Browse Articles

Quantitative spatial analysis of chromatin biomolecular condensates using cryoelectron tomography

Phase separation is an important mechanism to generate certain biomolecular condensates and organize the cell interior. Condensate formation and function remain incompletely understood due to difficulties in visualizing the condensate interior at high resolution. Here, we analyzed the structure of biochemically reconstituted chromatin condensates through cryoelectron tomography. We found that traditional blotting methods of sample preparation were inadequate, and high-pressure freezing plus focused ion beam milling was essential to maintain condensate integrity. To identify densely packed molecules within the condensate, we integrated deep learning–based segmentation with context-aware template matching. Our approaches were developed on chromatin condensates and were also effective on condensed regions of in situ native chromatin. Using these methods, we determined the average structure of nucleosomes to 6.1 and 12 Å resolution in reconstituted and native systems, respectively, found that nucleosomes form heterogeneous interaction networks in both cases, and gained insight into the molecular origins of surface tension in chromatin condensates. Our methods should be applicable to biomolecular condensates containing large and distinctive components in both biochemical reconstitutions and certain cellular systems.

Publisher Correction: Effect of berry maturity stages on the germination and protein constituents of African nightshade (Solanum scabrum) seeds

Methodological and conceptual considerations of the TCM evolution

Associations of serum uric acid to eGFR ratio with diabetic retinopathy in individuals with type 2 diabetes

Phylogenomics of the tetraploid Hawaiian lobeliads: Implications for their origin, dispersal history, and adaptive radiation

Hawaiian lobeliads exhibit extensive adaptive radiations and are considered the largest plant clade (143 species) endemic to any oceanic archipelago. Rapid insular radiations are prone to reticulate evolution, yet detecting hybridization is often limited by inadequate sampling of taxa or independent loci. We analyzed 633 nuclear loci (including tetraploid duplications) and whole plastomes for 89% of extant species to derive phylogenies for the Hawaiian lobeliads. Nuclear data provide strong support for nine major clades in both likelihood and ASTRAL analyses. All genera/sections are monophyletic except Clermontia and Cyanea . Nuclear and plastome phylogenies conflict on short, deep branches; the nuclear tree resolves a fleshy-fruited clade of Hawaiian Clermontia/Cyanea-Brighamia/Delissea , sister to Polynesian Sclerotheca , with both sister to a capsular-fruited Hawaiian clade. Incomplete lineage sorting in a rapid radiation starting 8.5–11.3 Ma is sufficient to explain uncertainty and cytonuclear discordance along the backbone. Sequence data support reticulation within Clermontia and especially Cyanea . Nuclear data identify 42 interisland dispersal events: 89% accord with the strict progression rule, involving movement to the next younger island in the hotspot chain, consistent with theory. Plastid data overestimate such events by 17%. Cyanea and Clermontia have undergone parallel adaptive radiations in elevational distribution and flower length on all major islands, with multiple founders and some interisland differences. Hawaiian lobeliad diversification was driven by an early intergeneric divergence in habitat, followed by parallel adaptive radiation and ecological speciation within Clermontia/Cyanea , combined with widespread single-island endemism, frequent interisland dispersal, and occasional hybridization.

Optimization of amorphous silicon solar cells through photonic crystals for enhanced optical properties

Muscle peripheral circadian clock drives nocturnal protein degradation via raised Ror/Rev-erb balance and prevents premature sarcopenia

How central and peripheral circadian clocks regulate protein metabolism and affect tissue mass homeostasis has been unclear. Circadian shifts in the balance between anabolism and catabolism control muscle growth rate in young zebrafish independent of behavioral cycles. Here, we show that the ubiquitin–proteasome system (UPS) and autophagy, which mediate muscle protein degradation, are each upregulated at night under the control of the muscle peripheral clock. Perturbation of the muscle transcriptional molecular clock disrupts nocturnal proteolysis, increases muscle growth measured over 12 h, and compromises muscle function. Mechanistically, the shifting circadian balance of Ror and Rev-erb regulates nocturnal UPS, autophagy, and muscle growth through altered TORC1 activity. Although environmental zeitgebers initially mitigate defects, lifelong muscle clock inhibition reduces muscle size and growth rate, accelerating aging-related loss of muscle mass and function. Circadian misalignment such as shift work, sleep deprivation, or dementia may thus unsettle muscle proteostasis, contributing to muscle wasting and sarcopenia.

Enhancing CO2 emissions prediction for electric vehicles using Greylag Goose Optimization and machine learning

Abstract Electric vehicle (EV) $$\hbox {CO}_2$$ emissions should be predicted and mitigated, which requires lowering EV emissions in line with global sustainability goals. Such accurate forecasting supports policymakers and other industry stakeholders make marketing decisions to reduce environmental impacts and optimize resource utilization. In this research, a novel Greylag Goose Optimization (GGO) algorithm is integrated with a Multi-Layer Perceptron (MLP) model to improve $$\hbox {CO}_2$$ emissions prediction. Finally, the study does a comparative analysis with some established optimization algorithms in hyperparameter tuning regarding an improved accuracy model. In addition, statistical analyses such as ANOVA, sensitivity analysis, and T-test were used to substantiate performance differentiation between models. For the optimal model, the GGO-optimized MLP significantly outperformed baseline models and other optimization techniques, having minimum error metrics such as correlation coefficient and RMSE and an MSE of $$4.72 \times 10^{-7}$$ . As a result, the emissions forecast is very reliable. The proposed approach provides actionable insights for environmental policies, EV adoption strategies, and infrastructure planning. The model enables stakeholders to achieve climate objectives, optimize EV charging systems and foster the creation of sustainable transportation systems, as said accurate emissions estimates are enabled.

