Search Results (10,074)

Excessive abdominal fat deposition reduces feed efficiency and edible carcass yield in chickens, yet its developmental and regional specialization remains poorly understood. We generated 93 bulk RNA sequencing (RNA-seq) libraries from 15 fat-associated anatomical regions at embryonic day 16 (E16) and 16 regions at 2 weeks post-hatch (2w) in six Xinghua chickens. Exploratory single-nucleus RNA sequencing was additionally performed on abdominal region (AR) tissue from one individual at each stage. Repeated-measures-aware analysis identified developmental stage as the major source of transcriptomic variation, with 4556 genes expressed at higher levels at E16 and 4528 at 2w. E16-associated programs were enriched for proliferation, morphogenesis, and structural development, whereas postnatal programs were dominated by immune and stimulus-response processes. Stage-specific weighted gene co-expression network analysis (WGCNA) identified substantial regional heterogeneity. AR showed stage-dependent signatures, including higher developmental and morphogenetic programs and lower lipid-metabolic programs at E16, and higher cell-cycle-related and lower developmental and fatty-acid-metabolic programs at 2w. Single-nucleus analysis identified adipose-lineage and multiple non-adipocyte populations, and cross-omics mapping showed that AR-associated signatures were distributed across multiple cellular compartments. These results suggest stage-dependent, multicellular transcriptional specialization of chicken AR tissue. Full article

Sequential non-thermal and thermal processing offers a route to jointly adjust the functionality, color/volatile profile and immunoreactivity of gluten-containing systems. This study aimed to evaluate the effects of sequential ultrasound-assisted enzymatic hydrolysis, wheat/rice starch incorporation and microwave heating on soluble gluten hydrolysate–starch composites, and to probe the underlying starch–gluten interactions. Gluten hydrolysates were blended with wheat or rice starch and microwave-heated to induce the Maillard reaction. Sequential processing enriched the <1 kDa peptide fraction (2.34%→13.05–14.99%) and raised ABTS·⁺ scavenging (0.25→0.40 mM Trolox/g). After starch compounding and microwaving, the composites exhibited increased protein-normalized TEAC (0.07–0.08 to 0.10–0.13 mM per mg/mL protein) and released more ninhydrin-reactive amino groups (>55 μmol/mg protein) after in vitro digestion. All microwave composites remained pale (L* > 94), with the coupled treated rice-starch composite showing the lowest color difference (ΔE = 0.25). GC-FID/electronic-nose profiling with PCA–DFA showed that the coupled treated composites retained a native cereal-like volatile profile, marked by the green/malty aldehyde 3-methylbutanal and hexanal, with only mild roasted-type Maillard volatiles and the clearest separation for rice starch. The lowest residual R5-reactive gluten reached 8.31–9.82 ppm for the coupled treated groups. Docking provided putative models of multi-site starch binding near immunodominant gliadin sequences (e.g., QQPYP, LQPFP) via Glu/Gln–glucose hydrogen bonds and hydrophobic contacts, with more diverse binding modes for rice starch. Overall, the sequential treatment improved functional and volatile properties and lowered R5-detectable immunoreactivity for composites, offering a process reference for the development of balanced gluten-derived functional ingredients and special dietary food formulations. Full article

Trihalomethanes (THMs) are carcinogenic disinfection by-products that pose severe environmental and health risks, yet effective microbial candidates’ resistance to THMs remains underexplored. In this study, twelve distinct bacterial strains wereisolated from activated sludge at a pharmaceutical wastewater treatment plant to identify potential THM-resistant bacteria. The isolates were characterized, evaluated for growth rates, and screened for tolerance in mineral salt agar medium exposed to 30 and 50 mg/L of mixed THMs over 72 h. Screening results revealed that four strains, i.e., BFMZ, EFMZ, FFMZ, and IFMZ, exhibited superior resilience, maintaining cell growth scores between +2 and +5 at elevated THM concentrations (50 mg/L), while other strains suffered in terms of growth. Molecular identification via 16S rDNA sequencing and phylogenetic analysis confirmed these tolerant strains as genus Tsukamurella sp. isolate BFMZ (score +5), Klebsiella sp. isolate EFMZ (score +3), Bacillus sp. isolate FFMZ (score +2), and Bacillus sp. isolate IFMZ (score +4). Notably, isolate BFMZ demonstrated the highest physiological resilience under high THM stress despite a moderate growth rate. These findings highlight the potential of THM-resistant bacteria and provide promising candidates for removing recalcitrant disinfection by-products. Full article

