Cofactor binding pocket and substrate binding site.

<p>(A) Interaction between SmyD2 and sinefungin. SmyD2 residues are represented by balls-and-sticks with their carbon atoms colored according to the scheme in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0021640#pone-0021640-g001" target="_blank">Figure 1</a>. Sinefungin is depicted by balls-and-sticks overlaid with 2F_o−F_c omit map calculated at 1.8 Å and contoured at 2.5 σ. Hydrogen bonds are illustrated as red broken lines. (B) Ribbon diagram of the putative substrate binding site, illustrating the interaction between SmyD2 and the modeled H3 peptide. The H3 peptide (1–10) from the Set7/9 structure (PDB code 1O9S) is displayed as balls-and-sticks with carbon atoms colored yellow. (C) Superposition of the target lysine-access channels of SmyD2, SmyD1, and SmyD3. The oval-shaped channel in SmyD2 is depicted by molecular surface. Residues in SmyD2 are represented by balls-and-sticks, while residues in SmyD1 and SmyD3 are displayed as sticks in purple and orange, respectively. Target lysine (H3K4) is colored in yellow.</p

<i>M. xanthus</i> strains used in this study.

<p><i>M. xanthus</i> strains used in this study.</p

Stereo view ribbon diagram of the domain interface of N- and C-terminal lobes.

<p>Residues are colored according to domain in which they reside, and hydrogen bonds are indicated as red dashed lines.</p

Combined Oral and Intravenous Immunization Stimulates Strong IgA Responses in Both Systemic and Mucosal Compartments

<div><p>To investigate the influence of immunization routes onIgG, IgA and IgM production in systemic and mucosal compartments, we immunized mice with keyhole limpet hemocyanin (KLH) via oral, intranasal (i.n.) or subcutaneous (s.c.) routes alone or combined with the intravenous (i.v.) route. We found that administering antigen intravenously could affect antibody production and formation of antibody secreting cells (ASCs) depending on the immunization route previously used. Combined oral/i.v. immunization but not s.c./i.v. immunization caused a great increase of IgA ASCs in the spleen and enhanced IgA production in the small intestine and serum. Combined i.n./i.v. immunization could also increase IgA ASCs in the spleen and enhance IgA production in serum but had no effect on IgA production in the small intestine. Oral/i.v. immunization caused increase of IgG ASCs in both the spleen and bone marrow. In comparison, combined i.n./i.v. and s.c./i.v. immunization could increase IgG ASCs in the spleen but not in bone marrow. Intravenous administration of KLH in mice that had been immunized via oral, i.n. or s.c. routes caused some increase of IgM ASCs in the spleen but not in bone marrow. In conclusion, combined oral and i.v. administration of an antigen can induce fast and strong immune responses, especially for IgA, in both systemic and mucosal compartments.</p></div

IHC analysis of IgA ASCs in the spleen.

<p>BALB/c mice were immunized with KLH via oral, i.n. or s.c. routes. Three days before sacrificing, mice were administered with KLH orally, intranasally, subcutaneously or intravenously. Spleens of mice were embedded in paraffin and sectioned into 3-μm slices and stained using anti-IgA antibody (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0168037#sec002" target="_blank">Materials and Methods</a>). Top row, mice were immunized with KLH orally, intranasally or subcutaneously. Three days before sacrificing, the mice received PBS via oral, i.n. or i.v. routes. The negative control was from mice that did not receive inoculations. Middle row, mice were immunized with KLH and received a final immunization with KLH before sacrificing either orally, intranasally or subcutaneously. Bottom row, mice were immunized orally, intranasally or subcutaneously and administered a final immunization with KLH intravenously. The isotype control was stained using rat IgG1 anti-human fibrinogen antibody. Data are representative ofeightmice(The s.c./s.c. group in the middle row were five mice). Scale bar = 50 μm.</p

An example illustrating how local cell density is counted.

<p>The local measuring domain of a cell is defined to be a square whose sides are taken to be equal to cell length. The measuring domain of cell <i>k</i> (colored in dark grey) is the square colored in yellow. Five of the neighboring cells, labeled by number 2, 3, 5, 6 and 7, lie or partly lie within this square, giving the local cell density of cell <i>k</i> to be 5. This diagram also illustrates cell turning and alignment of cells in close proximity.</p

Crystallographic data and refinement statistics.

a<p><i>R_merge</i> = Σ|I−〈I〉|/ΣI, where I is the observed intensity and 〈I〉 is the averaged intensity of multiple observations of symmetry-related reflections.</p>b<p>Numbers in parentheses refer to the highest resolution shell.</p>c<p><i>R_work</i> = Σ|F_o−F_c|/Σ|F_o|, where F_o is the observed structure factor, F_c is the calculated struture factor.</p>d<p><i>R_free</i> was calculated using a subset (5%) of the reflection not used in the refinement.</p

Ribbon diagram of the SmyD2 structures.

<p>(A) Side view (left) and top view (right) of the binary structure of SmyD2–sinefungin. (B) The structure of SmyD2–AdoHcy. Secondary structures of SmyD2, α-helices, 3₁₀-helices, and β-strands are labeled and numbered according to their position in the sequence. The S-sequence, MYND, SET-I, core SET, post-SET, and CTD are depicted in light green, blue, pink, green, cyan, and red, respectively, while sinefungin and AdoHcy are represented by balls-and-sticks and zinc ions are denoted by purple spheres. (C) Superposition of two SmyD2 structures in complex with sinefungin (red) and AdoHcy (cyan) based on their N-lobes. The maximum distance between the equivalent regions in the outer edge of their C-lobes is indicated. The intradomain motion is indicated by the straight arrow and the approximate rotation angle is given. (D) Ribbon diagram of the structure of SmyD1 and (E) SmyD3 with the domains colored the same as above.</p

The physical model of <i>M. xanthus</i> cell.

<p>A cell model with three nodes (N = 3) and its orientation are shown. For algorithm implementation purpose, each cell node is numbered with leading pole as node 1 and lagging pole as node . Any two consecutive nodes are connected by a segment of length L. Cell is allowed to turn or bend to some angle .</p

Effect of different active turning angle on aggregation center formation.

<p>Effect of different active turning angle on aggregation center formation.</p