Post-translational modifications of TIPE1.

<p>(A) NetPhosK Server was performed to predict kinase specific phosphorylation sites in TIPE1. (B) NetPhos Server was performed to predict generic phosphorylation sites in TIPE1. X axis represents amino acid sequence from N- to C- terminal. Y axis represents values computed by the software. The values above the threshold mean the most potential of phosphorylation.</p

Homology modeling and evaluation of model stability.

<p>(A) Homology modeling was performed by Swiss-Model Server and the predicted 3D structure of TIPE1 protein was shown. (B) Model quality was evaluated using the method of Ramachandran plot and the results represent the acceptable stability of 3D structure of TIPE1 protein.</p

Protein-protein interaction analysis for TIPE1.

<p>STRING platform is used to predict protein interactions. FBXW5, caspase8, caspase10, POMP and et al. were predicted to be interacted with TIPE1.</p

Prediction of signal peptide and transmembrane domain of TIPE1.

<p>Signal peptide (A) and transmembrane domain (B) of TIPE1 are predicted by SignaIP Server and TMpred Server, respectively. X axis represents amino acid sequence from N- to C- terminal. Y axis represents scores computed by each server.</p

Prediction of hydrophilicity, accessibility, polarity, flexibility, mutability and bulkiness of TIPE1.

<p>The hydrophilicity (A), accessibility (B), polarity (C), flexibility (D), mutability (E) and bulkiness (F) of TIPE1 are predicted using Protscale Server of expasy platform. X axis represents amino acid sequence from N- to C- terminal. Y axis represents scores computed by each algorithm.</p

APP deficiency enhances activation of Akt and MAPK upon NGF treatment.

<p>PC12 cells stably expressing APP shRNA and control cells expressing scrambled control (SC) shRNA were treated with 100 ng/mL NGF for the indicated time periods. Equal protein amounts of cell lysates were subjected to Western blotting to measure phosphorylation (p)/activation of Akt and MAPK. Protein levels were quantified by densitometry and normalized to those of controls for comparison (set as one arbitrary unit). Error bars indicate SEM, n = 3.</p

APP deficiency impairs neurite outgrowth and neuronal survival at basal levels, but promotes neurite outgrowth and neuronal survival more acutely upon NGF stimulation.

<p>(A) The day after plating embryonic day 17 rat primary neurons, neurons were infected with APP or scrambled control (SC) RNAi-containing lentivirus for 1 d. These neurons were then treated with or without 100 ng/mL NGF for 5 d, fixed, permeablized, immunostained with MAP2 antibody and a fluorescent-labeled secondary antibody, and observed under a fluorescent microscope. Infected cells were indicated by GFP fluorescence (in green) and neurons were indicated by positive MAP2 stainining (in red). The neurite lengths of infected neurons (>100) were measured for comparison. (B) Primary neurons from postnatal day 0 wild type (WT) and APP heterozygous (+/−) mice were treated with or without 100 ng/mL NGF for 5 d. These neurons were then treated with 25 µM Aβ for 1 d. After staining with propidium iodide (in red) and DAPI (in blue), the numbers of dead neurons (>300) were counted for comparison. Controls were set as one arbitrary unit. Error bars indicate SEM. *: <i>P</i><0.05, **: <i>P</i><0.01.</p

Expression of cis-encoded antisense of <i>dnaA.</i>

<p>A. The antisense RNA (<i>asdA</i>) encoded by the <i>dnaA</i> gene. B. Northern blot analysis of RNA isolated from wild-type S. Typhi grown to OD₆₀₀ 1.3 and probed with riboprobes obtained using the primer asdA-nF/asdA-nR. C. Alignment of <i>asdA</i> sequences showing the conservation of the promoter region. The transcription start site is indicated by an arrow and the −10 and −35 promoter elements are boxed. The asterisk (*) indicates the highly conserved sequences among various Enterobacteria. Abbreviations for bacterial species names are: <i>Salmonella</i> Typhi (STY), <i>Salmonella</i> Typhimurium (STM), <i>Escherichia coli</i> (ECO), <i>Shigella sp</i> (SHS), <i>Enterobacter sp</i> (ENC).</p

Overexpression analysis of <i>asdA</i>.

<p>qRT-PCR results of <i>dnaA</i> mRNA levels in A. 007-<i>asdA</i>, B. 007-pBAD, C. 007-<i>asdA</i>96 and D. Δrnc007<i>-asdA</i> and Δrne007-<i>asdA</i> strains. Total RNA was isolated from these strains grown to an OD₆₀₀ of 0.6 at 0, 5, 10, and 20 min after addition of L-arabinose (0.02% final concentration) to cultures.</p

Oligonucleotides used in this study.

<p>Oligonucleotides used in this study.</p