Aflatoxin contamination remains a critical challenge for food and feed safety, necessitating effective mitigation strategies. This study addresses the challenge of aflatoxin contamination by identifying four novel bacterial candidates capable of degrading four major aflatoxin congeners (B1, B2, G1, and G2). Quantitative HPLC and qualitative LC-HRMS with MS/MS profiling revealed that the isolated bacterial strains achieved high degradation efficiencies of 86–94%, proceeding through distinct demethylation and decarboxylation pathways. Oxford Nanopore whole-genome sequencing identified these potent degraders as Escherichia coli EC_2 and Klebsiella pneumoniae (KP_4, KP_5, and KP_6). To elucidate the genomic basis of this phenotype, we performed a comparative genomic analysis against two non-degrading E. coli strains. Functional annotation revealed complete aromatic degradation modules and intact enzymatic cascades present only in the degrading strains, demonstrating that this biodegradation capability is highly strain specific. Furthermore, molecular docking of key putative enzymes unique to these active cascades demonstrated highly favorable binding affinities (up to −8.70 kcal/mol) with all four aflatoxin congeners, stabilized by robust hydrogen bonding and hydrophobic networks. These findings provide a novel genomic and structural blueprint for aflatoxin biotransformation, highlighting the specific putative candidate enzymes, paaH and mhpB, for future investigations. Full article

Soil type imposes multilayered environmental filtering via physical structure, chemical properties, and resource availability, shaping microbial community assembly. Using 70 samples (black soil n = 27, meadow soil n = 32, and brown soil n = 11) from a typical black soil region of the Songnen Plain, we compared brown soil (forestland) with black soil and meadow soil (cropland) via 16S rRNA V3–V4 (primers 338F/806R) and fungal (ITS1, primers ITS1F/ITS2) amplicon sequencing and physicochemical analyses. The results showed (1) significantly higher organic carbon in brown soil than in black and meadow soils (p < 0.05); (2) a systematic shift along the r–K strategy axis, with K-strategists (e.g., Mortierellomycota and Acidobacteriota) dominating in brown soil, specializing in recalcitrant organic matter decomposition and carbon sequestration, and r-strategists (e.g., Proteobacteria, Bacteroidota, and Sordariaceae) enriched in black and meadow soils, rapidly utilizing labile carbon and driving carbon release. Redundancy analysis identified total organic carbon and pH as key environmental filters driving this shift. Our findings provide an ecological-strategy perspective for understanding land-use effects on soil microbiomes, informing carbon restoration and sustainable management in black soil regions. Full article

Esophageal adenocarcinoma (AC) incidence has increased markedly in the United States and other Western countries over recent decades. Gastro-esophageal reflux disease (GERD) can cause Barrett’s esophagus, which is strongly associated with the development of AC. However, the mechanisms underlying the pathogenesis of AC remain poorly elucidated. In this exploratory pilot study, we performed transcriptomic profiling by RNA sequencing (RNA-seq) on six normal esophagus (WT), four Barrett’s esophagus with low-grade dysplasia (BL), and six esophageal adenocarcinoma (AC) samples using RNA extracted via laser capture microdissection (LCM) of histologically confirmed formalin-fixed paraffin-embedded (FFPE) esophageal biopsies. Differential gene expression analysis demonstrated partial separation according to histological group, with overlap between BL and AC. BL and AC groups displayed a multitude of differentially expressed genes relative to WT samples; however, fewer differentially expressed genes were found when comparing BL and AC groups. We identified 3062 differentially expressed genes across comparisons (2289 WT vs. AC; 1854 WT vs. BL; 130 BL vs. AC). Using KEGG pathway analysis and functional annotation, candidate genes and pathways were identified. Genes related to the extracellular matrix, focal adhesion, and PI3K-AKT pathways were upregulated in BL and AC versus WT, while genes relating to keratinization, Ras/Rap1, and Hippo signaling were downregulated in BL and AC versus WT. A small set of genes (e.g., ANPEP, REG4, MEP1A) distinguished BL from AC and represent differentially expressed candidates for further investigation. This exploratory transcriptomic profiling provides insights into gene expression changes associated with AC pathogenesis and identifies candidate genes and pathways that warrant independent validation by qRT-PCR, immunohistochemistry, and functional studies. Full article

