Search Results (2,091)

Background: Human Metapneumovirus (HMPV) is a respiratory virus in the Pneumoviridae family. HMPV is an enveloped, negative-sense RNA virus encoding three surface proteins: SH, G, and F. The highly immunogenic fusion (F) protein is essential for viral entry and a key target for vaccine development. The F protein exists in two conformations: prefusion and postfusion. The prefusion form is highly immunogenic and considered a potent vaccine antigen. However, this conformation needs to be stabilized to improve its immunogenicity for effective vaccine development. Specific mutations are necessary to maintain the prefusion state and prevent it from changing to the postfusion form. Methods: In silico mutagenesis was performed on the C-terminal domain of the pre-F protein, focusing on five amino acids at positions 469 to 473 (LVDQS), using the established pre-F structure (PDB: 8W3Q) as the reference. The amino acid sequence was sequentially mutated based on hydrophobicity, resulting in mutants M1 (IIFLL), M2 (LLIVL), M3 (WWVLL), and M4 (YMWLL). Increasing hydrophobicity was found to enhance protein stability and structural rigidity. Results: Epitope mapping revealed that all mutants displayed significant B and T cell epitopes similar to the reference protein. The structure and stability of all mutants were analyzed using molecular dynamics simulations, free energy calculations, and secondary structure analysis. Based on the lowest RMSD, clash score, MolProbity value, stable radius of gyration, and low RMSF, the M1 mutant demonstrated superior structural stability. Conclusions: Our findings indicate that the M1 mutant of the pre-F protein could be the most stable and structurally accurate candidate for vaccine development against HMPV. Full article

Accurate cerebral vasculature segmentation using digital subtraction angiography (DSA) is critical for diagnosing and treating cerebrovascular diseases. However, conventional single-frame analysis methods often fail to capture fine vascular structures due to background noise, overlapping anatomy, and dynamic contrast flow. In this study, we propose a novel vessel-enhancing preprocessing technique using temporal differencing of DSA sequences to improve cerebrovascular segmentation accuracy. Our method emphasizes contrast flow dynamics while suppressing static background components by computing absolute differences between sequential DSA frames. The enhanced images were input into state-of-the-art deep learning models, U-Net++ and DeepLabv3+, for vascular segmentation. Quantitative evaluation of the publicly available DIAS dataset demonstrated significant segmentation improvements across multiple metrics, including the Dice Similarity Coefficient (DSC), Intersection over Union (IoU), and Vascular Connectivity (VC). Particularly, DeepLabv3+ with the proposed preprocessing achieved a DSC of 0.83 ± 0.05 and VC of 44.65 ± 0.63, outperforming conventional methods. These results suggest that leveraging temporal information via input enhancement substantially improves small and complex vascular structure extraction. Our approach is computationally efficient, model-agnostic, and clinically applicable for DSA. Full article

Bacterial cell morphology might result from natural selection to gain a competitive advantage under environmentally stressful conditions such as nutrient limitation. In nutrient-limited conditions, a higher surface-to-volume ratio is crucial for cell survival because it allows for a more efficient exchange of nutrients and waste products. A bacterial strain YC6860^T isolated from the rhizosphere of rice (Oryza sativa L.) showed pleomorphic behavior with smooth cell morphology and wrinkled surface rods depending upon nutritional conditions. Based on scanning and transmission electron microscopy studies, we hypothesized that the surface-to-volume ratio of cells would increase with decreasing nutrient concentrations and tested this quantitatively. The transition from smooth to wrinkled cell surface morphology could be one of the adaptation strategies by which YC6860^T maximizes its ability to access available nutrients. To characterize the properties of the wrinkled strain, we performed taxonomic and phylogenetic analyses. 16S rRNA gene sequencing results showed that the strain represented a novel, deep-rooting lineage within the order Rhizobiales with the highest similarity of 94.2% to Pseudorhodoplanes sinuspersici RIPI 110^T. Whole-genome sequencing was also performed to characterize its genetic features. The low phylogenetic and genetic similarity is probably related to the wrinkled morphology of the strain. Therefore, we propose that the strain YC6860^T might belong to a new genus and species, named Rugositalea oryzae. In addition, taxonomic analysis showed that YC6860^T is Gram-negative, aerobic, and rod-shaped with regular surface wrinkles under nutrient-limiting conditions, resembling a delicate twist of fusilli, with groove depths of 48.8 ± 3.7 nm and spacing of 122.5 ± 16.9 nm. This unique cell structure with regular rugosity could be the first finding that has not been reported in the existing bacterial morphology. Full article

