Project description:<p>Four species of phytoplankton representing important bloom-forming species from three globally important phyla (Bacillariophyta, Haptophyta, and Ochrophyte) were cultured in this study. These species include the cosmopolitan diatom <em>Chaetoceros affinis</em> CCMP159 (isolated from Great South Bay, NY, USA, 1958), the haptophytes<em> Chrysochromulina polylepis </em>CCMP1757 (isolated from the North Sea 1988) and <em>Gephyrocapsa oceanica</em> RCC1303 (isolated from Arachon Bay, France, Jan 1999), and the raphidophyte <em>Heterosigma akashiwo </em>strain CCMP 2393 (isolated from Rehoboth Bay, Delaware, USA). Cultures were grown under three conditions: nitrogen-stress, phosphorus-stress, and replete conditions. Intracellular metabolites were extracted from cultures and analyzed with targeted and untargeted mass spectrometry-based metabolomics methods.</p>
Project description:Deoxynivalenol (DON) is a type B trichothecene mycotoxin that is commonly found in cereals and grains worldwide. The presence of this fungal secondary-metabolite raises public-health concerns at both the agriculture and food industry level. The toxicity of DON is mainly characterized by its ability to inhibit ribosomal protein biosynthesis. Recently, we have shown that DON has a negative impact on gut integrity, a feature also noticed for Campylobacter (C.) jejuni. We further demonstrated that DON increased the load of C. jejuni in the gut and inner organs. In contrast, feeding the less toxic DON metabolite deepoxy-deoxynivalenol (DOM-1) to broilers reduced the Campylobacter load in vivo. Consequently, it can be hypothesized that DON and DOM-1 have a direct or indirect effect on the growth profile of C. jejuni. The aim of the present study was to further resolve the nature of this interaction in vitro by co-incubation and RNA-sequencing. The co-incubation of C. jejuni with DON resulted in significantly higher bacterial growth rates from 30 h of incubation onwards. On the contrary, the co-incubation of C. jejuni with DOM-1 reduced the CFU counts, indicating that this DON metabolite might contribute to reduce the burden of C. jejuni in birds, altogether confirming in vivo data. Furthermore, the transcriptomic profile of C. jejuni following incubation with either DON or DOM-1 differed. Co-incubation of C. jejuni with DON significantly increased the expression of multiple genes which are critical for Campylobacter growth, particularly members of the Flagella gene family, frr (ribosome-recycling factor), PBP2 futA-like (Fe3+ periplasmic binding family) and PotA (ATP-binding subunit). These organelles are required for pathogenicity-related phenotypes including motility, biofilm formation, host cell interactions, and host colonization, which may explain the high Campylobacter load in the intestine of DON-fed broiler chickens. On the contrary, DOM-1 downregulated the Flagella gene family and upregulated ribosomal proteins. The results highlight the adaptive mechanisms involved in the transcriptional response of C. jejuni to DON and its metabolite DOM-1, based on the following effects: (a) ribosomal proteins; (b) flagellar proteins; (c) engagement of different metabolic pathways. The results provide insight into the response of an important intestinal microbial pathogen against DON and lead to a better understanding of the luminal or environmental acclimation mechanisms in chickens.
Project description:All samples were gathered from mouse RAW 264.7 cells (macrophages). Control total RNA was extracted from untreated RAW 264.7 cells cultured for 1 hour. Test total RNA was extracted from lipopolysaccharide (100ng/ml) and lipopolysaccharide-binding protein (100pM) treated RAW 264.4 cells cultured for 1 hour. Experiment design included three control vs test arrays and three dye swap arrays. Keywords: other
Project description:To investigate gene expression changes in a bladder cancer cell line with RXRA p.S427F hotspot mutation after 24 hour treatment with PPARG agonist, rosiglitzone, and PPARG inverse-agonists; T0070907, SR10221, and BAY-4931
Project description:Wild type (Columbia-0) and hy5 loss of function mutants were treated with benzyl adenine (a synthetic cytokinin analog) for 1 hour and then mRNA was extracted for an RNA-seq differential expression experiment.
Project description:Zhao et al. Amplification Figure 1 This experiment was designed to evaluate the effect of in vitro transcription time on the fidelity, reproducibility, and yield of T7 based linear amplification. Duplicate reactions were performed at 37 degree for 2, 3, 4, 5, and 6 hours. Two additional 5-hour incubation reactions were stored at 4 degree overnight to determine the effect of low temperature incubation on amplification. BC2 total RNA was amplified using the Jeffrey lab protocol with the G50 column cleanup step. Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. Keywords: Logical Set