bluuebunny/crossref_metadata_2025_split huggingface dataset:
Helicase protein DDX11 as a novel antiviral factor promoting RIG-I-MAVS-mediated signaling pathway
Authors: Zhang Jiyu , Zhang Liaoyuan , Liu Dakai , Shi Hongyan , Zhang Xin , Chen Jianfei , Yang Xiaoman , Zeng Miaomiao , Zhang Jialin , Feng Tingshuai , Zhu Xiaoyuan , Jing Zhaoyang , Ji Zhaoyang , Shi Da , Feng Li 
Published: October 2024

ABSTRACT

Type Ι interferon (IFN) production mediated by retinoic acid-inducible gene 1 (RIG-I) and mitochondrial antiviral signaling protein (MAVS) is essential for antiviral innate immune responses. Here, we report the identification of a novel co-sensor for cytosolic nucleic acids: DEAD/H-box helicase 11 (DDX11), a member of the DExD/H (Asp-Glu-x-Asp/His)-box helicase family. Knockdown or knockout of DDX11 attenuated the ability of cells to increase IFN-β, IFN-stimulated gene 56, and C-X-C motif chemokine ligand 10 in response to SeV and poly (I:C) by blocking the activation of TANK-binding kinase 1 and IFN regulatory factor 3. Nucleic acid sensing by DDX11 was independent of the stimulator of IFN genes but was dependent on RIG-I and MAVS. DDX11 regulated RIG-I-MAVS-mediated IFN signaling by specifically interacting with nucleic acid, RIG-I, and MAVS to enhance RIG-I-double-strand RNA and RIG-I-MAVS binding affinity. Overall, our results identified a critical role for DDX11 in the innate immune response and provided molecular insights into the mechanisms by which DDX11 recognized cytosolic nucleic acid and interacted with RIG-Ι and MAVS for potent IFN signaling and antiviral immunity.

IMPORTANCE
Innate immunity is the first and most rapid host defense against virus infection. Recognition of viral RNA by the retinoic acid-inducible gene 1 (RIG-I)-like receptors (RLRs) initiates innate antiviral immune responses. How the binding of viral RNA to and activation of the RLRs are regulated remains enigmatic. In this study, we identified DEAD/H-box helicase 11 (DDX11) as a positive regulator of the RIG-I-mitochondrial antiviral signaling protein (MAVS)-mediated signaling pathways. Mechanistically, we demonstrated that DDX11 bound to viral RNA, interacted with RIG-I, and promoted their binding to viral RNA. DDX11 also promoted the interaction between RIG-I and MAVS and activation of RIG-I-MAVS signaling. Overall, our results elucidate the role of DDX11 in RIG-I-MAVS-dependent signaling pathways and may shed light on innate immune gene regulation.
S-palmitoylation of MAP kinase is essential for fungal virulence
Authors: Duan Yuhang , Li Pingping , Zhang Deyao , Wang Lili , Fang Yuan , Hu Hong , Mao Qiulu , Zhou Xiaolan , Zhao Panpan , Li Xuechun , Wei Jinfeng , Tang Jintian , Pan Li , Liu Hao , Chen Xiaolin , Chen Xiaoyang , Hsiang Tom , Huang Junbin , Zheng Lu 
Published: October 2024

ABSTRACT

S-palmitoylation is an important reversible protein post-translational modification in organisms. However, its role in fungi is uncertain. Here, we found the treatment of the rice false fungus
Ustilaginoidea virens
with S-palmitoylation inhibitor 2 BP resulted in a significant decrease in fungal virulence. Comprehensive identification of S-palmitoylation sites and proteins in
U. virens
revealed a total of 4,089 S-palmitoylation sites identified among 2,192 proteins and that S-palmitoylated proteins were involved in diverse biological processes. Among the five palmitoyltransferases, UvPfa3 and UvPfa4 were found to regulate the pathogenicity of
U. virens
. We then performed quantitative proteomic analysis of ∆
UvPfa3
and ∆
UvPfa4
mutants. Interestingly, S-palmitoylated proteins were significantly enriched in the mitogen-activated protein kinase and autophagy pathways, and MAP kinase UvSlt2 was confirmed to be an S-palmitoylated protein which was palmitoylated by UvPfa4. Mutations of S-palmitoylation sites in
UvSlt2
resulted in significantly reduced fungal virulence and decreased kinase enzymatic activity and phosphorylation levels. Simulations of molecular dynamics demonstrated mutation of S-palmitoylation sites in
UvSlt2
causing decreased hydrophobic solvent-accessible surface area, thereby weakening the bonding force with its substrate UvRlm1. Taken together, S-palmitoylation promotes
U. virens
virulence through palmitoylation of MAP kinase UvSlt2 by palmitoyltransferase UvPfa4. This enhances the enzymatic phosphorylation activity of the kinase, thereby increasing hydrophobic solvent-accessible surface area and binding activity between the UvSlt2 enzyme and its substrate UvRlm1. Our studies provide a framework for dissecting the biological functions of S-palmitoylation and reveal an important role for S-palmitoylation in regulating the virulence of the pathogen.

