Project description:In this study we investigate and compare DEGs of K. aerogenes macrocolonies during temperature entrainment (12:12, 35°C:36°C) and subsequent free running conditions (35°C). The goal of this experiment was to identify rhythmically expressed genes in K. aerogenes, the first human gut commensal bacterium with described circadian clock (Paulose et al. 2016). K. aerogenes circadian clock is sensitive to temperature entrainment (Paulose et al. 2019). To further investigate this temperature entrainment of K. aerogenes we performed RNA sequencing experiment. We identified 48 differentially expressed genes when comparing timepoints ZT6 to ZT18, 427 differentially expressed genes when comparing timepoints ZT6 to CT6, 6 differentially expressed genes between timepoints CT6 and CT18, and 2 differentially expressed genes between timepoints ZT18 and CT18.
Project description:In this study, we implemented RNA sequencing to identify melatonin sensitive transcripts during culture maturation. This work demonstrates that majority of melatonin sensitive genes are growth stage specific. Melatonin caused differential gene expression of 81 transcripts during the exponential growth and 30 during early stationary phase. This indole molecule affects genes related to the biofilm formation, fimbria biogenesis, transcriptional regulators, carbohydrate transport and metabolism, phosphotransferase system (PTS), stress response, metal ion binding and transport. It is likely that differential expression of biofilm and fimbria related genes is responsible for differences in macrocolony area. Additionally, melatonin potentially helps Klebsiella aerogenes in host colonization.
Project description:This gene expression experiment aimed to discover circiadian clock genes in yeast cells grown in a 1L fermentor culture Yeast were entrained for a period of time after the culture was released to a freerun (see growth protocol below). Samples were taken from fermenter cultures (1 × 109 yeast cells) every 3 hours over the first day of constant conditions (free-run), starting 1h before the temperature transition from 21°C to 28°C
Project description:The gastrointestinal bacterium Klebsiella (née Enterobacter) aerogenes expresses an endogenously generated, temperature-compensated circadian rhythm in swarming motility. We hypothesized that this rhythm may be synchronized/entrained in vivo by body temperature (TB). To determine entrainment, cultures expressing bioluminescence were exposed to temperature cycles of 1°C (35°C-36°C) or 3°C (34°C-37°C) in amplitude at periods (T-cycles) of T = 22, T = 24, or T = 28 h. Bacteria entrained to all T-cycles at both amplitudes and with stable phase relationships. A high-amplitude phase response curve (PRC) in response to 1-h pulses of 3°C temperature spike (34°C-37°C) at different circadian phases was constructed, revealing a Type-0 phase resetting paradigm. Furthermore, real-time bioluminescence imaging revealed a spatiotemporal pattern to the circadian rhythm. These data are consistent with the hypothesis that the K. aerogenes circadian clock entrains to its host via detection of and phase shifting to the daily pattern of TB.