Project description:The aim of the current study was to characterize the differential cellular and exosomal miRNAs during inflammation or high fat diet-induced obesity in mice. Mesenteric adipose tissue (MAT) and abdominal aorta (AA) from mice fed a normal chow diet (NCD) or a high fat diet (HFD) were harvested for miRNA profiling. MAT-derived adipocytes (MAT-Ad) challenged with either lipopolysaccharide (LPS, 1 µg/ml) or PBS were harvested for miRNA profiling. Meanwhile, miRNAs encapsulated in MAT-Ad-derived exosomes (MAT-Ad-EX) were also analyzed. Hierarchical clustering analysis performed on most significantly regulated miRNAs (HFD vs NCD in tissues; LPS challenge vs PBS in the cells) showed a set of miRNAs that are differentially expressed in obese versus lean MAT or AA tissues, and in LPS-challenged versus PBS-treated MAT-Ads. The dysregulated of miRNAs in MAT-Ad-EX was also generated and hierarchically clustered, induced by prolonged exposure to microbial product.
Project description:Tracing autotroph and heterotroph photosynthetic catalytic carbon cycling within a microbial mat, confirming biomass 13C incorporation into extracellular polymeric substances through proteomics.
Project description:Microbial communities respond to temperature with physiological adaptation and compositional turnover. Whether thermal selection of enzymes explains marine microbiome plasticity in response to temperature remains unresolved. By quantifying the thermal behaviour of seven functionally-independent enzyme classes (esterase, extradiol dioxygenase, phosphatase, beta-galactosidase, nuclease, transaminase, and aldo-keto reductase) in native proteomes of marine sediment microbiomes from the Irish Sea to the southern Red Sea, we record a significant effect of the mean annual temperature (MAT) on enzyme’s response (R2, 0.51–0.80, p < 0.01 in all cases). Activity and stability profiles of 228 esterases and 5 extradiol dioxygenases from sediment and seawater across 70 locations worldwide (latitude 62.2°S–16°N, MAT –1.4ºC–29.5ºC) validate this thermal pattern. Modelling the esterase phase transition temperature as a measure of structural flexibility, confirm the observed relationship with MAT. Furthermore, when considering temperature variability in sites with non-significantly different MATs, the broadest range of enzyme thermal behaviour and the highest growth plasticity of the enriched heterotrophic bacteria occur in samples with the widest annual thermal variability. These results indicate that temperature-driven enzyme selection shapes microbiome thermal plasticity and that thermal variability finely tunes such processes and should be considered alongside MAT in forecasting microbial community thermal response
Project description:This study aimed at identification of genetic regulations for desiccation tolerance in intertidal seaweed species Ulva lactuca most commonly experienced phenomenon of intertidal communities.
Project description:The vertebrate skeleton is mostly composed of three specific cell types: immature chondrocytes (IMM), mature (hypertrophic) chondrocytes (MAT), and osteoblasts (OST). These three cell types are distinct, but they also share the expression of many genes. This overlapping gene expression can be attributed to two transcription factors, SOX9 and RUNX2, which operate near the top of hierarchy of the gene regulatory network (GRN) underlying IMM, MAT, and OST. Sox9 drives IMM differentiation, whereas Runx2 regulates OST differentiation. Importantly, MAT do not form without the function of either Sox9 or Runx2, but little is known about mechanisms of GRN regulation in MAT. During MAT differentiation, the expression of Runx2 increases, and many genes regulated by this transcription such as Spp1, Mef2c, Ibsp, and Alpl are activated. To understand regulatory control of gene expression in mature chondrocytes, ChIP-seq experiments were performed using the mouse chondrogenic cell line ATDC5. These experiments identified in vitro RUNX2 binding sites at different stages of chondrogenesis. RUNX2 appeared to bind in most genes enriched in MAT at both day 3 of differentiation. The ChIP-seq analyses presented here verified the molecular mechanisms predicted here to regulate transcription of the many genomic loci in MAT, proving more insight into regulatory control during cartilage maturation.
Project description:Colonization of land from marine environments was a major transition for biological life on Earth, and intertidal adaptation was a key evolutionary event in the transition from marine- to land-based lifestyles. Multicellular intertidal red algae exhibit the earliest, systematic, and successful adaptation to intertidal environments, with Porphyra sensu lato (Bangiales, Rhodophyta) being a typical example. We used proteomic analyse to reveal the complex regulation of rapid responses to intertidal dehydration/rehydration cycling within Neoporphyra haitanensis. These adaptations include rapid regulation of its photosynthetic system, a readily available capacity to utilize ribosomal stores, an excess of methylation supply to rapidly synthesize proteins, and a strong anti-oxidation system to dissipate excess redox energy upon exposure to air. These novel insights into the unique adaptations of red algae to intertidal lifestyles inform our understanding of adaptations to intertidal ecosystems and the unique evolutionary steps required for intertidal colonization by biological life.
Project description:Protein stable isotope fingerprinting (P-SIF) is a method to measure the carbon isotope ratios of whole proteins separated from complex mixtures, including cultures and environmental samples. The goal of P-SIF is to expose the links between identity and function in microbial ecosystems by (i) determining the values of δ13C for different taxonomic divisions, and (ii) using those values as clues to the metabolic pathways employed by the respective organisms. This project measures >200 protein fractions and δ13C values for a sample of Cyanobacteria + Chloroflexi dominated microbial mat from Yellowstone National Park, USA.
Project description:Protein stable isotope fingerprinting (P-SIF) is a method to measure the carbon isotope ratios of whole proteins separated from complex mixtures, including cultures and environmental samples. The goal of P-SIF is to expose the links between identity and function in microbial ecosystems by (i) determining the values of δ13C for different taxonomic divisions, and (ii) using those values as clues to the metabolic pathways employed by the respective organisms. This project measures a limited number of protein fractions and δ13C values for a sample of floating, mat-like microbial biomass of an intensely phototrophic layer from Mahoney Lake, BC Canada.