Browse Articles

Soliton dynamics and stability analysis of a double-chain DNA model with various chaos detection tools

Correction for Bachellerie et al., Châtelperronian cultural diversity at its western limits: Shell beads and pigments from La Roche-à-Pierrot, Saint-Césaire

Triploid Atlantic salmon are physiologically disadvantaged at larger body sizes

Abstract Triploid Atlantic salmon are sterile and used in aquaculture to prevent escapees from breeding in the wild. Meanwhile, triploids suffer poor animal welfare in the latter marine growth phase. Previous experiments have mainly tested smaller fish, and physiological differences between triploids and diploids tended to be subtle or non-existing. We therefore hypothesized that triploidy first becomes a disadvantage at larger body sizes where scaling constraints become more magnified in triploids owing to them having larger cells with lower surface to volume ratios. We measured metabolic rates, stress responses, hypoxia tolerance, and critical thermal maximum in big (≈3 kg) triploid and diploid Atlantic salmon. Additionally, we assessed gill histology metrics. Big triploids had higher standard metabolic rates, lower aerobic scopes, and reduced tolerances to hypoxia and thermal stress. Oxygen extraction coefficients were overall lower in triploids, suggesting reduced efficiency in gill oxygen uptake. This was further supported by lower lamellar densities which indicate less gill surface area. In conclusion, big triploid Atlantic salmon were more vulnerable to environmental extremes driven by oxygen supply limitation and higher basal maintenance costs. This provides a mechanistic explanation for why triploids become prone to animal welfare issues in the latter growth phase of marine aquaculture.

<i>Rroid2</i> regulates effector-to-memory CD8 ⁺ T cell differentiation during infection in vivo

CD8 + T cell differentiation has been associated with changes in the expression of long noncoding RNAs (lncRNAs). Yet, which and how lncRNAs regulate CD8 + T cell responses following infection in vivo remains incompletely understood. We performed deep RNA-seq to map the lncRNA expression landscape of CD8 + T cell subsets during infection and generated lncRNA knockout mouse models to evaluate the in vivo relevance of six lncRNAs. We identified Rroid2 to regulate effector CD8 + T cell function and effector-to-memory differentiation. Rroid2 -deficient mice displayed increased CD44 dim Foxp3 + regulatory T cells while the development of other immune cells, such as natural killer cells, was not affected. In CD8 + T cells, Rroid2 deficiency resulted in a fine-tuned downregulation of transcription factors Id2 and T-bet and impaired KLRG1 + and KLRG1 − effector CD8 + T cell proliferation and cytotoxicity as well as effector-to-memory CD8 + T cell differentiation. The human orthologue of Rroid2 , LINC01814 , is also upstream of the transcriptional regulator ID2 and is highly expressed in human memory CD8 + T cells. Taken together, Rroid2 represents a key regulatory layer that controls CD8 + T cell differentiation.

The role of fine and submicron aerosol particles in urban air pollution in the context of meeting new air quality standards

Tropics-wide intraseasonal oscillations

The tropical climate variability is characterized by various oscillations across a range of timescales. Oscillations that imprint the tropical mean state are generally attributed to slow processes, such as the seasonal cycle or interannual variability. Here, we identify a pronounced tropics-wide intraseasonal oscillation (TWISO) in satellite observations and reanalyses. This oscillation, with a period of 30 to 60 d, is evident across multiple variables and involves interactions between convection, radiation, surface fluxes, and large-scale circulation. It is primarily manifested as convective perturbations in the tropical Indo-Pacific warm pool accompanied by oscillations in the large-scale tropical overturning circulation. Here, we examine the relationship between TWISO, the Madden–Julian Oscillation (MJO), and the instability of radiative-convective equilibrium. Certain phases of TWISO coincide with specific phases of the MJO, suggesting a potential connection between the two. However, although the MJO can amplify the oscillation amplitude of TWISO, it is not essential for TWISO to occur. Finally, due to its broad manifestation across the tropics, TWISO potentially exerts widespread influence on tropical weather and climate at regional scales.

Machine learning prediction of future land surface temperature from SAR optical fusion under urban expansion in Changsha, China

Stochastic responses and marginal valuation

The analysis of policy impacts in a dynamic and uncertain reality is vital to supporting informed economic policy design and implementation. Dynamic, stochastic economic models used in policy evaluation necessarily simplify the world as we know it. This motivates us to explore, refine, and extend tools aimed at producing marginal valuations that shed light on why some policies are optimal and how others, though suboptimal, can be improved. We present representations of these marginal valuations that embrace uncertainty and support robust implementation-even in environments characterized by “deep uncertainties.” These representations offer a more complete understanding of how interactions among multiple state variables, concerns about model misspecification, and uncertainties surrounding potentially long-term implications contribute to the cogent assessment of policies. We argue that these methods are particularly salient for evaluating the global cost of climate change and the global value of research and development with long-term prospects for success.