Background: Feces and cecum content are commonly involved in metabolomic analysis to understand the gut metabolic profile of the host, while, in fact, they are different. Feces represent the terminal excretory product after extensive host enzymatic digestion, absorption, and significant modification by the distal gut microbiota. In contrast, cecum content reflects the localized, in situ metabolic microenvironment at that specific site. However, it is worth noting that feces are the most accessible sample type for non-invasive studies, which could be considered proxies for cecum content in some specific cases. Unfortunately, the validity of fecal samples as an alternative to cecum content has rarely been assessed. Methods: The current study attempted to illustrate the distinct metabolomic and microbiota features of feces and cecum content in eight animals (mouse, pig, chicken, duck, rabbit, Gansu yak, Sichuan yak, and sheep) by means of ¹H-NMR and 16S rRNA, respectively. Results: A total of 116 molecules were characterized in feces and cecum content samples. Among them, 22 molecules were shared in all groups. Taking advantage of the univariate analysis, twenty-seven of the quantified molecules were significantly different between feces and cecum content, mainly pertaining to amino acids and organic acids. Moreover, in terms of mammals and non-mammals, short-chain fatty acids could be considered the main factor discriminating the metabolomic profiles between feces and cecum content. Furthermore, to better understand the mechanism of their metabolomic differences, 16S rRNA sequencing analysis was performed on feces and cecum content samples of mice, which is the most widely used animal model. The result showed that the Ace, Shannon, and Sobs indexes in feces were significantly higher than those of cecum content (p < 0.05). At the phylum and genus levels, the microbiota structures of feces and cecum content were similar, while the relative abundances of their microbiota exhibited distinct features. Conclusions: The present study could reduce this gap in information by characterizing, for the first time, the metabolomic differences between feces and cecum content using ¹H-NMR. Moreover, this study is meant as a reference guide for researchers wishing to apply a metabolomics approach to the gut of the host. Full article

Background: Corynebacterium ulcerans is an emerging zoonotic pathogen capable of cau-sing diphtheria-like infections in humans. Objectives: we report, for the first time in Brazil, the detection and phenotypic/genomic characterization of three atoxigenic ST-339 strains isolated from domestic animals, including one with a ciprofloxacin resistance profile linked to double GyrA mutations (S89L, D93G). Methods: species identification was performed by MALDI-TOF MS, followed by in vitro antimicrobial susceptibility testing, whole-genome sequencing, and bioinformatic analyses to predict virulence determinants, antimicrobial resistance genes, CRISPR–Cas systems, mobile genetic elements, and in silico structural analysis as well as phylogenetic reconstruction. Results: whole-genome sequencing confirmed species identity, revealed high genetic similarity, and identified distinct phylogenetic subclades, suggesting potential international dissemination. Genomic analyses showed conserved virulence determinants, such as incomplete pilus clusters, iron acquisition systems, and the pld gene, with the absence of the tox gene. Molecular modeling and dynamics simulations indicated that GyrA mutations disrupt critical ciprofloxacin–magnesium–water interactions, reducing binding stability. Mobile genetic elements, prophages, and CRISPR–Cas systems underscored the genomic plasticity of these isolates. Conclusions: these findings document a little-studied antimicrobial resistance mechanism in zoonotic C. ulcerans, highlighting the need for strengthened surveillance and further research on virulence and resistance, even in ato-xigenic strains. Full article

