676 research outputs found
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 -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 8 M orbiting in the
temperate zone around an M-star, with recently observed HO spectral
features in the infrared. We model Earth-like, Venus-like, as well as H-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-He atmosphere with limited amounts of HO and
CH. 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-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
Systemically Administered TLR7/8 Agonist and Antigen-Conjugated Nanogels Govern Immune Responses against Tumors
[Image: see text] The generation of specific humoral and cellular immune responses plays a pivotal role in the development of effective vaccines against tumors. Especially the presence of antigen-specific, cytotoxic T cells influences the outcome of therapeutic cancer vaccinations. Different strategies, ranging from delivering antigen-encoding mRNAs to peptides or full antigens, are accessible but often suffer from insufficient immunogenicity and require immune-boosting adjuvants as well as carrier platforms to ensure stability and adequate retention. Here, we introduce a pH-responsive nanogel platform as a two-component antitumor vaccine that is safe for intravenous application and elicits robust immune responses in vitro and in vivo. The underlying chemical design allows for straightforward covalent attachment of a model antigen (ovalbumin) and an immune adjuvant (imidazoquinoline-type TLR7/8 agonist) onto the same nanocarrier system. In addition to eliciting antigen-specific T and B cell responses that outperform mixtures of individual components, our two-component nanovaccine leads in prophylactic and therapeutic studies to an antigen-specific growth reduction of different tumors expressing ovalbumin intracellularly or on their surface. Regarding the versatile opportunities for functionalization, our nanogels are promising for the development of highly customized and potent nanovaccines
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