Ontology highlight
ABSTRACT:
PROVIDER: PRJNA573987 | ENA |
REPOSITORIES: ENA
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Project description:Microbial photoautotroph-heterotroph interactions underlie marine food webs and shape ecosystem diversity and structure in upper ocean environments. However, the high complexity of in situ ecosystems renders it difficult to study these interactions. Two-member co-culture systems of picocyanobacteria and single heterotrophic bacterial strains have been thoroughly investigated. However, in situ interactions comprise far more diverse heterotrophic bacterial associations with single photoautotrophic organisms. Here, bacterial community composition, lifestyle preference, and genomic- and proteomic-level metabolic characteristics were investigated for an open ocean Synechococcus ecotype and its associated heterotrophs over 91 days of co-cultivation. The associated heterotrophic bacterial assembly mostly constituted five classes including Flavobacteria, Bacteroidetes, Phycisphaerae, Gammaproteobacteria, and Alphaproteobacteria. The seven most abundant taxa/genera comprised >90% of the total heterotrophic bacterial community, and five of these displayed distinct lifestyle preferences (free-living or attached) and responses to Synechococcus growth phases. Six high-quality genomes from the co-culture system were reconstructed inclusive of Synechococcus and the five dominant heterotrophic bacterial populations. The only primary producer of the co-culture system, Synechococcus, displayed metabolic processes primarily involved in inorganic nutrient uptake, photosynthesis, and organic matter biosynthesis and release. Two of the flavobacterial populations, Muricauda and Winogradskyella, and an SM1A02 population, displayed preferences for initial degradation of complex compounds and biopolymers, as evinced by high abundances of TBDT, glycoside hydrolase, and peptidases proteins. In contrast, the alphaproteobacterium Oricola sp. population mainly utilized low molecular weight DOM, including Flavobacteria metabolism byproducts, through ABC, TRAP, and TTT transport systems. Polysaccharide-utilization loci present in the flavobacterial genomes encoded similar trans-membrane protein complexes as Sus/cellulosome and may influence their lifestyle preferences and close associations with phytoplankton. The heterotrophic bacterial populations exhibited complementary mechanisms for degrading Synechococcus-derived organic matter and driving nutrient cycling. In addition to nutrient exchange, removal of reactive oxygen species and vitamin trafficking also contributed to the maintenance of the Synechococcus / heterotroph co-culture system and the interactions shaping the system.
2020-05-27 | PXD015067 | Pride
Project description:Tumor cells are known to express immune-inhibitory ligands on their surface to mediate resistance against cytotoxic T lymphocytes. Using a high-throughput RNAi screening assay, we identified CCR9 as a potent tumor-specific immune checkpoint molecule that inhibited T cell-mediated tumor lysis. To understand the mode of CCR9-mediated immune resistance, MCF7 tumor cells were transfected with control or CCR9-specific siRNAs for 72 hours and co-cultured with survivin antigen-specific T cells for an additional 12 hours. T cells were then purified from the co-culture and total RNA was isolated for gene expression analysis.
2015-02-19 | E-MTAB-3244 | biostudies-arrayexpress
Project description:Translation of NRF1/NRF2 -mediated liver tissue biomarkers to an in vitro assay using an advanced micropatterned co-culture system (HEPATOPAC®) with primary hepatocytes from male Wistar-Hannover rats or humans
2020-06-22 | GSE150069 | GEO
Project description:Swine H1N1 influenza virus and streptococcus suis serotype 2 (SS2) are two important contributors to the porcine respiratory disease complex, which have significant economic impacts. Clinically, swine influenza virus and swine streptococcus suis co-infection is common, which will increase the mortality. However, the pathogenesis of the co-infection remains largely unkown. To explore it, gene expression profiling was to performed to detect comprehensive analysis of the global host response induced by H1N1 virus infection alone, SS2 infection alone, H1N1-SS2 co-infection and PBS control.
2016-09-10 | GSE60172 | GEO
Project description:Construction of a global gene co-expression network to determine gene relatedness and expand regulatory pathways in the model cyanobacterium Synechococcus 7002.
2015-09-11 | GSE72880 | GEO
Project description:Vascular aging and dysfunction are significant contributors to age-related cardiovascular and neurodegenerative diseases, both of which encompass major causes of death in the aged population. In particular, aging heavily impacts small vessels, damages vascular integrity leading to leakage events and inflammation, and can be further exacerbated by environmental factors that may result in more severe symptomatic presentation of disease. Here, we evaluate generalized, isogenic, co-culture in vitro models of microvasculature under perfusion with aged human serum over just four days, which results in a transcriptomic recapitulation of an aging phenotype, transcript and protein changes in junctional mediators, and functional loss of paracellular and transcellular barrier integrity. Additionally, in comparison with endothelial monoculture, we identify critical changes to basement membrane composition and aging-cue-mediated cell cycle shifts with pericyte co-culture. This modular approach reveals key impacts to further our understanding of vascular aging to leverage in designing therapeutic and preventative approaches.
2024-04-01 | GSE261154 | GEO
Project description:Hepatitis E virus (HEV) is an important causative pathogen of acute hepatitis. Because of the absence of an in vitro culture system for HEV, research has been greatly impeded. And interaction between HEV and host cells was mainly studied by tansfection/transinfection system, such as Adeno virus transinfection system. We developed an in vitro culture system for HEV in PLC/PRF/5 cells. With this in vitro culture system, we studied the gene expression profile change by HEV infection. Using a microarray assay, we analysed genes of PLC/PRF/5 cells, whose transcription level could be changed by HEV infection.
2014-01-01 | GSE53731 | GEO