Search Results (59)

Alternaria brown spot, caused by the tangerine pathotype of Alternaria alternata, is a destructive fungal disease affecting citrus production worldwide. Nucleotide-binding site-leucine-rich repeat (NBS-LRR) genes constitute a major class of plant immune receptors; however, their genome-wide characteristics and potential association with Alternaria brown spot resistance loci in citrus remain poorly understood. In this study, we performed a comprehensive genome-wide identification and comparative analysis of NBS-LRR genes across representative citrus species. A total of 417 and 326 NBS-LRR genes were identified in Citrus reticulata and Citrus clementina, respectively, and were classified into NL, CNL, TNL, and RNL subfamilies based on domain architecture. Phylogenetic reconstruction, gene structure analysis, conserved motif composition, chromosomal distribution, synteny relationships, and promoter cis-element profiling collectively revealed considerable structural variation and lineage-specific expansion of the NBS-LRR gene family in citrus genomes. By integrating previously reported quantitative trait locus (QTL) data for Alternaria brown spot, we identified several NBS-LRR genes located within a resistance-associated genomic interval on chromosome 3. Among these, a candidate gene, designated LRR2, exhibited differential transcriptional responses upon pathogen inoculation and displayed distinct sequence variations between citrus genotypes. Structural modeling and molecular docking analyses suggested potential binding interfaces between LRR2 and multiple host-selective toxins, although the biological relevance of these interactions requires further experimental validation. Subcellular localization assays in Nicotiana benthamiana showed that LRR2 is distributed in both the nucleus and cytoplasm. Notably, transient overexpression of LRR2 triggered hypersensitive response-like cell death and H₂O₂ accumulation. Collectively, this study provides a comprehensive overview of the citrus NBS-LRR gene family and presents a multifaceted characterization of a QTL-anchored candidate gene. These findings establish a genomic and molecular framework for further functional investigations of citrus–Alternaria interactions. Full article

The longitudinal study investigated the impact of age at first mating (AFM) on milk yield (MY) across the productive lifespan of Alpine goats born between 2005 and 2018. Data from 740 animals across three herds and 3200 lactations were analyzed. The AFM of the studied population ranged from 7 to 23 months. The impact of AFM on MY was estimated using a linear mixed model, accounting for the fixed effects of parity, litter size, season, herd, and suckling and milking durations, with the individual goat included as a random effect to control for repeated measures. The impact of AFM on lifetime production was estimated by regressing total milk yield (TMY) and number of lactations (TNL) on AFM, while accounting for herd effect. The study revealed a notable shift in productivity patterns across the animal’s life. Every additional month of AFM significantly increased milk yield in the first lactation (13.28 kg; p < 0.001), but this influence vanished in subsequent parities (p > 0.05). These higher initial yields were insufficient to compensate for the losses caused by a shortened productive lifespan. Specifically, each month of mating delay resulted in a loss of ~0.08 TNL and 34 kg TMY, totaling ~1 lactation and ~400 kg of milk for a 12-month delay. Results suggest that earlier mating may improve lifetime productivity under intensive production systems. Full article

The deltoid ligament (DL) is the primary stabilizer of the medial ankle; however, a limited understanding of the functional roles of its various bundles hinders rational surgical decision-making. This study aims to investigate the roles of individual DL bundles in maintaining ankle stability and articular contact pressure and thus seeks to guide decisions on whether reconstruction is required for specific injuries. A validated finite element foot model was used to simulate isolated and multiple deficiencies in the DL bundle. The articular displacements, rotations, and peak talar cartilage contact pressure were evaluated under anterior drawer force and under internal–external rotation, eversion, and plantarflexion–dorsiflexion moments. Compared with the intact model, anterior tibiotalar ligament (ATTL) deficiency resulted in the greatest anterior drawer displacement (increase: 29%). Talonavicular ligament (TNL) deficiency caused the largest internal–external rotation and plantarflexion (increases in external rotation: 69%; in internal rotation: 10%; in plantarflexion: 32%). Tibiocalcaneal ligament (TCL) deficiency caused the largest eversion (increase: 93%). Deep posterior tibiotalar ligament (dPTTL) deficiency caused the largest dorsiflexion (increase: 68%). The maximum talar cartilage contact pressure occurred in the TNL-deficient model under the plantarflexion condition. In conclusion, individual DL bundles exhibit specific functions in terms of controlling multidirectional ankle stability—the ATTL, TNL, TCL, and dPTTL are the primary stabilizers for anterior translation, rotation/plantarflexion, eversion, and dorsiflexion, respectively. These findings provide a biomechanical rationale for personalized surgical strategies. When comprehensive DL reconstruction is not feasible, clinicians can prioritize the reconstruction of specific bundles according to the patient’s instability severity and functional demands across degrees of freedom. Full article

