Transcriptome profiling of lung immune responses potentially related to acute respiratory distress syndrome in forest musk deer
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA790817 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR17278317_1.fastq.gz | Fastqsanger.gz | |||
| SRR17278317_2.fastq.gz | Fastqsanger.gz | |||
| SRR17278318_1.fastq.gz | Fastqsanger.gz | |||
| SRR17278318_2.fastq.gz | Fastqsanger.gz | |||
| SRR17278319_1.fastq.gz | Fastqsanger.gz |
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Project description:ARDS-mediated lung transcriptome alterations were identified in forest musk deer. Moreover, multiple transcripts/genes involved in lung development and lung defense responses to bacteria/viruses/fungi in ARDS were filtered out in forest musk deer.
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Project description:The Chinese forest musk deer (FMD; Moschus berezovskii) is an endangered artiodactyl mammal. Musk secreted by the musk gland of male FMD has extremely high economic and medicinal value. At present, little is known about the development of musk glands and the molecular mechanism of musk secretion. In the present research, using snRNA-seq and snATAC-seq association analysis performed on musk glands of forest musk deer, coupled with several bioinformatics analyses, the dynamic transcriptional cell atlas of musk gland development was revealed and the genes and transcription factors affecting musk secretion were determined. Based on uniform manifold approximation and projection (UMAP) analysis, we identified 12 cell types from musk glands, including two different acinar cells (clusters 0 and 10). In addition, the expression of core target genes and core transcription factors was verified by fluorescence in situ hybridization and immunohistochemistry. Combined with weighted gene co-expression network analysis (WGCNA), we obtained a deeper biological understanding of the relationship between core transcription factors, differentially expressed genes and musk secretion related pathways. This study lays a foundation for improving musk yield and meeting market demand. In the meantime, it also contributes to reducing the hunting and poaching of wild forest musk deer, protecting forest musk deer resources and maintaining ecological balance.
2023-08-31 | GSE182087 | GEO
Project description:Pneumonia can seriously threaten the life of forest musk deer (an endangered species). To gain a comprehensive understanding of pneumonia pathogenesis in forest musk deer, iTRAQ-based proteomics analysis was performed in diseased (Phe group) and normal (Ctrl group) lung tissues of forest musk deer that died of pneumonia. Results showed that 355 proteins were differentially expressed (fold change ≥ 1.2 and Q < 0.05) in Phe vs Ctrl experiments. GO/KEGG annotation and enrichment analyses showed that dysregulated proteins might play vital roles in bacterial infection and immunity. Given the close association of bacterial infection and pneumonia, 32 dysregulated proteins related to Staphylococcus aureus infection, bacterial invasion of epithelial cells, and pathogenic Escherichia coli infection were screened out. Among these 32 proteins, 13 proteins were mapped to the bovine genome. Given the close phylogenetic relationships of forest musk deer and bovine, the protein-protein interaction networks of the above-ment
2022-10-23 | PXD031240 |
Project description:BackgroundForest musk deer is an endangered species globally. The death of captive forest musk deer can be caused by certain respiratory system diseases. Acute respiratory distress syndrome (ARDS) is a huge threat to the life of forest muck deer that breed in our department.MethodsLung histopathologic analysis was conducted by hematoxylin and eosin (HE) staining. The lung gene changes triggered by ARDS were examined by RNA sequencing and related bioinformatics analysis in forest musk deer. The potential functions of unigenes were investigated by NR, SwissProt KOG, GO, and KEGG annotation analyses. Vital biological processes or pathways in ARDS were examined by GO and KEGG enrichment analyses.ResultsA total of 3265 unigenes were differentially expressed (|log2fold-change|> 2 and adjusted P value < 0.01) in lung tissues of 3 forest musk deer with ARDS compared with normal lung tissues of the non-ARDS group. These differentially expressed unigenes (DEGs) played crucial roles in immunity and defense responses to pathogens. Moreover, we identified the DEGs related to one or more of the following biological processes: lung development, immunity, and bacterial/viral/fungal infection. And six DEGs that might be involved in lung injury caused by immune dysregulation or viral/fungal infection were identified.ConclusionARDS-mediated lung gene alterations were identified in forest musk deer. Moreover, multiple genes involved in lung development and lung defense responses to bacteria/viruses/fungi in ARDS were filtered out in forest musk deer.