Phytopathogenic fungi secrete numerous effector proteins to disrupt plant defenses. At present, their sequence–structure–function relationships remain poorly understood owing to their diversity. Comprehensive understanding of conserved effectors is necessary to elucidate the molecular relationship between fungi and plants. To fill this research gap, we investigated the Colletotrichum higginsianum effector candidate (ChEC)-88 specifically expressed during infection. Notably, similar to the biotrophy-associated secreted protein 3 (BAS3) from Pyricularia oryzae, ChEC88 inhibited plant cell death caused by necrosis- and ethylene-inducing peptide 1-like protein (NLP1). Nuclear magnetic resonance analysis results revealed that ChEC88 adopted a novel pseudo two-fold symmetrical three-dimensional structure. Homology modeling suggested that BAS3 exhibited a ChEC88-like conformation despite sharing less than 50% sequence identity. Through PSI-BLAST searches, we found that ChEC88 homologs were conserved in various hemibiotrophic phytopathogenic fungi, including Colletotrichum, P. oryzae, and Fusarium species. Functional assays demonstrated that all of the representative homologs suppressed NLP1-induced plant cell death. Mutation experiments identified the residues critical for ChEC88 function. Overall, our findings suggest that hemibiotrophic phytopathogenic fungi share a conserved immune-suppression strategy mediated by ChEC88-like proteins and that such effectors possibly originated from a common ancestral lineage of phytopathogenic fungi. Full article

A new trinor-sesterterpenoid penitalarin D (1), with a 3,6-dioxabicyclo[3.1.0]hexane moiety, as well as two known compounds, penitalarin C (2) and nafuredin A (3), were obtained from the mangrove sediment-derived Talaromyces sp. SCSIO 41412. Their structures were determined by detailed NMR, MS spectroscopic analyses, and ECD calculations. Penitalarin D (1) and nafuredin A (3) showed toxicity or no toxicity against HepG2 cells at a concentration of 200 μM. The transcriptome sequencing and bioinformatics analysis revealed that 3 could be effective by regulating ferroptosis pathways in HepG2 cells, which was subsequently validated by RT-qPCR, demonstrating significant upregulation of ferroptosis-related genes. Pre-treatment with 3 could mitigate hypoxia-reoxygenation-induced damage in the oxygen glucose deprivation/reperfusion (OGD/R) cell model. Given the structural similarity of compounds 1, 2, and 3, we also screened compounds 1 and 2 in an AML12 OGD/R model. As no significant activity was observed, compound 3 was selected for subsequent in vivo studies. Subsequently, in vivo experiments demonstrated that 3 could significantly decrease pro-inflammatory cytokines and display the hepatoprotective effects against hepatic ischemia-reperfusion injury (HIRI). These findings identified nafuredin A (3) as a promising hepatoprotective agent for new drug development. Full article

The application of conductive polymers in wound dressings presents great potential for accelerated wound healing since their high electrical conductivity and biocompatibility facilitate the delivery of external electrical stimuli to cells and tissues, promoting cell differentiation and proliferation. Electrospinning is a very straightforward method for the preparation of polymeric wound dressings capable of mimicking the extracellular matrix of skin, promoting hemostasis, absorbing wound exudate, allowing atmospheric oxygen permeation and maintaining an appropriately moist environment. In this work, in situ chemically polymerized poly(3,4-ethylenedioxythiophene) (PEDOT) was achieved through hyaluronic acid-doping. The synthesized PEDOT was used for the production of conductive and biodegradable chitosan (CS)/gelatin (GEL)/PEDOT electrospun meshes. Additionally, the randomly aligned meshes were crosslinked with a 1,4-butanediol diglycidyl ether and their physicochemical and mechanical properties were investigated. The results show that the incorporation of a conductive polymer led to an increase in conductivity of the solution, density and fiber diameter that influenced porosity, water uptake, and dissolvability and biodegradability of the meshes, while maintaining appropriate water vapor permeation values. Due to their intrinsic similarity to the extracellular matrix and cell-binding sequences, CS/GEL/PEDOT electrospun nanofibrous meshes show potential as conductive nanofibrous structures for electrostimulated wound dressings in skin tissue engineering applications. Full article

