Stay-green protein, defective in Mendel's green cotyledon mutant, acts independent and upstream of pheophorbide a oxygenase in the chlorophyll catabolic pathway

Type C stay-green mutants are defined as being defective in the pathway of chlorophyll breakdown, which involves pheophorbide a oxygenase (PAO), required for loss of green color. By analyzing senescence parameters, such as protein degradation, expression of senescence-associated genes and loss of photosynthetic capacity, we demonstrate that JI2775, the green cotyledon (i) pea line used by Gregor Mendel to establish the law of genetics, is a true type C stay-green mutant. STAY-GREEN (SGR) had earlier been shown to map to the I locus. The defect in JI2775 is due to both reduced expression of SGR and loss of SGR protein function. Regulation of PAO through SGR had been proposed. By determining PAO protein abundance and activity, we show that PAO is unaffected in JI2775. Furthermore we show that pheophorbide a accumulation in the mutant is independent of PAO. When silencing SGR expression in Arabidopsis pao1 mutant, both pheophorbide a accumulation and cell death phenotype, typical features of pao1, are lost. These results confirm that SGR function within the chlorophyll catabolic pathway is independent and upstream of PA

Averaging over atom snapshots in linear-response TDDFT of disordered systems: A case study of warm dense hydrogen

Linear-response time-dependent density functional theory (LR-TDDFT) simulations of disordered extended systems require averaging over different snapshots of ion configurations to minimize finite size effects due to the snapshot--dependence of the electronic density response function and related properties. We present a consistent scheme for the computation of the macroscopic Kohn-Sham (KS) density response function connecting an average over snapshot values of charge density perturbations to the averaged values of KS potential variations. This allows us to formulate the LR-TDDFT within the adiabatic (static) approximation for the exchange-correlation (XC) kernel for disordered systems, where the static XC kernel is computed using the direct perturbation method [Moldabekov et al., J. Chem. Theory Comput. 19, 1286 (2023)]. The presented approach allows one to compute the macroscopic dynamic density response function as well as the dielectric function with a static XC kernel generated for any available XC functional. The application of the developed workflow is demonstrated for the example of warm dense hydrogen. The presented approach is applicable for various types of extended disordered systems such as warm dense matter, liquid metals, and dense plasmas

Assessing the accuracy of hybrid exchange-correlation functionals for the density response of warm dense electrons

We assess the accuracy of common hybrid exchange-correlation (XC) functionals (PBE0, PBE0-1/3, HSE06, HSE03, and B3LYP) within Kohn-Sham density functional theory (KS-DFT) for the harmonically perturbed electron gas at parameters relevant for the challenging conditions of warm dense matter. Generated by laser-induced compression and heating in the laboratory, warm dense matter is a state of matter that also occurs in white dwarfs and planetary interiors. We consider both weak and strong degrees of density inhomogeneity induced by the external field at various wavenumbers. We perform an error analysis by comparing to exact quantum Monte-Carlo results. In the case of a weak perturbation, we report the static linear density response function and the static XC kernel at a metallic density for both the degenerate ground-state limit and for partial degeneracy at the electronic Fermi temperature. Overall, we observe an improvement in the density response for partial degeneracy when the PBE0, PBE0-1/3, HSE06, and HSE03 functionals are used compared to the previously reported results for the PBE, PBEsol, LDA, AM05, and SCAN functionals; B3LYP, on the other hand, does not perform well for the considered system. Together with the reduction of self-interaction errors, this seems to be the rationale behind the relative success of the HSE03 functional for the description of the experimental data on aluminum and liquid ammonia at WDM conditions

Стратегічні пріоритети подолання демографічної кризи в Україні

We report a computational study on the spontaneous self-assembly of spherical particles into twodimensional crystals. The experimental observation of such structures stabilized by spherical objects appeared paradoxical so far.We implement patchy interactions with the patches point-symmetrically (icosahedral and cubic) arranged on the surface of the particle. In these conditions, preference for self-assembly into sheet-like structures is observed. We explain our findings in terms of the inherent symmetry of the patches and the competition between binding energy and vibrational entropy. The simulation results explain why hollow spherical shells observed in some Keplerate-type polyoxometalates (POM) appear. Our results also provide an explanation for the experimentally observed layer-by-layer growth of apoferritin - a quasi-spherical protein