IMPORTANCE

S-palmitoylation is an important post-translational lipid modification of proteins. However, its role in fungi is uncertain. In this study, we found that S-palmitoylation promotes virulence of rice false smut fungus
U. virens
through palmitoylation of MAP kinase UvSlt2 by palmitoyltransferase UvPfa4. This enhances the enzymatic phosphorylation activity of the kinase, thereby increasing hydrophobic solvent-accessible surface area and binding activity between the UvSlt2 enzyme and its substrate UvRlm1. Our studies provide a framework for dissecting the biological functions of S-palmitoylation and reveal an important role for S-palmitoylation in regulating the virulence of the pathogen. This is the first functional study to reveal the role of S-palmitoylation in fungal virulence.
Complete genome sequence of
Bulleidia
sp. 10714-15 isolated from human colon cancer patients
Authors: Ikeda Haruto , Oshibuchi Kota , Yang Jiayue , Fukuda Shinji , Arakawa Kazuharu 
Published: October 2024

ABSTRACT

Bulleidia
sp. is a non-spore-forming, obligatory anaerobic, Gram-positive bacterium isolated from the stool samples of human colon cancer patients. We report the complete genome sequence of
Bulleidia
sp. 10714-15, comprising a single linear chromosome of 2,218,984 bp with a G + C content of 36.6%.
Surfactin from
Bacillus subtilis
enhances immune response and contributes to the maintenance of intestinal microbial homeostasis
Authors: Jia Junpeng , Fu Mei , Ji Wenxin , Xiong Ningna , Chen Peng , Lin Jian , Yang Qian 
Published: October 2024

ABSTRACT

Surfactin, a lipopeptide biosurfactant produced by
Bacillus
spp., has emerged as a promising bioactive compound due to its potent inhibitory effects on bacterial and viral pathogens. This showcases its potential as a non-antibiotic strategy for managing infectious diseases. Our investigation reveals that surfactin administration significantly promotes weight gain and improves immune organ indices in mice, reflecting enhanced immunity and gut health. Surfactin augments phagocytic function in peritoneal macrophages and boosts proliferative responses in splenic lymphocytes post-chicken red blood cell immunization. Furthermore, it increases intestinal villi height, indicative of superior nutrient absorption. It elevates mucin secretion and expression of intestinal mucosal proteins, such as secretory IgA, Muc1, and Muc2, and tight junction proteins claudin-1, occludin, and Zo-1 in the jejunum and colon. Crucially, surfactin modifies the gut microbiota composition by reducing
Escherichia coli
populations and ameliorating cyclophosphamide-induced gut dysbiosis. Our data suggest that oral surfactin could be a valuable therapeutic modality to alleviate immune suppression and gut damage, proposing a new pathway for immunomodulatory treatment.

