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.
Project description:We use RNA-sequencing to generate gene expression profiles of fetal mammary cells with unique sorting strategies. These analyses reveal that sorting fetal mammary cells with Sox10 and EpCAM sorting markers provides a stroma-free fMaSC-enriched cell population. The gene expression profiling of these cells offers a resources to probe the molecular mechanisms that specify this unique cell state.
Project description:We use RNA-sequencing to generate gene expression profiles of fetal mammary cells with unique sorting strategies. These analyses reveal that sorting fetal mammary cells with Sox10 and EpCAM sorting markers provides a stroma-free fMaSC-enriched cell population. The gene expression profiling of these cells offers a resources to probe the molecular mechanisms that specify this unique cell state. Examination of 2 different sorting strategies for fetal mammary cells
Project description:To classify the cell population of lung alveolar macrophages in the presence (or absence) of lung cancer cells in vivo, single cell RNA sequence analysis was performed using orthotopic tumor bearing animal model with C57BL/6 mice and Lewis Lung Carcinoma (LLC) cells. CD45+, F4/80+, Siglec-F+ population was sorted as alveolar macrophage population with fluorescence-activated cell sorting (FACS) technique.
Project description:In summer 2014, we conducted experiments to determine the effects of different N substrates on phytoplankton communities in the North Pacific Ocean and in the transition zone of the California Current and gyre (Shilova, Mills et al., 2017). Samples were incubated with nitrate, ammonium, urea, and filtered deep water (FDW) for 48 hours (T48). Two treatments added iron, alone (Fe) or with a mix of N substrates (N+Fe), to determine the effects of Fe on the utilization of N substrates. All treatments resulted in changes in phytoplankton cell abundances and photosynthetic activity at both locations, with differences between phytoplankton groups. Prochlorococcus had large increases in biomass in response to ammonium and urea, while both eukaryotic phytoplankton and Synechococcus had only modest biomass increases in response to N+Fe and FDW. Moreover, distinct physiological responses were observed within sub-populations of Prochlorococcus and Synechococcus. In order to understand the variable responses to N substrates among phytoplankton groups and sub-populations in the California Current transition zone, the present work examines transcriptional changes that occurred 24 h after the substrates were added. Specifically, we hypothesize that transcription changes at 24 h indicate which phytoplankton taxa are N-limited, and thus help explain changes in cell abundances and photosynthetic activity by individual phytoplankton groups observed at 48 h. Furthermore, we hypothesize that the diversity in physiological responses within Prochlorococcus and Synechococcus are evident in the transcriptional responses measured at sub-population resolution.
Project description:Identification of genes enriched in putative stem/progenitor cells (CD133highPDGFRb- cell population) from the mouse embryonic pancreas that are purified by fluorescence activated cell sorting (FACS). Success in islet transplantation-based therapies for type 1 diabetes mellitus and an extreme shortage of pancreatic islets has motivated efforts to develop renewable sources of islet-replacement tissue. Only a few attempts have been made at prospective isolation of pancreatic stem/progenitor cells, due to the lack of specific markers and the development of cell culture method. This study demonstrates the isolation of pancreatic stem/progenitor cells from the embryonic pancreas by cell sorting. RT-PCR and microarray analysis demonstrated that pancreatic stem/progenitor cells are enriched in CD133highPDGFRb- cell population. During in vivo differentiation, these cell populations have the ability for self-renewal and multipotency, including the formation of insulin-producing cells. Since the strategy is based on the cell sorting using cell surface markers common to human and rodents, it may promote strategies to derive transplantable islet-replacement tissues from human pancreatic stem/progenitor cells. Experiment Overall Design: A couple of total RNAs derived from the different status of PDGFRb- cells was subjected to a dual-color microarray analysis, in which the RNAs from CD133highPDGFRb- cell population was labeled with Cy3 and that of CD133negPDGFRb- cell population with Cy5 respectively.
Project description:To investigate the interaction between lung alveolar macrophages and lung cancer cells in vivo, gene expression analysis was performed using orthotopic tumor bearing animal model with C57BL/6 mice and Lewis Lung Carcinoma (LLC) cells. CD45+, F4/80+, Siglec-F+ population was sorted as alveolar macrophage population with fluorescence-activated cell sorting (FACS) technique.