Nucleotide-binding site-leucine-rich repeat (NLR) proteins are key intracellular immune receptors in plants. Integrated domains (IDs) can occasionally be fused with NLRs, contributing to their functional diversity. However, the diversity and evolutionary patterns of NLR-IDs across angiosperms remain poorly understood. In this study, we analyzed 305 angiosperm genomes and found that the proportion of NLR genes containing IDs (NLR-ID genes) ranges from 0% to 38.3%, with an average of 10.6%. A total of 1226 unique IDs were identified, some of which are widely distributed, while others are specific to particular taxa. Notably, 415 of these IDs are homologous to plant proteins targeted by pathogen effectors, suggesting their role as candidate decoys. Comparative analysis of NLR-IDs in two subfamilies—TIR-NLR (TNL) and CC-NLR (CNL)—revealed that TNL genes have a significantly higher frequency of IDs, with the C-JID and DUF3542 domains being most prevalent. N-terminal fusion of the DUF3542 domain in CNL genes correlates with the loss of the MADA motif. Our findings expand the understanding of NLR-ID diversity and provide insights into the dynamic evolution of NLR protein architecture in angiosperms. Full article

Progesterone (P4) withdrawal is the key trigger for labour onset. Labour is a sterile inflammatory process involving monocyte infiltration, differentiation into M1 or M2 macrophages (Macs) and contributing to the inflammatory milieu in the uterus. Premature leukocyte influx may lead to preterm birth. Inflammatory stimuli induce intracellular progesterone (P4) withdrawal in myometrial cells (MYOs) through activation of P4 metabolizing enzyme 20alpha-hydroxysteroid dehydrogenase (20α-HSD). We hypothesized that (1) the pro-inflammatory M1-Macs induce 20α-HSD in MYO, which causes P4 withdrawal and MYO contractility, and (2) IL-1α produced by M1-Macs mediates the effect of M1-Macs on intracellular P4 withdrawal in MYO. Human myometrial biopsies from term pregnant women in labour (TL) and not in labour (TNL) revealed higher IL-1α in TL, with M1-Macs in TNL expressing more IL-1α than MYO. In vitro study shows (1) higher expression of IL-1α in M1-Macs compared to M2-Macs; (2) treatment of MYO with IL-1α or M1-Macs increased 20α-HSD and contractility; and (3) blockade of IL-1α, AP-1 transcription factors, or co-treatment with non-metabolizable progestin R5020 inhibit these effects. Our findings highlight the role of tissue-resident M1-Macs in regulating intracellular P4 metabolism and suggest that M1-Macs-derived IL-1α may facilitate P4-withdrawal and uterine contractility associated with labour onset. Full article

