Search Results (414)

The anti-Müllerian hormone type II receptor (Amhr2) is a critical component of the transforming growth factor-β (TGF-β) signaling pathway and plays essential roles in sex determination and gonadal development in teleosts. However, its function in the blotched snakehead (Channa maculata), an economically important fish in China, remains unexplored. In this study, we cloned and characterized the Amhr2 ortholog from C. maculata, designated CmAmhr2. The gene encodes a 443-amino acid protein containing a conserved STYKc kinase domain. Sequence and phylogenetic analyses revealed that CmAmhr2 is homologous to autosomal Amhr2 in other teleosts. Spatiotemporal expression analyses showed that CmAmhr2 was predominantly expressed in testes, particularly during critical windows of gonadal differentiation. In situ hybridization localized CmAmhr2 transcripts mainly in spermatogonia, with weaker signals in primary spermatocytes, Sertoli cells, and early-stage oocytes (oogonia and primary oocytes). Dietary administration of 30 mg/kg 17β-estradiol (E₂) from 15 to 45 days post-fertilization (dpf) for 30 days induced male-to-female sex reversal, producing neofemales (XY-F) and intersex individuals (XY-I). CmAmhr2 expression levels progressively declined with the degree of gonadal feminization: highest in normal XY male (XY-M) testes, intermediate in XY-I ovotestes, and lowest in fully feminized XY-F and normal XX female (XX-F) ovaries. Furthermore, CRISPR/Cas9-mediated mutagenesis of CmAmhr2 generated frameshift mutations predicted to disrupt the kinase domain. These findings suggest that CmAmhr2 is involved in male sex differentiation and testis development in C. maculata, providing novel molecular insights and a foundation for future sex-control research in aquaculture. Full article

China plays a multifaceted and pivotal role in the global snake trade network, with its trade dynamics heavily influenced by domestic market demand and international regulatory policies. Based on official CITES trade data from 1975 to 2023, this study systematically analyzes the scale, species composition, source dynamics, and potential risks of China’s legal snake trade by using Whole Organism Equivalents (WOEs) and trade measures adjusted for reporting effort. The results show that the cumulative trade volume exceeded 11.7 million WOEs and that China’s role underwent a major transformation from a “supply center” in the early 1990s to a “consumption hub” by 2012. Export patterns were dominated by colubrid snakes (81.5% of total exports), with the oriental ratsnake (Ptyas mucosa) alone accounting for 56.8%; this reflects a distinctive trade landscape shaped by the domestic culture of “medicine and food homology.” Although the proportion of captive-bred individuals has increased since 2010, a dual-supply system comprising both wild-sourced and captive-bred individuals persists. Furthermore, we identified several misreported species, exemplified by the non-native common cobra Naja naja being recorded as wild-sourced exports from China. Notably, the live venomous snake trade exhibits an extreme geographic concentration, with over 93% of exports directed to Hong Kong, thereby posing significant biosecurity and public health risks. In conclusion, future governance should move beyond simple trade bans by utilizing molecular tools to correct identification biases and by implementing regulatory frameworks modeled on the Hazard Analysis Critical Control Point (HACCP) system. This approach will address biosecurity risks within the trade chain and help achieve a scientifically informed balance between ecological conservation and livelihood security. Full article

Tomato brown rugose fruit virus (ToBRFV) poses a major threat to global tomato (Solanum lycopersicum) production, as it can overcome conventional resistance genes that are effective against tobamoviruses. In this study, a multiplex CRISPR/Cas9 system was developed to target the SlTOM1 susceptibility gene family (SlTOM1a–d), which encodes host factors essential for tobamovirus replication. Six guide RNAs (gRNAs), designed following 12 off-target analyses, were assembled into a multiplex CRISPR/Cas9 construct using a Golden Gate cloning strategy and introduced into tomato genotypes through an Agrobacterium-based tissue culture transformation procedure. Although primary T₀ transformants exhibited chimeric mutation patterns, stable inheritance and segregation of edited alleles were confirmed in the T₁ generation. Sequence analyses identified diverse indel mutations across target loci, with SlTOM1d exhibiting the highest editing efficiency. Multiplex genome editing successfully generated single-, double-, and triple-mutant combinations, with higher-order mutants displaying the strongest tolerance phenotypes. Following mechanical ToBRFV inoculation, edited T₁ plants exhibited markedly reduced symptom severity, low viral accumulation, and improved fruit health compared to wild-type controls. RT-qPCR analysis further confirmed significantly reduced viral RNA levels, supporting a host-factor-mediated tolerance mechanism. Importantly, edited lines maintained normal growth and agronomic performance. Collectively, these findings demonstrate that multiplex CRISPR/Cas9-mediated targeting of SlTOM1 homologs represents a promising and practical strategy for improving ToBRFV tolerance in tomato breeding programs. Full article