IMPORTANCE
The potential of surfactin as a microbial surfactant extends beyond its surfactant properties, impacting immune regulation and gut health. As the need for alternatives to traditional antibiotics continues to grow, surfactin’s ability to enhance host defense mechanisms against common pathogens without directly targeting them with antibiotics offers a strategic advantage. Understanding how surfactin shapes the immune landscape and the gut microbiome can inform innovative interventions against immunosuppression and intestinal impairment, particularly in contexts such as cyclophosphamide-induced toxicity.
Characterization of cross-reactive, non-neutralizing monoclonal antibodies against a pandemic GII.4 norovirus variant
Authors: Ford-Siltz Lauren A. , Tohma Kentaro , Kihn Kyle , Kendra Joseph A. , Deredge Daniel , Wintrode Patrick , Gao Yamei , Parra Gabriel I. 
Published: October 2024

ABSTRACT

Antibodies are thought to play a major role in protection against human norovirus infection. Mouse humoral responses closely mimic those of humans; thus, mouse models are used to characterize norovirus epitopes on the major viral capsid protein, VP1. We have developed a panel of mouse monoclonal antibodies (mAbs) produced against the last pandemic variant to emerge, Sydney 2012. While most mAbs (25/44) were mapped to variable antigenic sites on VP1, 19 of the mAbs were cross-reactive against multiple genotypes or GII.4 variants. Most (12/19) of the cross-reactive mAbs bound to the Shell domain and were cross-reactive with different GII noroviruses. Interestingly, mAb 30A11 exhibited cross-reactivity against all tested norovirus genotypes (GI, GII, GIV, and GIX). This mAb was mapped to a highly conserved region of the Shell domain (
51
PIDPWII
57
) using peptide ELISA and immunofluorescence. Of those mapping to the Protruding (P) domain, two (19C10 and 14B11) showed cross-reactivity with GII noroviruses. Using hydrogen-deuterium exchange mass spectrometry, we mapped 19C10 to a conserved region of the P domain near the P/Shell interface, which explains its cross-reactivity with different GII noroviruses and lack of histo-blood group antigen-blocking activity. Binding and mutational analyses showed that residues 518, 519, and 525 are important for 19C10 and 14B11 epitope recognition. While the antibodies described here are mostly non-neutralizing, they can be useful tools for research and diagnostics of noroviruses. The role of non-neutralizing, cross-reactive antibodies targeting different areas of the viral capsid merits further research to facilitate our understanding of immunity to norovirus infection and disease.

IMPORTANCE
To gain insights into the overall immune responses to human norovirus, we characterized non-neutralizing, cross-reactive monoclonal antibodies (mAbs) developed against a pandemic GII.4 norovirus. We determined the binding epitope of an antibody that exhibited cross-reactivity against all tested noroviruses, which makes it a useful tool for research and diagnostics. The epitope of two additional non-neutralizing mAbs was mapped to a less conserved region on the viral capsid protein, explaining their cross-reactivity patterns. Often overlooked, the role of non-neutralizing, cross-reactive mAbs merits further research to facilitate our understanding of immunity to norovirus infection and disease.
Biofilm-mediated antibiotic tolerance in
Staphylococcus aureus
from spinal cord stimulation device-related infections
Authors: Sivori Francesca , Cavallo Ilaria , Truglio Mauro , Pelagalli Lorella , Mariani Valerio , Fabrizio Giorgia , Abril Elva , Santino Iolanda , Fradiani Piera Assunta , Solmone Mariacarmela , Pimpinelli Fulvia , Toma Luigi , Arcioni Roberto , De Blasi Roberto Alberto , Di Domenico Enea Gino 
Published: October 2024

ABSTRACT

Staphylococcus aureus
is a predominant cause of infections in individuals with spinal cord stimulation (SCS) devices. Biofilm formation complicates these infections, commonly requiring both surgical and antibiotic treatments. This study explored the biofilm matrix composition and antimicrobial susceptibility of planktonic and biofilm-growing
S. aureus
isolates from individuals with SCS-related infections. Whole-genome sequencing (WGS) examined genotypes, virulome, resistome, and the pan-genome structure. The study also analyzed biofilm matrix composition, early surface adhesion, hemolytic activity, and antibiotic-susceptibility testing. WGS revealed genetic diversity among isolates. One isolate, though oxacillin susceptible, contained the
mec
A gene. The median number of virulence factor genes per isolate was 58. All isolates harbored the biofilm-related
ica
A/D genes. When assessing phenotypic characteristics, all strains demonstrated the ability to form biofilms
in vitro
. The antimicrobial susceptibility profile indicated that oxacillin, rifampin, and teicoplanin showed the highest efficacy against
S. aureus
biofilm. Conversely, high biofilm tolerance was observed for vancomycin, trimethoprim/sulfamethoxazole, and levofloxacin. These findings suggest that
S. aureus
isolates are highly virulent and produce robust biofilms. In cases of suspected biofilm infections caused by
S. aureus
, vancomycin should not be the primary choice due to its low activity against biofilm. Instead, oxacillin, rifampin, and teicoplanin appear to be more effective options to manage SCS infections.