Background/Objectives: Inteins are mobile genetic elements invading highly conserved genes across all domains of life and viruses. Five active intein insertion sites (MCM-a through e) had previously been identified and studied in the archaeal replicative helicase minichromosome maintenance (MCM) subunit gene mcm, making MCM an ideal system for dissecting the dynamics of multi-intein genes. However, work in this system thus far has been limited to particular archaeal groups. To better understand the dynamics and diversity of these inteins, MCM homologs spanning all archaeal groups were extracted from NCBI’s non-redundant protein sequence database, and the distribution and structural architectures of their inteins were characterized. Methods: The amino acid sequences of 4243 archaeal MCM homologs were retrieved from NCBI’s non-redundant protein sequence database. These sequences were systematically assessed for their intein content through within-group multiple sequence alignments. To characterize the inteins present at each site, extensive intein structure predictions and comparisons were performed. Phylogenetic analyses were used to investigate intein relatedness between and within sites, as well as the distribution of different MCM inteins in geographically overlapping populations of archaea. Results: In total, 11 active MCM intein insertion sites were identified, expanding on the previously known five. The insertion sites have varied invasion activity levels across archaeal groups, with Nanobdellati (DPANN) being the only group with all 11 sites active. In all but two (Methanonatronarchaeia and Hadarchaeota) of the archaeal groups studied where inteins were present, at least one MCM homolog was invaded by more than one intein. With respect to intein structure, within-intein insertions bearing semblance to DNA-binding domains were identified, with varied presence between inteins. Additionally, a study of archaeal MCM sequences of samples collected from the Atacama Desert in June 2013 revealed high MCM intein diversity levels. Conclusions: We identified six new active intein insertion sites in archaeal MCM, more than doubling the five previously known sites. All eleven intein insertion sites were either close to the ATP binding site, or the lined the channel through which the single-stranded DNA is pulled during the catalytic cycle of the helicase. Many of the analyzed inteins contained insertions bearing similarity to DNA-binding helix-turn-helix domains suggesting potential involvement in the intein homing process. Additionally, the high levels of MCM intein diversity observed in archaea from the Atacama Desert provide novel and strong support for a co-existence model of intein persistence. Full article

Mammals harbor diverse microbial communities across different body sites, which are crucial to physiological functions and host homeostasis. This study aimed to understand the structure and function of gut and lung microbiota of pregnant Pomona leaf-nosed bats using V3-V4 16S rRNA gene sequencing. Of the 350 bats captured using mist nets in Yunnan, nine pregnant Pomona leaf-nosed bats with similar body sizes were chosen. Gut and lung samples were aseptically collected from each bat following cervical dislocation and placed in sterile cryotubes before microbiota investigation. Microbial taxonomic annotation revealed that the phyla Firmicutes and Actinobacteriota were most abundant in the guts of pregnant bats, whereas Proteobacteria and Bacteroidota were abundant in the lungs. Family-level classification revealed that Bacillaceae, Enterobacteriaceae, and Streptococcaceae were more abundant in the guts, whereas Rhizobiaceae and Burkholderiaceae dominated the lungs. Several opportunistic and potentially pathogenic bacterial genera were present at the two body sites. Bacillus, Cronobacter, and Corynebacterium were abundant in the gut, whereas Bartonella, Burkholderia, and Mycoplasma dominated the lungs. Alpha diversity analysis (using Chao1 and Shannon indices) within sample groups examined read depth and species richness, whereas beta diversity using unweighted and weighted UniFrac distance metrics revealed distinct clustering patterns between the two groups. LEfSe analysis revealed significantly enriched bacterial taxa, indicating distinct microbial clusters within the two body sites. The two Random Forest classifiers (MDA and MDG) evaluated the importance of microbial features in the two groups. Comprehensive functional annotation provided insights into the microbiota roles in metabolic activities, human diseases, signal transduction, etc. This study contributes to our understanding of the microbiota structure and functional potential in pregnant wild bats, which may have implications for host physiology, immunity, and the emergence of diseases. Full article

