Search Results (193)

Background: Primary hepatocellular carcinoma (HCC) and liver metastases differ in origin, progression, and therapeutic response, yet a direct high-resolution spatial comparison of their tumor microenvironments (TMEs) within the liver has not previously been performed. Methods: We applied high-definition spatial transcriptomics to fresh-frozen specimens of one HCC and one liver metastasis (>16,000 genes per sample, >97% mapping rates) as a proof-of-principle two-specimen study, cross-validated in human proteomics and patients’ survival datasets. Transcriptional clustering revealed spatially distinct compartments, rare cell states, and pathway alterations, which were further compared against an independent systemic dataset. Results: HCC displayed an ordered lineage architecture, with transformed hepatocyte-like tumor cells broadly dispersed across the tissue and more differentiated hepatocyte-derived cells restricted to localized zones. By contrast, liver metastases showed two sharply compartmentalized domains: an invasion zone, where proliferative stem-like tumor cells occupied TAM-rich boundaries adjacent to hypoxia-adapted tumor-core cells, and a plasticity zone, which formed a heterogeneous niche of cancer–testis antigen–positive germline-like cells. Across both tumor types, we detected a conserved metabolic program of “porphyrin overdrive,” defined by reduced cytochrome P450 expression, enhanced oxidative phosphorylation gene expression, and upregulation of FLVCR1 and ALOX5, reflecting coordinated rewiring of heme and lipid metabolism. Conclusions: In this pilot study, HCC and liver metastases demonstrated fundamentally different spatial architectures, with metastases uniquely harboring a germline/neural-like plasticity hub. Despite these organizational contrasts, both tumor types converged on a shared program of metabolic rewiring, highlighting potential therapeutic targets that link local tumor niches to systemic host–tumor interactions. Full article

Species distribution models (SDMs) have become an important tool to inform conservation and pest surveillance programs about the potential biological invasion of insect pests. Nonetheless, to be operational, SDMs need to incorporate multiple environmental covariates and a representative number of occurrence points depicting the species’ ecological niche. The algorithm of choice, model of choice, and comparison can also have a great effect on the final prediction output. We created a dataset based on previously published records, plus 36 new occurrences and 37 environmental predictors, to generate the first global ensemble distribution model for Aulacaspis yasumatsui. We employed a strategy that aggregates SDMs with the best performance (i.e., greater accuracy) from six different algorithms, resulting in an averaged and weighted model, i.e., the ensemble model. We then selected models from algorithms whose true skill statistic (TSS) was above 0.5 in order to map the potential global distribution of A. yasumatsui. Our results suggest that covariate selection and the individual model algorithms used in the ensemble may be more important for achieving an accurate SDM than the number of occurrence points. Full article

The rapid expansion of ski tourism and climate change-induced snow shortages have led to intensified ski run maintenance, including extensive earthworks, artificial snowmaking, and regular snow grooming. While these activities are known to cause significant land degradation, quantitative geomorphological studies, specifically on the effects of snow grooming, are limited. This study addresses this knowledge gap by quantitatively assessing the impact of snow grooming on erosion processes and hillslope morphology by comparing them with natural landforms. We achieved this by determining the spatial distribution, morphometry, and long-term persistence of studied landforms. The study area consisted of a unique ski resort at Kasprowy Wierch, which does not use artificial snowmaking or extensive earthworks. We combined detailed field mapping with the analysis of multi-temporal Digital Elevation Models (DEMs) and orthophotos from 2012, 2019, 2020, and 2023. Our methodology also included the calculation of volumetric changes using the DEM of Difference (DoD) analysis. We distinguished two groups of eroded areas, natural landforms (e.g., shallow landslides, debris flow tracks, nivation niches) and snow groomer-induced forms, which were concentrated on ski runs. Natural landforms were elongated and deeper, with higher edges, clustered along debris flow tracks, and occurred on steeper slopes (mean 26.8°). They were more persistent and extensive, with a total area ranging from 3891 m² in 2012 to 3452 m² in 2023. In contrast, groomer-eroded landforms, located on gentler slopes (mean 23.4°), were smaller, more angular, less persistent, and concentrated on narrower, intensively used ski run sections. Their total area decreased from 2122.71 m² to 1762.25 m² over the same period, despite an increase in their count. The volumetric analysis revealed distinct dynamics: over the long term (2012–2023), natural forms showed a total deposition of +8.196 m³, while groomer-eroded forms experienced total erosion of −2.070 m³. During an extreme rainfall event in 2020, natural landforms experienced vast erosion of −163.651 m³, nearly five times greater than the −33.765 m³ observed on snow groomer-eroded landforms, demonstrating their greater susceptibility to high-magnitude events. Importantly, a comparison with other studies reveals that the scale of erosion from snow grooming is relatively small compared to the severe impacts of artificial snowmaking. Our findings are relevant for managing protected areas, such as Tatra National Park, where the focus should be on mitigating anthropogenic impacts to preserve natural processes, which in turn implies that the development of new ski infrastructure should be prohibited. Full article

