Mesodermal lineages in the developing respiratory system
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ABSTRACT:
SUBMITTER: Han L
PROVIDER: S-EPMC8547324 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:A mathematical model of respiratory system.
| 3a4 | Physiome Model Repository
Project description:Alternative splicing (AS) allows increased diversity and orthogonal regulation of the transcriptional products of mammalian genomes. To assess the distribution and variation of alternative splicing across cell lineages of the immune system, we comprehensively analyzed RNA sequencing and microarray data generated by the Immunological Genome Project Consortium. AS is pervasive: 60% of genes showed frequent AS isoforms in T or B lymphocytes, with 7,599 previously unreported isoforms. Distinct cell specificity was observed, with differential exon skipping in 5% of genes otherwise coexpressed in both B and T cells. The distribution of isoforms was mostly all or none, suggesting on/off switching as a frequent mode of AS regulation in lymphocytes. From the identification of differential exon use in the microarray data, clustering of exon inclusion/exclusion patterns across all Immunological Genome Project cell types showed that ?70% of AS exons are distributed along a common pattern linked to lineage differentiation and cell cycling. Other AS events distinguished myeloid from lymphoid cells or affected only a small set of exons without clear lineage specificity (e.g., Ptprc). Computational analysis predicted specific associations between AS exons and splicing regulators, which were verified by detection of the hnRPLL/Ptprc connection.
| S-EPMC3761616 | biostudies-literature
Project description:BackgroundThe evaluation of respiratory system health status in hospitalized patients is usually based on many laboratory examinations and imaging examinations. Medical examinations require a lot of manpower, material resources, financial resources, and may cause a certain degree of mechanical damage and radiation damage. It is not easily used widely and economically to assess the respiratory health status of community adults. Therefore, researchers developed a brief adult respiratory system health status scale-community version (BARSHSS-CV) and tested its reliability and validity.MethodsUsing clinical characteristics and pathogenic factors of respiratory system diseases as a theoretical basis and through reference to relevant literature, researchers developed an initial scale. A randomized cluster sampling strategy was used to recruit adults in the communities of Baoding City, Shijiazhuang City, Cangzhou city and Chifeng City in China. Researchers randomly selected 1 district from each city. Subsequently, 4 communities were respectively randomly selected from 4 districts. Then, researchers conducted the questionnaire survey in 4 communities. Finally, researchers investigated 615 community adults. 584 valid questionnaires were recovered. By applying exploratory factor analysis, confirmatory factor analysis, content validity index, Cronbach's ? coefficient, mean inter-item correlation coefficient and test-retest reliability, researchers tested the reliability and validity of scale and created the final BARSHSS-CV.ResultsBARSHSS-CV Cronbach's ?=0.951, content validity?=?0.933, test-retest reliability?=?0.963 and factor cumulative contribution rate?=?67.168% by exploratory factor analysis. By confirmatory factor analysis, Chi square value (?2) was 442.117, degrees of freedom (df) was 161, Chi square value/degrees of freedom (?2 /df) was 2.746, root-mean-square error of approximation (RMSEA) was 0.065, goodness of fit index (GFI) was 0.902, incremental fit index (IFI) was 0.955, comparative fit index (CFI) was 0.955, normed fit index (NFI) was 0.931, Tueker-Lewis index (TLI) was 0.947. BARSHSS-CV consisted of 20 items and 3 dimensions.ConclusionsBARSHSS-CV with good test-retest reliability and content/construct validity is a brief and economical tool for assessing the state of respiratory system amongst adult communities. BARSHSS-CV may help medical staff in community primary medical institutions quickly, conveniently and economically assess the status of respiratory system and the main problems of respiratory system in community adults.
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Project description:Nodal signaling plays crucial roles in vertebrate developmental processes such as endoderm and mesoderm formation, and axial patterning events along the anteroposterior, dorsoventral and left-right axes. In echinoderms, Nodal plays an essential role in the establishment of the dorsoventral axis and left-right asymmetry, but not in endoderm or mesoderm induction. In protostomes, Nodal signaling appears to be involved only in establishing left-right asymmetry. Hence, it is hypothesized that Nodal signaling has been co-opted to pattern the dorsoventral axis of deuterostomes and for endoderm, mesoderm formation as well as anteroposterior patterning in chordates. Hemichordata, together with echinoderms, represent the sister taxon to chordates. In this study, we analyze the role of Nodal signaling in the indirect developing hemichordate Ptychodera flava. In particular, we show that during gastrulation nodal transcripts are detected in a ring of cells at the vegetal pole that gives rise to endomesoderm and in the ventral ectoderm at later stages of development. Inhibition of Nodal function disrupts dorsoventral fates and also blocks formation of the larval mesoderm. Interestingly, molecular analysis reveals that only mesodermal, apical and ventral gene expression is affected while the dorsal side appears to be patterned correctly. Taken together, this study suggests that the co-option of Nodal signaling in mesoderm formation and potentially in anteroposterior patterning has occurred prior to the emergence of chordates and that Nodal signaling on the ventral side is uncoupled from BMP signaling on the dorsal side, representing a major difference from the molecular mechanisms of dorsoventral patterning events in echinoderms.