The advancement of autonomous robotic systems has led to significant capabilities in perception, localization, mapping, and control, yet a critical challenge remains in representing and preserving relational semantics, contextual reasoning, and cognitive transparency essential for collaboration in dynamic, human-centric environments. This paper introduces a unified architecture comprising the Ontology Neural Network (ONN) and the Ontological Real-Time Semantic Fabric (ORTSF) to address this challenge. The ONN formalizes relational semantic reasoning as a dynamic topological process by embedding Forman–Ricci curvature, persistent homology, and semantic tensor structures within a unified loss formulation, aiming to maintain relational integrity as scenes evolve. Building upon ONN, the ORTSF transforms reasoning traces into actionable control commands while compensating for system delays through predictive operators designed to preserve phase margins. Theoretical analysis and extensive simulations demonstrate that ORTSF maintains designed phase margins, offering advantages over classical delay compensation methods. Empirical studies indicate the framework’s effectiveness in unifying semantic cognition and robust control, providing a mathematically principled solution for cognitive robotics. Full article

Physalis grisea is an orphan crop with significant economic and medicinal potential. Although initial genome editing applications have recently emerged for Physalis species, the development and optimization of highly efficient, visually traceable Agrobacterium-mediated editing platforms remain crucial for advancing its functional genomics. This study uses the phytoene desaturase (PDS) gene—a key enzyme in the carotenoid biosynthetic pathway—as a visual reporter to develop a CRISPR/Cas9-mediated genome editing platform in P. grisea. A dual-target guide RNA (sgRNA) expression vector was constructed, and transgenic plants were successfully generated via Agrobacterium-mediated transformation of hypocotyl explants. Strikingly, phenotypic observations revealed that the regenerated mutants exhibited characteristic complete albino or green-white chimeric phenotypes, accompanied by distinct developmental retardation and dwarfing. Physiological quantitative analysis showed that total chlorophyll and carotenoid contents in the mutant leaves were significantly reduced by over 70% and 78%, respectively. Targeted sequencing further confirmed that the CRISPR/Cas9 system efficiently induced various mutations at the PgPDS locus (derived from Physalis grisea)—including fragment deletions, 1–4 bp insertions, and 2–3 bp substitutions—revealing a specific preference for non-homologous end joining (NHEJ) repair. In summary, this study not only validates the suitability of PgPDS as a reporter gene but also successfully establishes a robust genome editing technical system for P. grisea, providing a solid foundation for future functional genomics research and molecular breeding in this crop. Full article

