Biology-Basel最新文献

The accumulation of cocoons within brood cells of old combs is a key factor causing a series of negative impacts on bee colonies. Previous studies did not sufficiently address this dynamic nature as the core microenvironment for preimaginal bee development. During this accumulation, the enrichment of potentially harmful microorganisms and chemical substances may pose a latent threat to colony health. This study combined microbiome and metabolomics analyses to systematically investigate the potential colony health risks posed by multi-generational accumulation of cocoons in Apis mellifera combs. The results demonstrated that with the growing number of brood rearing generations, the microbial diversity within the cocoons underwent significant shifts. For the bacterial community within multiple-generation cocoons, the Simpson index exhibited a significant increase, whereas indices including Sobs, Ace, and Chao showed significant decreases (p < 0.05). In the fungal community, the Shannon and Pielou_e indices significantly increased, while the Simpson and Faith_pd indices significantly declined (p < 0.05). Potential pathogens such as Melissococcus and the mycotoxin-producing fungus Wallemia became significantly enriched, reaching alarming relative abundances of 42.70% and 13.52%, respectively, in the multiple-generation cocoons. Metabolomic analysis further revealed the enrichment of 685 differential metabolites, including persistent exogenous pesticides such as cyanazine and pymetrozine, etc. Correlation analysis uncovered a significant positive relationship (r > 0.8) between these pesticide residues and pathogen abundance, indicating interactions between pollutants and pathogens that may exacerbate risks. This study reveals the aggravation of microecological imbalance and chemical pollution load within the cocoons of old combs and therefore provides strong scientific support for risk assessment of comb age in colony health management and offers practical guidance for the sustainable development of beekeeping.

Background and Purpose: We present a pilot benchmark dataset of 378 preclinical histological samples for evaluating large language model (LLM) performance on multi-dimensional classification tasks. This dataset addresses the lack of standardized benchmarks for assessing LLMs in preclinical histopathology, encompassing species identification (mouse, rabbit, rat), organ recognition, staining methods, and preparation techniques. Methods: We evaluated the LLMs GPT-4.1, GPT-4o-mini, and Llama 3.2 on 378 histological samples across four classification dimensions: species identification (mouse, rabbit, rat), organ recognition (kidney, liver, prostate, spleen), staining method classification (H&E, Elastica van Gieson, collagen, iron, IHC-elastin, MOVAT's pentachrome), and preparation type determination (frozen vs. paraffin-embedded). Performance was assessed using sensitivity and specificity metrics with confusion matrix analysis. Results: Model performance varied substantially across tasks and exhibited strong sensitivity to class imbalance. For preparation type classification, GPT-4.1 achieved the most balanced performance (50% frozen sensitivity, 85.7% paraffin sensitivity), while Llama 3.2 failed to recognize paraffin samples (0% sensitivity). In species classification, Llama 3.2 was the only model capable of identifying all three species (rabbit: 75% sensitivity, rat: 85.7% sensitivity) despite poor mouse recognition (0.3% sensitivity). GPT-4.1 achieved higher mouse sensitivity within this dataset (70.4% sensitivity) but failed with minority species. For staining classification, Llama 3.2 demonstrated highest overall performance, achieving >88% sensitivity for most staining types, while GPT-4o-mini showed perfect H&E recognition (100% sensitivity). Conclusions: Current LLMs demonstrate variable performance for histological classification with substantial sensitivity to class imbalance. While not suitable for standalone diagnostic use, they may serve as useful screening tools in research settings with appropriate human oversight.

