that sessile oaks were able to regenerate almost only where they were dominant in the overstorey

Modelos de endemicidad a lo largo de un gradiente altitudinal en Sierra Nevada (España) y Lefka Ori (Creta, Grecia)

Aim: High mountains in the Mediterranean region of Europe are particularly rich in endemic vascular plants. We aimed to compare the altitudinal patterns of vascular plant species richness and the proportion of endemic species in two Mediterranean region: Lefka Ori on the island of Crete (Greece) and Sierra Nevada on the Iberian peninsula. Location: Sierra Nevada, Granada (Spain); Lefka Ori, Crete (Greece). Methods: Data from standardised permanent plots settings on summit sites (comprising eight plot sectors, covering the upeermost 10 altitudinal metres) of different elevations were used (GLORIA Multi-Summit approach; www.gloria.ac.at). Species numbers, rates of endemic species, and soils temperature were compared by means of ANCOVA and linear regression. Results: The two regions, though climatically similar, showed strikingly different patterns: In Sierra Nevada, the proportion of endemic vascular plants (species restricted to Sierra Nevada) showed a stepwise increase from the lowest to the highest summit. In contrast, the proportion of endemic species restricted to Crete was not significantly different between the four summits in Lefka Ori. In both regions the observed trends were largely consistent with the altitudinal distribution of the endemic species obtained from standard floras. Main conclusions: The geographic positions of the two regions, i.e. island versus mainland and the higher elevation of Sierra Nevada are suggested to be the primary causes of the observed differences. The high degree of endemism in the cold environments of Mediterranean mountains’ upper bioclimatic zones indicates a pronounced vulnerability to the impacts of climate change. A continued and intensified species monitoring in the mountains around the Mediterranean basin, therefore, should be considered as a priority research task.Objetivo: Las zonas de alta montaña en la región mediterránea europea son particularmente ricas en plantas vasculares endémicas. Nuestro objetivo es comparar los modelos altitudinales para la riqueza de plantas vasculares y la proporción de endemismos en dos regiones mediterráneas: Lefka Ori en la isla de Creta (Grecia) y Sierra Nevada en la Península Ibérica. Localización: Sierra Nevada, Granada (España); Lefka Ori, Creta (Grecia). Método: Los datos proceden de un muestreo estandarizado en varias cimas situadas a diferentes altitudes (GLORIA Multi-Summit approach; www.gloria.ac.at). El número de especies, tasas de endemicidad, y temperatura del suelo se compararon por medio de ANCOVA y regresión lineal. Resultados: Las dos regiones objeto de análisis, aunque similares climáticamente, muestran patrones llamativamente diferentes: en Sierra Nevada, la proporción de plantas vasculares endémicas (especies restringidas a Sierra Nevada) muestra un incremento gradual desde la cima más baja a la más alta. En contraste, la proporción de endemismos restringidos a Creta no fue significativamente diferente entre las cuatro cimas de Lefka Ori. Las tendencias observadas en ambas regiones fueron en gran parte consistentes con la distribución de las especies endémicas obtenida de las floras para cada región. Conclusiones principales: La posición geográfica de ambas regiones, por ejemplo. isla frente a continente, y la mayor elevación de Sierra Nevada se sugieren como las principales causas de las diferencias observadas. El alto grado de endemicidad en los ambientes fríos de las zonas bioclimáticas superiores de las montañas mediterráneas evidencia una marcada vulnerabilidad a los impactos del cambio climático. Por lo tanto, el seguimiento continuado e intensivo de las especies de montaña alrededor de la cuenca mediterránea, debería considerarse como una tarea investigadora prioritaria.He set up of the permanent plots and data collection was supported by the FP-5 project GLORIA-Europe (2001-2003) No EVK2-2000-00056 of the European Commission

ACCESS: Confirmation of a Clear Atmosphere for WASP-96b and a Comparison of Light Curve Detrending Techniques