We report the first occurrence of an arboreal spiny rat of the tribe Echimyini in the Early Holocene of southern South America. The specimen, a lower deciduous premolar, was recovered from fluvial deposits exposed along the right bank of Doll Creek, in northeastern Argentina. Morphological comparisons indicate strong affinities with the extant Amazonian genus Lonchothrix, although the fossil exhibits distinct traits such as thicker enamel and a transverse, short posterior mesofossettid. The available evidence of strong climatic niche conservatism in Echimyini supports its interpretation as an indicator of the transient presence of humid, Amazonian-like forests in the region around 10,000 years ago. Sedimentological and stratigraphic evidence correlates this warming phase with an Early Holocene transgression in the Paraná Delta. The absence of aff. Lonchothrix in the recent fauna may be the result of a post-optimum extinction event triggered by a drier phase during the Middle Holocene. This discovery provides novel evidence for a short-lived biogeographic connection between Amazonia and the southern cone during a climatic window of expansion for tropical biotas. It also highlights the role of the fossil record of Echimyidae as a sensitive proxy for reconstructing paleoenvironmental changes in temperate South America. Full article

The majority of extant studies concentrate on the reactivation of dormant Anammox biomass or the recovery of activity under specific storage conditions. Research on rehabilitation strategies for anaerobic ammonium oxidation (Anammox) systems is limited, with the exception of research on inhibitory factors. The recovery characteristics of biofilm systems after collapse induced by varying degrees of ammonia-nitrogen and small-molecular organic compound composite shocks have not been thoroughly elucidated. This study addresses the collapse of Anammox biofilm systems caused by sodium acetate inhibition through multi-phase rehabilitation strategies, stoichiometric analysis, and microbial community succession dynamics. Two regression algorithms—Support Vector Regression (SVR) and eXtreme Gradient Boosting (XGBoost)—were employed to construct predictive models for Total Nitrogen Removal Efficiency (TNRE) and Total Nitrogen Removal Rate (TNRR) in the CANON system, with model performance evaluated via coefficient of determination (R²) and root mean square error (RMSE). Results demonstrated that after terminating moderate-to-high sodium acetate dosing (300 mg/L and 500 mg/L), reactors R300 and R500 achieved TNRE recovery to 57.98% and 58.86%, respectively, and TNRR of 0.281 and 0.275 kgN/m³·d within 60–100 days, indicating the reversibility of high-concentration sodium acetate inhibition but a positive correlation between recovery duration and inhibition intensity. Microbial community analysis revealed that Planctomycetota (including Candidatus_Kuenenia) rebounded to 46–49% relative abundance in R100, synchronized with TNRE improvement. In contrast, R300 and R500 exhibited ecological niche replacement of denitrifiers (Denitratisoma) and partial TNRE restoration despite enhanced performance. Model comparisons showed SVR outperformed XGBoost in TNRE prediction, whereas XGBoost demonstrated superior TNRR prediction accuracy with R² approaching 1 and RMSE nearing 0, significantly surpassing SVR. This work provides critical insights into recovery mechanisms under organic inhibition stress and establishes a robust predictive framework for optimizing nitrogen removal performance in CANON systems. Full article

Microbial transplantation represents a sustainable strategy to address productivity gaps in agricultural soils by transferring microbiomes that enhance nutrient cycling, pathogen suppression, and stress tolerance. This study evaluates whether probiotic consortia from high-yield soybean soils (donor soil) could improve crop performance in less productive fields (recipient soil). We developed a host-adapted inoculant from soybean rhizospheres grown in donor soil and applied it to seeds at five concentrations (0.25–10 g/kg seed) in recipient soil, with untreated controls for comparison. To assess crop-specific microbial recruitment, we prepared a parallel bean-derived inoculant under identical conditions. Through 16S rRNA sequencing and growth/yield analysis, we found the following: (1) Distinct bacteriome assemblies between soybean- and bean-derived inoculants, confirming host specificity; (2) Successful enrichment of beneficial taxa (Enterobacteriaceae increased by 15–22%, Rhizobiaceae by 7–12%) despite native community resilience; and (3) Consistent yield improvement trends (4.8–6.2%), demonstrating potential to bridge productivity gaps. These results show that transplanted microbiomes can effectively modulate rhizosphere communities while maintaining ecological balance. This work establishes a scalable approach to address soil productivity limitations through microbiome transplantation. Future research should optimize (a) inoculant composition for specific productivity gaps; (b) delivery systems; and (c) compatibility with resident microbiomes, particularly in systems where niche-specific processes govern microbial establishment. Full article