IMPORTANCE

SCS devices are increasingly used to manage chronic pain, but infections associated with these devices, particularly those caused by
Staphylococcus aureus
, present significant clinical challenges. These infections are often complicated by biofilm formation, which protects bacteria from immune responses and antibiotic treatments, making them difficult to eradicate. Understanding the genetic diversity, virulence, and biofilm characteristics of
S. aureus
isolates from SCS infections is critical to improving treatment strategies. Our study highlights the need to reconsider commonly used antibiotics like vancomycin, which shows reduced activity against biofilm-growing cells. Identifying more effective alternatives, such as oxacillin, rifampin, and teicoplanin, provides valuable insight for clinicians when managing biofilm-related
S. aureus
infections in patients with SCS implants. This research contributes to the growing evidence that biofilm formation is crucial in treating device-related infections, emphasizing the importance of tailoring antimicrobial strategies to the biofilm phenotype.
Integrated multi-omics analysis of the microbial profile characteristics associated with pulmonary arterial hypertension in congenital heart disease
Authors: Xie Jiahui , Zhang Xiaoyu , Cheng Liming , Deng Yao , Ren Haobo , Mu Minghua , Zhao Liang , Mu Chunjie , Chen Jiaxiang , Liu Kai , Ma Runwei 
Published: October 2024

ABSTRACT

Dysregulation of immune and inflammatory cells around blood vessels and metabolic dysfunction are key mechanisms in the development of pulmonary arterial hypertension (PAH). The homeostasis of the human microbiome plays a crucial role in regulating immune responses and the progression of diseases. For pulmonary arterial hypertension associated with congenital heart disease involving body-lung shunt (PAH-CHD), the potential impact of the microbiome on the “gut-lung axis” remains underexplored. This study recruited 15 healthy individuals and 15 patients with pulmonary arterial hypertension due to congenital heart disease from Fuwai Yunnan Hospital, Chinese Academy of Medical Sciences, and Kunming Children's Hospital. We performed differential analyses of metabolites and microbiota from both the gut and lower respiratory tract for these two groups. The goal was to investigate the “gut-lung axis” microbiome and metabolome profiles in children with PAH-CHD and to analyze the interrelationships between these profiles. Ultimately, we aim to propose the potential value of these profiles in aiding diagnosis. The results indicated that the gut and pulmonary microbiota of children with PAH-CHD are characterized by an increased abundance of beneficial symbionts, which are closely linked to changes in the metabolome. Metabolite functional enrichment analysis revealed energy metabolism reprogramming in the PAH-CHD group, with active metabolic pathways associated with bile acid secretion and carnitine homeostasis. Moreover, the differential expression of metabolites was correlated with right heart function and growth development.

IMPORTANCE
Previous studies have primarily focused on the relationship between the gut microbiome and PAH. However, the impact of microbial homeostasis on the progression of PAH-CHD from the perspective of the gut-lung axis has not been adequately elucidated. Our study utilizes an integrated multi-omics approach to report on the differential characteristics of gut and lung microbiota between children with PAH-CHD and reference subjects. We found that microbiota influence the pathological changes and disease manifestations of PAH-CHD through their metabolic activity. Additionally, alterations in metabolites impact the microbial ecological structure. Our findings suggest that modulating the microbiome composition may have positive implications for maintaining and regulating the immune environment and pathological progression of PAH-CHD.
Real-time plasmid transmission detection pipeline
Authors: Scherff Natalie , Rothgänger Jörg , Weniger Thomas , Mellmann Alexander , Harmsen Dag 
Published: October 2024

