Journal of foot and ankle researchBenjamin Peterson, John Osborne, Ameer Nor Azhar, Matthew Carroll, Peta Tehan
BACKGROUND: There is growing research evidence related to musculoskeletal and sports podiatry published by Australian researchers. This short report presents data from the musculoskeletal and sports podiatry stream of a national bibliometric review which aimed to map all Australian podiatry-related research from 1970 to 2024. METHODS: A systematic search of the literature was conducted via Scopus until December 2024. Studies were screened for eligibility using Covidence. Study meta-data was analysed using Biblioshiny to describe publications volume, authors, institutions, journals, and research collaborations. Via manual processes, each publication was categorised for: level of evidence using National Health and Medical Research Council criteria; research type using the United Kingdom Clinical Research Collaboration Health Research Classification System; and funding source, using Higher Education Research Data Collection specifications. RESULTS: The search strategy yielded 288 records published by 774 authors (19% international), with a total 12,593 citations, with 44.1 mean citations per article from 1991 to 2024 were included. A total of 65 articles (23%) were categorised as level I evidence. The British Journal of Sports Medicine and the Journal of Science and Medicine in Sport were equally the most frequent publication sources, publishing 23 (8%) articles respectively. Podiatry-related musculoskeletal and sports research is usually undertaken without dedicated funding (67%). The majority of published articles focussed on the evaluation of treatments and therapeutic interventions (36%) and on the aetiology of conditions (34%). CONCLUSION: The musculoskeletal and sports podiatry stream was the most widely researched, with the highest proportion of level I evidence among all streams of the national bibliometric review. Given the high burden of disease and adverse impacts on activities of daily living associated with musculoskeletal conditions, further attention in preventative care and the promotion of wellbeing in sports and musculoskeletal research would be beneficial.
The plant genomeLuan Cutti, Daniel Fernando da Silva Filho, Geisson Edwin Guadir Lara, Jessica Matheson, Nicholas A Johnson, Jacob Montgomery, Nathan Hall, Brent Murphy, Todd …
The International Weed Genomics Consortium (IWGC) has sequenced and annotated the genomes of over 30 weed species, generating genomic resources to understand their biology, evolution, and adaptation. The objective of this study was to evaluate the semi-automated, isoform sequencing (Iso-seq)-based, IWGC genome annotation pipeline by reannotating the genome of the model species Arabidopsis thaliana with various amounts and types of extrinsic data and to measure the impact that varying inputs had on the annotation completeness and quality. Annotations were run comparing the effects of (1) the quantity and source of Iso-seq reads, (2) annotated proteins from botanically closely related or distantly related species, and (3) the number of proteins provided to the annotation program "MAKER-P." Reannotations were compared to each other and to the published annotation of the A. thaliana genome. The IWGC annotation pipeline annotated almost all the genes without manual curation when informed with an Iso-seq dataset and proteins of related species. In general, the pipeline produced more accurate, annotated genes with more input proteins, especially from closely related species, in the gene model prediction step. Furthermore, the combination of proteins from several closely related species increased the number of annotated genes. The number or source of Iso-seq reads did not have a significant effect if many proteins from closely related species were utilized. The annotation pipeline annotated nearly 90% of genes from additional crop species genomes. The IWGC genome annotation pipeline is robust in reannotating the A. thaliana genome and therefore is most likely performing well in the several non-model weed species it has been used on so far.