Malaria is a major global health concern caused by Plasmodium parasites, among which Plasmodium falciparum is responsible for the most severe and fatal cases. The emergence of drug resistance to existing antimalarial therapies necessitates the discovery of novel molecular targets and chemically distinct inhibitors. Current study employed an integrated in silico drug discovery pipeline combining high-throughput structure-based virtual screening of 1549 deep-sea marine microbial metabolites with MM-GBSA binding free-energy estimation, QikProp-based ADME/Tox profiling, and 100 ns molecular dynamics (MD) simulations to link rapid screening with dynamic verification of binding stability. Molecular docking against Plasmodium falciparum dihydroorotate dehydrogenase (PfDHODH; PDB ID: 7KZ4) yielded five top-ranked compounds with Glide scores ranging from -12.02 to -10.61 kcal·mol^-1, which is higher than the Primaquine (-6.920 kcal·mol^-1; a clinically approved antimalarial reference compound). MM-GBSA analysis further refined hit selection, producing binding free energies (ΔG_bind) between -63.28 and -31.37 kcal·mol^-1. The selected lead compounds included (±)-puniceusine P, aspergilol F, tersaphilone C, 4-carbglyceryl-3,3'-dihydroxy-5,5'-dimethyldiphenyl ether, and 15-O-methyl ML-236A. The top hits were subjected to 100 ns MD simulations in Desmond, demonstrating stable protein-ligand complexes, particularly for (±)-puniceusine P and 15-O-methyl ML-236A (protein backbone root mean square deviation (RMSD; ~0.8-1.0 Å). ADME profiling indicated acceptable predicted physicochemical and pharmacokinetic properties. Overall, these in silico findings highlight deep-sea marine microbial metabolites as promising PfDHODH inhibitor candidates requiring experimental validation.

Post-translational modification (PTM) encompasses diverse modifications, including phosphorylation, methylation, ubiquitin-like modifications (UBLs), and so on, which profoundly influence cellular functions. UFMylation is a recently identified ubiquitin-like modification, which is mediated by the Ubiquitin-like Ubiquitin Fold Modifier 1 (UFM1) conjugation system. The UFM1 conjugation system comprises UFM1, Ubiquitin-like protein activating enzyme 5 (UBA5), UFM1-conjugating enzyme 1 (UFC1), UFM1-specific ligase 1 (UFL1), UFM1-specific protease 1 (UFSP1), UFM1-specific protease 2 (UFSP2), UFM1-binding protein 1 (UFBP1), and CDK5 regulatory subunit-associated protein 3 (CDK5RAP3). Accumulating research has demonstrated that the UFM1 conjugation system regulates various cellular stress responses, including endoplasmic reticulum (ER) stress, protein trafficking, DNA damage repair, and autophagy. Additionally, abnormal stress adaptations of the UFM1 conjugation system contribute to the pathophysiological complications of inflammatory diseases and cancer, underscoring its significance as a key regulatory node in human health and disease. Therefore, this review provides a comprehensive exploration of the structural characteristics of UFM1 conjugation system members and the mechanistic roles of UFMylation by UFM1 conjugation system-mediated diseases related to cellular stress responses, which will not only facilitate the identification of novel diagnostic and prognostic indicators but also enable the identification of specific therapeutic targets for UFM1 conjugation system-related diseases.

Drought stress is a major limiting factor for canola production in arid and semi-arid regions, particularly during seed germination, seedling and flowering stages. In this study, we evaluated drought responses of doubled haploid (DH) lines derived from interspecific hybrids of B. napus × B. rapa and their parental cultivars under simulated (PEG-6000) and soil-based drought conditions. Drought stress significantly reduced germination, growth, and physiological performance in all genotypes; however, DH lines consistently exhibited superior tolerance. Under PEG-induced osmotic stress, DH lines maintained higher germination rates, root elongation, and relative water content compared with parental genotypes. During seedling and flowering stages drought, DH lines showed lower accumulation of hydrogen peroxide and malondialdehyde, alongside markedly higher antioxidant enzyme activities (CAT and POD) and improved photosynthetic efficiency (Fv/Fm). Gene expression analysis revealed strong induction of drought-responsive genes, including WRKY28, MYB, LTP, WSP, metallothionein, and protein kinase family genes, particularly in DH lines at prolonged stress exposure. Multivariate analyses (PCA and correlation) confirmed a close association between enhanced antioxidant capacity, transcriptional activation, and drought tolerance traits. Overall, our results demonstrate that homozygous doubled haploid lines derived from distant hybridization between B. napus and B. rapa exhibit enhanced drought tolerance at both early and reproductive stages. These genotypes represent valuable genetic resources for breeding drought-tolerance canola cultivars.

