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Characterization of Human Lung Airway APC Subsets

ABSTRACT: The respiratory system is a complex network of many cell types, including subsets of macrophages and dendritic cels, that work together to maintain steady-state respiration. Due to limitations in acquiring cells from healthy human lung, these subsets remain poorly characterized transcriptionally and phenotypically. We set out to systemically identify these subsets in human airways, by developing a schema of isolating large numbers of cells by whole lung bronchoalveolar lavage. Six subsets of phagocytic antigen presenting cells were consistently observed, which varied in their ability to internalize bacterial particles. Subsets could be further separated by their inherent capacities to upregulate CD83, CD86, and CCR7. Whole genome transcriptional profiling revealed a clade of “true dendritic cells” distinct from a “macrophage/monocyte” clade. Each clade, and each member of both clades, could be discerned by specific genes of increased expression, which would serve as markers for future studies in healthy and diseased states.

ORGANISM(S): Homo sapiens

PROVIDER: GSE79706 | GEO | 2017/03/07

SECONDARY ACCESSION(S): PRJNA316804

REPOSITORIES: GEO

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Symbiodinium clade content drives host transcriptome more than thermal stress in the coral Montastraea faveolata (part 1)

Project description:Given the overwhelming evidence that symbiont genotypes differentially affect host processes such as growth, bleaching susceptibility, and nutrient acquisition, we set out to measure gene expression differences in fragments of Montastraea faveolata harboring two different clades of Symbiodinium. On the reefs near Puerto Morelos, México, colonies of M. faveolata are known to shift algal symbiont clade with depth, often associating with clade A at the top, clade B in the middle, and clade C near the bottom of the colony. By measuring photosynthetic efficiency and gene expression in control and heat-stressed fragments containing either clade B, clade C, or a mix of both, we found that: 1) the algal response to thermal stress is due to both host and algal factors; 2) fragments of M. faveolata express different genes in response to sub-bleaching thermal stress depending on algal genotype; 3) the overall effect of heat stress on coral gene expression is less significant than the effect of housing different zooxanthellae types. Overall, we present convincing evidence that different Symbiodinium clades may be functionally distinct, which in turn, greatly influences host gene expression.

2009-05-31 | GSE12809 | GEO

Copper toxicity response influences mesotrophic Synechococcus community structure

Project description:Picocyanobacteria from the genus Synechococcus are ubiquitous in ocean waters. Their phylogenetic and genomic diversity suggests ecological niche differentiation, but the selective forces influencing this are not well defined. Marine picocyanobacteria are sensitive to Cu toxicity, so adaptations to this stress could represent a selective force within, and between, “species” also known as clades. We compared Cu stress responses in cultures and natural populations of marine Synechococcus from two co-occurring major mesotrophic clades (I and IV). Using custom microarrays and proteomics to characterize expression responses to Cu in the lab and field, we found evidence for a general stress regulon in marine Synechococcus. However, the two clades also exhibited distinct responses to copper. The Clade I representative induced expression of genomic island genes in cultures and Southern California Bight populations, while the Clade IV representative downregulated Fe-limitation proteins. Copper incubation experiments suggest that Clade IV populations may harbor stress-tolerant subgroups, and thus fitness tradeoffs may govern Cu-tolerant strain distributions. This work demonstrates that Synechococcus has distinct adaptive strategies to deal with Cu toxicity at both the clade and subclade level, implying that metal toxicity and stress response adaptations represent an important selective force for influencing diversity within marine Synechococcus populations.

2016-10-28 | GSE89262 | GEO

Evolutionary Instability of CUG-Leu in the Genetic Code of Budding Yeasts

Project description:The standard genetic code is almost universal, and the evolutionary factors that caused a few organisms to deviate from it are poorly understood. We report that three independent changes of the genetic code occurred during the evolution of budding yeasts, each of which was a reassignment of the codon CUG from leucine to another amino acid. We identify five major yeast clades that differ by translating CUG as either Ser (2 clades), Ala (1 clade), or Leu (2 clades). The newly discovered Ser2 clade is in the final stages of transition from one genetic code to another. It appears to use only a novel tRNASer (tSCAG) to translate CUG codons, but the gene for the ancestral tRNALeu (tLCAG) is still intact in most species in the clade, consistent with the ‘ambiguous intermediate’ theory. We propose that the three parallel changes of the genetic code in yeasts were not driven by natural selection in favor of their effects on the proteome, but by selection to eliminate the ancestral tLCAG, possibly in response to a killer toxin.