Single-object vision–language tracking has become an important research topic due to its potential in applications such as intelligent surveillance and autonomous driving. However, existing cross-modal alignment methods typically rely on contrastive learning and struggle to effectively address semantic ambiguity or the presence of multiple similar objects. This study aims to explore how to achieve more robust vision–language alignment under these challenging conditions, thereby achieving accurate object localization. To this end, we propose a text heatmap mapping (THM) module that enhances the spatial guidance of textual cues in tracking. The THM module integrates visual and language features and generates semantically aware heatmaps, enabling the tracker to focus on the most relevant regions while suppressing distractors. This framework, developed based on UVLTrack, combines a visual transformer with a pre-trained language encoder. The proposed method is evaluated on benchmark datasets such as OTB99, LaSOT, and TNL2K. The main contribution of this paper is the introduction of a novel spatial alignment mechanism for multimodal tracking and its effectiveness on various tracking benchmarks. Results demonstrate that the THM-based tracker improves robustness to semantic ambiguity and multi-instance interference, outperforming baseline frameworks. Full article

Visual–language tracking often faces challenges like target deformation and confusion caused by similar objects. These issues can disrupt the alignment between visual inputs and their textual descriptions, leading to cross-modal semantic drift and feature-matching errors. To address these issues, we propose SATrack, a Semantic-Aware Alignment framework for visual–language tracking. Specifically, we first propose the Semantically Aware Contrastive Alignment module, which leverages attention-guided semantic distance modeling to identify hard negative samples that are semantically similar but carry different labels. This helps the model better distinguish confusing instances and capture fine-grained cross-modal differences. Secondly, we design the Cross-Modal Token Filtering strategy, which leverages attention responses guided by both the visual template and the textual description to filter out irrelevant or weakly related tokens in the search region. This helps the model focus more precisely on the target. Finally, we propose a Confidence-Guided Template Memory mechanism, which evaluates the prediction quality of each frame using convolutional operations and confidence thresholding. High-confidence frames are stored to selectively update the template memory, enabling the model to adapt to appearance changes over time. Extensive experiments show that SATrack achieves a 65.8% success rate on the TNL2K benchmark, surpassing the previous state-of-the-art UVLTrack by 3.1% and demonstrating superior robustness and accuracy. Full article

The NBS-LRR genes constitute the largest class of resistance (R) proteins in plants, capable of recognizing pathogen-secreted effectors to trigger immune responses. However, systematic studies of NBS-LRR genes in medicinal plants have not yet been reported. In this study, we performed a comprehensive genome-wide identification and analysis of the NBS-LRR gene family in the medicinal plant Salvia miltiorrhiza. A total of 196 NBS-LRR genes were identified, among which 62 possessed complete N-terminal and LRR domains. Multiple NBS-LRR proteins extracted from other model plants can be classified and distinguished on the phylogenetic tree according to subfamilies CNL, TNL, and RNL. Comparative analysis revealed a marked reduction in the number of TNL and RNL subfamily members within the Salvia species. Analysis of the expression patterns of SmNBS-LRR genes with transcriptomes data revealed a close association between SmNBS-LRRs and secondary metabolism. Promoter analysis demonstrated an abundance of cis-acting elements in SmNBS genes related to plant hormones and abiotic stress. Our study enhances the understanding of the NBS-LRR gene family in medicinal plants and provides a foundation for future functional characterization of the NBS-LRR genes in S. miltiorrhiza and its potential application in disease-resistance breeding. Full article

Introduction: Rice, a cornerstone of global food security, faces escalating demands for enhanced yield and disease resistance. We collected 300 high-quality genomes, representing both cultivated (Oryza sativa indica, O. sativa japonica, and O. sativa aus) and wild species (O. rufipogon, O. glaberrima, and O. barthii). Methods: Leveraging HMMER, NLR-Annotator, and OrthoFinder, we systematically identified 148,077 leucine-rich repeat (LRR) and 143,459 nucleotide-binding leucine-rich repeat (NLR) genes, with LRR receptor-like kinases (LRR-RLKs) dominating immune receptor proportions, followed by coiled-coil domain containing (CNL)-type NLRs and LRR receptor-like proteins (LRR-RLPs). Results: Benchmarking Universal Single-Copy Orthologs (BUSCO) assessments confirmed robust genome quality (average score: 94.78). Strikingly, 454 TIR-NB-LRR (TNL) genes—typically rare in monocots—were detected, challenging prior assumptions. Phylogenetic analysis with Arabidopsis TNLs highlighted five O. glaberrima genes clustering with dicot TNLs; these genes featured truncated PLN03210 motifs fused to nucleotide-binding adaptor shared by APAF-1, R proteins, and CED-4 (NB-ARC) and LRR domains. Conclusions: By bridging structural genomics, evolutionary dynamics, and domestication-driven adaptation, this work provides a foundation for targeted breeding strategies and advances functional studies of plant immunity in rice. Full article