The emergence of Sundaland during the Pleistocene glaciation has played a crucial role, as the Indo-Pacific Barrier (IPB), in shaping the genetic structure of marine taxa and coastal flora, specifically mangroves. This study investigated the genetic diversity, population structure, demographic history and phylogeography of Avicennia marina and two other Indo-West Pacific (IWP) Avicennia species, Avicennia alba and Avicennia officinalis, across the Andaman Sea (Indian Ocean) and the Gulf of Thailand (Pacific Ocean). Using Restriction-site-Associated DNA sequencing (RADseq), we generated thousands of genome-wide SNPs for 362 Avicennia individuals and revealed a pronounced East-West genetic divergence, separating the Andaman and Gulf of Thailand populations. Phylogeographic and demographic analyses suggest that colonization events by distinct ancestral lineages (Indian and West Pacific Ocean lineages), the Indo-Pacific Barrier (Sundaland), and Pleistocene sea-level fluctuations shaped the population structure and contributed to low genetic diversity (H_o = 0.073-0.083) and high inbreeding coefficients (F_IS = 0.169-0.501). This study highlights the importance of Thailand, as part of the Indo-Pacific interface, in harboring genetic resources from both Indian and West Pacific Ocean lineages, as exemplified in A. marina. Consequently, Andaman and Thai Gulf populations should be managed as distinct evolutionarily significant units (ESUs).

Myocardial ischemia-reperfusion injury remains a major unresolved challenge in cardiovascular medicine. Although timely restoration of blood flow is essential to limit ischemic damage, reperfusion triggers a complex network of maladaptive biological responses, including oxidative stress, calcium overload, mitochondrial dysfunction, metabolic impairment, and sterile inflammation. These processes converge on cardiomyocyte death, adverse ventricular remodeling, and long-term functional deterioration. Mesenchymal stem cells have been widely investigated as cardioprotective agents; however, accumulating evidence indicates that their beneficial effects are predominantly mediated by paracrine mechanisms. Among these, extracellular vesicles released by mesenchymal stem cells have emerged as key biological effectors. Experimental studies demonstrate that mesenchymal stem cell-derived extracellular vesicles modulate multiple signaling pathways involved in ischemia-reperfusion injury, including activation of the phosphoinositide 3-kinase (PI3K) and protein kinase B (PKB) axis, regulation of signal transducer and activator of transcription 3 (STAT3) signaling in a cell-specific manner, suppression of nuclear factor kappa B (NF-κB)-driven inflammatory responses, and stabilization of hypoxia-inducible factor-1α (HIF-1α)-dependent adaptive programs. At the subcellular level, these vesicles preserve mitochondrial structure and function, support energy metabolism, regulate mitophagy, and limit oxidative damage. Their molecular cargo, comprising regulatory microRNAs, metabolic enzymes, and stress-response proteins, enables coordinated modulation of survival, inflammatory, and reparative pathways rather than single-target effects. This review synthesizes current experimental evidence on the mechanistic basis of mesenchymal stem cell-derived extracellular vesicle-mediated cardioprotection and discusses their potential as cell-free, mechanism-based therapeutic strategies to limit myocardial ischemia-reperfusion injury.

