Red panda and ferret
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1098497 | ENA |
REPOSITORIES: ENA
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Project description:we applied RNA-seq to detect novel expressed transcripts in 12 tissues of giant pandas, using a transcriptome reconstruction strategy combining reference-based and de novo methods. Then we used mass spectrometry method to identify proteomes of five selected tissues, aiming at validating these novel full-length genes we identified.
2015-12-23 | PXD002917 | Pride
Project description:The giant panda (Ailuropoda melanoleuca) stands as a flagship and umbrella species, symbolizing global biodiversity. While traditional assisted reproductive technology faces constraints in safeguarding the genetic diversity of giant pandas and bolstering the population size of giant pandas, induced pluripotent stem cells (iPSCs) known for their capacity to differentiate into diverse cells types, including germ cells, present a transformative potential for conservation of endangered animals. In our study, we isolated primary fibroblast cells from an individual giant panda and successfully generated giant panda induced pluripotent stem cells (GPiPSCs) through a non-integrating episomal vectors reprogramming method. Characterization of these GPiPSCs revealed their state of primed pluripotency and demonstrated their potential for differentiation. Furthermore, we innovatively formulated a species-specific chemically defined FACL medium and unraveled the intricate signaling pathway networks responsible for maintaining the pluripotency and fostering cell proliferation of GPiPSCs. This study provides key insights into rare species iPSCs, offering materials for panda characteristics research and laying the groundwork for in vitro giant panda gamete generation, potentially aiding endangered species conservation.
2024-09-25 | GSE250292 | GEO
Project description:Many patients who are diagnosed with coronavirus disease 2019 (COVID-19) suffer from venous thromboembolic complications despite the use of stringent anticoagulant prophylaxis. Studies on the exact mechanism(s) underlying thrombosis in COVID-19 are limited as animal models commonly used to study venous thrombosis pathophysiology (i.e. rats and mice) are naturally not susceptible to Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Ferrets are susceptible to SARS-CoV-2 infection, successfully used to study virus transmission, and were previously used to study activation of coagulation and thrombosis during influenza virus infection. Here, we used plasma and lung material from SARS-CoV-2-inoculated ferrets to explore their use in studying COVID-19-associated changes in coagulation and thrombosis. Lungs of ferrets inoculated intranasally with SARS-CoV-2 demonstrated alveolar septa that were mildly expanded by macrophages, and diffuse interstitial histiocytic pneumonia. However, no macroscopical or microscopical evidence of vascular thrombosis in the lungs of SARS-CoV-2-inoculated ferrets was found. Longitudinal plasma profiling using a mass spectrometry-based approach revealed minor differences in plasma protein profiles in SARS-CoV-2-inoculated ferrets up to 2 weeks post-infection. Apart from fibrinogen, the majority of plasma coagulation factors were stable and demonstrated a low coefficient of variation. We conclude that while ferrets are an essential and well-suited animal model to study SARS-CoV-2 transmission, their use to study SARS-CoV-2-related changes relevant to thrombotic disease is limited.
2022-07-19 | PXD027582 | Pride
Project description:Influenza A viruses (IAVs) present major public health threats from annual seasonal epidemics and pandemics as well as from viruses adapted to a variety of animals including poultry, pigs, and horses. Vaccines that broadly protect against all such IAVs, so-called “universal” influenza vaccines, do not currently exist, but are urgently needed. Here, we demonstrated that an inactivated, multivalent whole virus vaccine, delivered intramuscularly or intranasally, was broadly protective against challenges with multiple IAV hemagglutinin and neuraminidase subtypes in both mice and ferrets. The vaccine is comprised of four beta-propiolactone-inactivated low pathogenicity avian influenza A virus subtypes of H1N9, H3N8, H5N1, or H7N3. Vaccinated mice and ferrets demonstrated substantial protection against a variety of IAVs, including the 1918 H1N1 strain, the highly pathogenic avian H5N8 strain, and H7N9. We also observed protection against challenge with antigenically variable and heterosubtypic avian, swine, and human viruses. Compared to mock vaccinated animals, vaccinated mice and ferrets demonstrated marked reductions in viral titers, lung pathology, and host inflammatory responses. This vaccine approach indicates the feasibility of eliciting broad, heterosubtypic IAV protection and identifies a promising candidate for influenza vaccine clinical development.
2022-07-21 | GSE205840 | GEO
Project description:Severe fever with thrombocytopenia syndrome phlebovirus (SFTSV), listed in the WHO most dangerous pathogens, has 12-30% fatality rates with a characteristic thrombocytopenia syndrome. With a majority of clinically diagnosed SFTSV patients older than ~50 years, age is a critical risk factor for SFTSV morbidity and mortality. Here, we report an age-dependent ferret model of SFTSV infection and pathogenesis that fully recapitulates the clinical manifestations of human infections. While young adult ferrets (≤2 years old) did not show any clinical symptoms and mortality, SFTSV-infected aged ferrets (≥4 years old) demonstrated severe thrombocytopenia, reduced white blood cells, and high fever with 93% mortality rate. Moreover, significantly higher viral load was observed in aged ferrets. Transcriptome analysis of SFTSV-infected young ferrets revealed strong interferon-mediated anti-viral signaling, whereas inflammatory immune responses were markedly upregulated and persisted in aged ferrets. Thus, this immunocompetent age-dependent ferret model should be useful for anti-SFTSV therapy and vaccine development.
