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The Sonic hedgehog (Shh) gene is expressed in the areas that mediate central nervous system (CNS) and limb polarity, indicating its role in the inductive interactions that form the CNS. The Shh and two other closely related genes encode putative secreted proteins and are possibly involved in cell-cell interactions. Ectopic expression of Shh in the mouse CNS triggers the flow of plate-expressed genes.

Abstract Background The topology of a biological pathway provides clues as to how a pathway operates, but rationally using this topology information with observed gene expression data remains a challenge. Results We introduce a new general-purpose analytic method called Mechanistic Bayesian Networks (MBNs) that allows for the integration of gene expression data and known constraints within a signal or regulatory pathway to predict new downstream pathway targets. The MBN framework is implemented in an open-source Bayesian network learning package, the Python Environment for Bayesian Learning (PEBL). We demonstrate how MBNs can be used by modeling the early steps of the sonic hedgehog pathway using gene expression data from different developmental stages and genetic backgrounds in mouse. Using the MBN approach we are able to automatically identify many of the known downstream targets of the hedgehog pathway such as Gas1 and Gli1, along with a short list of likely targets such as Mig12. Conclusions The MBN approach shown here can easily be extended to other pathways and data types to yield a more mechanistic framework for learning genetic regulatory models.

Cre-lox technology has revolutionized research in renal physiology by allowing site-specific genetic recombination in individual nephron segments. The distal convoluted tubule (DCT), consisting of distinct early (DCT1) and late (DCT2) segments, plays a central role in Na+ and K+ homeostasis. The only established Cre line targeting the DCT is Pvalb-Cre, which is limited by noninducibility, activity along DCT1 only, and activity in neurons. Here, we report the characterization of the first Cre line specific to the entire DCT. CRISPR/Cas9 targeting was used to introduce a tamoxifen-inducible IRES-Cre- ERT2 cassette downstream of the coding region of the Slc12a3 gene encoding the NaCl cotransporter (NCC). The resulting Slc12a3-Cre- ERT2 mice were crossed with R26R-YFP reporter mice, which revealed minimal leakiness with 6.3% of NCC-positive cells expressing yellow fluorescent protein (YFP) in the absence of tamoxifen. After tamoxifen injection, YFP expression was observed in 91.2% of NCC-positive cells and only in NCC-positive cells, revealing high recombination efficiency and DCT specificity. Crossing to R26RTdTomato mice revealed higher leakiness (64.5%), suggesting differential sensitivity of the floxed site. Western blot analysis revealed no differences in abundances of total NCC or the active phosphorylated form of NCC in Slc12a3-Cre-ERT2 mice of either sex compared with controls. Plasma K+ and Mg2+ concentrations and thiazide-sensitive Na+ and K+ excretion did not differ in Slc12a3-Cre-ERT2 mice compared with controls when sex matched. These data suggest genetic modification had no obvious effect on NCC function. Slc12a3-Cre- ERT2 mice are the first line generated demonstrating inducible Cre recombinase activity along the entire DCT and will be a useful tool to study DCT function. [ABSTRACT FROM AUTHOR]

[super 15]N-HSQC based NMR titration experiments are used for a 12-residue peptide substrate with AcpS to identify six specifically interacting residues without the formation of any notable secondary structure. The genetic insertion of the eight residue coding sequence into the proteins sonic hedgehog and transferrin receptor has enabled good in vitro and in vivo PPTase-mediated modification by a series of fluorescent CoAs, which has led to a set of fluorescent proteins with a peptide tag minimally perturbant to protein folds.

The generation and characterization of a genetically engineered mouse model in which all animals develop short latency malignant osteosarcoma is described. The model based on osteoblast-restricted deletion of p53 and pRb showed strong similarities between murine osteosarcoma and human osteosarcoma could be used to address the molecular genetics of osteosarcoma and develop novel therapeutic strategies.

The signaling of Sonic Hedgehog (Shh) morphogen is promoted by Gas 1 and Cdo proteins. The Shh signaling is crucial for the development of various parts of the central nervous system.