Human vaccines & immunotherapeuticsXiaolong Tian, Yingping Zhang, Chen Zhang, Dongdong Liu, Yanmin Ma
This study aims to analyze the global research patterns and emerging trends in CAR-T cell therapy for ALL through a bibliometric analysis. Publications were retrieved from the Web of Science Core Collection database. The bibliometric analysis utilized VOSviewer, CiteSpace, and the R package "bibliometrix" to visualize collaborations, keyword co-occurrences, and emerging research trends. A total of 844 articles from 253 journals by 6,459 authors across 44 countries were analyzed, showing an annual growth rate of 40.08%. The USA (372 articles, 38,065 citations) and China (275 articles, 5,636 citations) dominated research output. The University of Pennsylvania (353 articles), Memorial Sloan Kettering Cancer Center (170), and Children's Hospital of Philadelphia (131) were the most productive institutions, while Blood (41 articles) published the most articles. Stephan A. Grupp (38 articles, H-index = 30), Carl H. June (26 articles, H-index = 24), and Shannon L. Maude (25 articles, H-index = 20) were the most influential authors. Keyword analysis revealed five research clusters, including basic mechanisms, CAR design, population treatment integration, clinical outcomes, and toxicity management. Burst keyword analysis showed the evolution from basic science (2010-2013) to clinical translation (2014-2016), toxicity management (2017-2019), and recently to long-term outcomes and risk assessment (2020-2024), with "term follow-up" and "risk" as the only keywords with active bursts in 2024. This bibliometric analysis reveals that research on CAR-T therapy for ALL has progressed from foundational concepts to clinical implementation and now focuses on optimizing long-term outcomes and patient selection. Future research should prioritize biomarker development, next-generation CAR designs, and combination strategies to overcome persistence, toxicity, and resistance limitations in ALL treatment.
European journal of psychotraumatologyJohn Ahern, Donal G Fortune
Background: Complex post-traumatic stress disorder (C-PTSD) has been included in the International Classification of Diseases, 11th revision (ICD-11) to recognize the impact of significant trauma(s) on an affected individual. C-PTSD has the core symptoms of post-traumatic stress disorder (PTSD) with additional symptoms of disturbances of self-organization. While the ICD-11 has been in use globally since 2022, research is limited on how clinicians working in routine adult mental health (AMH) services adapt to diagnosing and treating C-PTSD.Objective: To investigate the experiences of clinicians in applying and treating C-PTSD with adults in a public AMH setting.Method: A reflexive thematic analysis approach was used to code and analyse results from semi-structured interviews conducted with 20 psychologists and psychiatrists.Results: Three key themes were identified from clinicians' experiences: (1) 'C-PTSD is beyond a simple diagnosis', reflecting challenges regarding understanding trauma history and differential diagnosis; (2) 'Balancing treatment on a tightrope', highlighting trust as a foundation required in the therapeutic relationship before attempting trauma processing through various treatment modalities; and (3) 'Resourcing for C-PTSD treatment success', emphasizing how adequate resources, regular supervision, training, and attuned trauma services are needed to overcome barriers to treatment of C-PTSD in public AMH settings.Conclusions: Clinicians reported key challenges in working with C-PTSD diagnosis in AMH settings. While clinicians are aware of the diagnostic criteria, building a therapeutic relationship with C-PTSD clients remains a challenge before engaging in effective interventions. The need for adequate access to resources, such as evidence-based treatment pathways, further training on C-PTSD across multidisciplinary teams, regular supervision, and trauma-informed services that are attuned to individuals' needs, is a key issue for clinicians that requires addressing in public AMH services.
Journal of obstetrics and gynaecology : the journal of the Institute of Obstetrics and GynaecologyFeng Sun, Mengyao Huan, Huimin Niu, Chuning Lin, Xinyi Zhang, Yuxin Liu, Feng Jiang, Chuyan Wu
BACKGROUND: Polycystic Ovary Syndrome (PCOS) imposes substantial metabolic and reproductive burdens. Exercise has emerged as a crucial lifestyle intervention, and corresponding scientific interest has expanded. This study provides a comprehensive bibliometric analysis of global research on the intersecting PCOS and exercise. METHODS: Relevant publications (2005-2025) were collected from the Web of Science Core Collection (WoSCC). CiteSpace, VOSviewer, and bibliometrix were applied to map publication trends, international collaboration patterns, and evolving research hotspots. RESULTS: A total of 1,146 publications were identified, demonstrating sustained growth. The United States and Australia dominated productivity, collaborating primarily with India, the United Kingdom (UK), and Switzerland. Key research hotspots included metabolic syndrome, endothelial function, cardiovascular disease, and increasing emphasis on exercise-based interventions. Monash University and the University of Adelaide played central roles in institutional networks. Emerging themes, including oxidative stress and anxiety, have emerged in the broader PCOS literature and are closely linked to exercise-related biological pathways. CONCLUSIONS: Exercise is an increasingly prominent research focus in PCOS management. This analysis outlines the field's structural and thematic evolution and identifies opportunities for advancing scientific understanding. Strengthened international and multidisciplinary collaboration remains essential.
