Project description:Skeletal elements from the feather star Anneissia japonica were isolated and stripped of organic material. The skeleton was then demineralized and the occluded proteins isolated. The proteins were separated by SDS-PAGE and fractions were analyzed by LC-MS/MS. The results were compared to predicted proteins encoded by the genome. The proteins found in the organic matrix of the skeleton were compared to those found in other skeletons both within Echinodermata and to other taxa.
Project description:We employed HITS-CLIP to map genome wide Star-PAP mRNA binding and define the role of RBM10 on global Star-PAP mRNA association. We show a transcriptome-wide association of Star-PAP which is diminished on cellular Star-PAP depletion. HITs-CLIP data analysis of RBM10 knockdown and pulldown with anti Star-PAP antibody on HEK293 cells indicates significance of RBM10 in Star-PAP and mRNA association.
Project description:Strain ∆staRPZnstaR was obtained to investigate genome-wide differential gene expresion when staR gene is reppressed or overexpressed by adding Zn to the culture medium. In addition, gene expression profile alterations produced upon inhibition of gyrase with Novobiocin were studied in the absence and presence of StaR.
Project description:Purpose: The aim of this study is to determine the expression profile in whole blood samples of children infected with respiratory syncytial virus and other respiratory viruses. Method: Host mRNA profiles in whole blood samples of children were generated by next-generation sequencing using Illumina Hiseq. Sequence reads were trimmed for adapter using skewer, mapped to reference human genome using STAR, and quantified using RSEM. Differential expression analysis was performed using DESeq2. Results: Transcriptional module analysis revealed dysregulation of genes related to inflammatory response, neutrophils, monocytes, B-cell and T-cell response. Conclusion: This study showed an imbalance in innate and adaptive immune responses in children with respiratory virus infections. This study also showed that NGS provides a comprehensive assessment of transcripts in whole blood samples.
Project description:Pooled genetic screening with CRISPR/Cas9 has enabled genome-wide high-resolution assignment of genes to phenotypes. To assess the effect of a given genetic perturbation, each sgRNA must be evaluated in hundreds of cells to overcome stochastic genetic drift and obtain robust results. In complex models that display particularly high heterogeneity, such as organoids or tumors transplanted into mice however, sufficient representation typically requires unreasonable scaling, thus preventing genome-wide screens at high resolution. Here we present CRISPR-StAR, a screening paradigm that overcomes intrinsic and extrinsic heterogeneity as well as genetic drift in bottlenecks by leveraging internal controls generated through activating sgRNAs only in half of the progenies of each cell. We use CRISPR-StAR to reveal in vivo-specific genetic dependencies in a genome-wide screen in mouse melanoma. Benchmarking to a conventional screening setup highlights the improved data quality this technology delivers. We anticipate CRISPR-StAR to set a new standard for genetic screening in complex models, foremost in vivo.
Project description:Pooled genetic screening with CRISPR/Cas9 has enabled genome-wide high-resolution assignment of genes to phenotypes. To assess the effect of a given genetic perturbation, each sgRNA must be evaluated in hundreds of cells to overcome stochastic genetic drift and obtain robust results. In complex models that display particularly high heterogeneity, such as organoids or tumors transplanted into mice however, sufficient representation typically requires unreasonable scaling, thus preventing genome-wide screens at high resolution. Here we present CRISPR-StAR, a screening paradigm that overcomes intrinsic and extrinsic heterogeneity as well as genetic drift in bottlenecks by leveraging internal controls generated through activating sgRNAs only in half of the progenies of each cell. We use CRISPR-StAR to reveal in vivo-specific genetic dependencies in a genome-wide screen in mouse melanoma. Benchmarking to a conventional screening setup highlights the improved data quality this technology delivers. We anticipate CRISPR-StAR to set a new standard for genetic screening in complex models, foremost in vivo.