The Lovozero and Khibiny alkaline massifs (Kola Peninsula, Russian Arctic) are the prominent sources of REE minerals, with the Lovozero loparite deposit being the only currently active REE mine in Russia. A new ashcroftine-related mineral phase KA with the idealized chemical formula K₆(Na₄Ca)(Y₈Ca₃Mn)[Si₂₈O₆₈(OH)₂](CO₃)₈F₂·9H₂O was found in the Khibiny alkaline massif. Its empirical formula determined by electron microprobe analysis is Na_4.14K_6.11Ca_3.89Mn_0.59Y_6.10Ce_0.08 Gd_0.32Tb_0.15Dy_0.78Ho_0.19Er_0.35Tm_0.15Yb_0.12Lu_0.06Si₂₈C₈O_93.02F_2.08·9H₂O. The crystal structure was determined and refined by means of single-crystal X-ray diffraction analysis. The KA phase is tetragonal, I4/mmm, a = 24.1661(3), c = 17.5914(4) Å, V = 10,273.4(3) ų. The crystal structure contains two Y sites. The Y1 site is [8]-coordinated and hosts more heavy REEs, whereas the Y2 site is predominantly [7]-coordinated and accumulates lighter REEs and Mn. The crystal structure is based upon the [Si₂₈X₇₀] nanotubes (X = O,OH) elongated along the c-axis and composed of corner-sharing SiX₄ tetrahedra. The external diameter of the tubules is equal to ~19.54 Å, i.e., slightly less than 2 nm. The silicate nanotubes are running parallel to the c-axis and centered along the (00z) and (½½z) directions. The tubules are linked by walls of YO_n polyhedra that also involve triangular CO₃ groups. The K⁺, Na⁺, and Ca²⁺ cations, as well as H₂O molecules, are located either inside or outside the tubules. The crystal-chemical formula of the KA phase can be written as {K_6.14Na_4.30Ca_0.81}[Y_5.88Ca_3.12Dy_0.88Mn²⁺_0.60Gd_0.32 Ho_0.24Er_0.24Tb_0.16Tm_0.16Er_0.12Yb_0.12Ce_0.08Lu_0.08](Mn³⁺_0.09) [Si₂₈O_68.36(OH)_1.65](CO₃)₈F₂·8.97H₂O, which agrees well with the idealized formula. According to the information-based complexity analysis, the KA phase has a very complex structure and belongs to less than 3.5% of the very complex minerals known today. The presence of silicate tubules is the key reason for the exceptional structural complexity of the phase. It is impossible to establish exact relations between the KA phase and ashcroftine-(Y) on the basis of the currently available data, since the last chemical analysis of the latter mineral was done in 1924. Therefore, the mineralogical identity of ashcroftine-(Y) is currently an unresolved problem. The silicate tubule in the KA phase is topologically related to the Linde zeolite A (the LTA zeolite framework) and can be produced from the latter by a series of topological operations. The KA phase forms a homological row with caysichite-(Y) and miyawakiite-(Y), along which the Si content is increasing, and silicate chains in caysichite-(Y) transform into silicate tubules in miyawakiite-(Y) and into silicate nanotubules in the KA phase. Indeed, the M:Si:C ratio (where M = Y, REEs, Ca, Mn, Fe) changes from 1:1:0.75 for caysichite-(Y) through 0.75:1:0.5 for miyawakiite-(Y) to 0.43:1:0.29 for ashcroftine-(Y) (and KA). The increasing role of silica along the row results in the formation of zeolite-derived porous one-dimensional units. The KA phase possesses two important crystal chemical properties that distinguish it from other minerals known to date: it hosts a variety of REEs and is based upon nanoscale zeolite-like silicate units. The KA phase, ashcroftine-(Y), caysichite-(Y), and miyawakiite-(Y) have never been prepared under laboratory conditions. The mineralogical occurrence of the KA phase in the Khibiny massif points out to its secondary origin, i.e., its formation under relatively soft, low-temperature hydrothermal conditions. Thus, the discovery of the KA phase in nature may provide important hints toward its synthesis in the laboratory by means of a soft-chemistry approach. Full article

Accurate prediction of protein function is fundamental to progress in biotechnology and biomedicine, yet progress remains severely hampered by the widening chasm between exponentially growing genomic data and the limited capacity for functional annotation. High-throughput sequencing and metagenomics have driven an explosion in sequence data that far outstrips experimental characterization. UniProt now contains over 203 million protein entries, of which only ~2% have been experimentally validated. This widening “sequence–function gap” exceeds the reach of traditional homology-based tools such as BLAST (v2.17.0) and HMMER (v3.2), which are inherently constrained by sequence identity thresholds. The emergence of Protein Language Models (PLMs), including ESM and ProtTrans, has introduced a transformative paradigm, thereby shifting functional inference from similarity-based retrieval to geometric reasoning within learned semantic spaces. Nevertheless, current approaches remain largely confined to unimodal or narrowly bimodal frameworks, failing to capture the inherently multidimensional determinants of enzymatic function, including active-site geometry, chemical reaction logic, and literature-embedded semantic context. This review systematically adopts a multimodal global-fusion perspective, elucidating how three-dimensional geometric features, chemical reaction semantics, and textual knowledge graphs are synergistically integrated around PLMs as a core backbone. We delineate complementary mechanisms and integration strategies that together enable fine-grained protein function annotation beyond the performance ceiling of single-sequence methods. Furthermore, we survey the translational potential of such frameworks from computational prediction to real biological applications, and critically examine persistent bottlenecks including activity cliffs, transition-state inference, and conformational dynamics. We identify the integration of physics-informed machine learning with dynamics-aware architectures as a pivotal direction toward a causal, mechanism-level understanding of protein function. Full article