European journal of psychotraumatologyMai Jiaying Xu, Chenyang Zhao, Hao Qin, Haimou Ye, Weiwen Wang, Hang Xu
Background: Adolescence is a developmentally sensitive period for trauma-related psychopathology, yet posttraumatic stress disorder (PTSD) is defined differently across diagnostic systems. The DSM-5 conceptualises PTSD broadly, whereas the ICD-11 distinguishes PTSD from complex PTSD (CPTSD), raising questions about diagnostic alignment and clinical meaning in youth.Objective: This study examined the diagnostic concordance between DSM-5 PTSD and ICD-11 PTSD and the differentiation between DSM-5 PTSD and ICD-11 CPTSD in adolescents, further evaluating whether adverse childhood experiences (ACEs) differentially predicted diagnoses.Method: Participants included 585 adolescents aged 13-20 years from psychiatric outpatient clinics and 2146 control adolescents from schools. DSM-5 PTSD was assessed using the PTSD Checklist for DSM-5, ICD-11 PTSD and CPTSD were assessed with the International Trauma Questionnaire (ITQ), and ACEs were measured using the ACE International Questionnaire (ACE-IQ). Least absolute shrinkage and selection operator (LASSO) logistic regression and receiver operating characteristic (ROC) analyses were used to identify stable adversity-based predictors and evaluate model discrimination.Results: DSM-5 PTSD prevalence was substantially higher than ICD-11 PTSD prevalence in both samples. ACEs showed minimal predictive value for ICD-11 PTSD but strong associations with DSM-5 PTSD and ICD-11 CPTSD, particularly cumulative adversity and community violence. DSM-5 PTSD aligned more closely with ICD-11 CPTSD than with ICD-11 PTSD in adolescents, and ACEs predicted diagnostic differentiation primarily in samples with lower trauma exposure.Conclusions: By directly mapping diagnostic overlap and adversity-based differentiation within adolescent cohorts, this study addresses a critical gap in the literature regarding the age-specific validity and clinical meaning of DSM-5 and ICD-11 trauma diagnoses.
Life science allianceHoussemeddine Derbel, Evan Kinnear, Justin J-L Wong, Qian Liu
DNA methylation is a fundamental epigenetic mechanism, and its significant changes (i.e., differential methylation) regulate gene expression, cell-type specification, and disease progression without altering the underlying DNA sequence. Differential methylation has traditionally been detected by statistical comparison of two groups using existing tools and has supported a wide range of downstream analyses in human disease studies. However, few toolboxes efficiently integrate robust detection, annotation, and visualization of differential methylation, and the reproducibility of detected signals across tools remains limited. Moreover, existing methods have rarely been evaluated on long-read methylomes, despite their increasing availability. Here, we present DiffMethylTools, an end-to-end framework designed to address analytical and computational challenges in differential methylation studies. DiffMethylTools generates robust differential methylation detection with comprehensive annotation and visualization modules to streamline analysis workflows. Benchmarking across six datasets, including three long-read methylomes, shows that DiffMethylTools outperforms four widely used tools in detecting differential methylation, with improved overall performance and reproducibility. In addition, DiffMethylTools offers compatibility with upstream methylation-calling pipelines, and facilitates downstream biological interpretation through flexible annotation and visualization capabilities.
