Resting cyst formation is a remarkable survival strategy used by ciliates in response to the adverse environmental conditions. However, the mechanisms underlying encystment are poorly understood. Here, the genetic basis of encystment in Colpoda aspera was examined through RNA sequencing to identify transcriptome-wide changes in gene expression between vegetative and encystment stages. After de novo assembly, 49,543 transcripts were identified. Gene annotation and pathway mapping analysis reveale ...[more]
Project description:The goals of this study is to investigate the function of CDK19 and CYC9 of Tetrahymena thermophila. Overall design: Compare the expression of genes amnong WT, ∆CDK19 and ∆CYC9 cells in starvation and costimulation.
Project description:The goals of this study is to investigate the function of Cdk3 of Tetrahymena thermophila. Overall design: Compare the expression of genes amnong WT and cdk3∆ cells in C1, C2 and C3.
Project description:The goals of this study is to investigate the function of Cyc17 of Tetrahymena thermophila. Overall design: Compare the expression of genes amnong WT and CYC17KO cells in C4, C5, C6 anc C7.
Project description:The goals of this study are to investigate the function of Dpl2 of Tetrahymena thermophila. Overall design: Compare the expression of genes amnong WT and dpl∆ cells in C3, C4, C5, C6 and C7.
Project description:Specific binding proteins are crucial for the correct spatiotemporal expression of mRNA. To understand this process, a method is required to characterize RNA-protein interactions in single living cells with subcellular resolution. We combined endogenous single RNA and protein detection with two-photon fluorescence fluctuation analysis to measure the average number of proteins bound to mRNA at specific locations within live cells. We applied this to quantify the known binding of zipcode binding protein 1 (ZBP1) and ribosomes to ?-actin mRNA within subcellular compartments of primary fibroblasts and neurons. ZBP1-mRNA binding did not occur in nuclei, contrary to previous conclusions. ZBP1 interaction with ?-actin mRNA was enhanced perinuclearly in neurons compared to fibroblasts. Cytoplasmic ZBP1 and ribosome binding to the mRNA were anti-correlated depending on their location in the cell. These measurements support a mechanism whereby ZBP1 inhibits translation of localizing mRNA until its release from the mRNA peripherally, allowing ribosome binding.
Project description:The goals of this study is to investigate the function of E2fl-1 of Tetrahymena thermophila. Overall design: Compare the expression of genes amnong WT and e2fl-1∆ cells in C2, C3, C4, C5, C6 and C7.
Project description:The goals of this study are to compare the difference between DBP knock-down group and control group in mesangial cells Overall design: DBP was knock-down by siRNA and NC siRNA was set as control.
Project description:We report the development of the multiplexed nanoflare, a nanoparticle agent that is capable of simultaneously detecting two distinct mRNA targets inside a living cell. These probes are spherical nucleic acid (SNA) gold nanoparticle (Au NP) conjugates consisting of densely packed and highly oriented oligonucleotide sequences, many of which are hybridized to a reporter with a distinct fluorophore label and each complementary to its corresponding mRNA target. When multiplexed nanoflares are exposed to their targets, they provide a sequence specific signal in both extra- and intracellular environments. Importantly, one of the targets can be used as an internal control, improving detection by accounting for cell-to-cell variations in nanoparticle uptake and background. Compared to single-component nanoflares, these structures allow one to determine more precisely relative mRNA levels in individual cells, improving cell sorting and quantification.
Project description:Methods for normalization of RNA-sequencing gene expression data commonly assume equal total expression between compared samples. In contrast, scenarios of global gene expression shifts are many and increasing. Here we compare the performance of three normalization methods when polyA(+) RNA content fluctuates significantly during zebrafish early developmental stages. As a benchmark we have used reverse transcription-quantitative PCR. The results show that reads per kilobase per million (RPKM) and trimmed mean of M-values (TMM) normalization systematically leads to biased gene expression estimates. Biological scaling normalization (BSN), designed to handle differences in total expression, showed improved accuracy compared to the two other methods in estimating transcript level dynamics. The results have implications for past and future studies using RNA-sequencing on samples with different levels of total or polyA(+) RNA.