ABSTRACT: The changes in transcript titers are described for Drosophila Kc167 cells following 5-48 hr treatment with 20-hydroxyecdysone. Keywords: hormone response RNA from ecdysone-treated cells was compared to RNA from cells treated with carrier alone. A total of 3-13 slides were analyzed for each time point, each from a separate biological sample; dye-swaps were included.
Project description:The changes in transcript titers are described for Drosophila ML-DmBG3-c2 cells following 5-48 hr treatment with 20-hydroxyecdysone. Keywords: hormone response RNA from ecdysone-treated cells was compared to RNA from cells treated with carrier alone. A total of 4 slides were analyzed for each time point, each from a separate biological sample; dye-swaps were included.
Project description:The changes in transcript titers are described for Drosophila CME W1 Cl.8+ cells following 5-48 hr treatment with 20-hydroxyecdysone. Keywords: hormone response RNA from ecdysone-treated cells was compared to RNA from cells treated with carrier alone. A total of 4 slides were analyzed for each time point, each from a separate biological sample; dye-swaps were included.
Project description:The changes in transcript titers are described for Drosophila ML-DmD4-c1 cells following 5-48 hr treatment with 20-hydroxyecdysone. Keywords: hormone response RNA from ecdysone-treated cells was compared to RNA from cells treated with carrier alone. A total of 3-4 slides were analyzed for each time point, each from a separate biological sample; dye-swaps were included.
Project description:Two different strains of Aedes aegypti mosquito, Moyo-in-dry and Moyo-S, are profiled for their response through time to infection with Dengue 2 virus. Expression is measured using a two-colour custom spotted cDNA array. A mixed strain uninfected sample is hybridized as the reference.
Project description:Gene expression profiles reflect unique aspects of individual biologic phenotypes and may characterize the heterogeneity of solid tumors. Using previously-described methodologies that employ DNA microarray data, a 50-gene expression profile (metagene) that predicts risk of recurrence in early stage colon carcinoma was identified. This analysis used an initial discovery cohort of 52 patients. The performance of the 50-gene predictor was evaluated in an independent validation cohort of 73 patients. Using a connectivity map analysis of the 50-gene model, we identified candidate agents and then tested the in vitro efficacy of these compounds in colon cancer cell lines. 73 samples that had patient recurrence data with stage information were used in the analysis. Keywords: Disease state analysis A total of 73 samples were spotted on microarray slides. No replicates are included in the study.
Project description:Rhabdomyosarcoma (RMS) is the most common childhood sarcoma and is identified as either the embryonal or alveolar (ARMS) subtype. In approximately 75% of cases, ARMSs are characterized by specific chromosomal translocations that involve PAX and FKHR genes. ARMS gene expression signatures vary, depending on the presence or absence of the translocations. Insulin-like growth factor-binding protein 2 (IGFBP2) is strongly overexpressed in translocation-negative RMS. Because IGFBP2 is associated with tumorigenesis, we investigated its functional role in RMS. An analysis of IGFBP2 distribution in RMS cell lines revealed a strong accumulation in the Golgi complex, in which morphological characteristics appeared peculiarly modified. After silencing IGFBP2 expression, our microarray analysis revealed mostly cell cycle and actin cytoskeleton gene modulations. In parallel, IGFBP2-silenced cells showed reduced cell cycle and rates of invasion and decreased seeding in the lungs after tail vein injections in immunodeficient mice. An analysis of IGFBP2 mRNA and protein localization in human tumors showed abnormal protein accumulation in the Golgi complex, mostly in PAX/FKHR-negative RMS. Moreover, an analysis of patients with RMS revealed the presence of conspicuous circulating levels of IGFBP2 proteins in children with highly aggressive RMS tumors. Taken together, our data provide evidence that IGFBP2 contributes to tumor progression and that it could be used as a marker to better classify clinical and biological risks in RMS. Three independent silencing experiments on RH36, an embryonal rhabdomyosarcoma cell line, were performed to study the role of IGFBP2 oncogene in this childhood tumor. Each of 3 biological replicates has its own control which is represented by cell culture treated with a non-targeting siRNA (siCONTROL). 3 controls were used to produce a M-bM-^@M-^\control poolM-bM-^@M-^] that has been used as reference in all microarray experiments. Each microarray experiment consists of a competitive hybridization between test and reference RNA (e.g. silenced cells vs. control), labelled with Cy3 or Cy5. Two microarray experiments were performed for each of three silencing experiment (technical replicate). Each slide was scanned and the data was normalized and analyzed.