Improving color reliability of digital textile images via optimized acquisition and preprocessing

Correction for Tse et al., Large-scale combination screens reveal small-molecule sensitization of antibiotic-resistant gram-negative ESKAPE pathogens

Predicting spatiotemporal changes in flood prone regions using PSO-ML coupling under climate change scenarios

From nematode to Nobel: How community-shared resources fueled the rise of <i>Caenorhabditis elegans</i> as a research organism

Experimental organisms such as the nematode Caenorhabditis elegans are fundamental to biological discovery. The success of C. elegans research has been greatly enabled by infrastructure that allows thousands of scientists to share and access research materials and unpublished information efficiently. Here, we celebrate the worm by interweaving vignettes describing four Nobel Prize–winning discoveries with descriptions of how the major NIH-supported research resources—the Caenorhabditis Genetics Center, WormBase, and WormAtlas—provide invaluable support for all C. elegans research. The synergy between investigation and the availability of shared resources for the C. elegans community is a paradigm for all model organism research, and the continued support of such community research resources will be essential for maximizing impactful discoveries in the future.

Capsaicin camphor and caffeic acid reduce adipogenesis and promote lipolysis with TRPV1 involvement

Abstract Excess fat accumulation contributes to metabolic disorders such as insulin resistance, type 2 diabetes, cardiovascular disease and increases risk of dementia. Promoting lipolysis and inhibiting adipogenesis through natural compounds offers a promising therapeutic approach to obesity. This study investigates the lipolytic and anti-adipogenic effects of capsaicin, camphor, and caffeic acid in human Simpson-Golabi-Behmel Syndrome (SGBS) adipocyte model. First, we determined appropriate treatment concentrations using MTT assays, which demonstrated a dose dependent reduction in cell viability for all three compounds. Selected doses were applied to differentiating SGBS cells until day 14. Lipid droplet accumulation and free fatty acid release were assessed using Oil Red O (ORO) staining and a lipolysis assay kit, respectively. Gene expression of adipogenic and lipolytic markers was analysed by RT-PCR and TRPV1 receptor involvement was examined by immunofluorescence. A network pharmacology approach incorporating GeneCards, STITCH, and other databases revealed downregulation of PPARG, CEBPA, and FABP4, and upregulation of HSL, ATGL, and PLIN1. TRPV1 activation was prominent in capsaicin treated cells. Network analysis identified shared regulatory hubs such as PPARG, STAT3, and MTOR. All treatments significantly reduced lipid accumulation and increased lipolysis, with capsaicin showing the strongest effects. Combination treatments, especially capsaicin with caffeic acid, exhibited synergistic effects. While the previous studies showed interference of these compounds in the molecular pathways involved in fat cell metabolism, our work establishes for the first time potential thermogenic capacity of camphor individually and of combinatory effects of three compounds to inhibit adipogenesis and promote lipolysis in human adipocytes, potentially through TRPV1 signalling and modulation of metabolic gene networks. These findings highlight their therapeutic potential for metabolic disorders.

Genomic ancestry, behavior, and the domestication of the dog

Fundamental insights into gallium leaching for sustainable electronic waste recovery

Abstract This study systematically concerns the leaching behavior and dissolution kinetics of gallium (Ga). The objective was to identify sustainable leaching agents by incorporating organic acid reagents. Using a novel approach involving pH-adjusted experiments, the findings elucidated the dissolution behavior, delineating acidolysis and complexolysis. The screening results demonstrated the efficacy of oxalic acid (10 mM), which extracted 1105.2 ± 61.4 mg/L of Ga at pH 1.2. Dissolution kinetics based on the shrinking core model (SCM) revealed a synergistic mechanism governed by film diffusion and surface chemical reaction control, with chemical reaction control dominating at higher temperatures. One-factor-at-a-time (OFAT) experiments clarified the influence of experimental parameters on Ga leaching yield. In addition, the Box-Behnken design (BBD) was employed to evaluate parameter interactions, confirming the significance of the process parameters, including interaction terms, while characterizing the model in terms of a quadratic expression. Under optimized conditions: 710.55 mM acid concentration, a reaction temperature of $$84.5^\circ$$ C, and a solid loading of 50 g/L, 37% of Ga was effectively extracted within 3.2 hours. These findings underscore the selectivity and operational compatibility of oxalic acid compared to conventional leaching agents, emphasizing its promising integration into biogenic production pathways and sustainable closed-loop gallium recovery processes.

Neural representation of the decisional reference point in monkeys

The decisional reference point serves as a hidden benchmark for evaluating options in decision-making. Despite extensive behavioral evidence for the existence of the reference point, its neural instantiation remains unclear. To identify reference point encoding at both the single-neuron and population levels, we analyzed neural activity from macaques performing a wealth accumulation task that dissociated objective reward values from the reference point. Across six frontal regions, we found that reference-related signals were broadly distributed at the single-neuron level. However, at the population level, only the ventral bank of the anterior cingulate cortex (vbACC) encoded the reference point significantly. In contrast, the dorsal bank of ACC and dorsolateral prefrontal cortex showed population-level encoding of reference-dependent subjective value signals. The temporal sequence of these signals and their known anatomical connectivity hints at a dedicated neural circuit for reference dependence, with the vbACC potentially serving as a global source of reference point signal modulating activity in downstream value-encoding regions.