Acidophilic kinases are serine/threonine protein kinases that preferentially phosphorylate substrates bearing negatively charged determinants near the phosphoacceptor site. These determinants may be encoded by aspartate or glutamate, or introduced by prior phosphorylation of serine, threonine, or tyrosine residues. CK2 is the most representative of this historically small group of kinases because of its high basal activity, broad localization, and extensive substrate repertoire. Kinome-wide specificity profiling covering more than 84% of the active human S/T kinome has now provided a near-comprehensive view of acidophilic kinases across several families. Here, we compare these enzymes through three interconnected features: subcellular localization, substratome size, and consensus-motif specificity. We broadly categorize them as D/E-directed kinases or phosphate-directed/primed kinases, while recognizing that these preferences are not mutually exclusive. We then compare intrinsic preferences measured with peptide libraries with those observed in bona fide substrates. Despite their shared preference for negative charge, acidophilic kinases display markedly different positional requirements for acidic or phosphorylated determinants. For kinases that rely strongly on consensus-sequence recognition, these preferences can generate distinctive kinase-specific fingerprints that can support the attribution of experimentally validated phosphosites, particularly when combined with subcellular localization. Full article

Background: Aortic dissection (AD) is a life-threatening vascular disease with high mortality, yet its molecular pathogenesis remains incompletely understood. This study investigated the role of regulated in development and DNA damage responses 1 (REDD1) in vascular smooth muscle cells (VSMCs) apoptosis and the underlying mechanisms. Methods: Single-cell RNA sequencing data from GSE222318 were analyzed to investigate the expression levels of REDD1 in VSMCs and its role in inducing apoptosis and autophagy. The target gene was silenced in C57BL/6J mice via tail-vein injection of Adeno-associated virus.β-aminopropionitrile (BAPN) was used for AD induction. Western blotting was used to assess REDD1, LC3B, p62, BAX, BCL-2 in aortic tissues. Aortic histopathological alterations were examined by hematoxylin and eosin (H&E), Elastica van Gieson (EVG), and Masson’s trichrome staining. Immunofluorescence was performed to examine REDD1 expression and its localization in α-SMA-positive vascular smooth muscle cells. REDD1, LC3B, p62, BAX, BCL-2, mTOR, and p-mTOR were also examined by Western blotting in cultured cells. Mitochondrial membrane potential was evaluated by JC-1 staining, and apoptosis was assessed by flow cytometry. Results: REDD1 expression levels were significantly increased in human AD tissues and localized predominantly to medial VSMCs. REDD1 levels were positively correlated with BAX and LC3B and negatively correlated with BCL-2 and p62. Knockdown of REDD1 in AD mice was associated with increased levels of BAX and p62 and decreased levels of BCL-2 and LC3B in aortic tissues, accompanied by more severe pathological manifestations. REDD1 silencing in VSMCs increased BAX, p62 and p-mTOR while reducing BCL-2 and LC3B, accompanied by increased apoptosis and loss of mitochondrial membrane potential, whereas rapamycin reduced apoptosis and alleviated mitochondrial injury. Conclusions: REDD1 appears to play a protective, compensatory role in AD. Increased REDD1 expression may help preserve mitochondrial membrane potential and attenuate VSMC apoptosis under pathological stress, accompanied by changes in static autophagy-related markers that suggest a possible association with increased autophagic activity. Loss of REDD1 activity promotes mitochondrial injury and VSMC apoptosis, thereby aggravating AD. Targeting REDD1 may therefore represent a potential therapeutic strategy for AD. Full article

