The mean fluorescence values obtained from the flow cytometry histogram were plotted against incubated Aβ_1–42 concentration in the presence of serum (A) and under serum deprived condition (B).

<p>The mean fluorescence values obtained from the flow cytometry histogram were plotted against incubated Aβ_1–42 concentration in the presence of serum (A) and under serum deprived condition (B).</p

Detection of fibrillar Aβ_1–42 induced Aβ_1–40 production by flow cytometry.

<p>For the analysis of Aβ_1–40 synthesis in amyloidic condition, Hep-1 cells were treated with fibrillar Aβ_1–42 in the presence (A) or absence (B) of serum, stained with anti Aβ_1–40 antibodies (biotinylated) and streptavidin conjugated phycoerythrin. Histograms are shown for the control with no added amyloid (ctrl) and for cells incubated with various concentrations of Aβ_1–42.as indicated in the figure.</p

Fibrillar Aβ_1–42 induced APP upregulation in Hep-1 cells.

<p>Morphology of fibrillar Aβ_1–42 was confirmed by TEM (A).Cells were untreated or treated with 2 µM, 10 µM, 20 µM Aβ_1–42 for 24 hrs. Cell lysates were subjected to Western blot analysis using 8E5 antibody (B). The blot was quantitated by densitometric analysis (C). The fold increase of APP production compared to untreated control cells were shown as mean ± SD (n = 4). *, P<0.05; **, P<0.01 compared to control.</p

Aβ_1–40 expression monitored by immunofluorescence microscopy.

<p>Endothelial cells were incubated with different concentrations of fibrils for 12 hrs and processed as described in the <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0058194#s2" target="_blank">materials and method</a>. Phase contrast (left panels) and fluorescence images (right panel) were taken showing the same field.</p

The morphological changes of Hep-1 cells incubated with Aβ_1–42 in the presence and absence of serum analyzed by scattering data.

<p>The effect of Aβ_1–42 concentration (A, D: 0 µM; B, E: 5 µM; C, F: 10 µM) in both forward and side scatter values is given in the dot plot.</p

Affects of exogenous Aβ_1–42 on the level of eNOS and autophagy in endothelial cells.

<p>Endothelial cells were treated with 5 µM and 10 µM Aβ_1–42 and incubated for 12 hrs. Protein levels of eNOS, nNOS, caveolin-1 and the autophagy marker LC3B were analyzed by Western blotting (A). (B), quantitation of protein levels of eNOS, nNOS and caveolin-1 normalized to β-actin control. Results are mean ± SD (n = 3–5). (C), quantitation of LC3B II/I ratio normalized to β-actin control. Results are mean ± SD (n = 3). **, P<0.01 compared to control.</p

Examples of NIA-Only cDNA Clones and RT–PCR Results

<p>Expression pattern of 19 novel cDNA clones in 16 different cell lines or tissues: unfertilized egg, E3.5 blastocyst, E7.5 whole embryo (embryo plus placenta), E12.5 male mesonephros (gonad plus mesonephros), newborn brain, newborn ovary, newborn kidney, embryonic germ (EG) cell, embryonic stem (ES) cell (maintained as undifferentiated in the presence of LIF), trophoblast stem (TS) cell, mesenchymal stem (MS) cell, osteoblast, neural stem/progenitor (NS) cell, NS differentiated (differentiated neural stem/progenitor cells), and hematopoietic stem/progenitor (HS) cells. Glyceraldegyde-3-phosphate dehydrogenase (GAP-DH) was used as a control. A U number is assigned to each gene in the gene index (see <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0000074#sd002" target="_blank">Dataset S2</a>). The exon number was predicted from alignment with the mouse genome sequence, and the amino acid sequence was predicted with the ORF finder from NCBI.</p

PCA Analysis of EST Frequency

<p>The results were obtained by analyzing 2,812 genes that exceeded 0.1% in at least one library. (A) 3D biplot that shows both cell types (red spheres) and genes (yellow boxes). (B) 2D PCA of cell types. EST frequencies were log-transformed before the analysis. Names of some cells and tissues are abbreviated as follows: 6.5 EP, E6.5 whole embryo (embryo plus placenta); 7.5 EP, E7.5 whole embryo (embryo plus placenta); 8.5 EP, E8.5 whole embryo (embryo plus placenta); 9.5 EP, E9.5 whole embryo (embryo plus placenta); 7.5 E, E7.5 embryonic part only; 7.5 P, E7.5 extraembryonic part only; NbOvary, newborn ovary; NbBrain, newborn brain; NbHeart, newborn heart; NbKidney, newborn kidney; 13.5 VMB, E13.5 ventral midbrain dopamine cells; 12.5 Gonad (F), E12.5 female gonad/mesonephros; 12.5 Gonad (M), E12.5 male gonad/mesonephros; HS (Kit⁻, Sca1⁻), hematopoietic stem/progenitor cells (Lin⁻, Kit⁻, Sca1⁻); HS (Kit⁻, Sca1⁺), hematopoietic stem/progenitor cells (Lin⁻, Kit⁻, Sca1⁺); HS (Kit⁺, Sca1⁻), hematopoietic stem/progenitor cells (Lin⁻, Kit⁺, Sca1⁻); HS (Kit⁺, Sca1⁺), hematopoietic stem/progenitor cells (Lin⁻, Kit⁺, Sca1⁺); and NS-D, differentiated NS cells.</p

Signature Genes for Specific Groups of Early Embryos and Stem Cells

<p>Signature Genes for Specific Groups of Early Embryos and Stem Cells</p