Additional file 1: of Protein remote homology detection based on bidirectional long short-term memory

The SCOP ID of the independent SCOPe testing dataset. (PDF 7601 kb

Initial field.zip

This folder contains the initial condition of Advanced Regional Prediction (ARPS, version5.3.3) for the wind-blown sand simulations

The effect of the <i>hMLH1</i> -93G>A genotype on <i>hMLH1</i> expression.

<p><b>(A)</b> Schematic of reporter gene constructs containing the core promoter region of <i>hMSH1</i> (a 282-bp fragment from -299 to -17) with the G or A allele at the -93 polymorphic site (upper). The luciferase expression of two constructs (pGL3-93G and pGL3-93A) in 293T and SK-OV-3 cells cotransfected with pRL-SV40 to standardize the transfection efficiency is shown (lower). Each group has six replicates, and the transfection experiments were repeated three times. The data are the means ± standard error of the mean. The asterisk indicates a significant change. (<b>B</b>) <i>hMLH1</i> expression level in twenty-eight ovarian cancer tissues with different -93G>A genotypes (6 -93GG, 10 -93AG and 12 -93AA); the data are the means ± standard error of the mean. The expression level of the -93GG and -93AG genotypes were significantly higher than that of the AA genotype (<i>P</i><0.001).</p

Color and Texture Morphing with Colloids on Multilayered Surfaces

Dynamic morphing of marine species to match with environment changes in color and texture is an advanced means for surviving, self-defense, and reproduction. Here we use colloids that are placed inside a multilayered structure to demonstrate color and texture morphing. The multilayer is composed of a thermal insulating base layer, a light absorbing mid layer, and a liquid top layer. When external light of moderate intensity (∼0.2 W cm^–2) strikes the structure, colloids inside the liquid layer will be assembled to locations with an optimal absorption. When this system is exposed to continuous laser pulses, more than 18 000 times of reversible responses are recorded, where the system requests 20 ms to start the response and another 160 ms to complete. The flexibility of our concept further allows the system to be built on a variety of light-absorbing substrates, including dyed paper, gold thin film, and amorphous silicon, with the top layer even a solid

Localization of p47-roGFP in skeletal muscle.

<p>(A) Immunostaining of enzymatically dissociated single FDB myofibers for endogenous p47^phox and the ryanodine receptor shows that p47^phox co-localizes with the ryanodine receptor at the triad. (B) Fluorescent live cell image of an FDB electroporated with p47-roGFP and counter stained with the membrane and t-tubule dye FM4-64® shows that p47-roGFP is localized at the t-tubule. The line plots represent the longitudinal spatial profile of fluorescence averaged over the transverse direction within the boxed regions.</p

p47-roGFP allows for live-cell imaging of redox changes during RAW264.7 cell activation.

<p>(<i>A</i>) Representative confocal image of RAW264.7 cells transfected with p47-roGFP shows cytosolic distribution of p47-roGFP in control cells (−LPS). Upon LPS-mediated activation (20 ng/ml, 45 min) p47-roGFP localized with the membrane dye FM4-64®. (B) Representative time course of LPS-induced p47-roGFP oxidation. Biosensor oxidization occurred dynamically upon LPS-induced activation (black squares), while in the presence of the Nox peptide inhibitor gp91ds (5 µm, 60 min) minimal oxidation occurred (red circles). After 45 min of LPS, cells were treated with 1 mM H₂O₂ to maximally oxidize followed by addition of 10 mM DTT to maximally reduce the biosensors. (C) Average (±SEM) of 9 cells for each condition from (B) during the last 3 minutes of LPS. ** p<0.01 (Tukey statistical analysis for p value).</p

Construction of the Nox biosensor p47-roGFP.

<p>The coding sequences of human p47^phox and roGFP2, carrying a 30-amino-acid linker, were PCR amplified from pcDNA3.1-p47^phox and pLPCX-Grx1-roGFP2, respectively as described in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0063989#s2" target="_blank">Materials and Methods</a>. The forward and reverse primers for the two reactions were designed to incorporate HindIII, SpeI and NotI restriction sites. Both PCR products were purified and ligated to form a linear p47^phox-linker-roGFP expression cassette, which was cloned into the pcDNA3.1 vector using HindIII and NotI restriction sites.</p

p47-roGFP biosensor shows specificity to the Nox complex in primary spleen macrophages.

<p>(A) Macrophage cells from wild-type mice (C57Bl/6j) expressing transiently transfected p47-roGFP showed homogeneous cytosolic distribution of p47-roGFP in the absence of LPS-mediated activation (−LPS). Upon LPS-mediated activation p47-roGFP localized with the membrane dye FM4-64® (+LPS). (B) In the absence of LPS (−LPS), p47-roGFP is distributed homogeneously throughout the cytosol of macrophages isolated from Nox2 deficient (Nox2^−/y) mice. Upon LPS stimulation (+LPS), p47-roGFP translocated to the cell membrane of Nox2^−/y macrophages, localizing with FM4-64®. (C) LPS stimulation of primary spleen macrophages resulted in rapid oxidation of p47-roGFP in wild-type macrophages (black squares). Cells incubated with gp91ds (5 µM, 60 min.) demonstrated a significant reduction in the rate and extent of p47-roGFP oxidation (red squares). In Nox2^−/y macrophages (blue squares) LPS did not induce oxidation of p47-roGFP. There was no oxidation of p47-roGFP in the absence of LPS (Time CTRL, green squares). Error bars represent s.e. from the mean. Representative images (A & B) are shown from at least 9 cells. Data (C) are representative of <i>n</i>_animals = 6 per strain, 3 cells per animal. ** p<0.01, * p<0.05 (Tukey statistical analysis for p value).</p

p47-roGFP measures Nox dependent ROS produced in the extracellular space.

<p>Catalase (4 µM) in the extracellular space prevented the oxidation of p47-roGFP (A) but did not alter the oxidation of Grx1-roGFP2 (B) during electrical stimulation of FDB myofibers.</p

LPS-induced stimulation increases the rate of DCF fluorescence in macrophage cells from 8–10 wk old mice.

<p>(A) Representative data (ΔF/F₀) from macrophages of WT (C57Bl/6J, black line), p47^phox−/− (red line) and Nox2^−/y (blue line) mice showing the temporal change in DCF fluorescence upon LPS-treatment (20 ng/ml). F₀ is the basal fluorescence taken over the first 100 seconds prior to LPS. (B) LPS-induced stimulation (boxed areas of A) significantly increased the normalized rate of DCF fluorescence (black bar) compared to pre-stimulated values (white bar). The increased intensity of DCF fluorescence was significantly higher in WT macrophages compared to macrophages from p47^phox−/− and Nox2^−/y mice. Error bars represent s.e. from the mean. Data are analyzed from <i>n</i>_animals = 6 per strain, 6 replicates per animal. * p<0.05 (Tukey statistical analysis for p value).</p