Carbohydrate researchMaxim S Kokoulin, Yulia V Savicheva, Ksenia V Isaeva, Lyudmila A Romanenko, Marina P Isaeva
Bacteria of the genus Vibrio dwelling in marine environment produce structurally diverse lipopolysaccharides (LPS) that play critical roles in environmental adaptation and host interactions. Here we report the complete structural elucidation of two O-polysaccharides (OPS) from the LPS of Vibrio sp. KMM 9700, isolated from the red alga Polysiphonia sp. Genomic analysis revealed an O-antigen gene cluster containing sulfotransferases (STs), glycosyltransferases (GTs), a PAPS biosynthesis operon, and the dTDP-Rha pathway. A GT and ST pair similar to that in the capsular polysaccharide cluster of V. chaetopteri KMM 8419T suggested the synthesis of a polysaccharide with α-l-rhamnopyranose (α-L-Rhap) 3-O-sulfate. An additional GT and ST pair in the cluster indicated the biosynthesis of another sulfated polysaccharide. Using chemical analyses, selective modifications, and NMR spectroscopy, we showed that both OPS coexist in the LPS preparation. The major OPS is a tetrasaccharide repeating unit with alternating 6-substituted α-D-Glcp and 2-substituted α-L-Rhap residues, featuring sulfate at O-3 and O-acetyl at O-4 of one α-L-Rhap residue. The minor OPS is a pentasaccharide repeating unit composed exclusively of α-L-Rhap residues with three 3-linked and two 2-linked residues, bearing sulfate groups at O-2 of two specific α-L-Rhap residues. Neither structure has been previously reported in bacterial glycans. The presence of two distinct sulfated OPS in a single Vibrio strain expands the known chemotypic diversity within the genus and suggests a sophisticated surface adaptation mechanism in marine environments.
Life science allianceSøren W Gersting, Julia V Cramer, Philipp Guder, Amelie S Lotz-Havla, Barbara Wolf, Heidi Noll-Puchta, Ralf Erdmann, Ania C Muntau, Mathias Woidy
Peroxisomal dysfunction contributes to a broad spectrum of multisystem disorders, yet mechanistic understanding and therapeutic options remain limited, posing significant challenges for clinical management. Network-based computational strategies support hypothesis generation, biomarker discovery, and drug repurposing, but their usage is constrained by incomplete human interactome coverage-especially by scarcity of high-confidence protein-protein interaction (PPI) data for peroxisomal proteins. We present the first comprehensive map of the peroxisomal interactome, generated using an automated, informatics-guided bioluminescence resonance energy transfer strategy. We profiled PPIs for 92 peroxisomal proteins and six isoforms, validating 68% of known interactions and identifying 333 novel ones. Integration with curated PPIs yielded an expanded peroxisomal interactome, enriched for drug targets and disease-associated proteins. A disease-linked subnetwork enabled prioritization of drug repurposing candidates. Tissue-specific expanded peroxisomal interactome variants, derived from transcriptomic data, revealed distinct functional submodules across nine tissues. Gene ontology analysis of 1,272 non-peroxisomal interactors suggested pathways contributing to tissue-specific vulnerability. Our approach provides a systems-level framework for mechanistic insight in peroxisomal disease, the identification of treatment targets, and application to other organelle systems.
