Summary
By the time the complete genome sequence of the soil bacterium Pseudomonas putida KT2440 was published in 2002 (Nelson et al., ) this bacterium was considered a potential agent for ...environmental bioremediation of industrial waste and a good colonizer of the rhizosphere. However, neither the annotation tools available at that time nor the scarcely available omics data—let alone metabolic modeling and other nowadays common systems biology approaches—allowed them to anticipate the astonishing capacities that are encoded in the genetic complement of this unique microorganism. In this work we have adopted a suite of state‐of‐the‐art genomic analysis tools to revisit the functional and metabolic information encoded in the chromosomal sequence of strain KT2440. We identified 242 new protein‐coding genes and re‐annotated the functions of 1548 genes, which are linked to almost 4900 PubMed references. Catabolic pathways for 92 compounds (carbon, nitrogen and phosphorus sources) that could not be accommodated by the previously constructed metabolic models were also predicted. The resulting examination not only accounts for some of the known stress tolerance traits known in P. putida but also recognizes the capacity of this bacterium to perform difficult redox reactions, thereby multiplying its value as a platform microorganism for industrial biotechnology.
C1 inhibitor (C1Inh) deficiency is responsible for hereditary angioedema (C1‐INH‐HAE) and caused by variants of the SERPING1/C1INH/C1NH gene. C1Inh is the major control of kallikrein–kinin system. ...C1Inh deficiency leads to its uncontrolled activation, with subsequent generation of the vasoactive peptide bradykinin. This update documents 748 different SERPING1 variants, including published variants and additional 120 unpublished ones. They were identified as heterozygous variants (n = 729), as homozygous variants in 10 probands and as compound heterozygous variants (nine combinations). Six probands with heterozygous variants exhibited gonadal mosaicism. Probands with heterozygous (n = 72) and homozygous (n = 1) variants were identified as de novo cases. Overall, 58 variants were found at positions showing high residue conservation among serpins, and have been referred to as a mousetrap function of C1Inh: reactive center loop, gate, shutter, breach, and hinge. C1Inh phenotype analysis identified dysfunctional serpin variants with failed serpin–protease association and a residual 105‐kDa species after incubation with target protease. Regarding this characteristic, in conditions with low antigenic C1Inh, 74 C1‐INH‐HAE probands presented with an additional so‐called intermediate C1‐INH‐HAE phenotype. The present update addresses a comprehensive SERPING1 variant spectrum that facilitates genotype–phenotype correlations, highlighting residues of strategic importance for serpin function and for identification of C1Inh deficiency as serpinopathy.
Context.
Clouds are ubiquitous in exoplanet atmospheres and they represent a challenge for the model interpretation of their spectra. When generating a large number of model spectra, complex cloud ...models often prove too costly numerically, whereas more efficient models may be overly simplified.
Aims.
We aim to constrain the atmospheric properties of the directly imaged planet HR 8799e with a free retrieval approach.
Methods.
We used our radiative transfer code petitRADTRANS for generating the spectra, which we coupled to the PyMultiNest tool. We added the effect of multiple scattering which is important for treating clouds. Two cloud model parameterizations are tested: the first incorporates the mixing and settling of condensates, the second simply parameterizes the functional form of the opacity.
Results.
In mock retrievals, using an inadequate cloud model may result in atmospheres that are more isothermal and less cloudy than the input. Applying our framework on observations of HR 8799e made with the GPI, SPHERE, and GRAVITY, we find a cloudy atmosphere governed by disequilibrium chemistry, confirming previous analyses. We retrieve that C/O = 0.60
−0.08
+0.07
. Other models have not yet produced a well constrained C/O value for this planet. The retrieved C/O values of both cloud models are consistent, while leading to different atmospheric structures: either cloudy or more isothermal and less cloudy. Fitting the observations with the self-consistent Exo-REM model leads to comparable results, without constraining C/O.
Conclusions.
With data from the most sensitive instruments, retrieval analyses of directly imaged planets are possible. The inferred C/O ratio of HR 8799e is independent of the cloud model and thus appears to be a robust. This C/O is consistent with stellar, which could indicate that the HR 8799e formed outside the CO
2
or CO iceline. As it is the innermost planet of the system, this constraint could apply to all HR 8799 planets.