Project description:Genomic, proteomic, and metabolomic technologies continue to receive increasing interest from environmental toxicologists. This interest is due to the great potential of these technologies to identify detailed modes of action and to provide assistance in the evaluation of a contaminant?s risk to aquatic organisms. Our experimental model is the zebrafish (Danio rerio) exposed to reference endocrine disrupting compounds in order to investigate compound-induced changes in gene transcript profiles. Adult, female zebrafish were exposed to 0, 15, 40, and 100 ng/L of 17 alpha-ethynylestradiol (EE2) and concentration and time-dependent changes in hepatic gene expression were examined using Affymetrix GeneChip® Zebrafish Genome Microarrays. At 24, 48, and 168 hours, fish were sacrificed and liver mRNA was extracted for gene expression analysis (24 and 168 hours only). In an effort to link gene expression changes to effects on higher levels of biological organization, body and ovary weights were measured and blood was collected for measurement of plasma steroid hormones (17 beta-estradiol (E2), testosterone (T)) and vitellogenin (VTG) using ELISA. EE2 exposure significantly affected GSI, E2, T, VTG and gene expression. We observed 1575 genes that were significantly affected (up- or down-regulated by at least 1.5-fold (p ? 0.001) in a concentration-dependent manner by EE2 exposure at either 24 or 168 hours. EE2 exposure altered transcription of genes involved in steroid hormone homeostasis, cholesterol homeostasis, retinoic acid metabolism, and cell growth and proliferation. Plasma VTG was significantly increased at 24, 48, and 168 hours (p<0.05) at 40 and 100 ng/L and at 15 ng/L at 168 hours. E2 and T were significantly reduced following EE2 exposure at 48 and 168 hours. GSI was decreased in a dose-dependent manner at 168 hours. In this study, we identified genes involved in a variety of biological functions that have the potential to be used as markers of exposure to estrogenic substances. Future work will evaluate the use of these genes in zebrafish exposed to weak estrogens to determine if these genes are indicative of exposure to estrogens with varying potencies.
Project description:Biomolecular condensates are implicated in many cellular processes, and are thought to create subcellular microenvironments that regulate specific biochemical activities. For example, in vitro experiments suggest that condensates enable non-stoichiometric enrichment of small molecules within condensates. However, probing the microenvironments of condensates in cells is a major challenge, because tools to selectively manipulate specific condensates in living cells are limited. Here we developed a non-natural micropeptide (i.e., the “killswitch”) and a Nanobody-based recruitment system as a universal approach to probe endogenous condensates, and demonstrate direct links between condensate microenvironments and function in cells. The killswitch is a hydrophobic, aromatic-rich sequence with an ability to self-associate, and no homology to human proteins. When recruited to endogenous and disease-specific condensates in human cells, the killswitch arrested the dynamics of the condensate-forming proteins, which led to predicted and unexpected effects. Targeting the killswitch to the nucleolar protein NPM1 altered nucleolar composition, and inhibited the dynamics of a ribosomal protein within nucleoli. Targeting the killswitch to fusion oncoprotein condensates inhibited the dynamics of effector proteins in the condensates, altered condensate composition, and inhibited proliferation of condensate-driven leukemia cells. In adenoviral nuclear condensates, the killswitch inhibited partitioning of capsid protein into condensates, and suppressed viral particle assembly. The results suggest that the microenvironment within cellular condensates has an essential contribution to non-stoichiometric enrichment and the dynamics of effector proteins. The killswitch is a widely applicable tool to alter the material properties of endogenous condensates, and as a consequence, to probe functions of condensates linked to diverse physiological and pathological processes in living systems.