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Project description:Swine pathogens have a long history of zoonotic transmission to humans, occasionally leading to sustained outbreaks or pandemics. Through a retrospective epidemiological study of swine populations in China, we describe novel lineages of porcine hemagglutinating encephalomyelitis virus (PHEV) complex coronaviruses (CoVs) that cause exclusively respiratory symptoms with no signs of the neurological symptoms typically associated with classical PHEV infection. Through large-scale epidemiological surveillance, we show that these novel lineages have circulated in at least eight provinces in southeastern China. Phylogenetic and recombination analyses of twenty-four genomes identified two major viral lineages causing respiratory symptoms with extensive recombination within them, between them, and between classical PHEV and the novel respiratory variant PHEV (rvPHEV) lineages. Divergence times among the sampled lineages in the PHEV virus complex date back to 1886-1958 (mean estimate 1928), with the two major rvPHEV lineages separating approximately 20 years later. Many rvPHEV viruses show amino acid substitutions at the carbohydrate-binding site of hemagglutinin esterase (HE) and/or have lost the cysteine required for HE dimerization. This resembles the early adaptation of human CoVs, where HE lost its hemagglutination ability to adapt to growth in the human respiratory tract. Our study represents the first report of the evolutionary history of rvPHEV circulating in swine and highlights the importance of characterizing CoV diversity and recombination in swine to identify pathogens with outbreak potential that could threaten swine farming.
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Project description:Cortical neurogenesis follows a simple lineage: apical Radial Glia Cells (RGC) generate basal progenitors, and these produce neurons. How this occurs in species with expanded germinal zones and a folded cortex, like human, remains unclear. We used single-cell RNA sequencing from individual cortical germinal zones in ferret, and barcoded lineage tracking, to determine the molecular diversity of progenitor cells and their lineages. We identified multiple RGC classes that initiate parallel lineages, converging onto a common class of newborn neuron. Parallel RGC classes and transcriptomic trajectories were repeated across germinal zones and conserved in ferret and human, but not mouse. Neurons followed parallel differentiation trajectories in gyrus and sulcus, with different expression of human cortical malformation genes. Progenitor cell lineage multiplicity is conserved in the folded mammalian cerebral cortex. This SuperSeries is composed of the SubSeries listed below.
2024-03-27 | GSE234305 | GEO
Project description:Hypoxemia is associated with worse outcomes in COPD. The aim of the study was to investigate the prevalence, incidence, and risk factors of hypoxic respiratory failure (HRF) in COPD.This was a longitudinal analysis of data from the Swedish National Register of COPD. HRF was defined as resting saturation ≤88% or long-term oxygen therapy. Risk factors for developing HRF were analyzed using multiple logistic regression and receiver operating characteristic curve analysis.A total of 3,061 patients were included; mean forced expiratory volume in 1 second was 1.47 L; mean age was 70 years; and 54% were females. Median follow-up time was 1.8 years (interquartile range 1.3-2.4 years). HRF was present in 43 (1.4%) patients at baseline and 74 (2.4%) patients at follow-up. Among patients without HRF at baseline, 49 (1.6%) developed HRF during follow-up. The risk was highest for patients in Global initiative for Chronic Obstructive Lung Disease (GOLD) 2017 stage IV or groups C or D at baseline. Developing HRF was independently predicted by lower forced expiratory volume in 1 second and lower COPD Assessment Test score, with a c-statistic of 0.84 (95% CI, 0.70-0.91). When the multivariable model used the GOLD 2017 variables stages I-IV and the dichotomized variables frequent exacerbations and COPD Assessment Test ≥10; the c-statistic increased slightly to 0.86 (95% CI, 0.80-0.92; P<0.0001).In patients with COPD, the prevalence and incidence of HRF was low and was predicted well by more severe air flow limitation and worse health status. The risk is highest in patients with GOLD stage IV and GOLD groups C or D.
