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The spatial distribution of RNA sequences during early development of the ascidian, Styela plicata, was determined by in situ hybridization with poly(U) and cloned DNA probes. Styela eggs and embryos contain three colored cytoplasmic regions of specific morphogenetic fates, the ectoplasm, endoplasm, and myoplasm. These cytoplasmic regions participate in(More)
Dual-channel long oligonucleotide microarrays are in widespread use. Although much attention has been given to proper experimental design and analysis regarding long oligonucleotide microarrays, relatively little information is available concerning the optimization of protocols. We carried out a series of microarray experiments designed to investigate the(More)
Growth factors and the extracellular matrix have been shown to fulfill vital developmental roles in many embryonic systems. Our hypothesis is that a developmental role played by the extracellular matrix in sea urchins may be the binding of a PDGF-like growth factor to promote signaling activity. We report here that anti-human PDGF-B antibodies and(More)
mRNAs for Spec 1 and Spec 2 of Strongylocentrotus purpuratus and LpS1 of Lytechinus pictus accumulate only in the aboral ectoderm of developing embryos. In vitro nuclear transcription assays were done to study the transcriptional regulation of these cell type-specific genes. Spec 1, Spec 2c, and Spec 2d genes all appeared to be transcriptionally activated(More)
The influence of the extracellular matrix (ECM) on differential gene expression during sea urchin development was explored using cell-type-specific cDNA probes. The ECM of three species of sea urchin, Strongylocentrotus purpuratus, Lytechinus variegatus and Lytechinus pictus, was disrupted with the lathrytic agent beta-aminopropionitrile (BAPN), which(More)
The LpS1 genes of the sea urchin Lytechinus pictus are activated early in development in aboral ectoderm cells. They therefore have ontogenic properties similar to their counterparts in Stronglyocentrotus purpuratus, the Spec genes. Both gene families encode proteins belonging to the calmodulin superfamily as evidenced by the presence of distinct EF-hand(More)
The aryl hydrocarbon receptor (AHR) is a ligand-activated transcription factor that mediates the toxic effects of its xenobiotic ligands and acts as an environmental checkpoint during the cell cycle. We expressed stably integrated, Tet-Off-regulated AHR variants in fibroblasts from AHR-null mice to further investigate the AHR role in cell cycle regulation.(More)
RET/PTC rearrangements represent key genetic events involved in papillary thyroid carcinoma (PTC) initiation. The aim of the present study was to identify the early changes in gene expression induced by RET/PTC in thyroid cells. For this purpose, microarray analysis was conducted on PCCL3 cells conditionally expressing the RET/PTC3 oncogene. Gene expression(More)
With no known exceptions, every published microarray study to determine differential mRNA levels in eukaryotes used RNA extracted from whole cells. It is assumed that the use of whole cell RNA in microarray gene expression analysis provides a legitimate profile of steady-state mRNA. Standard labeling methods and the prevailing dogma that mRNA resides almost(More)
Homeobox genes from the urochordates Styela clava (AHox2) and S. plicata (AHox3) were cloned and analyzed. The two genes are homologous and Antennapedia-like. The homeobox regions have 87% identity at the nucleotide level and are identical at the amino-acid level. No introns are present in the homeobox region of AHox3, and AHox3 is represented at a low copy(More)