Hybrid magnetic–plasmonic nanoparticles offer a promising platform for cancer therapy by combining localized photothermal heating with nanoscale mechanical stimulation under remote laser irradiation and low-frequency alternating magnetic fields. However, the therapeutic potential of combining these effects remains insufficiently explored. In this study, we investigated the individual and combined effects of photothermal therapy (PTT) and magnetomechanical therapy (MMT) on the viability of Huh7 hepatocarcinoma cells in vitro using two types of layered Au–Fe microdisks (~1000 nm in diameter) with different layer sequences, i.e., Au(10)/Fe(70)/Au(10) (AFA) and Fe(50)/Au(10)/Fe(50) (FAF), where the values in parentheses denote the layer thicknesses in nanometers. The photothermal conversion efficiencies of the AFA and FAF microdisks in agarose were 35% and 53%, respectively, exceeding the values measured in aqueous solutions. After 24 h of incubation, both types of microdisks exhibited low intrinsic cytotoxicity up to concentrations of 100 µg/mL, at which the cell viability was reduced by no more than 7%. Application of either PTT or MMT enhanced cytotoxicity for both microdisk types. PTT was more effective for AFA microdisks, resulting in 29% cell death, whereas MMT showed greater efficacy for FAF microdisks, inducing 17% cell death. Notably, simultaneous PTT and MMT produced the strongest and synergistic therapeutic effect, leading to approximately 50% cell death. These findings demonstrate the potential of hybrid Au–Fe microdisks as multifunctional agents for combined photothermal and magnetomechanical cancer therapy. Full article

Asian black bears (Ursus thibetanus) and brown bears (Ursus arctos) are commonly kept in captivity in zoos, where captive conditions may alter fecal pathogenic bacterial communities and affect host health, although systematic studies remain limited. This study used 16S rRNA sequencing to characterize the composition, diversity, and community assembly mechanisms of fecal pathogenic bacteria in captive brown bears and black bears. Brown bear samples clustered relatively closely, whereas black bear samples were more dispersed, with juveniles and adults clearly separated; the Shannon index of adult black bears was significantly higher than that of brown bears (p < 0.001). Animal pathogenic bacteria (3.37–80.30%) and zoonotic potentially pathogenic bacterial taxa (18.00–96.60%) were the dominant types in both species, with Escherichia coli showing the highest abundance in most samples, and zoonotic potentially pathogenic taxa abundance was higher in adults (83.67%) than in juveniles (74.77%). These findings indicate that captivity and host age shape fecal MBPD-annotated potentially pathogenic bacterial communities in ursids, with enrichment of MBPD-annotated zoonotic potentially pathogenic taxa, including E. coli–assigned sequences, providing a scientific basis for health management of captive bears and potential public health risk assessment. Full article

Agricultural practices based on sustainable principles (e.g., conservation tillage, crop rotation, cover cropping, and the application of organic inputs) have been tested for their potential to improve soil structure, enhance soil organic matter, and support agrobiodiversity. These practices are directly linked to soil microbial diversity. Diverse soil microbial communities play multiple roles in promoting beneficial interactions between plants and their environment and in maintaining functional agroecosystems. Key functions enabled by soil microorganisms are carbon dynamics, nutrient cycling, soil structure improvement, pathogen suppression, plant growth promotion, and stress tolerance. Soil microorganisms are increasingly recognized as a promising but still underexploited source in tackling sustainability challenges in agricultural production. However, their potential varies depending on the interactions among abiotic and biotic factors, as well as the applied cultivation practices. In recent decades, advances in DNA extraction from soil and next-generation sequencing (NGS) technologies have enabled comprehensive characterization of microbial diversity, community composition, and functional potential for assessing soil health and agroecosystem functioning. Understanding, predicting, and exploring relevant plant–soil–microbiome interactions are essential for enhancing agroecosystem capacity for sustainable production. This review paper highlights how different factors and agricultural practices affect microbiome biodiversity. The focus is on microbiome approaches that integrate information on community composition with assessments of functional potential and measured microbial activity and ecosystem processes, combining state-of-the-art molecular monitoring, ecological indicators, and predictive modeling to support evidence-based management recommendations, distinguishing approaches that are currently applicable in agricultural practice from those that require further experimental validation. Full article