Loss of lipid asymmetry facilitates plasma membrane blebbing by decreasing membrane lipid packing

Membrane blebs have important roles in cell migration, apoptosis, and intercellular communication through extracellular vesicles (EVs). While plasma membranes (PM) typically maintain phosphatidylserine (PS) on their cytoplasmic leaflet, most blebs have PS exposed on their outer leaflet, revealing that loss of steady-state lipid asymmetry often accompanies PM blebbing. How these changes in PM lipid organization regulate membrane properties and affect bleb formation remains unknown. We confirmed that lipid scrambling through the scramblase TMEM16F is essential for chemically induced membrane blebbing across cell types, with the kinetics of PS exposure being tightly coupled to the kinetics of bleb formation. Measurement of lipid packing with environment-sensitive probes revealed that lipid scrambling changes the physical properties of the PM, reducing lipid packing and facilitating the bilayer bending required for bleb formation. Accordingly, reducing lipid packing of the PM through cholesterol extraction, elevated temperature, or treatment with biological amphiphiles promoted blebbing in the absence of TMEM16F. Consistent with these cellular observations, blebbing in Caenorhabditis elegans embryos measured via EV production was significantly reduced by depleting the TMEM16-homolog ANOH-2. Our findings suggest that changing membrane biophysical properties by lipid scrambling is an important contributor to the formation of blebs and EVs and potentially other cellular processes involving PM deformation.

Study on the anti-penetration randomness of metal protective structures based on optimized artificial neural network

Author Correction: Risk factors for and incidence of osteoporosis in patients with breast cancer by gender : a nationwide cohort study

Paradoxical indeed

Author Correction: Caprini score combined with thrombotic molecular markers for predicting DVT in patients with traumatic fractures

Eat, flee, freeze: Division of labor in the larval zebrafish visuomotor system

Association between Neutrophil Percentage-to-Albumin ratio and anemia risk: a population-based study

Exploiting luminescent solar concentrators in indoor visible light communication systems

Effect of heterozygous deletions on phenotypic changes and dosage compensation in Arabidopsis thaliana

Abstract Heterozygous deletions, which include a large number of genes, are often caused by the induction of mutations. The induction of gene dosage compensation should be considered when assessing the effects of heterozygous deletions on phenotypic changes. This mechanism is known to balance the expression levels of genes with different copy numbers in sex chromosomes, but it is also known to operate in autosomes. In the present study, 12 Arabidopsis thaliana BC1 mutants with heterozygous deletions were produced by crossing wild-type Col-0 plants with mutants induced by heavy ion beams. The sizes of the deletions ranged from 50.9 kb to 2.03 Mb, and the number of deleted genes ranged from 8 to 92. Nine of the 12 BC1 mutants showed phenotypic changes in fresh weight 14 days after cultivation or during the flowering period. RNA-sequencing (RNA-seq) analyses of 14-day-old leaves, 40-day-old leaves, and flower buds showed that dosage compensation did not occur in any stage or tissue tested. These results indicate that heterozygous deletions cause phenotypic changes owing to the absence of dosage compensation.

Simulating regional workforce impacts of decarbonizing integrated steelmaking

Global efforts to mitigate climate change are increasing pressure on heavy manufacturing industries to decarbonize production. The iron and steel industry is responsible for 7% of CO 2 emissions globally (2% in the United States) and is often a major employer in the regions where iron and steel is produced. Understanding the future prospects for workers in regions with high CO 2 emitting industries—including impacts of phasing out or evolving such industries—will be critical for informing regional economic and clean energy strategies. We simulate the impact of an “in-place” transition that replaces today’s integrated production with direct reduced iron (DRI) used in electric arc furnaces (EAFs), using Southwest Pennsylvania as an application of our generalizable approach. Our results suggest that the integrated steelmaking workforce today has the skills, knowledge, and abilities (SKAs) to fill over 95% of all jobs required by DRI/EAF facilities, but the number of jobs is only 25% of those at integrated plants. We also find that some occupational groups have greater general transferability into the broader job market, while other groups, such as production workers, are ill-equipped today based on current SKAs to transition out of the iron and steel industry. Our methodology further suggests factors that limit transitions: Around 85% of occupations are more limited by missing skills, while 15% are more limited by insufficient wages. These results may help to improve the design of social policy and the targeting of retraining programs, while the simulation approach can be readily adapted for other regions and industries.

Improving frequency stability in grid-forming inverters with adaptive model predictive control and novel COA-jDE optimized reinforcement learning

Pre-Hispanic ritual use of psychoactive plants at Chavín de Huántar, Peru

Ritual is broadly accepted as an important locus of social interaction in the pre-Hispanic Central Andes, and research into the development of durable sociopolitical inequality in the region often focuses on the social and political roles of public rituals. At the Middle-Late Formative Period (ca. 1200–400 BCE) monumental center of Chavín de Huántar, as well as at contemporary sites, ritual has long been hypothesized to include the use of psychoactive plants. However, neither psychoactive plant remains nor chemical traces of psychoactive compounds in likely ritual contexts have been identified at any of these sites. Recently excavated deposits sealed in an underground gallery at Chavín contained twenty-three artifacts of forms (especially bone tubes) associated with consumption of psychoactive plants elsewhere in the region. We here report, based on independent microbotanical and chemical analyses, two kinds of direct evidence for use of psychoactive plants in institutionalized ritual at Chavín. These results are direct evidence of psychoactive plants in archaeological bone tubes used as inhalers and the northernmost direct evidence of vilca and Nicotiana use in the pre-Hispanic Andes.