Rice blast, caused by the fungus Magnaporthe oryzae, is one of the most devastating threatening to global rice production. The narrow genetic background of modern rice cultivars exacerbates the shortage of durable resistance resources. In contrast, the wild rice species Oryza officinalis harbors abundant stress-resistance alleles and represents a valuable gene pool for identifying novel broad blast-resistance genes. The cloned resistance gene Pid2 is encoded in a receptor-like protein kinase conferring race-specific resistance against the M. oryzae isolate ZB15. In this study, three Pid2 homologs were isolated from O. officinalis. The special allele Pid2of-MD33 was transformed into “Yunjing 37(YG37), a blast-susceptible japonica rice cultivar” via Agrobacterium-mediated transformation. Quantitative real-time PCR analysis showed that Pid2of-MD33 was consistently expressed in various tissues of O. officinalis, with the highest transcript abundance detected in leaf mesophyll cells and plasma membranes. Inoculation with the M. oryzae isolate ZB15 revealed that transgenic YG37 lines expressing Pid2of-MD33 displayed significantly reduced lesion size and pathogen proliferation, suggesting recovered race-specific resistance. These results enrich the resistance gene resources for rice blast research and provide a promising candidate gene for rice blast resistance breeding. Full article

The NAC (NAM, ATAF1/2, and CUC1/2) family of transcription factors (TFs) play critical roles in regulating salt tolerance across diverse plant species. This study identified and characterized 101 NAC TFs in eggplant (Solanum melongena L.), revealing their diverse physicochemical properties, chromosomal distributions, and evolutionary relationships. Based on its salt stress-induced expression pattern and homology to known salt-responsive NAC factors, SmNAC28 was selected as a key candidate for functional investigation of salt tolerance. Expression profiling indicated that SmNAC28 is preferentially expressed in roots and stems, and its transcript levels are modulated by salt stress. Subcellular localization confirmed that SmNAC28 localizes to both the plasma membrane and nucleus, a dynamic distribution regulated by S-palmitoylation. Under normal conditions, SmNAC28 is anchored to the plasma membrane and nucleus via S-palmitoylation; upon salt stress exposure, it undergoes depalmitoylation and translocates to the nucleus. Using a hairy root transformation system in eggplant, we demonstrated that overexpression of SmNAC28 in roots significantly enhanced salt tolerance by mitigating oxidative damage, maintaining ion homeostasis, and promoting osmotic adjustment. Analysis of transcript levels further revealed that SmNAC28 overexpression upregulated ion transporter genes (NHX2, CHXs), signaling genes (CIPKs), and the proline biosynthesis gene (P5CS), which demonstrated that SmNAC28 integrates antioxidant defense, ion homeostasis, and osmotic regulation to confer salt tolerance. This study reveals the response mechanism of SmNAC28 to salt stress of the eggplant transcription factor SmNAC28 under salt stress, and provided a research foundation for salt tolerance breeding. Full article