PsychoneuroendocrinologyC Winters, W Gorssen, S E Ulbrich, S Goumon
Salivary oxytocin is a widely used peripheral measure for investigating neuroendocrine correlates of social, stress-related, and adaptive physiological processes. While theoretical interpretations of oxytocin have evolved substantially beyond early prosocial accounts and recognized context dependency, individual variability, and regulatory functions, more recent studies introducing oxytocin measures in non-human species often rely exclusively on early prosocial interpretations. This striking limitation to just one of several conceptualizations prompted us to examine how theoretical perspectives are represented in the literature on salivary oxytocin. To address this, we conducted a bibliometric and semantic analysis of 445 publications on salivary oxytocin (2005-2026) to identify historical trends, citation patterns, thematic concentrations, and alignment with current theoretical frameworks. A citation analyses revealed the dominance of early canonical studies, with a small number of papers accounting for a disproportionate share of citations. Keyword and semantic cluster analyses identified seven thematic domains, including stress research, parental care, and clinical studies, while integration across species was limited. Explicit citation of selected landmark publications representing major conceptual frameworks of oxytocin function was uncommon (16.6% of studies), with human studies primarily referencing the publication representing social salience theory and animal studies primarily referencing the publication representing the prosocial framework. Thus, despite its evolutionary conservation and translational potential, salivary oxytocin research showed limited explicit theoretical engagement, while citation and semantic patterns remained disproportionately centered on early socially oriented literature. Together, these findings suggest that the rapid expansion of the field has not been accompanied by comparable structural diversification. This highlights the need for future research to apply models, integrate findings, and contextualize applications to produce informed insights into oxytocin's physiological, behavioral, and adaptive functions.
FlyJumriani Jumriani, Ratnawati Ratnawati, Youdiil Ophinni, Emil Salim, Firzan Nainu
Pharmaceutical waste has been recognized as an emerging contaminant that is increasingly detected in the environment and may pose ecotoxicological risks. This review aims to describe the global development of research on pharmaceutical waste within the field of ecotoxicology and to examine the role of insects in trophic food-chain exposure pathways. A bibliometric analysis was conducted using the Scopus database, comprising 1,051 articles published between 2010 and 2025. The results show a consistent upward trend in publications, with pharmaceutical ecotoxicology research predominantly focused on aquatic environments, environmental risk assessment, contaminant monitoring, and toxicological evaluation. Keyword analysis further indicates that terrestrial exposure pathways remain comparatively less emphasized within the current bibliometric landscape. The narrative review indicates that pharmaceutical waste can accumulate in organisms and be transferred through the food chain, leading to various physiological and systemic toxic effects, even at low environmental concentrations. In this context, insects play a strategic role as mediators of trophic exposure. Hermetia illucens is relevant in waste management and biotransformation processes, while Drosophila melanogaster is a well-established model organism for investigating physiological and molecular responses to pharmaceutical compound exposure. Thus, this review discusses the potential of an insect-based ecotoxicology framework in which H. illucens may serve as a bioconversion model for waste processing and D. melanogaster as a mechanistic model for toxicological studies. We also highlight the need for a more integrative ecotoxicological approach to pharmaceutical waste that explicitly considers insect involvement and food chain - based exposure pathways.
European journal of psychotraumatologyMałgorzata Dragan, Magdalena Grabowska, Zofia Hecht, Aleksandra Mołodysz, Marwa Amiri, Philip Hyland
Background: The International Trauma Questionnaire (ITQ) is a widely used measure of ICD-11 Posttraumatic Stress Disorder (PTSD) and Complex PTSD (CPTSD), enabling the estimation of the prevalence rates of these disorders in general population and clinical samples. Due to concerns related to the use of self-report measures, authors of the original version introduced the concept of 'clinical checks', which are added in the new version to ensure initial responses reflected the intended clinical meaning of the scale items.Objective: As the concept is new and needs testing in different cultural settings, the aim of this study was to measure and compare the prevalence of probable PTSD and CPTSD in a representative sample of Poles with the use of a new version of the ITQ (ITQ-CC) and an original one.Method: We collected data from a representative sample of adults from Poland (N = 1,816) via an internet research panel.Results: Comparison of the results obtained with the use of ITQ versus ITQ-CC revealed that individual symptom endorsements decreased by between 18.9% and 41.6%. Disorder prevalence estimates without the clinical checks were 5.3% for PTSD and 6.1% for CPTSD. These estimates dropped to 2.4% for PTSD, and to 3.5% for CPTSD, when the clinical checks were used; thus the relative decrease was 55.7% for PTSD, and 48.7% for CPTSD, giving a total relative reduction rate of 48.8%.Conclusion: The study results indicate a significant influence of clinical checks on post-traumatic symptoms screening. This resulted in a substantial reduction in the estimated PTSD and CPTSD prevalence rates.