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Project description:Single-nucleus transcriptomics and chromatin accessibility analysis of musk gland in Chinese forest musk deer
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Project description:The musk gland in an adult male forest musk deer is an organ that synthesizes, stores, and secretes musk, a cream-colored liquid upon initial secretion that gradually transforms into a blackish-brown solid substance upon full maturation. In this study, four healthy adult male forest musk deer were selected and a total of 12 musk samples were collected for analysis. The samples were in three different states depending on the different seasonal collection dates, which were in June, August, and October. High-throughput 16S-rRNA gene sequencing technology was used to detect microbiota changes in the gland. The results indicate that microbial richness gradually declined during the musk maturation process. The microbiota composition between the initial liquid and final solid musk samples was varied significantly (P < 0.05). The dominant bacterial phyla were similar at all three stages included Firmicutes, Proteobacteria, Actinobacteria, and Bacteroidetes. However, the abundances were differences in terms of the dominant bacterial genera. PICRUSt analysis showed the highest represented category was "Amino acid transport and metabolism" (24.8%), followed by "Transcription" (22.04%), and "Carbohydrate transport and metabolism" (20.74%). Our findings indicate that the microbiota in the musk gland plays an important role in the maturation process of musk.
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Project description:Musk microbiota from the Chinese forest musk deer strain:Firmicutes, Actinobacteria, Fusobacteria, Proteobacteria, Euryarchaeota, Bacteroidetes | isolate:mated or unmated | breed:Corynebacterium, Fusobacterium, Jeotgalicoccus, Mannheimia and Planomicrobium | cultivar:musk microbiota Raw sequence reads
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Project description:Male musk deer secrete musk from the musk gland located between their naval and genitals. Unmated male forest musk deer generate a greater amount of musk than mated males, potentially allowing them to attract a greater number of females. In this study, we used gas chromatography and mass spectrometry (GC/MS) to explore musk chemical composition of the musk pods of captive mated and unmated sexually mature Chinese forest musk deer and used next-generation sequencing to intensively survey the bacterial communities within them. Analysis of the chemical composition of the musk showed that unmated males have more muscone and cholesterol. Features of the musk16S rRNA gene showed that mated Chinese forest musk deer have both a greater Shannon diversity (p < 0.01) and a greater number of estimated operational taxonomic units than unmated ones; many bacterial genera were overrepresented in unmated Chinese forest musk deer males. Members of these genera might be involved in musk odor fermentation. PICRUSt analysis revealed that metabolic pathways such as aldosterone-regulated sodium reabsorption, metabolism of terpenoids and polyketides, flavone and flavonol biosynthesis, and isoflavonoid biosynthesis were enriched in the musk of unmated Chinese forest musk deer males.
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Project description:Forest musk deer is the most important animal for natural musk production, and the musk composition changes periodically during musk secretion, accompanied by variation in the com-position of deer-symbiotic bacteria. GC-MS and 16S rRNA sequencing were conducted in this study, the dynamic changes to correlated chemical composition and the microbiota across musk secretion periods (prime musk secretion period, vigorous musk secretion period and late musk secretion period) were investigated by integrating its serum testosterone level in different mating states. Results showed that the testosterone level, musk composition and microbiota changed with annual cycle of musk secretion and affected by its mating state. Muscone and the testosterone level peaked at vigorous musk secretion period, and the microbiota of this stage was distinct from the other 2 periods. Actinobacteria, Firmicutes and Proteobacteria were dominant bacteria across musk secretion period. PICRUSt analysis demonstrated that bacteria were ubiquitous in musk pod and involved in the metabolism of antibiotics and terpenoids in musk. "Carbohydrates and amino acids," "fatty acids and CoA" and "secretion of metabolites" were enriched at 3 periods, respectively. Pseudomonas, Corynebacterium, Clostridium, Sulfuricurvum were potential biomarkers across musk secretion. This study provides a more comprehensive understanding of genetic mechanism during musk secretion, emphasizing the importance of Actinobacteria and Corynebacterium in the synthesis of muscone and etiocholanone during musk secretion, which required further validation.
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Project description:The development of the neuromuscular synapse depends on signaling processes which involve protein phosphorylation as a crucial regulatory event. The receptor tyrosine kinase MuSK is the key signaling molecule at the neuromuscular synapse whose activity is required for the formation of a mature and functional neuromuscular synapse. However, the signaling cascade downstream of MuSK and the regulation of the different components is still poorly understood. Here we present data from a quantitative phosphoproteomics approach to study MuSK-dependent processes. Muscle cells were stimulated with the heparansulfate proteoglycan agrin, which activates MuSK and downstream signaling events. To get an insight into the signaling dynamics we used three different time points (unstimulated, 15 min, 60 min and 4 hrs).
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