The environment (within 9 Å) of the semi-dominant gain-of-function <i>unc-8</i> allele <i>e49</i>, here A266T, in the 4 superimposed models of a subunit of UNC-8.

<p>For clarity, only ribbons are drawn. Yellow, blue, green and orange denote the different modeled subunits of <i>unc-8</i>. The sidechain of A266 was substituted in the picture by T266 and is shown in red.</p

Structural alignment used for modeling of MEC-4 and UNC-8.

<p>MEC-4_A, MEC-4_B, MEC-4_C, MEC-4_H and UNC-8_A, UNC-8_B, UNC-8_C, UNC-8_H were treated independently from one another. Each subunit is modeled to the superimposed subunits of 2QTS or 3HGC, respectively. Secondary structural elements are color-coded (red: helices, blue: β-strands). Asterisks below the sequences denote identical, and dots similar residues. Amino acid substitutions corresponding to mutant alleles are depicted in bold and are underlined, for specifics see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0012814#pone-0012814-t001" target="_blank">Table 1</a>. Solid lines above the alignment denote parts of the modeled hand (turquoise: forearm, light blue: fingers, yellow: thumb).</p

Stereo views of the environment of the dominant, gain-of-function <i>mec-4</i> allele <i>u231</i> (here A408V).

<p>The sidechain of A408 was substituted by Val and is shown in red. I and II denote transmembrane helices I and II. <b>a</b>: Yellow, blue and green denote the different subunits of <i>mec-4</i> modeled to the three different subunits of the crystal structure 2QTS. <b>b</b>: Yellow, blue and green denote the crystallographic equivalent subunits of the trimer derived by application of crystallographic symmetry. The subunit was modeled to the subunit of 3HGC. The same helical segments are shown as in Figure 3a.</p

Superposition of the four subunits of MEC-4 modeled on the 3 subunits of the crystal structure of the closed acid sensing ion channel of chicken (PDB ID: 2QTS) and on the minimal function channel (PDB ID: 3HGC).

<p>Colors denote the model confidence factor of the SWISS-MODEL server; dark blue regions denote high confidence, green to red gradually lower reliability. Lower reliability is assigned if the template residues (in A, B and C of 2QTS and 3HGC) differ from one another or to sparse loops incorporated from other structures. The arrow marks the position of <i>e49</i> in the modeled UNC-8 subunits (not shown). NC1 and NC2 denote the position of two blocks of sequence in MEC-4 which have no counterpart in the alignment and therefore are not modeled.</p

Ion channel mutants.

<p>The molecular characteristics, the associated mutant phenotypes and the localization of amino-acid substitutions on the model are indicated. TM: Transmembrane.</p

Expression domains of common response genes and symptoms associated with infection

GFP. In contrast, no GFP expression or vacuolization was seen in the intestines of non-infected worms.<p><b>Copyright information:</b></p><p>Taken from "Genome-wide investigation reveals pathogen-specific and shared signatures in the response of to infection"</p><p>http://genomebiology.com/2007/8/9/R194</p><p>Genome Biology 2007;8(9):R194-R194.</p><p>Published online 17 Sep 2007</p><p>PMCID:PMC2375032.</p><p></p

Comparison of host gene expression profiles following infection with different pathogens

Expression levels are indicated by a color scale and represent normalized differences between infected and control animals. Grey denotes genes not considered to be differentially regulated under that condition. The numbers on the vertical axis correspond to differentially regulated genes. Each column shows the expression levels of individual genes (represented as rows) following infection by the pathogens as indicated on the horizontal axis (, ; , ; , ; , ). Genes differentially regulated in an infection with and their comparative expression levels with other pathogens. Genes defining a pathogen-specific signature specifically up-regulated with infection. Groupings, as indicated by the horizontal bars, formed after clustering using non-redundant sets of genes that were up- and down-regulated by at least two pathogens (trees not shown). Genes commonly up-regulated following , and infections.<p><b>Copyright information:</b></p><p>Taken from "Genome-wide investigation reveals pathogen-specific and shared signatures in the response of to infection"</p><p>http://genomebiology.com/2007/8/9/R194</p><p>Genome Biology 2007;8(9):R194-R194.</p><p>Published online 17 Sep 2007</p><p>PMCID:PMC2375032.</p><p></p

Third harmonic generation microscopy for lipid deposition imaging.