To address the complex challenge of recognizing mixed handwritten text in practical scenarios such as examination papers and to overcome the limitations of existing methods that typically focus on a single category, this paper proposes MHTR, a Multimodal Handwritten Text Adaptive Recognition algorithm. The framework comprises two key components, a Handwritten Character Classification Module and a Handwritten Text Adaptive Recognition Module, which work in conjunction. The classification module performs fine-grained analysis of the input image, identifying different types of handwritten content such as Chinese characters, digits, and mathematical formula. Based on these results, the recognition module dynamically selects specialized sub-networks tailored to each category, thereby enhancing recognition accuracy. To further reduce errors caused by similar character shapes and diverse handwriting styles, a Context-aware Recognition Optimization Module is introduced. This module captures local semantic and structural information, improving the model’s understanding of character sequences and boosting recognition performance. Recognizing the limitations of existing public handwriting datasets, particularly their lack of diversity in character categories and writing styles, this study constructs a heterogeneous, integrated handwritten text dataset. The dataset combines samples from multiple sources, including Chinese characters, numerals, and mathematical symbols, and features high structural complexity and stylistic variation to better reflect real-world application needs. Experimental results show that MHTR achieves a recognition accuracy of 86.63% on the constructed dataset, significantly outperforming existing methods. Furthermore, the context-aware optimization module demonstrates strong adaptive correction capabilities in various misrecognition scenarios, confirming the effectiveness and practicality of the proposed approach for complex, multi-category handwritten text recognition tasks. Full article

Scorpion venom contains various insecticidal peptides. Previously, through transcriptome analysis of the venom gland of Liocheles australasiae, we identified precursor sequences of several peptides that share sequences similar to those acting on K⁺ channels. In this study, we chemically synthesized five of the peptides which were found in the venom and evaluated their insecticidal activity against crickets. This revealed that one of the peptides, named LaIT6, exhibited significant insecticidal activity without mammalian toxicity. To identify amino acid residues important for the insecticidal activity of LaIT6, nine analogs were synthesized mainly by substituting acidic, basic, and aromatic residues with alanine. This revealed that two basic residues and an aromatic residue in the C-terminal region are important for the activity. This characteristic of structure-activity relationships, known as a functional dyad, is commonly observed in peptides that act on K⁺ channels, suggesting that the action target of LaIT6 is K⁺ channels. As expected, LaIT6 showed significant inhibitory activity against insect K⁺ channels. Since no activity against human K⁺ channels was observed, we concluded that the selectivity of LaIT6 is determined by differences in the action on K⁺ channels between insects and mammals. Full article

