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mRNA injection into the ventral blastomeres of Xenopus embryos of mRNA encoding Wnt pathway genes induces a secondary axis with complete head structures. To identify target genes of the pre-MBT dorsalization pathway that might be responsible for head formation in zebrafish, we have cloned zebrafish dickkopf1 (dkk1), which is expressed in tissues implicated(More)
Nodal signals induce mesodermal and endodermal progenitors during vertebrate development. To determine the role of Nodal signaling at a genomic level, we isolated Nodal-regulated genes by expression profiling using macroarrays and gene expression databases. Putative Nodal-regulated genes were validated by in situ hybridization screening in wild type and(More)
Proteins of the Extramacrochaetae and Id subfamily of Helix-Loop-Helix (HLH) proteins are negative regulators of bHLH transcription factors. We cloned a cDNA from zebrafish which encodes a member of the id3 subfamily. High levels of transcripts accumulated in the germ ring and in the embryonic shield. Towards the end of gastrulation, Id3 was highly(More)
The need for fast and accurate predictors of pharmaceutically important properties has been increasing due to pressure from high-throughput screening, in-silico screening, and the need to more rapidly identify potential pharmacokinetic issues before drugs advance to the more expensive clinical development stages. A novel method for making predictive models(More)
The bacteriophage population is large, dynamic, ancient, and genetically diverse. Limited genomic information shows that phage genomes are mosaic, and the genetic architecture of phage populations remains ill-defined. To understand the population structure of phages infecting a single host strain, we isolated, sequenced, and compared 627 phages of(More)
A new application of the grand canonical thermodynamics ensemble to compute ligand-protein binding is described. The described method is sufficiently rapid that it is practical to compute ligand-protein binding free energies for a large number of poses over the entire protein surface, thus identifying multiple putative ligand binding sites. In addition, the(More)
BACKGROUND Gene expression analyses based on complex hybridization measurements have increased rapidly in recent years and have given rise to a huge amount of bioinformatic tools such as image analyses and cluster analyses. However, the amount of work done to integrate and evaluate these tools and the corresponding experimental procedures is not high.(More)
It has been recognized that drug-induced QT prolongation is related to blockage of the human ether-a-go-go-related gene (hERG) ion channel. Therefore, it is prudent to evaluate the hERG binding of active compounds in early stages of drug discovery. In silico approaches provide an economic and quick method to screen for potential hERG liability. A diverse(More)
Dietary accumulation of four chiral organochlorine compounds--alpha-hexachlorocyclohexane (alpha-HCH), trans-chlordane, and chlorobiphenyls (CBs) 95 and 136-by immature rainbow trout (Oncorhynchus mykiss) was studied to determine if fish can accumulate and eliminate these compounds enantioselectively. Fish rapidly accumulated all four compounds from food(More)