2018-10-30 | GSE121911 | GEO
Project description:Gonadectomy (GDX) induces sex steroid-producing adrenocortical tumors in certain mouse strains and in the domestic ferret. Complementary approaches, including DNA methylation mapping and microarray expression profiling, were used to identify novel genetic and epigenetic markers of GDX-induced adrenocortical neoplasia in female DBA/2J mice. Markers were validated by quantitative RT-PCR, laser capture microdissection, in situ hybridization, and immunohistochemistry. Two genes with hypomethylated promoters, Igfbp6 and Foxs1, were upregulated in post-GDX adrenocortical neoplasms. The neoplastic cells also exhibited hypomethylation of the fetal adrenal enhancer of Sf1, an epigenetic signature that typifies descendants of fetal adrenal rather than gonadal cells. Expression profiling demonstrated upregulation of gonadal-like genes, including Spinlw1, Insl3, and Foxl2, in GDX-induced adrenocortical tumors of the mouse. One of these markers, FOXL2, was detected in adrenocortical tumor specimens from gonadectomized ferrets. These new markers may prove useful for studies of steroidogenic cell development and for diagnostic testing. Total RNA extracted from whole adrenal glands of gonadectomized and non-gonadectomized mice.
2014-07-31 | E-GEOD-54393 | biostudies-arrayexpress
Project description:Speciation leads to adaptive changes in organ cellular anatomy and physiology. These evolutionary changes create challenges for studying rare cell type functions that diverge between human and mice. Rare CFTR-rich pulmonary ionocytes exist throughout the cartilaginous airways of humans, but limited presence and divergent biology in the proximal trachea of mice has prevented the use of traditional transgenic models to elucidate ionocyte functions in the airway. Here we describe the creation and use of novel conditional genetic ferret models to dissect pulmonary ionocyte biology and function by enabling ionocyte lineage tracing (FOXI1-CreERT2::ROSA-TG), ionocyte ablation (FOXI1-KO), and ionocyte-specific deletion of CFTR (FOXI1-CreERT2::CFTRL/L). By comparing these models to cystic fibrosis (CF) ferrets, we demonstrate that ionocytes control airway surface liquid (ASL) absorption, secretion, pH, and mucus viscosity—leading to reduced ASL volume and impaired mucociliary clearance in CF, FOXI1-KO, and FOXI1-CreERT2::CFTRL/L ferrets. These processes were regulated by CFTR- dependent ionocyte transport of Cl– and HCO3–, as determined electrophysiologically and by single-cell imaging with a conditionally activated halide fluorescent sensor. Single-cell transcriptomics, using pulse-seq of lineage-traced ionocyte-enriched cultures, revealed three subtypes of pulmonary ionocytes with unique biologic functions and a common rare cell progenitor of ionocytes, tuft, and neuroendocrine cells. Thus, rare pulmonary ionocytes perform critical CFTR-dependent functions in the proximal airway that are hallmark features of CF airway disease. These studies provide a road map for using conditional genetics in the first non- rodent mammal to address gene function, cell biology, and disease processes that have greater evolutionary conservation between humans and ferrets.
2023-08-01 | GSE233654 | GEO
Project description:Gene differential expression studies can serve to explore and understand the laws and 16 characteristics of animal life activities, and the difference in gene expression between different 17 animal tissues have been well demonstrated and studied. However, for the world-famous rare 18 and protected species giant panda (Ailuropoda melanoleuca), only the transcriptome of the blood 19 and spleen has been reported separately. Here, in order to explore the transcriptome differences 20 between the different tissues of the giant panda, transcriptome profiles of the heart, liver, spleen, 21 lung, and kidney from five captive giant pandas were constructed with Illumina HiSeq 2500 22 platform. The comparative analysis of the inter-tissue gene expression patterns was carried out 23 based on the generated RNA sequencing datasets. Analyses of Gene Ontology (GO) enrichment, 24 Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment, and protein-protein interaction 25 (PPI) network were performed according to the identified differentially expressed genes (DEGs). 26 We generated 194.52 GB clean base data from twenty-five sequencing libraries and identified 27 18,701 genes, including 3492 novel genes. With corrected p-value < 0.05 and |log2FoldChange| > 28 2, we finally obtained 921, 553, 574, 457, and 638 tissue-specific DEGs in the heart, liver, spleen, 29 lung, and kidney, respectively. In addition, we identified TTN, CAV3, LDB3, TRDN, and 30 ACTN2 in the heart; FGA, AHSG, and SERPINC1 in the liver; CD19, CD79B, and IL21R in the 31 spleen; NKX2-4 and SFTPB in the lung; GC and HRG in the kidney as hub genes in the PPI 32 network. The results of the analyses showed a similar gene expression pattern between the spleen 33 and lung. This study provided for the first time the heart, liver, lung, and kidney’s transcriptome 34 resources of the giant panda, and it provided a valuable resource for further genetic research or 35 other potential research.
2020-08-31 | GSE138294 | GEO
Project description:Light, as both energy source and informational signal, profoundly influences plant growth and development during the whole life span from seed germination to flowering. To dissect the role for red light signaling in regulate the seedling development, we analyzed the gene expression profile of red light- and dark-grown WT seedlings by high throughput sequencing.
2020-07-25 | GSE101873 | GEO
Project description:As described in our paper "Aspm knockout ferret reveals an evolutionary mechanism governing cerebral cortical size" (Johnson et al., Nature 2018), we used the standard Drop-seq method and analysis of Macosko et al. (2015) to capture, sequence, and analyze mRNA from single cells from Aspm wild-type, heterozygous, and knock-out littermate ferrets at embryonic day 35. Bulk reference samples were processed using standard Illumina mRNA-seq library prep and sequencing protocols, and the samples were described previously (Johnson, Wang et al., Nature Neurosci 2015)
2018-04-18 | GSE110010 | GEO