Plants are challenged regularly with multiple types of biotic stress factors, such as pathogens or insect herbivores, in their environment. To detect and defend against pathogens, plants have evolved an innate immune system in which intracellular receptors in the so-called effector-triggered immunity play a vital role. In Arabidopsis thaliana the Toll/interleukin-1 receptors (TIRs) domain is related to intracellular immunity receptors, for example in TIR-NBS-LRR (TNL) proteins. Among the TIR domain carrying proteins, very little is known about the function of the TIR-X proteins. Here, we focus on the recently described TIR-X (TIRP; At5g44900) to analyze its role in phytohormone-mediated plant defense through gene expression and phytohormone quantification. Therefore, we employed two fungal pathogens, the necrotrophic Alternaria brassicicola and the hemibiotrophic Verticillium dahliae, to infect A. thaliana WT (Col-0), TIRP knock-out, and TIRP overexpressing lines for comparative analyses. Furthermore, we included the insect herbivore Spodoptera littoralis and a treatment with S. littoralis egg extract on the plants to analyze any role of TIRP during these attacks. We found that both A. brassicicola and V. dahliae infections increased TIRP gene expression systemically. The salicylic acid content was higher in the TIRP overexpressing line, corresponding to a better S. littoralis larval growth performance in feeding assays. However, since we never observed clear infection-related differences in jasmonate or salicylic acid levels between the wild type and the two transgenic Arabidopsis lines, our results rule out the possibility that TIRP acts via the regulation of phytohormone synthesis and accumulation. Full article

The comprehensive analysis of NBS-LRR resistance genes in the pepper (Capsicum annuum L.) genome reveals their structural diversity, evolutionary history, and functional importance in plant immunity. A total of 252 NBS-LRR genes were identified, distributed unevenly across all chromosomes, with 54% forming 47 gene clusters. These clusters, driven by tandem duplications and genomic rearrangements, underscore the dynamic evolution of resistance genes. Phylogenetic analysis demonstrated the dominance of the nTNL subfamily over the TNL subfamily, reflecting lineage-specific adaptations and evolutionary pressures. Structural analyses identified six conserved motifs (P-loop, RNBS-A, kinase-2, RNBS-B, RNBS-C, and GLPL) essential for ATP/GTP binding and resistance signaling. Subfamily-specific differences in motif composition and sequence similarity highlight their functional divergence and specialization. Comparative analyses across species further revealed a greater prevalence of nTNL genes in angiosperms, with significant losses of TNL genes in monocots. This study enhances our understanding of the evolution and diversification of plant-resistance genes and provides a foundation for developing disease-resistant crops through targeted breeding strategies. Full article

Anthropogenic structures such as overhead powerlines pose potentially high collision risks to flying animals, particularly birds, leading to millions of fatalities each year. Studies of bird collisions with powerlines to date, however, have estimated different numbers of collision per year and per kilometer in highly variable landscapes. This study aimed to clarify the risk of bird collisions with powerlines in an average landscape, to overcome the bias towards studies in collision hotspots. We conducted experiments to determine searcher efficiency, removal, and decomposition rates of collided birds as well as searching for collision victims and recording flight movements and flight reactions towards the powerlines. Annual bird-strike rates and flight phenology were analyzed using generalized additive models (GAMs). We estimated 50.1 collision victims per powerline kilometer per year and demonstrated that pigeons (especially Wood Pigeon, Columba palumbus) accounted for the largest proportion of collision victims (approximately 65%). Our study thus offers the opportunity to estimate the number of bird collisions (and the range of species) that can be expected in areas that are not particularly rich in bird life or sensitive, especially in view of the planned intensive expansion of energy structures in the context of the green energy transition. Full article