<p>(<b>a</b>) Schematic representation of the non-linear microscope configuration. Two paths are used for detection, one in reflection (for TPEF signals) and the other in transmission mode (for THG signals). ND: Neutral Density filters, GM: Galvanometric mirrors, PMT: photomultiplier tube, L1, L2: telescope lenses, DM: Dichroic mirror, F1, F2: Filters, O: Objective lens, C: Condenser lens, M: Mirror. (<b>b</b>) Geometry of third harmonic generation (fundamental frequency ω), via non-linear optical interaction with a medium (). (<b>c</b>) The respective energy-level diagram describing the interaction of three photons of angular frequency ω with a non-linear material, to form one photon of triple frequency (and thus energy) compared to initial incident photons. (<b>d</b>) When a Gaussian beam is focused within the volume of a birefringent medium that perfectly compensates dispersion for the fundamental and third harmonic frequencies, THG waves symmetrical to the beam waist position (blue and dotted line respectively) interfere destructively due to a phase shift by π radians, and no signal is obtained. Destructive interference taking place in such a birefringent material can be avoided if the regions before and after the beam waist position possess unequal third order susceptibility values, since the generated third harmonic waves differ in amplitude. (<b>e</b>) For a material presenting a perfect dispersion compensation between frequencies ω and 3ω (implying that the phase matching condition Δk = 3k_ω - k_3ω = 0 is satisfied), the momentum conservation of the respective photons can be met. However, no signal is generated due to destructive interference of THG waves (shown in panel d). For common normal dispersive material (n_3ω>n_ω), momentum conservation condition cannot be met in any manner; and therefore, effective THG is not possible. If n_3ωω, efficient THG can occur since the angularly spread wave vectors of the focused fundamental beam can be added effectively so that the total momentum before and after the nonlinear interaction is conserved.</p

Protein dynamics in a longitudinal ageing study in <i>C</i>. <i>elegans</i>.

<p>(A) Representative images of 3 single animals grown at 25°C at day 1, 3 and 5. Animals co-express p_<i>ife-2</i>IFE-2::GFP and p_{<i>dcap-1</i>}DCAP-1::dsRED (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0127869#pone.0127869.s008" target="_blank">S4 Video</a>). Individuals show differences in protein localization during ageing. Size bars correspond to 100μm. (B) IFE-2::GFP and (C) DCAP-1::dsRED fluorescent intensity quantification of the 3 animals in (A).</p

A versatile imaging platform for light sheet microscopy and FRAP.

<p>(A) 3D scheme of the LSM and components (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0127869#pone.0127869.s005" target="_blank">S1 Video</a> for full 3D overview of the setup and compare photographs in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0127869#pone.0127869.s001" target="_blank">S1 Fig</a>). The red line indicates the path of the laser beam. The laser beam is guided by a flexible mirror set to pass through the cylindrical lens, where a laser light sheet is created and focused on the sample, which is immersed in an index matching fluid bath. A 3D stage is used to move the sample along x-, y- and z-axis into position for imaging via the CCD camera with tube lens attachment, which is placed orthogonal to the light sheet. Components for FRAP performance are encircled and consist of a flip mirror and a focal lens to concentrate the beam for fluorescent photobleaching of the sample. A detailed description is provided in Materials and Methods. (B) Basic 2D scheme of the setup showing its essential components. LAS = laser, SH = shutter, FM = flip mirror, CL = cylindrical lens, FL1 = focal lens 1, FL2 = focal lens 2, OS = 3D stage, RBS = Refractive index matching fluid bath and sample, LED = white light LED, CCD = CCD camera, TL = tube lens, I = iris, F = fluorescent filter set, OL = objective lens.</p