Bacterial communities in diverse environmental niches respond to various external stimuli for survival. A primary means of communication between bacterial cells involves one-component (OC) and two-component signal transduction systems (TCSs). These systems are key for sensing environmental changes and regulating bacterial physiology. TCSs, which are the more complex of the two, consist of a sensor histidine kinase for receiving an external input and a response regulator to convey changes in bacterial cell physiology. For numerous reasons, TCSs have emerged as significant targets for antibacterial drug design due to their role in regulating expression level, bacterial viability, growth, and virulence. Diverse studies have shown the molecular mechanisms by which TCSs regulate virulence and antibiotic resistance in pathogenic bacteria. In this study, we performed a thorough analysis of the data from multiple public databases to assemble a comprehensive catalog of the principal detection systems present in both the non-pathogenic Pseudomonas putida KT2440 and the pathogenic Pseudomonas aeruginosa PAO1 strains. Additionally, we conducted a sequence analysis of regulatory elements associated with transcriptional proteins. These were classified into regulatory families based on Helix-turn-Helix (HTH) protein domain information, a common structural motif for DNA-binding proteins. Moreover, we highlight the function of bacterial TCSs and their involvement in functions essential for bacterial survival and virulence. This comparison aims to identify novel targets that can be exploited for the development of advanced biotherapeutic strategies, potentially leading to new treatments for bacterial infections. Full article

Copper (Cu) is an essential metal micronutrient, and a fungal pathogen’s ability to thrive in diverse niches across a broad range of bioavailable copper levels is vital for host colonization and fungal propagation. Recent transcriptomic studies have implied that trace metal acquisition is important for the propagation of the white nose syndrome (WNS) causing fungus, Pseudogymnoascus destructans, on bat hosts. This report characterizes the P. destructans transcriptional response to Cu-withholding and Cu-overload stress. We identify 583 differently expressed genes (DEGs) that respond to Cu-withholding stress and 667 DEGs that respond to Cu-overload stress. We find that the P. destructans Cu-transporter genes CTR1a and CTR1b, as well as two homologs to Cryptococcus neoformans Cbi1/BIM1 VC83_03095 (BLP2) and VC83_07867 (BLP3), are highly regulated by Cu-withholding stress. We identify a cluster of genes, VC83_01834 – VC83_01838, that are regulated by copper bioavailability, which we identify as the Cu-Responsive gene Cluster (CRC). We find that chronic exposure to elevated copper levels leads to an increase in genes associated with DNA repair and DNA replication fidelity. A comparison of our transcriptomic datasets with P. destructans at WNS fungal infection sites reveals several putative fungal virulence factors that respond to environmental copper stress. Full article

The import of ornamental plants has become a major source of alien invasive plants in China, posing threats to local ecosystems. However, research on their invasive potential and management strategies remains limited. This study evaluated the invasion risks of nine representative introduced ornamental plants (including naturalized and invasive species) in China (IOPCs). Using ecospat to perform climatic niche comparisons, we found significant unfilling and expansion (>50%) in most introduced ornamental plants, indicating strong invasiveness. Species distribution models (SDMs) were applied to predict the current and future distributions of these IOPCs under four shared socioeconomic pathways (SSPs: SSP1-2.6, SSP2-4.5, SSP3-7.0, and SSP5-8.5) across four time periods (2021–2040, 2041–2060, 2061–2080, and 2081–2100). The SDM results showed that the current high-risk areas are concentrated in southern China. Under future climate change, moderate- and high-risk zones are projected to shift northward, with the total areas increasing significantly, namely moderate-risk areas by 106.10% and high-risk areas by 64.35%, particularly in the border regions of Jiangxi, Fujian, and Zhejiang. We recommend establishing restricted introduction lists for non-native ornamental plants, enhancing monitoring and management in high-risk regions, and implementing early eradication measures. This study quantified the invasion risks and potential distributions of representative invasive ornamental plants, providing a scientific basis for effective control strategies. Full article