Isolated cool white dwarf stars more often have strong magnetic fields than young, hotter white dwarfs, which has been a puzzle because magnetic fields are expected to decay with time but a cool ...surface suggests that the star is old. In addition, some white dwarfs with strong fields vary in brightness as they rotate, which has been variously attributed to surface brightness inhomogeneities similar to sunspots, chemical inhomogeneities and other magneto-optical effects. Here we describe optical observations of the brightness and magnetic field of the cool white dwarf WD 1953-011 taken over about eight years, and the results of an analysis of its surface temperature and magnetic field distribution. We find that the magnetic field suppresses atmospheric convection, leading to dark spots in the most magnetized areas. We also find that strong fields are sufficient to suppress convection over the entire surface in cool magnetic white dwarfs, which inhibits their cooling evolution relative to weakly magnetic and non-magnetic white dwarfs, making them appear younger than they truly are. This explains the long-standing mystery of why magnetic fields are more common amongst cool white dwarfs, and implies that the currently accepted ages of strongly magnetic white dwarfs are systematically too young.
Celotno besedilo
Dostopno za:
DOBA, IJS, IZUM, KILJ, KISLJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
The carbon (C) storage capacity of northern latitude ecosystems may diminish as warming air temperatures increase permafrost thaw and stimulate decomposition of previously frozen soil organic C. ...However, warming may also enhance plant growth so that photosynthetic carbon dioxide (CO2) uptake may, in part, offset respiratory losses. To determine the effects of air and soil warming on CO2 exchange in tundra, we established an ecosystem warming experiment – the Carbon in Permafrost Experimental Heating Research (CiPEHR) project – in the northern foothills of the Alaska Range in Interior Alaska. We used snow fences coupled with spring snow removal to increase deep soil temperatures and thaw depth (winter warming) and open‐top chambers to increase growing season air temperatures (summer warming). Winter warming increased soil temperature (integrated 5–40 cm depth) by 1.5 °C, which resulted in a 10% increase in growing season thaw depth. Surprisingly, the additional 2 kg of thawed soil C m−2 in the winter warming plots did not result in significant changes in cumulative growing season respiration, which may have been inhibited by soil saturation at the base of the active layer. In contrast to the limited effects on growing‐season C dynamics, winter warming caused drastic changes in winter respiration and altered the annual C balance of this ecosystem by doubling the net loss of CO2 to the atmosphere. While most changes to the abiotic environment at CiPEHR were driven by winter warming, summer warming effects on plant and soil processes resulted in 20% increases in both gross primary productivity and growing season ecosystem respiration and significantly altered the age and sources of CO2 respired from this ecosystem. These results demonstrate the vulnerability of organic C stored in near surface permafrost to increasing temperatures and the strong potential for warming tundra to serve as a positive feedback to global climate change.
Understanding the factors and processes that shape intra-specific sensitivity to heat stress is fundamental to better predicting the vulnerability of benthic species to climate change. Here, we ...investigate the response of a habitat-forming Mediterranean octocoral, the red gorgonian Paramuricea clavata (Risso, 1826) to thermal stress at multiple biological and geographical scales. Samples from eleven P. clavata populations inhabiting four localities separated by hundreds to more than 1500 km of coast and with contrasting thermal histories were exposed to a critical temperature threshold (25 °C) in a common garden experiment in aquaria. Ten of the 11 populations lacked thermotolerance to the experimental conditions provided (25 days at 25 °C), with 100% or almost 100% colony mortality by the end of the experiment. Furthermore, we found no significant association between local average thermal regimes nor recent thermal history (i.e., local water temperatures in the 3 months prior to the experiment) and population thermotolerance. Overall, our results suggest that local adaptation and/or acclimation to warmer conditions have a limited role in the response of P. clavata to thermal stress. The study also confirms the sensitivity of this species to warm temperatures across its distributional range and questions its adaptive capacity under ocean warming conditions. However, important inter-individual variation in thermotolerance was found within populations, particularly those exposed to the most severe prior marine heatwaves. These observations suggest that P. clavata could harbor adaptive potential to future warming acting on standing genetic variation (i.e., divergent selection) and/or environmentally-induced phenotypic variation (i.e., intra- and/or intergenerational plasticity).