Background: Telomeres are repetitive DNA sequences at chromosome ends that maintain genomic stability and shorten with age. Mutations in genes such as DKC1, TERC, TERT, NOP10, TINF2 and NHP2 cause Telomere Spectrum Disorders (TSD), leading to shortened telomeres. Acquired TSDs arise from environmental or occupational exposures and commonly affect veterans, truck drivers, and industrial workers. These exposures generate reactive oxygen species associated with cancer, liver disease, pulmonary disease, and bone marrow complications. Idiopathic Pulmonary Fibrosis (IPF) is most common pulmonary manifestation, followed by hepatic fibrosis/cirrhosis, hematologic disorders (e.g., aplastic anemia, MDS), and rarely gastrointestinal findings. This case describes a Gulf War veteran with suspected acquired short telomeres and multisystem involvement (idiopathic cirrhosis, pulmonary fibrosis, cytopenias) and uniquely found to have gastrointestinal (Gastric Antral Vascular Ectasia, GAVE), a potential unsuspected manifestation of TSD. Methods/Case: A 76-year-old male with atrial fibrillation (post-Watchman), cryptogenic cirrhosis, COPD, IPF, diabetes, and anemia presented with severe shortness of breath and hypoxia. Admitted for Sepsis and Acute Hypoxic Respiratory Failure. Treated with AVAPS, IV Zosyn, IV Lasix, steroids, bronchodilators, and diuretics. His condition improved, and he was discharged on baseline 3L O2. His Gl history included GAVE, an unsuspected bleeding complication causing chronic iron-deficiency anemia. Hematologic findings included chronic anemia, thrombocytopenia, and a hypocellular bone marrow with 12% atypical NK cells. Discussion/Results: The patient's Gulf War exposure to oil fire pollutants (benzene, toluene, PAHs, lead, cadmium, and particulate matter) likely contributed to telomere shortening and TSD-related multisystem disease. Given his shortened telomeres, testing for TERC and TERT mutations is warranted. GAVE (“watermelon stomach”) is a rare cause of GI bleeding characterized by dilated gastric vessels and chronic anemia and has been linked to TSD but no current reports have documented this association. Its occurrence in this patient suggests an unrecognized gastrointestinal manifestation of TSD as the patient does not have known history of portal hypertension. Conclusions: This represents an potentially underreported manifestation of acquired TSD presenting with combined hepatic, pulmonary, hematologic, and gastrointestinal (GAVE) involvement. Full article

This study evaluated the genetic diversity and population structure of wild M. nipponense populations in the Pearl River Basin based on mitochondrial DNA (mtDNA) D-loop sequences. A total of 14 wild populations were collected from the West River, North River, and Pearl River Delta, and genetic diversity and population differentiation were assessed using haplotype analysis, analysis of molecular variance (AMOVA), pairwise F_ST, and principal component analysis (PCA). A total of 351 variable sites were identified. The overall haplotype diversity (h) and nucleotide diversity (π) were 0.947 and 0.03665, respectively, indicating high genetic diversity across the Pearl River Basin. Significant genetic differentiation was detected among populations (F_ST = 0.3785, p-value < 0.001), with 37.85% of genetic variation occurring among populations. PCA revealed distinct genetic relationships among populations, supporting the presence of population genetic structure within the Pearl River Basin. Populations from Tian’e County, Xilin County, Dahua Yao Autonomous County, and other upper tributaries of the West River exhibited distinct genetic characteristics compared with populations from Zhaoqing City, Guiping City, Guangzhou City, and the middle and lower reaches of the West River and the Pearl River estuary. Among the 14 populations, those from Zhaoqing City, Guiping City, and Guangzhou City exhibited relatively high genetic diversity and distinctive genetic characteristics. These findings suggest that the complex hydrological structure and historical connectivity of the Pearl River Basin have contributed to the observed population genetic structure. The genetically diverse populations identified in this study represent valuable wild germplasm resources for the conservation and selective breeding of M. nipponense. Full article