Biogenesis of a mitochondrial outer membrane protein in Trypanosoma brucei : targeting signal and dependence on an unique biogenesis factor

The mitochondrial outer membrane (OM) contains single and multiple membrane-spanning proteins which need to contain signals that ensure correct targeting and insertion into the OM. The biogenesis of such proteins has so far essentially only been studied in yeast and related organisms. Here we show that POMP10, an OM protein of the early diverging protozoan Trypanosoma brucei, is signal-anchored. Transgenic cells expressing variants of POMP10 fused to GFP demonstrate that the N-terminal membrane-spanning domain flanked by a few positively charged or neutral residues is both necessary and sufficient for mitochondrial targeting. Carbonate extraction experiments indicate that, while the presence of neutral instead of positively charged residues did not interfere with POMP10 localization, it weakened its interaction with the OM. Expression of GFP-tagged POMP10 in inducible RNAi cell lines shows that its mitochondrial localization depends on pATOM36 but does neither require Sam50 nor ATOM40, the trypanosomal analogue of the Tom40 import pore. pATOM36 is a kinetoplastid-specific OM protein that has previously been implicated in the assembly of OM proteins and in mitochondrial DNA inheritance. In summary, our results show that while the features of the targeting signal in signal-anchored proteins are widely conserved, the protein machinery that mediates their biogenesis is not

Mistargeting of aggregation prone mitochondrial proteins activates a nucleus-mediated posttranscriptional quality control pathway in trypanosomes.

Mitochondrial protein import in the parasitic protozoan Trypanosoma brucei is mediated by the atypical outer membrane translocase, ATOM. It consists of seven subunits including ATOM69, the import receptor for hydrophobic proteins. Ablation of ATOM69, but not of any other subunit, triggers a unique quality control pathway resulting in the proteasomal degradation of non-imported mitochondrial proteins. The process requires a protein of unknown function, an E3 ubiquitin ligase and the ubiquitin-like protein (TbUbL1), which all are recruited to the mitochondrion upon ATOM69 depletion. TbUbL1 is a nuclear protein, a fraction of which is released to the cytosol upon triggering of the pathway. Nuclear release is essential as cytosolic TbUbL1 can bind mislocalised mitochondrial proteins and likely transfers them to the proteasome. Mitochondrial quality control has previously been studied in yeast and metazoans. Finding such a pathway in the highly diverged trypanosomes suggests such pathways are an obligate feature of all eukaryotes

Does Vascular Calcification Accelerate Inflammation?: A Substudy of the dal-PLAQUE Trial.

BACKGROUND: Atherosclerosis is an inflammatory condition with calcification apparent late in the disease process. The extent and progression of coronary calcification predict cardiovascular events. Relatively little is known about noncoronary vascular calcification. OBJECTIVES: This study investigated noncoronary vascular calcification and its influence on changes in vascular inflammation. METHODS: A total of 130 participants in the dal-PLAQUE (Safety and efficacy of dalcetrapib on atherosclerotic disease using novel non-invasive multimodality imaging) study underwent fluorodeoxyglucose positron emission tomography/computed tomography at entry and at 6 months. Calcification of the ascending aorta, arch, carotid, and coronary arteries was quantified. Cardiovascular risk factors were related to arterial calcification. The influences of baseline calcification and drug therapy (dalcetrapib vs. placebo) on progression of calcification were determined. Finally, baseline calcification was related to changes in vascular inflammation. RESULTS: Age >65 years old was consistently associated with higher baseline calcium scores. Arch calcification trended to progress more in those with calcification at baseline (p = 0.055). There were no significant differences between progression of vascular calcification with dalcetrapib compared to that with placebo. Average carotid target-to-background ratio indexes declined over 6 months if carotid calcium was absent (single hottest slice [p = 0.037], mean of maximum target-to-background ratio [p = 0.010], and mean most diseased segment [p < 0.001]), but did not significantly change if calcification was present at baseline. CONCLUSIONS: Across multiple arterial regions, higher age is consistently associated with higher calcium scores. The presence of vascular calcification at baseline is associated with progressive calcification; in the carotid arteries, calcification appears to influence vascular inflammation. Dalcetrapib therapy did not affect vascular calcification.The study was supported by F. Hoffmann-La Roche Ltd, Basel, Switzerland. Some editorial assistance was provided by Prime Healthcare and was funded by F. Hoffmann-La Roche Ltd, Basel, Switzerland. Partial support is acknowledged from NIH/NHLBI R01 HL071021 (ZAF). We thank Elisabetta Damonte for helping with statistical analyses.This is the author accepted manuscript. The final version is available from Elsevier via http://dx.doi.org/10.1016/j.jacc.2015.10.05