Robust genetic tools are a prerequisite for causal, perturbation-based tests of redox physiology in acetogens. Here we establish practical genetic entry points for Sporomusa sphaeroides DSM 2875 under strictly anaerobic handling. We first attempted genome editing via double-crossover allelic exchange targeting pyrF using a non-replicative pUC19-based knockout construct and 5-fluoroorotic acid counterselection. Diagnostic PCR identified ΔpyrF candidates with the expected size shifts, demonstrating that homologous recombination is technically feasible in DSM 2875; however, the ΔpyrF genotype exhibited severe growth defects and could not be stably maintained over repeated passages, indicating a key limitation of a pyrF-based workflow under our current conditions. We then evaluated multiple E. coli–anaerobe shuttle plasmids for introduction and maintenance. Among the tested vectors, pJIR751 reproducibly yielded erythromycin-resistant transformants after prolonged incubation and supported serial passaging on selective media. Plasmid retention was confirmed by diagnostic PCR from liquid cultures in all tested isolates. Importantly, this maintainable plasmid platform enables genetically grounded perturbation-and-rescue experiments under electrode- or Fe⁰-assisted conditions, allowing mechanistic hypotheses in bioelectrochemical acetogenesis to be tested causally rather than inferred from phenotypes alone. Together, these results define current practical boundaries for S. sphaeroides genetics and establish pJIR751 as a practical foundation for downstream genetic manipulation in bioelectrochemical studies. Full article

Cardiac fibrosis is a hallmark of cardiac aging and a major contributor to development of heart failure. However, therapeutic strategies that specifically target cardiac fibrosis remain limited. In this study, we demonstrate that small-molecule compound ML216 exerts protective effects against aging-associated or β-adrenoceptor agonist isoproterenol-induced cardiac fibrosis in vitro or in vivo. Mechanistically, ML216 inhibits transforming growth factor-β1 (TGF-β1) signaling by reducing TGF-β1 protein levels, thereby attenuating Mothers against decapentaplegic homolog (SMAD) phosphorylation and downstream induction of connective tissue growth factor (CTGF). This leads to a marked suppression of fibrotic genes Col1a1, Cnn2, and Acta2, ultimately resulting in reduced fibrosis. Additionally, the inhibition of the TGF-β1 pathway alleviates cardiomyocytes apoptosis, which may further limit inflammatory responses and contributes to the overall attenuation of cardiac fibrosis. Collectively, these findings demonstrate that ML216 mitigates cardiac fibrosis through the inhibition of TGF-β1 pathway-mediated fibrotic signaling and apoptosis, highlighting its potential as a therapeutic candidate for the treatment of cardiac fibrosis. Full article

The pervasive environmental dispersal of glyphosate has established this herbicide as a dominant anthropogenic xenobiotic, necessitating advanced bioremediation strategies to restore soil integrity. This study assessed the bioremediation efficacy of biosurfactants produced by Serratia ureilytica BM01-BS in glyphosate-contaminated soils, establishing their adsorption dynamics and ecotoxicological safety. The strain S. ureilytica BM01-BS gave a biosurfactant yield of 3.7 g·L⁻¹ with promising surface properties, utilizing babassu (Attalea speciosa) waste as the sole nutrient source. Whole-Genome Sequencing and Biosynthetic Gene Cluster mining identified a Nonribosomal Peptide Synthetase cluster homologous to rhizomide-type lipopeptides responsible for biosurfactant production. Bioremediation assays in glyphosate-contaminated soils demonstrated a removal efficiency exceeding 95% in approximately 60 min, outperforming the synthetic surfactant SDS (20–30% efficiency). Kinetic and isothermal modeling suggest that the bioremediation process is governed by chemisorption, adhering to a pseudo-second-order model (R² = 0.998) with a maximum adsorption capacity of 845 µg·kg⁻¹. Fourier-Transform Infrared spectroscopy confirmed that the biosurfactant effectively removes glyphosate and restores the soil’s mineral integrity, as evidenced by the complete disappearance of glyphosate-associated phosphonic and carboxylic bands. Ecotoxicological assessments verified the environmental safety of the bioremediation process. These findings position the BM01-BS biosurfactant as a sustainable, biodiversity-based adjuvant for enhancing ecological resilience in glyphosate-impacted landscapes. Full article