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Project description:During development of the mammalian central nervous system (CNS), neurons and glial cells (astrocytes and oligodendrocytes) are generated from common neural precursor cells (NPCs). However, neurogenesis precedes gliogenesis, which normally commences at later stages of fetal telencephalic development. Astrocyte differentiation of mouse NPCs at embryonic day (E) 14.5 (relatively late gestation) is induced by activation of the transcription factor STAT3, whereas at E11.5 (mid-gestation) NPCs do not differentiate into astrocytes even when stimulated by STAT3-activating cytokines such as leukemia inhibitory factor (LIF). This can be explained in part by the fact that astrocyte-specific gene promoters are highly methylated in NPCs at E11.5, but other mechanisms are also likely to play a role. We therefore sought to identify genes involved in the inhibition of astrocyte differentiation of NPCs at midgestation. We first examined gene expression profiles in E11.5 and E14.5 NPCs, using Affymetrix GeneChip analysis, applying the Percellome method to normalize gene expression level. We then conducted in situ hybridization analysis for selected genes found to be highly expressed in NPCs at midgestation. Among these genes, we found that N-myc and high mobility group AT-hook 2 (Hmga2) were highly expressed in the E11.5 but not the E14.5 ventricular zone of mouse brain, where NPCs reside. Transduction of N-myc and Hmga2 by retroviruses into E14.5 NPCs, which normally differentiate into astrocytes in response to LIF, resulted in suppression of astrocyte differentiation. However, sustained expression of N-myc and Hmga2 in E11.5 NPCs failed to maintain the hypermethylated status of an astrocyte-specific gene promoter. Taken together, our data suggest that astrocyte differentiation of NPCs is regulated not only by DNA methylation but also by genes whose expression is controlled spatio-temporally during brain development. Experiment Overall Design: Neuroepithelial cells(NPCs) were prepared from telencephalons of E11.5 and E14.5 mice and cultured in N2-supplemented Dulbecco's Modified Eagle's Medium with F12 (GIBCO) containing 10 ng/ml basic FGF (R&D Systems) (N2/DMEM/F12/bFGF) on culture dishes (Nunc) or chamber slide (Nunc) which had been precoated with poly-L-ornithine (Sigma) and fibronectin (Sigma). E11.5 NPCs were cultured for one day and E14.5 NPCs were for four days.
2008-10-20 | E-GEOD-10796 | biostudies-arrayexpress
Project description:Respiratory viral pathogens like influenza and coronaviruses such as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have caused outbreaks leading to millions of deaths. Vaccinations are, to date, the best and most economical way to control such outbreaks and have been highly successful for several pathogens. Currently used vaccines for respiratory viral pathogens are primarily live attenuated or inactivated and can risk reversion to virulence or confer inadequate immunity. The recent trend of using potent biomolecules like DNA, RNA, and protein antigenic components to synthesize vaccines for diseases has shown promising results. Still, it remains challenging to translate due to their high susceptibility to degradation during storage and after delivery. Advances in bioengineering technology for vaccine design have made it possible to control the physicochemical properties of the vaccines for rapid synthesis, heightened antigen presentation, safer formulations, and more robust immunogenicity. Bioengineering techniques and materials have been used to synthesize several potent vaccines, approved or in trials, against coronavirus disease 2019 (COVID-19) and are being explored for influenza, SARS, and Middle East respiratory syndrome (MERS) vaccines as well. Here, we review bioengineering strategies such as the use of polymeric particles, liposomes, and virus-like particles in vaccine development against influenza and coronaviruses and the feasibility of adopting these technologies for clinical use.
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Project description:Neural crest cells (NCCs) are vertebrate stem cells that give rise to various cell types throughout the developing body in early life. Here, we utilized single-cell transcriptomic analyses to delineate NCC-derivatives along the posterior developing vertebrate, zebrafish, during the late embryonic to early larval stage, a period when NCCs are actively differentiating into distinct cellular lineages. We identified several major NCC/NCC-derived cell-types including mesenchyme, neural crest, neural, neuronal, glial, and pigment, from which we resolved over three dozen cellular subtypes. We dissected gene expression signatures of pigment progenitors delineating into chromatophore lineages, mesenchyme cells, and enteric NCCs transforming into enteric neurons. Global analysis of NCC derivatives revealed they were demarcated by combinatorial hox gene codes, with distinct profiles within neuronal cells. From these analyses, we present a comprehensive cell-type atlas that can be utilized as a valuable resource for further mechanistic and evolutionary investigations of NCC differentiation.
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