Vicia villosa Roth var. glabrescens (smooth vetch) is an economically important legume cover crop valued for its nitrogen-fixing capacity, high biomass yield, and adaptability across diverse agroecosystems. Here, we present a chromosome-scale, high-quality genome assembly of V. villosa var. glabrescens, constructed using PacBio HiFi sequencing combined with Hi-C scaffolding. The assembly spans 3.70 Gb with a scaffold N50 of 4.69 Mb and exhibits lower heterozygosity (0.9%) compared to V. villosa Roth (3.1%). Genome analysis revealed significant expansion of long terminal repeat retrotransposons (LTR-RTs), as well as lineage-specific proliferation of miniature inverted-repeat transposable elements (MITEs) in V. villosa var. glabrescens. Comparative genomics with V. villosa Roth highlighted gene family expansions associated with trichome development, providing insights into the genetic basis of morphological and adaptive differences within the Vicia species. This reference genome provides a foundational resource for accelerating the breeding of V. villosa varieties with enhanced agronomic traits and contributes to a broader understanding of legume genomics and plant genome evolution.

Marine fish are a good dietary source of important macro- and micronutrients. In addition to fresh fish, fish with varying degrees of industrial processing-frozen, marinated, smoked, canned, etc.-is used extensively in the food market. This study comprehensively characterizes the protein content, fat content, and fatty acid composition of various commercially available canned marine fish species. All canned fish muscle and cod liver were in salted brine, to eliminate the influence of other ingredients. All samples obtained from muscle had a relatively high protein content, mostly between 15 and 21 g/100 g. The fat content was highly variable, ranging from a few tenths to 15 g/100 g. Of the fatty acids, PUFAs predominated in almost all samples. The fatty acid composition of canned fish was very similar to the fatty acid composition of fresh fish. The fact that the content of highly oxylabile PUFAs practically did not differ compared to fresh fish indicates that the preservation process does not lead to significant oxidative damage to this type of product. A significant benefit of eating marine fish is the intake of highly unsaturated fatty acids EPA and DHA of the omega-3 fatty acid series. Mainly mackerel and sardines are an excellent source of these two acids. Atlantic salmon and sockeye salmon are also very good sources. As a result, consuming an average of 3 g of cod liver, 10 g of mackerel, 15 g of sardines, or 30 g of Atlantic and sockeye salmon is sufficient to ensure the recommended daily intake of EPA and DHA.

Diabetes mellitus (DM) is a chronic metabolic disorder characterized by persistent systemic inflammation, which contributes to progressive multi-organ dysfunction, particularly in metabolically active tissues such as the liver and kidneys. Bee bread (Perga), a fermented bee pollen product rich in bioactive compounds, has been reported to exert anti-inflammatory and organ-protective effects; however, its tissue-specific influence on inflammatory responses under diabetic conditions remains incompletely defined. Thirty-two male Wistar Albino rats were randomly assigned to four groups: Control, DM, DM + Perga, and Perga. Diabetes was induced by streptozotocin (STZ; 55 mg/kg, i.p.). Perga was administered orally at a dose of 0.5 g/kg/day for 28 days. Pro-inflammatory cytokine levels (CRP, TNF-α, IL-1β, and IL-6) were quantified in liver and kidney tissues using ELISA. Histopathological alterations were evaluated by hematoxylin and eosin staining. DM significantly increased the IL-1β, IL-6, and CRP levels in hepatic tissue and elevated TNF-α, IL-1β, IL-6, and CRP levels in renal tissue. Perga administration attenuated these inflammatory responses, particularly reducing IL-1β and IL-6 levels in the liver and all measured cytokines in the kidney. Histopathological analyses revealed hepatocyte degeneration and necrosis, sinusoidal dilatation, tubular epithelial degeneration, and glomerular damage in diabetic rats, whereas Perga treatment partially improved hepatic alterations and improved renal structural integrity. These findings indicate that Perga exerts tissue-specific anti-inflammatory and protective effects in experimental diabetes, with a more pronounced impact on renal inflammation than on hepatic responses. Although its effects on hepatic TNF-α and CRP levels were limited, Perga may act as a natural modulator of cytokine-mediated inflammatory processes. Further studies are warranted to elucidate the underlying molecular mechanisms.