We test here the prediction capabilities of the new generation of deep learning predictors in the more challenging situation of multistate multidomain proteins by using as a case study a coiled-coil family of Nucleotide-binding Oligomerization Domain-like (NOD-like) receptors from A. thaliana and a few extra examples for reference. Results reveal a truly remarkable ability of these platforms to correctly predict the 3D structure of modules that fold in well-established topologies. A lower performance is noticed in modeling morphing regions of these proteins, such as the coiled coils. Predictors also display a good sensitivity to local sequence drifts upon the modeling solution of the overall modular configuration. In multivalued 1D to 3D mappings, the platforms display a marked tendency to model proteins in the most compact configuration and must be retrained by information filtering to drive modeling toward the sparser ones. Bias toward order and compactness is seen at the secondary structure level as well. All in all, using AI predictors for modeling multidomain multistate proteins when global templates are at hand is fruitful, but the above challenges have to be taken into account. In the absence of global templates, a piecewise modeling approach with experimentally constrained reconstruction of the global architecture might give more realistic results. Full article

The Solanaceae family occupies a significant position, and the study of resistance genes within this family is extremely valuable. Therefore, our goal is to examine disease resistance genes based on the high-quality representative genomes of Solanaceae crops, and to develop corresponding Simple Sequence Repeat (SSR) molecular markers. Among nine representative Solanaceae species, we identified 819 NBS-LRR genes, which were further divided into 583 CC-NBS-LRR (CNL), 54 RPW8-NBS-LRR (RNL), and 182 TIR-NBS-LRR (TNL) genes. Whole genome duplication (WGD) has played a very important role in the expansion of NBS-LRR genes in Solanaceae crops. Gene structure analysis showed the striking similarity in the conserved motifs of NBS-LRR genes, which suggests a common ancestral origin, followed by evolutionary differentiation and amplification. Gene clustering and events like rearrangement within the NBS-LRR family contribute to their scattered chromosomal distribution. Our findings reveal that the majority of NBS-LRR family genes across all examined species predominantly localize to chromosomal termini. The analysis indicates the significant impact of the most recent whole genome triplication (WGT) on the NBS-LRR family genes. Moreover, we constructed Protein–Protein Interaction (PPI) networks for all 819 NBS-LRR genes, identifying 3820 potential PPI pairs. Notably, 97 genes displayed clear interactive relationships, highlighting their potential role in disease resistance processes. A total of 22,226 SSRs were detected from all genes of nine Solanaceae species. Among these SSRs, we screened 43 NBS-LRR-associated SSRs. Our study lays the foundation for further exploration into SSR development and genetic mapping related to disease resistance in Solanaceae species. Full article

NLR genes are crucial components of the effector-triggered immunity (ETI) system, responsible for recognizing pathogens and initiating immune responses. Although NLR genes in many plant species have been extensively studied, the diversity of NLR genes in citrus remains largely unknown. Our analysis revealed significant variations in the copy numbers of NLR genes among these species. Gene duplication and recombination were identified as the major driving forces behind this diversity. Additionally, horizontal gene transfer (HGT) emerged as the principal mechanism responsible for the increase in NLR gene copy number in A. buxifolia. The citrus NLR genes were classified into four categories: TIR-NBS-LRR (TNL), CC-NBS-LRR (CNL), RPW8-NBS-LRR (RNL), and NL. Our findings indicate that TNL, RNL, and CNL genes originated from NL genes through the acquisition of TIR and RPW8 domains, along with CC motifs, followed by the random loss of corresponding domains. Phylogenetic analysis suggested that citrus NLR genes originated alongside the species and underwent adaptive evolution, potentially playing crucial roles in the global colonization of citrus. This study provides important insights into the diversity of citrus NLR genes and serves as a foundational dataset for future research aimed at breeding disease-resistant citrus varieties. Full article