Human vaccines & immunotherapeuticsTiecheng Liu, Xiangnv Meng, Yongsheng Li, Fu Mi, Xi Yang, Sha Sha
Immune checkpoint inhibitors (ICIs) have transformed oncologic practice, but their expanding use has heightened concern about potentially fatal cardiovascular toxicity. This bibliometric study mapped the global research landscape and temporal evolution of ICI-associated cardiotoxicity from 2016 to 2025. Records were retrieved from the Web of Science Core Collection on January 1, 2026. After excluding letters, conference abstracts, editorials, and other non-research items, 1,127 original articles and reviews were analyzed. A thesaurus file standardized synonyms, abbreviations, spelling variants, and singular-plural forms before keyword co-occurrence analysis. VOSviewer and CiteSpace were used to evaluate publication trends, collaboration networks, citation structures, keyword clusters, temporal patterns, and burst terms. The corpus involved 67 countries, 2,430 institutions, and 8,842 authors. Annual output increased from 9 publications in 2016 to 236 in 2025, representing a 26.2-fold rise and a compound annual growth rate of 43.8%; cumulative publication output was well fitted by a quadratic polynomial model (R2 = 0.9973). China produced the most publications, whereas the United States achieved the highest citation count. The University of Texas MD Anderson Cancer Center, Javid Moslehi, and Frontiers in Oncology were the leading institution, author, and journal, respectively; The New England Journal of Medicine was the most frequently co-cited journal. Keyword mapping delineated three domains: immune-mediated cardiovascular phenotypes, PD-1/PD-L1-related mechanisms, and multidisciplinary risk management. Temporal and burst analyses indicated a shift from toxicity recognition toward mechanistic elucidation, diagnostic standardization, risk stratification, and cardiovascular outcome assessment. Emerging low-frequency but rapidly strengthening terms highlight growing attention to combination-regimen safety, patient-level risk assessment, evidence synthesis, and long-term cardiovascular outcomes.
Biochemical and biophysical research communicationsGabriela A Galeazzo, Douglas M M Soares, Danilo T Amaral, Patricia Sartorelli, Ana Clara L N Silva, Eliana Samuels, Marcelo R S Melo, Cassius V Stevani, Anders…
Bioluminescence is visible light produced by living organisms through luciferase-catalyzed oxidation of luciferins. Although widespread in anthozoans, the molecular basis of their light emission remains poorly defined. Characterization has focused on Renilla reniformis, leaving anthozoan luciferase diversity underexplored. Here, we report the identification and characterization of a coelenterazine-dependent luciferase from the Murray's sea pen Anthoptilum murrayi (AnmLuc). Transcriptome analysis identified a transcript encoding a ∼35-kDa protein with characteristic motifs. The coding sequence was cloned and the recombinant protein was expressed in Escherichia coli. The reaction catalyzed by the purified enzyme resulted in an intense blue light emission (λmax ≈ 495 nm) in the presence of coelenterazine, with an activity optimum near 15 °C and 30-40% of maximal activity still measurable at 2-5 °C. These findings provide the first molecular characterization of a deep-sea anthozoan luciferase, expanding known diversity, and offering insights into Anthozoan light emission.