Detecting highly divergent or previously unknown viruses is a critical bottleneck in clinical diagnostics and pathogen surveillance. While alignment-based methods often fail to classify sequences lacking homology to known references, deep learning offers a powerful alternative for signal extraction from ‘viral dark matter.’ In this work, we present a high-performance ensemble of deep convolutional neural networks specifically designed to identify viral contigs in complex human metagenomic datasets. Our framework processes sequences acquired from high-throughput biological sensors and integrates complementary architectures to capture both local motifs and global genomic signatures. The proposed ensemble achieves state-of-the-art performance, reaching an AUROC of 0.939 on 300 bp contigs and significantly outperforming existing models such as transformer-based approaches, ViraMiner, and DeepVirFinder. Crucially, our results demonstrate high robustness to data degradation, maintaining stable predictive power even with a 10% random nucleotide substitution rate, a common challenge in degraded clinical samples. Furthermore, the model generalizes to ‘unseen’ viral families not present during training, demonstrating its utility for emerging threat detection. To ensure full reproducibility and facilitate further research in clinical sensing, the complete code and datasets are publicly available on Github. Full article

The widespread adoption of hybrid rice has played a pivotal role in ensuring food security in China. However, the heavy reliance on wild-abortive (WA) cytoplasmic male sterility (CMS) systems raises potential biosafety concerns. In this study, we screened a global collection of wild rice (Oryza rufipogon) accessions using orf182-specific molecular markers to characterize the geographic distribution patterns of this gene. Mitochondrial sequencing and assembly of 11 representative wild rice species harboring orf182 revealed 16 novel genes. A total of 469 mitochondrial genes were classified into 23 gene families, with nine families containing single-copy homologous genes, indicating significant gene duplication in mitochondria. We observed a strong positive correlation between mitochondrial genome size and the quantity and size of repetitive sequences. Collinearity analysis revealed extensive mitochondrial variation and large-scale inversions in Guangdong wild rice. Comparative genome analysis uncovered inversions, translocations, and several variations surrounding orf182, with a 71 bp repeat sequence mediating the formation of the orf182-nad6 chimeric gene. Gene copy number analysis (GCNV) revealed variable orf182 gene copy counts (1, 2, and 3) in wild rice species. Additionally, successful transformation of orf182 from various sources into sterile lines was achieved. These findings provide valuable resources for advancing hybrid rice development in China, thus contributing to enhanced food security. Full article

Dengue fever (DF) is an acute mosquito-borne infectious disease caused by dengue virus (DENV), primarily transmitted by Aedes aegypti and Aedes albopictus. Nearly 4 billion people worldwide are at risk of infection, and the 2024 epidemic reached an unprecedented scale. Severe cases can lead to hemorrhage, shock, and even death, prompting the WHO to classify it as a potential pandemic pathogen. Current prevention and control measures face prominent bottlenecks, including limited applicable populations for vaccines, lack of specific antiviral drugs, and increasing insecticide resistance in mosquito vectors. Notably, susceptible animal models serve as core tools for elucidating the pathogenic mechanisms of dengue virus, screening antiviral drugs, and evaluating vaccine protective efficacy, holding irreplaceable significance. This review systematically summarizes the characteristics, application scenarios, and research progress of mainstream and potential susceptible animal models, including non-human primates, mice, pigs, tree shrews, and bats. It covers model systems with different immune statuses, genetically modified types, and species-specific traits. Among these, mouse models are the most widely used due to their high flexibility and controllable cost, while non-human primate models have become key carriers for preclinical vaccine evaluation by virtue of their high homology with human immune responses. However, current models generally suffer from core bottlenecks, such as incomplete simulation of core severe phenotypes, insufficient restoration of immune mechanisms, unclear viral receptor mechanisms, and lack of unified standards for inoculation doses and evaluation indicators. These limitations make it difficult to accurately replicate key severe disease mechanisms, including antibody-dependent enhancement (ADE) and cytokine storms. Future model development should focus on core requirements—including intact immunity, broad-spectrum susceptibility, and accurate simulation of clinical pathological features—prioritize solving the simulation challenges of ADE and cytokine storms, and establish standardized experimental systems and evaluation criteria. By comprehensively summarizing the advantages and limitations of the existing models, this review provides a systematic reference for the optimization and upgrading of dengue virus-susceptible animal models. It also holds important guiding significance for promoting the in-depth development of basic dengue research, innovation in prevention and control technologies, and clinical transformation and application. Full article