Consistently Simulating a Wide Range of Atmospheric Scenarios for K2-18b with a Flexible Radiative Transfer Module

The atmospheres of small, potentially rocky exoplanets are expected to cover a diverse range in composition and mass. Studying such objects therefore requires flexible and wide-ranging modeling capabilities. We present in this work the essential development steps that lead to our flexible radiative transfer module, REDFOX, and validate REDFOX for the Solar system planets Earth, Venus and Mars, as well as for steam atmospheres. REDFOX is a k-distribution model using the correlated-k approach with random overlap method for the calculation of opacities used in the $\delta$-two-stream approximation for radiative transfer. Opacity contributions from Rayleigh scattering, UV / visible cross sections and continua can be added selectively. With the improved capabilities of our new model, we calculate various atmospheric scenarios for K2-18b, a super-Earth / sub-Neptune with $\sim$8 M$_\oplus$ orbiting in the temperate zone around an M-star, with recently observed H$_2$O spectral features in the infrared. We model Earth-like, Venus-like, as well as H$_2$-He primary atmospheres of different Solar metallicity and show resulting climates and spectral characteristics, compared to observed data. Our results suggest that K2-18b has an H$_2$-He atmosphere with limited amounts of H$_2$O and CH$_4$. Results do not support the possibility of K2-18b having a water reservoir directly exposed to the atmosphere, which would reduce atmospheric scale heights, hence too the amplitudes of spectral features inconsistent with the observations. We also performed tests for H$_2$-He atmospheres up to 50 times Solar metallicity, all compatible with the observations.Comment: 28 pages, 13 figures, accepted for publication in Ap

Cross-Disciplinary Genomics Approaches to Studying Emerging Fungal Infections

Emerging fungal pathogens pose a serious, global and growing threat to food supply systems, wild ecosystems, and human health. However, historic chronic underinvestment in their research has resulted in a limited understanding of their epidemiology relative to bacterial and viral pathogens. Therefore, the untargeted nature of genomics and, more widely, -omics approaches is particularly attractive in addressing the threats posed by and illuminating the biology of these pathogens. Typically, research into plant, human and wildlife mycoses have been largely separated, with limited dialogue between disciplines. However, many serious mycoses facing the world today have common traits irrespective of host species, such as plastic genomes; wide host ranges; large population sizes and an ability to persist outside the host. These commonalities mean that -omics approaches that have been productively applied in one sphere and may also provide important insights in others, where these approaches may have historically been underutilised. In this review, we consider the advances made with genomics approaches in the fields of plant pathology, human medicine and wildlife health and the progress made in linking genomes to other -omics datatypes and sets; we identify the current barriers to linking -omics approaches and how these are being underutilised in each field; and we consider how and which -omics methodologies it is most crucial to build capacity for in the near future

Retracing the molecular basis and evolutionary history of the loss of benzaldehyde emission in the genus Capsella

The transition from pollinator‐mediated outbreeding to selfing has occurred many times in angiosperms. This is generally accompanied by a reduction in traits attracting pollinators, including reduced emission of floral scent. In Capsella, emission of benzaldehyde as a main component of floral scent has been lost in selfing C. rubella by mutation of cinnamate‐CoA ligase CNL1. However, the biochemical basis and evolutionary history of this loss remain unknown, as does the reason for the absence of benzaldehyde emission in the independently derived selfer Capsella orientalis. We used plant transformation, in vitro enzyme assays, population genetics and quantitative genetics to address these questions. CNL1 has been inactivated twice independently by point mutations in C. rubella, causing a loss of enzymatic activity. Both inactive haplotypes are found within and outside of Greece, the centre of origin of C. rubella, indicating that they arose before its geographical spread. By contrast, the loss of benzaldehyde emission in C. orientalis is not due to an inactivating mutation in CNL1. CNL1 represents a hotspot for mutations that eliminate benzaldehyde emission, potentially reflecting the limited pleiotropy and large effect of its inactivation. Nevertheless, even closely related species have followed different evolutionary routes in reducing floral scent

Target specificity among canonical nuclear poly(A) polymerases in plants modulates organ growth and pathogen response

Polyadenylation of pre-mRNAs is critical for efficient nuclear export, stability, and translation of the mature mRNAs, and thus for gene expression. The bulk of pre-mRNAs are processed by canonical nuclear poly(A) polymerase (PAPS). Both vertebrate and higher-plant genomes encode more than one isoform of this enzyme, and these are coexpressed in different tissues. However, in neither case is it known whether the isoforms fulfill different functions or polyadenylate distinct subsets of pre-mRNAs. Here we show that the three canonical nuclear PAPS isoforms in Arabidopsis are functionally specialized owing to their evolutionarily divergent C-terminal domains. A strong loss-of-function mutation in PAPS1 causes a male gametophytic defect, whereas a weak allele leads to reduced leaf growth that results in part from a constitutive pathogen response. By contrast, plants lacking both PAPS2 and PAPS4 function are viable with wild-type leaf growth. Polyadenylation of SMALL AUXIN UP RNA (SAUR) mRNAs depends specifically on PAPS1 function. The resulting reduction in SAUR activity in paps1 mutants contributes to their reduced leaf growth, providing a causal link between polyadenylation of specific pre-mRNAs by a particular PAPS isoform and plant growth. This suggests the existence of an additional layer of regulation in plant and possibly vertebrate gene expression, whereby the relative activities of canonical nuclear PAPS isoforms control de novo synthesized poly(A) tail length and hence expression of specific subsets of mRNAs