Early disease detection using biosensors is a significant challenge in modern medicine. This study aimed to investigate Lactobacillus rhamnosus GG (LGG) as a bacterial biosensor for biomarkers indicative of oral and systemic health conditions. For this purpose, LGG was cultured and then exposed to phosphate buffer, 10 wt.% sucrose solution, pH = 4.0, lactic acid, and filter-sterile saliva from five subjects. A total of 10 groups consisted of filter-sterile, freshly pooled saliva of subject 1 (SANT), subject 2 (SLAN), subject 3 (SLFU), subject 4 (SLPA), subject 5 (SLPO), phosphate buffer solution (pH = 7.4, BUF), and PBS with resin. Subsequently, the proteomic profiling of the samples was done by high-resolution mass spectrometry, focusing on the expression of bacterial proteins. The samples were evaluated for the biosensing capacity of LGG through its proteomic expression. Statistical comparisons were performed to outline proteomic changes, clustering upregulated and downregulated proteins relevant to stress response, metabolism, and environmental adaptation. The identification of key proteins associated with metabolic regulation, response to oxidative stress, and bacterial adaptation was possible using heatmaps and volcano plots. Each subject’s salivary composition also presented its unique, characteristic proteomic signature. Results showed a massive downregulation of proteins linked with stress under nutrient-rich conditions. In conclusion, the early detection of protein expression modifications related to environmental niche changes has shown that LGG can serve as a promising novel diagnostic tool, potentially overcoming many drawbacks of current physicochemical transducer-based biosensors. Full article

Climate change presents major challenges to global biodiversity and ecosystems. Related species distributed in the same region may exhibit differential response patterns to global climate change, resulting in divergent conservation strategies. East Africa is a critical hub for the diversity and distribution of giant Lobelia. In this study, we examined the potential distribution of seven giant Lobelia species (Lobelia aberdarica, L. telekii, L. gibberoa, L. bambuseti, L. deckenii, L. gregoriana, and L. rhynchopetalum) across six East African countries (Kenya, Ethiopia, Tanzania, Rwanda, Uganda, and Burundi) under projected climate change scenarios both RCP4.5 and RCP8.5. Species distribution models yielded high predictive accuracy (TSS > 0.8), with the mean temperature of the driest quarter (bio9) emerging as the most influential climatic variable determining future species distribution. The study found considerable variation in the species’ climatic niches, identifying distinct regions of climatically suitable habitats for each. Lobelia species at lower altitudes, such as L. giberroa and L. bambuseti, showed greater stability and expansion. In comparison, species at higher altitudes, such as L. telekii, L. deckenii, and L. rhynchopetalum, faced significant contraction in suitable habitats. These high-altitude species are particularly vulnerable and require urgent conservation interventions. This research highlights the importance of climate change considerations in the conservation of Lobelia species and provides a basis for developing targeted sustainable conservation. Full article

The conversion of tropical forests into urban and agriculture landscapes may alter insect populations through habitat disturbance and impact the diets of aerial insectivores. Most dietary studies on aerial insectivores have limitation on identifying prey at higher taxonomic levels in broad landscapes, restricting species-level identification and thus making a detailed dietary comparison impossible. This study examines the dietary changes through adaptation of house-farm swiftlets (Aerodramus sp.) and Pacific swallows (Hirundo tahitica) across three distinct habitats in Peninsular Malaysia: mixed-use landscapes, oil palm plantations, and paddy fields. High-throughput DNA metabarcoding with ANML primers targeting mitochondrial CO1 gene, identified 245 arthropod prey species, with six dominant orders: Coleoptera, Diptera, Blattodea, Hemiptera, Hymenoptera, and Lepidoptera. Mixed-use landscapes supported the highest dietary diversity and niche breadth, reflecting their ecological complexity. Paddy fields exhibited moderate diversity, while oil palm plantations demonstrated the lowest diversity, influenced by simplified vegetation structures and limited prey availability. The consumption of agricultural pests and vector species highlights the critical ecological role of aerial insectivorous birds in natural pest management and mitigating vector-borne disease risks. This research emphasizes the importance of conserving habitat heterogeneity to sustain the ecological services provided by these birds, benefiting both agricultural productivity and public health. Full article