PaTaS: Quality Assurance for Model-driven Software Development

The quality of software products in safety critical applications, extensively found within the space domain, is a key success factor but also a major cost driver. To ensure high quality of the software product, quality assurance processes with quality models and metrics are applied. With these tools and processes, product assurance managers and software developers are able to quantify the quality of the software under development. Within the ESA-funded study PaTaS (Product Assurance with TASTE Study), a product quality model with software and model metrics was developed and implemented in an end-to-end model-driven software development (MDSD) life cycle demonstrator. The goal of this study was to identify applicable concepts to maintain quality and dependability levels when MDSD is applied. This requires the definition of connected model and software quality indicators. These indicators were integrated into ESA’s reference software product quality model (ECSS-Q-HB-80-04A). The resulting adapted quality model got incorporated in a model-driven software development life cycle demonstrator. To evaluate this demonstrator and the integrated quality indicators in a realistic development scenario, mission-critical parts of the command and data handling subsystem of a satellite mission were modelled and subsequently coded. The aim of the activity was to demonstrate the effect of the end-to-end life cycle in combination with the developed quality model on the final onboard software product. In this paper we present the result of the study. The focus is on the quality model for MDSD and new quality metrics for models, which can be embedded in an end-to-end model-driven product development life cycle

PaTaS - Quality Assurance in Model-Driven Software Engineering for Spacecraft

Within PATAS (Product Assurance with TASTE Study), a product quality model with software and model metrics is developed and implemented in an end-to-end model-driven software engineering (MDSE) lifecycle demonstrator, based on TASTE. The goal of this study is to find applicable concepts to maintain quality and dependability levels, when MDSE is applied. This requires the definition of connected model and software quality indicators. These indicators are identified and integrated with ESA's reference software product quality model (ECSS-Q-HB-80-04A). The resulting quality model is integrated in a model-based software development lifecycle demonstrator, based on TASTE. To evaluate this demonstrator and the integrated quality indicators, mission-critical parts of the command and data handling subsystem of a satellite mission are modelled and subsequently coded, simulating a realistic development scenario as use case. The aim of the activity is to demonstrate the effect of the end-to-end lifecycle in combination with the developed quality model on the final onboard software product. The final results will set the baseline for recommendations to improve Quality Assurance in MDSE at ESA. In this talk, we present the on-going study and its latest results

TbLOK1/ATOM19 is a novel subunit of the noncanonical mitochondrial outer membrane protein translocase of Trypanosoma brucei

TbLOK1 has previously been characterized as a trypanosomatid-specific mitochondrial outer membrane protein whose ablation caused a collapse of the mitochondrial network, disruption of the membrane potential and loss of mitochondrial DNA. Here we show that ablation of TbLOK1 primarily abolishes mitochondrial protein import, both in vivo and in vitro. Co-immunprecipitations together with blue native gel analysis demonstrate that TbLOK1 is a stable and stoichiometric component of the archaic protein translocase of the outer membrane (ATOM), the highly diverged functional analogue of the TOM complex in other organisms. Furthermore, we show that TbLOK1 together with the other ATOM subunits forms a complex functional network where ablation of individual subunits either causes degradation of a specific set of other subunits or their exclusion from the ATOM complex. In summary these results establish that TbLOK1 is an essential novel subunit of the ATOM complex and thus that its primary molecular function is linked to mitochondrial protein import across the outer membrane. The previously described phenotypes can all be explained as consequences of the lack of mitochondrial protein import. We therefore suggest that in line with the nomenclature of the ATOM complex subunits, TbLOK1 should be renamed to ATOM19