2018-05-21 | PXD008827 | Pride

THE DNA BINDING LANDSCAPE OF THE MAIZE AUXIN RESPONSE FACTOR FAMILY [DAP-seq]

Project description:DAP-seq was used to generate genome-wide DNA:TF interaction maps for fourteen maize ARFs from the evolutionarily conserved class A ‘activator’ and class B ‘repressor’ clades. Among the distinct binding sites that were identified, we observed a high degree of overlap for ARFs of the same class, but found substantial differences in motif sequence, spacing, site preference, and association with auxin induced genes among clade A and clade B ARFs.

2018-09-14 | GSE111795 | GEO

THE DNA BINDING LANDSCAPE OF THE MAIZE AUXIN RESPONSE FACTOR FAMILY [RNA-seq]

2018-09-14 | GSE111792 | GEO

Fingerprinting the Asterid species using subtracted diversity array reveals novel species-specific sequences.

Project description:Asterids is one of the major plant clades comprising of many commercially important medicinal species. One of the major concerns in medicinal plant industry is adulteration/contamination resulting from misidentification of herbal plants. This study reports the construction and validation of a microarray capable of fingerprinting medicinally important species from the Asterids clade.

2014-07-31 | GSE31242 | GEO

nCounter (NanoString) expression analysis of CD19+CD27-IgD- and CD19+CD27+IgD- B cells cultured with plasmacytoid dendritic cells and RNA containing immune complexes in vitro for 6 days

Project description:Comparison of two B cell subsets isolated from healthy individuals after stimulation in vitro with SLE-related immune complexes and in the presence of plasmacytoid dendritic cells.

2017-09-07 | E-MTAB-5740 | biostudies-arrayexpress

Gene expression profile comparison of DC subsets

Project description:To evaluate gene expression profiles on different dendritic cell subsets isolated from spleens of mice We used whole genome microarrays to identify genes specific to pDCs and not other DC subsets in the absence of disease pDCs, CD11b+ cDCs, and CD8+ cDCs were FACS-purified from spleens of healthy C57bl/6 mice

2015-12-10 | E-GEOD-75834 | biostudies-arrayexpress

Acoel single-cell transcriptomics: cell-type analysis of a deep branching organism

Project description:Bilaterian animals display a wide variety of cell types, organized into defined anatomical structures and organ systems, which are mostly absent in pre-bilaterian animals. Xenacoelomorpha are an early branching bilaterian phylum displaying an apparently relatively simple anatomical organization that have greatly diverged from other Bilaterian clades. In this study, we use whole-body single-cell transcriptomics on the acoel Isodiametra pulchra to identify and characterize different cell types. Our analysis identifies the existence of at least 11 major cell-type categories in acoels all contributing to the main biological functions of the organism: metabolism, locomotion and movements, behavior, defense and development. Interestingly, while most cell clusters express core fate markers shared with other animal clades, we also describe a surprisingly large numbers of clade-specific marker genes, suggesting the emergence of clade-specific common molecular machineries functioning in distinct cell types. Together, these results provide novel insight into the evolution of bilaterian cell-types and open the door to a better understanding of the origins of the bilaterian body plan and their constitutive cell types.

2020-07-09 | GSE154049 | GEO

The Detection and Subtyping of Seasonal Influenza A H1N1 Isolates Using a Microarray

Project description:An influenza A microarray was used to type influenza A H1N1 specimens collected in Washington State and the results compared with identification by both culture and real time RT PCR. The microarray was more sensitive than conventional influenza testing. Cluster analysis of the microarray data discriminated specimens into distinct clades. Specimens from two pediatric decedents formed a unique clade upon H1 analysis. Keywords: Comparative genome study; Influenza A strains; Subtype H1N1

2008-11-01 | GSE12226 | GEO

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