Oaks in the genus Quercus L. are keystone species in the forest ecosystem and are considered ideal models for the study of plant evolution. In this research, we applied population genetics, ecological niche analysis and phenotypic traits to explore patterns of species differentiation and demographic history of two Chinese montane oak species (Quercus baronii Skan and Quercus dolicholepis A. Camus) from Quercus section Ilex across species distribution ranges. Analyses of population genetics with ten nuclear microsatellite loci on 33 populations of the two oak species indicated great interspecific genetic variations with distinct genetic backgrounds for the two oaks. Simulations on species demography suggested a speciation-without-migration model as the best to explain species divergence, while an approximate Bayesian computation analysis indicated that the two studied oak species probably split at about 17.80–28.48 Ma. A comparison of two core bioclimatic factors and ecological niche tests revealed strong niche differentiation between the two oak species, and association analysis also found a significantly positive correlation between interspecific genetic variations and bioclimatic distances. Additionally, analyses of the leaf morphology of 117 specimens with five quantitative characteristics showed clear species discrepancy between Q. baronii and Q. dolicholepis. Based on this evidence from genetic, ecological and phenotypic analyses, our research indicated clear species differentiation between Q. baronii and Q. dolicholepis, possibly in relation to an early species divergence and varying adaptative features of the two oaks shaped by heterogeneous environments within Qinling-Daba Mountains and surroundings. This study provides an example for future investigation of species differentiation and evolution among related oak species with integrated analyses and highlights the importance of ecological conditions on adaptive evolution and genetic conservation of endemic tree species in montane regions. Full article

The seasonal phenological segregation observed among various species within a plant community can be interpreted as a form of niche differentiation that facilitates the coexistence of these species. In the present study, life forms and phenological attributes of dominant plant species in temperate semi-natural grasslands of Central Himalaya, India, were assessed between January 2022 and December 2022. This study was carried out in three sites in different forest zones, viz. oak, cypress and pine. In each site, plots measuring 0.5 hectares were established and phenological assessments were conducted within each of these plots. A total of 50, 36, and 49 herbaceous species were identified in the grasslands of oak, cypress and pine zones, respectively, with these species categorized into five distinct life form classes. In the grasslands of both oak and pine zones, hemicryptophytes emerged as the predominant life form, whereas in the cypress zone grasslands, it was found that chamaephytes take precedence. The differences observed in the classifications of life forms can be ascribed to the geographical distribution and the biotic interactions present in these sites. The three grasslands exhibit comparable climatic conditions and day lengths, resulting in no significant variations in soil temperature, light intensity or overall climatic factors. The majority of species commenced their flowering phase during the monsoon season, attributed to the favorable conditions characterized by warm, humid weather and adequate soil moisture. Various phenological events, including germination, growth, and senescence, are significantly affected by weather and climate, and their timing subsequently influences ecosystem processes in a reciprocal manner. This study provides valuable foundational data for ecological and environmental research, aiding in the comparison and distinction of plant compositions across the Himalayas and its ecosystems. Full article

Background/Objectives: Youth with type 1 diabetes (T1D) who experience avoidable complications often have dangerously high and consistently elevated HbA1c values. Novel Interventions in Children’s Healthcare (NICH), a program designed to effectively intervene with this population, has demonstrated success with reducing avoidable complications and improving HbA1c in these youth. However, prior examinations of program outcomes have not included a comparison group. This is the first study to compare electronic health record (EHR) outcomes (i.e., HbA1c values, hospital utilization) of NICH youth to a comparison group. Methods: Youth with T1D and avoidable complications were referred to NICH (n = 101; NICH = 40; comparison = 61) from the Pacific Northwest region of the United States. Retrospective EHR review included one year prior to and two years post NICH referral. Outcomes included hospitalization utilization and HbA1c values. There were no significant demographic differences between NICH and unserved youth (M age = 14.05 years; 50% female). Results: Within-group analyses revealed that NICH youth demonstrated a significant reduction in mean (M) admissions from one year prior to two years post-referral (M = 1.55 to M = 0.99; p = 0.011) as well as reduced HbA1c values from pre-referral to one year post-referral (M = 11.64%; 287 mg/dL; 15.9 mmol/L to M = 10.87; 265 mg/dL; 14.7 mmol/L; (p = 0.006)). Between-group analyses revealed NICH youth had lower proportions of individuals with an HbA1c over 10% (240 mg/dL; 13.3 mmol/L) (p = 0.03) compared to comparison group youth at one year post-referral. ANOVA analyses showed a significant reduction in admissions in linear interaction F (1,95) = 4.036, (p = 0.047), indicating that NICH youth demonstrated a significantly greater reduction in admissions over time compared to comparison youth. Conclusions: This study was the first to compare the health outcomes of NICH youth to a comparison group. NICH youth demonstrated significant reductions in admissions and HbA1c values over time. Full article