Low-Reynolds-number gravity-driven migration and deformation of bubbles near a free surface

International audienceWe investigate numerically the axisymmetric migration of bubbles toward a free surface, using a boundary-integral technique. Our careful numerical implementation allows to study the bubble(s) deformation and film drainage; it is benchmarked against several tests. The rise of one bubble toward a free surface is studied and the computed bubble shape compared with the results of Princen [J. Colloid Interface Sci. 18, 178 (1963)]. The liquid film between the bubble and the free surface is found to drain exponentially in time in full agreement with the experimental work of Debre'geas et al. [Science 279, 1704 (1998)]. Our numerical results also cast some light on the role played by the deformation of the fluid interfaces and it turns out that for weakly deformed interfaces (high surface tension or a tiny bubble) the film drainage is faster than for a large fluid deformation. By introducing one or two additional bubble(s) below the first one, we examine to which extent the previous trends are affected by bubble-bubble interactions. For instance, for a 2-bubble chain, decreasing the bubblebubble separation increases the deformation of the last bubble in the chain. Finally, the exponential drainage of the film between the free surface and the closest bubble is preserved, yet the drainage is enhanced

Could Greater Time Spent Displaying Waking Inactivity in the Home Environment Be a Marker for a Depression-Like State in the Domestic Dog?

Dogs exposed to aversive events can become inactive and unresponsive and are commonly referred to as being “depressed”, but this association remains to be tested. We investigated whether shelter dogs spending greater time inactive “awake but motionless” (ABM) in their home-pen show anhedonia (the core reduction of pleasure reported in depression), as tested by reduced interest in, and consumption of, palatable food (KongTM test). We also explored whether dogs being qualitatively perceived by experts as disinterested in the food would spend greater time ABM (experts blind to actual inactivity levels). Following sample size estimations and qualitative behaviour analysis (n = 14 pilot dogs), forty-three dogs (6 shelters, 22F:21M) were included in the main study. Dogs relinquished by their owners spent more time ABM than strays or legal cases (F = 8.09, p = 0.032). One significant positive association was found between the KongTM measure for average length of KongTM bout and ABM, when length of stay in the shelter was accounted for as a confounder (F = 3.66, p = 0.035). Time spent ABM also correlated with scores for “depressed” and “bored” in the qualitative results, indirectly suggesting that experts associate greater waking inactivity with negative emotional states. The hypothesis that ABM reflects a depression-like syndrome is not supported; we discuss how results might tentatively support a “boredom-like” state and further research directions.</jats:p

Insight Into the Anti-staphylococcal Activity of JBC 1847 at Sub-Inhibitory Concentration

Multidrug-resistant pathogens constitute a serious global issue and, therefore, novel antimicrobials with new modes of action are urgently needed. Here, we investigated the effect of a phenothiazine derivative (JBC 1847) with high antimicrobial activity on Staphylococcus aureus, using a wide range of in vitro assays, flow cytometry, and RNA transcriptomics. The flow cytometry results showed that JBC 1847 rapidly caused depolarization of the cell membrane, while the macromolecule synthesis inhibition assay showed that the synthesis rates of DNA, RNA, cell wall, and proteins, respectively, were strongly decreased. Transcriptome analysis of S. aureus exposed to sub-inhibitory concentrations of JBC 1847 identified a total of 78 downregulated genes, whereas not a single gene was found to be significantly upregulated. Most importantly, there was downregulation of genes involved in adenosintrifosfat (ATP)-dependent pathways, including histidine biosynthesis, which is likely to correlate with the observed lower level of intracellular ATP in JBC 1847–treated cells. Furthermore, we showed that JBC 1847 is bactericidal against both exponentially growing cells and cells in a stationary growth phase. In conclusion, our results showed that the antimicrobial properties of JBC 1847 were primarily caused by depolarization of the cell membrane resulting in dissipation of the proton motive force (PMF), whereby many essential bacterial processes are affected. JBC 1847 resulted in lowered intracellular levels of ATP followed by decreased macromolecule synthesis rate and downregulation of genes essential for the amino acid metabolism in S. aureus. Bacterial compensatory mechanisms for this proposed multi-target activity of JBC 1847 seem to be limited based on the observed very low frequency of resistance toward the compound

Business constraints and growth potential of micro and small manufacturing enterprises in Uganda

Ugandan micro and small enterprises (MSEs) still perform poorly. Studies associating poor performance of manufacturers with lack of finance and low investment ignore micro enterprises. Those focusing on MSEs are either exploratory in nature or employ a descriptive analysis, which cannot show the extent to which business constraints explain the performance of MSEs. Thus, this paper tries to examine the extent to which the growth of MSEs is associated with business constraints while controlling for owners’ attributes and firms’ characteristics. The results reveal that MSEs’ growth potential is negatively associated with limited access to productive resources (finance and business development services), high taxes and lack of market access