Practical management of chronic breathlessness

Wickham, Helena; Spathis, Anna; Chin, Chloe; Ryan, Richella; Booth, Sara

doi:10.1136/sbmj.h6200

Cited by 4 publications

(3 citation statements)

References 18 publications

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“…The differential abundance of taxa across individual days between co-culture and control samples was identified with metagenomeSeq from the microbiomeMarker R package (v.1.2.2) ( 37 ) with a P -adjusted value cutoff of <0.05. All plots were generated using the ggplot2 (v.3.4.2) ( 38 ) and phylosmith (v.1.0.6) ( 39 ) R packages, and all statistical analyses were performed on RStudio 2022.07.1 Build 554.…”

Section: Methodsmentioning

confidence: 99%

Rhodobacteraceae are key players in microbiome assembly of the diatom Asterionellopsis glacialis

Isaac,

Mohamed,

Amin

2024

Appl Environ Microbiol

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The complex interactions between bacterioplankton and phytoplankton have prompted numerous studies that investigate phytoplankton microbiomes with the aim of characterizing beneficial or opportunistic taxa and elucidating core bacterial members. Oftentimes, this knowledge is garnered through 16S rRNA gene profiling of microbiomes from phytoplankton isolated across spatial and temporal scales, yet these studies do not offer insight into microbiome assembly and structuring. In this study, we aimed to identify taxa central to structuring and establishing the microbiome of the ubiquitous diatom Asterionellopsis glacialis . We introduced a diverse environmental bacterial community to A. glacialis in nutrient-rich or nutrient-poor media in a continuous dilution culture setup and profiled the bacterial community over 7 days. 16S rRNA amplicon sequencing showed that cyanobacteria ( Coleofasciculaceae ) and Rhodobacteraceae dominate the microbiome early on and maintain a persistent association throughout the experiment. Differential abundance, co-abundance networks, and differential association analyses revealed that specific members of the family Rhodobacteraceae , particularly Sulfitobacter amplicon sequence variants, become integral members in microbiome assembly. In the presence of the diatom, Sulfitobacter species and other Rhodobacteraceae developed positive associations with taxa that are typically in high abundance in marine ecosystems ( Pelagibacter and Synechococcus ), leading to restructuring of the microbiome compared to diatom-free controls. These positive associations developed predominantly under oligotrophic conditions, highlighting the importance of investigating phytoplankton microbiomes in as close to natural conditions as possible to avoid biases that develop under routine laboratory conditions. These findings offer further insight into phytoplankton–bacteria interactions and illustrate the importance of Rhodobacteraceae , not merely as phytoplankton symbionts but as key taxa involved in microbiome assembly. IMPORTANCE Most, if not all, microeukaryotic organisms harbor an associated microbial community, termed the microbiome. The microscale interactions that occur between these partners have global-scale consequences, influencing marine primary productivity, carbon cycling, and harmful algal blooms to name but a few. Over the last decade, there has been a growing interest in the study of phytoplankton microbiomes, particularly within the context of bloom dynamics. However, long-standing questions remain regarding the process of phytoplankton microbiome assembly. The significance of our research is to tease apart the mechanism of microbiome assembly with a particular focus on identifying bacterial taxa, which may not merely be symbionts but architects of the phytoplankton microbiome. Our results strengthen the understanding of the ecological mechanisms that underpin phytoplankton–bacteria interactions in order to accurately predict marine ecosystem responses to environmental perturbations.

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Section: Methodsmentioning

confidence: 99%

Rhodobacteraceae are key players in microbiome assembly of the diatom Asterionellopsis glacialis

Isaac,

Mohamed,

Amin

2024

Appl Environ Microbiol

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“…The “limma” R package (v3.44.3) [ 13 ] was used to identify differentially expressed genes (DEGs) between HCM and normal tissues in the GSE36961 dataset with a cutoff value of |log2fold change| > 0.5 and a false discovery rate (FDR) < 0.05, which were visualized using the “ggplot” (v3.3.2) [ 14 ]and “heatmap” R packages (v0.7.7). These were further intersected with the 493 hypoxia-related genes to obtain differentially expressed hypoxia-related genes.…”

Section: Methodsmentioning

confidence: 99%

Identification and analysis of key hypoxia- and immune-related genes in hypertrophic cardiomyopathy

et al. 2023

Biol Res

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Background Hypertrophic cardiomyopathy (HCM), an autosomal dominant genetic disease, is the main cause of sudden death in adolescents and athletes globally. Hypoxia and immune factors have been revealed to be related to the pathology of HCM. There is growing evidence of a role for hypoxia and inflammation as triggers and enhancers in the pathology in HCM. However, the role of hypoxia- and immune-related genes in HCM have not been reported. Methods Firstly, we obtained four HCM-related datasets from the Gene Expression Omnibus (GEO) database for differential expression analysis. Immune cells significantly expressed in normal samples and HCM were then screened by a microenvironmental cell population counter (MCP-counter) algorithm. Next, hypoxia- and immune-related genes were screened by the LASSO + support vector machine recursive feature elimination (SVM-RFE) and weighted gene co-expression network analysis (WGCNA). Single-gene enrichment analysis and expression validation of key genes were then performed. Finally, we constructed a competing endogenous RNA (ceRNA) network of key genes. Results In this study, 35 differentially expressed hypoxia genes were found. By using LASSO + SVM-RFE analysis, 10 more targets with differentially expressed hypoxia genes were identified. The MCP-count algorithm yielded five differentially expressed immune cells, and after assessing them for WGCNA characteristics, 612 immune genes were discovered. When hypoxia and immune genes were combined for cross-tabulation analysis, three hypoxia- and immune-related genes (ATP2A2, DDAH1, and OMA1) were identified. Conclusion Based on hypoxia characteristic genes, three key genes were identified. These were also significantly related to immune activation, which proves a theoretical basis and reference value for studying the relationship between HCM and hypoxia and immunity. Graphical Abstract

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“…DEGs with a P-adjusted (Padj) value less than 0.05 were considered significant. Volcano plots were generated using the R package ggplot2 68 .…”

Section: Methodsmentioning

confidence: 99%

The Novel Role of hnRNP UL1 in Human Cell Nucleoli

Cichocka¹,

Karlik²,

Plewka³

et al. 2022

Int. J. Biol. Sci.

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hnRNP UL1 plays an important role in cell nuclei, where it is recruited to DNA damage sites and is involved in the repair of DNA double-strand breaks. Furthermore, this protein is known as a transcriptional repressor of RNA polymerase II genes. In the present study, we have shown that hnRNP UL1 is also localized in the nucleoli of human cells. Upon investigating its function, we found that hnRNP UL1 stimulates ribosomal DNA (rDNA) gene transcription. Moreover, we observed that cells with hnRNP UL1 silencing exhibited increased sensitivity to DNA damage. We also showed that hnRNP UL1 interacts with γH2A.X, RPA32, XRCC1, and Chk1 in cell nucleoli, suggesting its involvement in the repair of rDNA damage.

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Practical management of chronic breathlessness

Abstract: Breathlessness is a common condition that is often undermanaged and distressing for patients

Cited by 4 publications

References 18 publications

Rhodobacteraceae are key players in microbiome assembly of the diatom Asterionellopsis glacialis

Rhodobacteraceae are key players in microbiome assembly of the diatom Asterionellopsis glacialis

Identification and analysis of key hypoxia- and immune-related genes in hypertrophic cardiomyopathy

The Novel Role of hnRNP UL1 in Human Cell Nucleoli

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