Ultra-hot Jupiters are emerging as a new class of exoplanets. Studying their chemical compositions and temperature structures will improve our understanding of their mass loss rate as well as their ...formation and evolution. We present the detection of ionized calcium in the two hottest giant exoplanets – KELT-9b and WASP-33b. By using transit datasets from CARMENES and HARPS-N observations, we achieved high-confidence-level detections of Ca II using the cross-correlation method. We further obtain the transmission spectra around the individual lines of the Ca II H&K doublet and the near-infrared triplet, and measure their line profiles. The Ca II H&K lines have an average line depth of 2.02 ± 0.17% (effective radius of 1.56 Rp) for WASP-33b and an average line depth of 0.78 ± 0.04% (effective radius of 1.47 Rp) for KELT-9b, which indicates that the absorptions are from very high upper-atmosphere layers close to the planetary Roche lobes. The observed Ca II lines are significantly deeper than the predicted values from the hydrostatic models. Such a discrepancy is probably a result of hydrodynamic outflow that transports a significant amount of Ca II into the upper atmosphere. The prominent Ca II detection with the lack of significant Ca I detection implies that calcium is mostly ionized in the upper atmospheres of the two planets.
We use a highly complete subset of the Galaxy And Mass Assembly II (GAMA-II) redshift sample to fully describe the stellar mass dependence of close pairs and mergers between 108 and 1012 M⊙. Using ...the analytic form of this fit we investigate the total stellar mass accreting on to more massive galaxies across all mass ratios. Depending on how conservatively we select our robust merging systems, the fraction of mass merging on to more massive companions is 2.0–5.6 per cent. Using the GAMA-II data we see no significant evidence for a change in the close pair fraction between redshift z = 0.05 and 0.2. However, we find a systematically higher fraction of galaxies in similar mass close pairs compared to published results over a similar redshift baseline. Using a compendium of data and the function γ
M
= A(1 + z)
m
to predict the major close pair fraction, we find fitting parameters of A = 0.021 ± 0.001 and m = 1.53 ± 0.08, which represents a higher low-redshift normalization and shallower power-law slope than recent literature values. We find that the relative importance of in situ star formation versus galaxy merging is inversely correlated, with star formation dominating the addition of stellar material below
$\mathcal {M}^*$
and merger accretion events dominating beyond
$\mathcal {M}^*$
. We find mergers have a measurable impact on the whole extent of the galaxy stellar mass function (GSMF), manifest as a deepening of the ‘dip’ in the GSMF over the next ∼Gyr and an increase in
$\mathcal {M}^*$
by as much as 0.01–0.05 dex.
Amyloid beta (Aβ) peptides are the major components of senile plaques, one of the main pathological hallmarks of Alzheimer disease (AD). However, Aβ peptides' functions are not fully understood and ...seem to be highly pleiotropic. We hypothesized that plasma Aβ peptides concentrations could be a suitable endophenotype for a genome-wide association study (GWAS) designed to (i) identify novel genetic factors involved in amyloid precursor protein metabolism and (ii) highlight relevant Aβ-related physiological and pathophysiological processes. Hence, we performed a genome-wide association meta-analysis of four studies totaling 3 528 healthy individuals of European descent and for whom plasma Aβ1-40 and Aβ1-42 peptides levels had been quantified. Although we did not observe any genome-wide significant locus, we identified 18 suggestive loci (P<1 × 10(-)(5)). Enrichment-pathway analyses revealed canonical pathways mainly involved in neuronal functions, for example, axonal guidance signaling. We also assessed the biological impact of the gene most strongly associated with plasma Aβ1-42 levels (cortexin 3, CTXN3) on APP metabolism in vitro and found that the gene protein was able to modulate Aβ1-42 secretion. In conclusion, our study results suggest that plasma Aβ peptides levels are valid endophenotypes in GWASs and can be used to characterize the metabolism and functions of APP and its metabolites.
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