Physiological responses and histological alterations induced by pollution in the Nile tilapia from the Rosetta branch of the River Nile, Egypt

Abstract The Nile River is the primary source of freshwater in Egypt and supports nearly all the anthropogenic activities in the region and, consequently, it is highly susceptible to pollution from diverse sources. Aquatic ecosystems in the Nile basin face increasing threats originated from pollution and seasonal fluctuations, both of which can profoundly affect the health and resilience of fish populations. Hence, addressing this issue is a must. This study investigated the impact of heavy metals (Fe, Zn, Cu, Cr and Cd) on key physiological and biochemical parameters for the Nile tilapia, Oreochromis niloticus sampled from two sites on the Rosetta Branch of the River Nile: El-Qanater (reference site) and El-Qatta (polluted site) during summer and winter of 2023. In addition, histological analysis was conducted on vital organs covering the winter season. Both site and season were detected with impacts on the hormonal concentrations in the fish samples. Compared to the reference site, fish individuals from the polluted site exhibited pronounced alterations in hormonal balance, with elevated cortisol levels and a marked decline in thyroid hormones (T3 and T4), while TSH levels were increased, particularly during winter. Elevated serum glucose, total protein, and albumin levels were evidenced for metabolic stress. Liver enzyme activity (ALT and AST) and kidney function biomarkers (urea, uric acid, and creatinine) were significantly increased, especially in winter. Profound responses to pollution were recorded with higher levels of SOD, CAT, GPx, and GST, aligned with a substantial decline in GSH levels. Moreover, higher malondialdehyde (MDA) levels were detected in winter. For fish organs histologically examined, a severe damage was remarkably observed in liver, gills, and kidney of fish from El-Qatta site. This study reveals the combined impact of pollution and seasonal changes on the Nile tilapia health, emphasizing the need for continuous monitoring and effective pollution control. Implementing targeted water quality programs in the Rosetta Branch is recommended to preserve fish health, biodiversity, and sustainable fisheries.

VGLL1 contributes to both the transcriptome and epigenome of the developing trophoblast compartment

The trophectoderm (TE), the first lineage specified during mammalian development, initiates implantation and gives rise to placental trophoblasts. While animal models have elucidated key conserved signaling pathways involved in early TE specification, including bone morphogenetic protein (BMP), WNT, and HIPPO, species-specific differences during early development emphasize the need for human-specific models. We previously identified VGLL1, a coactivator of TEAD transcription factors, as a human-specific placental marker. In this study, we employed a pluripotent stem cell (PSC)-based model of TE induction by BMP4 to investigate chromatin remodeling and transcriptional dynamics during TE formation. BMP4-induced chromatin accessibility changes promoted a trophoblast gene expression program, while mesoderm lineage markers were only transiently expressed upon canonical WNT activation. We found that VGLL1 was expressed downstream of key TE transcription factors (GATA2/3, TFAP2A/C) but was essential for establishment of full trophoblast identity by up-regulating the epidermal growth factor receptor (EGFR) and reinforcing GATA3 expression through positive feedback. Notably, VGLL1 enhanced canonical WNT signaling via direct regulation of WNT receptors and effectors. We also identified KDM6B, a histone demethylase that removes H3K27me3 repressive marks, as a direct VGLL1 target. KDM6B facilitated activation of bivalent promoters associated with TE markers, linking epigenetic regulation to lineage identity. Our findings establish a mechanistic framework positioning VGLL1 as a central regulator that integrates HIPPO, BMP, and WNT signaling pathways to drive establishment of human TE.

Enhanced log ratio calibration methods for stratified variance estimation in survey sampling

A legacy of genetic entanglement with wolves shapes modern dogs

Dogs evolved through interactions between people and gray wolves during the Late Pleistocene and have been ubiquitous in human societies ever since. Instances of wolf-to-dog introgression are rare, but adaptive introgression has been shown in association with high-altitude survival. Any widespread gene flow, however, has fallen below thresholds of detection in genome-wide statistical assessments. To reexamine evidence of dog–wolf gene flow, we analyzed 2,693 published dog and wolf genomes and combined highly sensitive local ancestry inference and phylogenomic analyses of nuclear genes, mitochondrial genomes, and Y-chromosome sequences. Although dogs and wolves segregate decisively at the nuclear level, no individual nuclear gene tree supports dog monophyly. Uniparental markers show mixed and interleaved dog and wolf clades with strong support and incongruent phylogenetic topologies. Using local ancestry inference, we find that 64.1% of modern breed dogs carry wolf ancestry from admixture that occurred nearly a thousand generations ago on average and now covers ~0.14% of their individual nuclear genomes. Among modern free-living village dogs (n = 280), 100% of analyzed genomes carry wolf ancestry. We find that wolf ancestry in dog breeds correlates with functional traits including size, breed category, and personality characteristics. In village dogs, wolf ancestry is enriched at olfactory receptor genes, suggesting adaptive introgression for sensory acuity that may have helped these free-living dogs survive in more challenging environments. In total, dog–wolf admixture has likely been an important factor in shaping the evolution of modern dogs.