ABSTRACT

The spread of antimicrobial resistance among bacteria by horizontal plasmid transmissions poses a major challenge for clinical microbiology. Here, we evaluate a new real-time plasmid transmission detection pipeline implemented in the SeqSphere
+
(Ridom GmbH, Münster, Germany) software. Within the pipeline, a local Mash plasmid database is created, and Mash searches with a distance threshold of 0.001 are used to trigger plasmid transmission early warning alerts (EWAs). Clonal transmissions are detected using core-genome multi-locus sequence typing allelic differences. The tools MOB-suite, NCBI AMRFinderPlus, CGE MobileElementFinder, pyGenomeViz, and MUMmer, integrated in SeqSphere+, are used to characterize plasmids and for visual pairwise plasmid comparisons, respectively. We evaluated the pipeline using published hybrid assemblies (Oxford Nanopore Technology/Illumina) of a surveillance and outbreak data set with plasmid transmissions. To emulate prospective usage, samples were imported in chronological order of sampling date. Different combinations of the user-adjustable parameters sketch size (1,000 vs 10,000) and plasmid size correction were tested, and discrepancies between resulting clusters were analyzed with Quast. When using a sketch size of 1,000 with size correction turned on, the SeqSphere
+
pipeline agreed with the published data and produced the same clonal and carbapenemase-carrying plasmid clusters. EWAs were in the correct chronological order. In summary, the developed pipeline presented here is suitable for integration into clinical microbiology settings with limited bioinformatics knowledge due to its automated analyses and alert system, which are combined with the GUI-based SeqSphere
+
platform. Thus, with its integrated sample database, (near) real-time plasmid transmission detection is within reach in bacterial routine-diagnostic settings when long-read sequencing is employed.

IMPORTANCE

Plasmid-mediated spread of antimicrobial resistance is a major challenge for clinical microbiology, and monitoring of potential plasmid transmissions is essential to combat further dissemination. Whole-genome sequencing is often used to surveil nosocomial transmissions but usually limited to the detection of clonal transmissions (based on chromosomal markers). Recent advances in long-read sequencing technologies enable full reconstruction of plasmids and the detection of very similar plasmids, but so far, easy-to-use bioinformatic tools for this purpose have been missing. Here, we present an evaluation of an innovative real-time plasmid transmission detection pipeline. It is integrated into the GUI-based SeqSphere
+
software, which already offers core-genome multi-locus sequence typing-based pathogen outbreak detection. It requires very limited bioinformatics knowledge, and its database, automated analyses, and alert system make it well suited for prospective clinical application.
Making medical education great again: analysing trainee feedback to identify key drivers of trainee satisfaction and improve experience
Authors: Ferin Katheryn , Hufflett Tony , Rance Thomas , Round Jonathan 
Published: October 2024

ObjectivesThe London School of Paediatrics (LSP) surveys trainees annually regarding their training placements. There is a wide variation in satisfaction. We explored the last 5 years of data to identify trends and determine predictors of overall trainee satisfaction.MethodsThe survey is distributed annually to all London paediatric trainees with response rates of 86–90%. It explores overall placement satisfaction, followed by key questions covering staffing, supervision, teaching, facilities and other facets. The survey blends both quantitative and qualitative feedback.Satisfaction levels were analysed using time series trend analysis. Overall levels were compared using t-tests. Associations between satisfaction and components of the survey were identified using a convergence of multiple regression and other multivariate analyses.ResultsOverall trainee satisfaction increased steadily until 2020. There was a considerable variation across sites, some having consistently higher or lower scores than the median, while others showed an upward or downward trend, or very variable pattern.By training levels, ST3 trainees consistently rated their placement below average and ST7 trainees above average. There was also a considerable variation in responses by training level with regard to perceived staffing levels and teaching.To understand the influences on overall satisfaction, regression coefficients were derived between specific metrics and overall satisfaction using multiple regression and then normalised to 100%. The explanatory power of this list to explain satisfaction overall is high at 82% R2.Trainee satisfaction was most strongly correlated with workplace atmosphere and consultant support. Staffing, educational supervision, facilities and wider MDT (Multidisciplinary Team) support are associated with overall satisfaction, but to a lesser degree.ConclusionsTrainee satisfaction is crucial, affecting patient safety, retention and trainee mental health. Our analysis identified significant associations with satisfaction including modifiable elements such as consultant engagement and team morale. Staffing levels were less related to satisfaction than expected.Experimental data exploring the components of clinical training in real-world situations are lacking. These data use the natural experiment of placing trainees in different training locations to explore the factors that relate to their overall experience.