Background/Objectives: Postoperative MRI is crucial for detecting residual tumor, identifying complications, and planning subsequent therapy. This study evaluates accelerated deep learning reconstruction (DLR) versus standard clinical protocols for early postoperative MRI following tumor resection. Methods: This study uses a multidisciplinary approach involving a neuroradiologist, neurosurgeon, neuro-oncologist, and radiotherapist to evaluate qualitative aspects using a 5-point Likert scale, the preferred reconstruction variant and potential residual tumor of DLR and conventional reconstruction (CR) of FLAIR, T1-weighted non-contrast and contrast-enhanced (T1), and coronal T2-weighted (T2) sequences for 1.5 and 3 T MRI. Quantitative analysis included the image quality metrics Structural Similarity Index (SSIM), Multi-Scale SSIM (MS-SSIM), Feature Similarity Index (FSIM), Noise Quality Metric (NQM), signal-to-noise ratio (SNR), and Peak SNR (PSNR) with CR as a reference. Results: All raters strongly preferred DLR over CR. This was most pronounced for FLAIR images at 1.5 and 3 T (91% at 1.5 T and 97% at 3 T) and least pronounced for T1 at 1.5 T (79% for non-contrast-enhanced and 84% for contrast-enhanced sequences) and for T2 at 3 T (69%). DLR demonstrated superior qualitative image quality for all sequences and field strengths (p < 0.001), except for T2 at 3 T, which was observed across all raters (p = 0.670). Diagnostic confidence was similar at 3 T with better but non-significant differences for T2 (p = 0.134) and at 1.5 T with better but non-significant differences for non-contrast-enhanced T1 (p = 0.083) and only marginally significant results for FLAIR (p = 0.033). Both the SSIM and MS-SSIM indicated near-perfect similarity between CR and DLR. FSIM performs worse in terms of consistency between CR and DLR. The image quality metrics NQM, SNR, and PSNR showed better results for DLR. Visual assessment of residual tumor was similar at 3 T but differed at 1.5 T, with more residual tumor detected with DLR, especially by the neurosurgeon (n = 4). Conclusions: An accelerated DLR protocol demonstrates clinical feasibility, enabling high-quality reconstructions in challenging postoperative MRIs. DLR sequences received strong multidisciplinary preference, underscoring their potential to improve neuro-oncologic decision making and suitability for clinical implementation. Full article

Mycoplasmal pneumonia of sheep (MPS), caused by Mesomycoplasma (Mycoplasma) ovipneumoniae, profoundly impacts ovine productivity and survival. Although gut–lung microbiota interactions are increasingly recognized in respiratory diseases, whether similar crosstalk occurs between the lung and rumen microbiota in MPS-affected sheep remains unknown. To investigate alterations in the lung and rumen microbiota of sheep with MPS, the crosstalk between these microbial communities, and their impacts on growth phenotypes. From a cohort of 414 naturally infected six-month-old male Hu sheep, we selected 10 individuals with severe pulmonary pathology and 10 healthy controls for detailed phenotypic and microbiome analyses. Assessment of 359 phenotypic traits revealed that MPS significantly impairs feed efficiency and growth rate (p < 0.05). Through 16S rRNA gene sequencing, we found that MPS significantly altered the pulmonary microbiota community structure (p < 0.01), with a noticeable impact on the rumen microbiota composition (p = 0.059). Succinivibrionaceae_UCG-001 was significantly depleted in both the rumen and lungs of diseased sheep (p < 0.05) and strongly associated with reduced average daily feed intake (p < 0.05). In addition, pulmonary Pasteurella and ruminal Succinivibrionaceae_UCG-002 were significantly enriched in MPS-affected sheep, showed a strong positive correlation (p < 0.05), and were both negatively associated with feed efficiency (p < 0.05). Notably, Pasteurella multocida subsp. gallicida may act as a keystone species influencing feed efficiency. These findings point to a previously unrecognized rumen-lung microbial axis that may modulate host productivity in sheep affected by MPS. This work provides new insights into the pathogenesis of MPS and offers potential targets for therapeutic intervention and management. Full article

Polynucleotide (PN) and polydeoxyribonucleotide (PDRN) are DNA-derived biopolymers increasingly recognized for their potential in dermatology. Despite their structural similarities, PN and PDRN exhibit distinct functions due to differences in polymer length and molecular weight. PN, composed of longer DNA fragments, plays a key role in extracellular matrix remodeling. Conversely, PDRN, composed of relatively shorter oligonucleotide sequences than those of PN, enhances skin condition through adenosine receptor activations and supports nucleotide synthesis via both the salvage and de novo pathways. This review provides a critical comparison of the molecular characteristics and functions of PN and PDRN with particular emphasis on their dermatological applications. By delineating their respective roles in esthetic and regenerative medicine, we aim to highlight recent advances that may guide the development of optimized treatment strategies and foster evidence-based clinical practice. Full article