Fish & shellfish immunologyXuewu Zhu, Weibin Zhang, Shuang Li, Fangyi Chen, Ke-Jian Wang
Vibrio species are ubiquitous in aquatic environments and represent significant pathogens in marine aquaculture, with Vibrio alginolyticus being a primary threat to farmed aquatic animals. The limited availability of therapeutic drugs in aquaculture, compounded by widespread antibiotic resistance, necessitates the development of new antibacterial strategies. In this study, a previously uncharacterized functional gene, designated as Spamprin, was identified in Scylla paramamosain. Its transcripts exhibited tissue-specific distribution and were markedly upregulated following LPS stimulation. Through bioinformatics analysis and prediction using antimicrobial peptide databases, a truncated peptide, Spamprin4-23 derived from Spamprin was screened. The peptide demonstrated potent antimicrobial activity against a wide range of microorganisms in vitro. Mechanistically, Spamprin4-23 significantly increased bacterial membrane permeability and induced morphological changes in target microorganisms. Importantly, it exhibited no cytotoxic effects against crab hemocytes or mammalian HEK293T cells. Although Spamprin4-23 showed no direct bactericidal activity against V. alginolyticus in vitro, it reduced bacterial burden in host tissues and conferred significant protection, leading to improved survival of V. alginolyticus-challenged mud crabs. This effect was most likely associated with the immunomodulatory activity of the peptide, as evidenced by the modulation of immune-related gene expression. Collectively, these findings suggest that Spamprin4-23 may serve as a promising immunomodulatory agent for disease control in aquaculture, offering a viable alternative to conventional antibiotic-based strategies.
Ophiocordyceps (Ophiocordyceps sinensis) is a precious medicinal and edible fungus widely utilized in nutraceuticals and functional foods. However, the structural intricacies and biological potential of its high-molecular-weight polysaccharides remain largely unknown. In the present study, a novel high-molecular-weight neutral polysaccharide, designated as CSP1b, was isolated and purified from cultured ophiocordyceps via water extraction, ethanol precipitation, and sequential column chromatography. Characterization revealed that CSP1b possesses an extraordinary molecular weight of 2.65 × 107 Da and consists predominantly of glucose (73.98%), mannose (13.35%), and galactose (12.67%). Structural elucidation identified CSP1b as a galactomannoglucan with a backbone of →4)-α-D-Glcp-(1 → 6)-α-D-Glcp-(1→, branched at the O-6 position by side chains containing →6)-α-D-Glcp-(1→, α-D-Manp-(1→, and various galactose residues, resulting in a branching degree of 32.06%. The polysaccharide exhibited a filamentous and ribbon-like intertwined surface morphology. In vitro immunomodulatory assays demonstrated that CSP1b significantly enhanced the proliferation and phagocytic capacity of RAW 264.7 (mouse macrophage cell line), as well as induced the secretion of nitric oxide (NO) and cytokines (TNF-α, IL-6) in a dose-dependent manner. In summary, a novel high-molecular-weight galactomannoglucan (CSP1b) was isolated for the first time from cultured ophiocordyceps and exhibited potent immunostimulatory activity. These findings enrich the polysaccharide library of ophiocordyceps and support its application in immunoregulatory products.
Analytical biochemistryWenbo Zhou, Nguyen Quoc Khanh Le, Matthew Chin Heng Chua
Protein function prediction remains a central problem in bioinformatics, with broad implications for understanding biological processes, disease mechanisms, and drug discovery. Due to the high cost and time required for experimental characterization, only a small fraction of proteins have reliable functional annotations, highlighting the need for accurate computational approaches. Recent advances in protein structure prediction, particularly AlphaFold2, have enabled large-scale access to high-quality three-dimensional structures, creating new opportunities for structure-informed function prediction. In this study, we propose UniRES-GO (Unified Residue-level Early Fusion for Gene Ontology prediction), a novel framework that integrates protein sequence features with AlphaFold2-predicted structural information via residue-level early fusion. The fused representations are modeled as protein contact graphs and processed using a Graph Attention Network to capture both local residue interactions and global structural context, yielding discriminative protein-level embeddings for multi-label function prediction. We evaluate UniRES-GO on a human protein dataset across the three Gene Ontology categories: Biological Process, Cellular Component, and Molecular Function. Experimental results demonstrate that UniRES-GO consistently outperforms representative sequence- and interaction-based methods across multiple evaluation metrics, including Fmax, AUC, and AUPR. In particular, UniRES-GO achieves strong performance in Molecular Function prediction, reaching an AUC of 0.970, while maintaining high stability across multiple runs. Ablation studies further confirm the effectiveness of the residue-level fusion strategy and graph-based modeling. Overall, UniRES-GO provides an effective and generalizable approach for protein function prediction by leveraging predicted structural information, offering practical advantages for annotating proteins lacking homologous sequences or interaction data.