Background: Psoriasis is a chronic, immune-mediated inflammatory skin disorder that frequently exhibits spontaneous clinical remission during pregnancy. However, the underlying cell-type-specific transcriptomic alterations—particularly the involvement of dermal fibroblasts and hormone receptor signaling—remain poorly understood. Methods: We established an imiquimod (IMQ)-induced psoriasis-like dermatitis model in BALB/c mice comparing pregnant and non-pregnant cohorts. Multi-omics profiling combing bulk and single-cell RNA sequencing was integrated with computational intercellular communication and trajectory analysis. In vitro hormone-stimulation assays with ELISA quantification and in situ multiplex immunofluorescence were performed for experimental evaluation. Results: Compared with non-pregnant IMQ-treated mice, pregnant mice exhibited reduced psoriasis area and severity index scores and diminished epidermal thickening. Bulk RNA sequencing revealed downregulated Th1/Th17 inflammatory transcripts and upregulated hormone-associated genes (e.g., Pgr, Esr1, Ghr). Single-cell RNA sequencing identified 11 distinct cell types, with fibroblasts displaying distinct hormone receptor profiles and functional heterogeneity. Fibroblasts displayed transcripts encoding both anti-inflammatory factors (e.g., Tgfb2, Gas6, Grn) and pro-inflammatory factors (e.g., Fgf7, Mif). Keratinocytes exhibited an anti-inflammatory transcriptional phenotype with attenuated proliferation signatures. Monocytes/macrophages shifted toward M2-like transcriptional signatures and displayed computationally predicted communication with fibroblasts via candidate pathways including GRN and Gas6. Experimentally, primary mouse dermal fibroblasts stimulated with estradiol, progesterone, and growth hormone in vitro significantly increased secretion of PGRN. Gas6 secretion was significantly augmented by estradiol and growth hormone, whereas progesterone induced a modest elevation with borderline significance (p = 0.060). In contrast, TGF-β2 protein remained undetectable in culture supernatants. Furthermore, multiplex immunofluorescence demonstrated significantly increased expression of the Gas6 receptor MerTK on dermal macrophages in the IMQ + pregnancy group. Conclusions: Pregnancy-induced hormonal fluctuations may be associated with the amelioration of IMQ-induced psoriatic dermatitis, which correlates with a fibroblast-involved immunoregulatory network. These findings highlight the association of stromal-immune crosstalk in disease remission and suggest the GRN and Gas6 pathways as candidate pathways for future functional validation. Full article

Surface soil moisture forecasting is important for drought monitoring, irrigation management, and land–atmosphere process analysis but remains challenging because near-surface soil moisture is jointly influenced by antecedent precipitation, atmospheric drying, soil properties, vegetation conditions, and irregular multi-source observations. This study proposes an Antecedent-Precipitation-Informed Surface Soil Water Balance and Time-Aware Mamba–Mixture-of-Experts (API-SWB-Mamba-MoE) framework for forecasting in situ volumetric soil moisture at approximately 5 cm depth using only information available before the target time. The framework combines a process-guided API-SWB physical prior, a time-aware Mamba temporal encoder, a context-conditioned MoE residual decoder, and gated residual fusion. The U.S. source-domain stations were evaluated using five independently repeated station-level random holdout splits, with approximately 70%, 15%, and 15% of the stations assigned to training, validation, and testing in each repetition, respectively. The five resulting U.S.-trained models were further applied without target-domain retraining or fine-tuning to six German and French stations for zero-shot transfer evaluation. Across the U.S. test prediction–observation pairs pooled from the five repetitions, the proposed model achieved a Pearson correlation coefficient (R) of 0.934, a root mean square error (RMSE) of 0.035 cm³ cm⁻³, a Kling–Gupta efficiency (KGE) of 0.922, and a mean bias error (MBE) of −0.001 cm³ cm⁻³. Pooled zero-shot predictions yielded RMSE values of 0.036 and 0.038 cm³ cm⁻³ and KGE values of 0.885 and 0.917 for Germany and France, respectively. The pooled U.S. test RMSE was 7.9–22.2% lower than that of the ablation variants and 20.5–32.7% lower than that of the benchmark models. These results suggest that combining a process-guided prior with time-aware sequence modeling and context-conditioned expert routing offers a promising approach for station-scale soil moisture forecasting under irregular multi-source observations. The external results provide preliminary evidence of zero-shot transferability at the six selected sites, although broader regional validation remains necessary. Full article