One of the strongest ${\rm Na~I}$ features was observed in WASP-96b. To confirm this novel detection, we provide a new 475-825nm transmission spectrum obtained with Magellan/IMACS, which indeed confirms the presence of a broad sodium absorption feature. We find the same result when reanalyzing the 400-825nm VLT/FORS2 data. We also utilize synthetic data to test the effectiveness of two common detrending techniques: (1) a Gaussian processes (GP) routine, and (2) common-mode correction followed by polynomial correction (CMC+Poly). We find that both methods poorly reproduce the absolute transit depths but maintain their true spectral shape. This emphasizes the importance of fitting for offsets when combining spectra from different sources or epochs. Additionally, we find that for our datasets both methods give consistent results, but CMC+Poly is more accurate and precise. We combine the Magellan/IMACS and VLT/FORS2 spectra with literature 800-1644nm HST/WFC3 spectra, yielding a global spectrum from 400-1644nm. We used the PLATON and Exoretrievals retrieval codes to interpret this spectrum, and find that both yield relatively deeper pressures where the atmosphere is optically thick at log-pressures between $1.3^{+1.0}_{-1.1}$ and 0.29$^{+1.86}_{-2.02}$ bars, respectively. Exoretrievals finds a solar to super-solar ${\rm Na~I}$ and ${\rm H_2O}$ log-mixing ratios of $-5.4^{+2.0}_{-1.9}$ and $-4.5^{+2.0}_{-2.0}$, respectively, while PLATON finds an overall metallicity of $log_{10}(Z/Z_{\odot}) = -0.49^{+1.0}_{-0.37}$dex. Therefore, our findings are in agreement with literature and support the inference that the terminator of WASP-96b has few aerosols obscuring prominent features in the optical to near-infrared (near-IR) spectrum.Comment: ACCEPT by AJ July 5th 202

ACCESS, LRG-BEASTS, & MOPSS: Featureless Optical Transmission Spectra of WASP-25b and WASP-124b

We present new optical transmission spectra for two hot Jupiters: WASP-25b (M = 0.56~M$_J$; R = 1.23 R$_J$; P =~3.76 days) and WASP-124b (M = 0.58~M$_J$; R = 1.34 R$_J$; P = 3.37 days), with wavelength coverages of 4200 - 9100\AA\ and 4570 - 9940\AA, respectively. These spectra are from the ESO Faint Object Spectrograph and Camera (v.2) mounted on the New Technology Telescope (NTT) and Inamori-Magellan Areal Camera & Spectrograph on Magellan Baade. No strong spectral features were found in either spectra, with the data probing 4 and 6 scale heights, respectively. \texttt{Exoretrievals} and \texttt{PLATON} retrievals favor stellar activity for WASP-25b, while the data for WASP-124b did not favor one model over another. For both planets the retrievals found a wide range in the depths where the atmosphere could be optically thick ($\sim0.4\mu$ - 0.2 bars for WASP-25b and 1.6 $\mu$ -- 32 bars for WASP-124b) and recovered a temperature that is consistent with the planets' equilibrium temperatures, but with wide uncertainties (up to $\pm$430$^\circ$K). For WASP-25b, the models also favor stellar spots that are $\sim$500-3000$^\circ$K cooler than the surrounding photosphere. The fairly weak constraints on parameters are owing to the relatively low precision of the data, with an average precision of 840 and 1240 ppm per bin for WASP-25b and WASP-124b, respectively. However, some contribution might still be due to an inherent absence of absorption or scattering in the planets' upper atmospheres, possibly because of aerosols. We attempt to fit the strength of the sodium signals to the aerosol-metallicity trend proposed by McGruder et al. 2023, and find WASP-25b and WASP-124b are consistent with the prediction, though their uncertainties are too large to confidently confirm the trend.Comment: Accepted in AJ July 202

Fair game: exploring the dynamics, perception and environmental impact of ‘surplus’ wild foods in England 10kya-present

This paper brings together zooarchaeological data from Neolithic to Post-medieval sites in England to explore the plasticity of cultural attitudes to the consumption of wild animals. It shows how, through time, game has been considered variously as ‘tabooed’ and ‘edible’, each having implications for patterns of biodiversity and wildlife management. The essential points being made are that deeper-time studies can reveal how human perceptions of ‘surplus foods’ have the potential to both create and remedy problems of environmental sustainability and food security. Perhaps more significantly, this paper argues that understanding the bio-cultural past of edible wild animal species has the potential to transform human attitudes to game in the present. This is important at a time when food security and the production of surplus are pressing national and global concerns