Biochemical and biophysical research communicationsMayu Shibata, Yasuko Kuramitsu, Etsuko T Matsuura, Rumi Kondo, Kei Yura
Respiratory complex I generates proton gradient through coupled NADH: ubiquinone oxidoreduction and proton pumping for ATP synthesis in aerobic respiration. Structural studies showed the involvement of the third transmembrane helix in ND6 subunit (TMH3ND6) in the global open-closed conformational change of RCI was important for the functional coupling. However, the atomistic mechanism for the conformational change of TMH3ND6 remains unclear. Here, we computationally analyzed the network graphs of coevolving residue contacts of the core functional subunits derived from Escherichia coli and Ovis aries. We identified four conserved paths connecting the quinone-binding site and TMH3ND6. Together with structural frustration and genomic variant analyses, we suggest that these paths can transmit structural disturbance upon quinone binding, facilitating the conformational change of TMH3ND6.
Biochemical and biophysical research communicationsWaka Sugiura, Motoko Ikeda, Rina Hamajima
The transcription factor p53 is widely conserved among vertebrates and invertebrates and regulates various stress responses, including apoptosis. p53 proteins identified in the lepidopteran insects Bombyx mori (Bm-p53) and Spodoptera frugiperda exhibit proapoptotic activity through transient expression; however, the mechanism of apoptosis induction by lepidopteran p53 remains unclear, particularly regarding the domains required and the role of transcriptional activity. Here, we investigated the domains required for Bm-p53 activity using transient expression assays with domain/region deletion mutants. Bm-p53 contains three domains-TAD (transcriptional activation domain), DBD (DNA-binding domain), and NLS (nuclear localization signal)-which are conserved in mammalian and Drosophila p53s. However, Bm-p53 lacks an oligomerization domain, which is conserved in the C-terminal region of mammalian and Drosophila p53s. We found that all examined domains/region-TAD, DBD, NLS, and the C-terminal region (CR)-are crucial for the full proapoptotic activity of Bm-p53. Additionally, Bm-p53 can activate transcription from a promoter containing human p53-binding sites. This activity is completely lost in cells expressing Bm-p53 with deletions in the DBD, NLS, and CR, whereas TAD deletion results in a modest reduction. Both the proapoptotic and transcriptional activities were suppressed in Bm-p53 with point mutations corresponding to human p53 mutational hotspots. Collectively, our findings demonstrate that Bm-p53 induces apoptosis primarily through transcriptional activation of downstream genes, requiring nuclear localization via the NLS and DNA binding via the DBD, and supported by the TAD and CR. Notably, transcription-independent mechanisms may also contribute to apoptosis induction, indicating a more complex regulatory model of Bm-p53 function.
Food research international (Ottawa, Ont.)Zhe Liu, Xuetuan Wei, Qingyan Pan, Xifeng Zuo, Ailing Guo
In this study, three novel antimicrobial peptides (AMPs) were isolated and purified from the fermentation supernatant of B. amyloliquefaciens, and their amino acid sequences were identified by LC-MS/MS as LLLLKKPLLL, LLLPKK, and LLLSKKLL, respectively. Among them, AMP hz-01 demonstrated the highest inhibitory effects on L. monocytogenes, with a MIC of 0.12 mg/mL and MBC of 0.98 mg/mL. Its antibacterial mechanism involves disrupting cell membrane integrity, thereby causing cell death. Molecular docking and molecular dynamics simulations suggested that AMP hz-01 may interact with β-ketoacyl-acyl carrier protein synthase III through hydrogen bonding and may associate with the membrane phospholipid bilayer, supporting a proposed dual mechanism of charge-driven membrane targeting and hydrophobicity-induced membrane perturbation. These findings provide a theoretical foundation for the development of AMPs as promising, natural, and effective agents for controlling pathogenic bacteria.