diffRepeats: Quantify repeat element enrichment with next-generation sequencing data

<p>Quantify repeat element enrichment with next-generation sequencing data</p

Electrostatic Adsorption of Heme Proteins Alternated with Polyamidoamine Dendrimers for Layer-by-layer Assembly of Electroactive Films

A novel thin film of heme proteins, including hemoglobin (Hb), myoglobin (Mb), and catalase (Cat), was successfully assembled layer by layer with polyamidoamine (PAMAM) dendrimers on different solid surfaces. At pH 7.0, protonated PAMAM possesses positive surface charges, whereas the proteins have net negative surface charges at pH above their isoelectric points. Thus, layer-by-layer {PAMAM/protein}n films were assembled with alternate adsorption of oppositely charged PAMAM and proteins from their aqueous solutions mainly by electrostatic interaction. The assembly process was monitored by quartz crystal microbalance (QCM), UV−vis spectroscopy, and cyclic voltammetry (CV). The growth of the protein multilayer films was regular and linear, whereas the electroactivity of the films was only extended to a few bilayers. CVs of {PAMAM/protein}n films showed a pair of well-defined and nearly reversible peaks characteristic of the protein heme Fe(III)/Fe(II) redox couples. Although {PAMAM/Hb}n and {PAMAM/Mb}n films showed very similar properties, {PAMAM/Cat}n films displayed different and unique characters. The substrates with biological or environmental significance, such as oxygen, hydrogen peroxide, trichloroacetic acid, and nitrite, were catalytically reduced at {PAMAM/protein}n film electrodes, showing the potential applicability of the films as new types of biosensors or bioreactors based on direct electrochemistry of the proteins. Both the electrochemical and electrocatalytic activity of {PAMAM/protein}n films can be tailored precisely by controlling the number of bilayers or the film thickness

Histograms of GFP-expression in cells from pooled colonies analyzed by flow cytometry.

<p>The plots from Experiment 2 of <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0015704#pone-0015704-t002" target="_blank">Table 2</a> show the gating for the threshold of GFP-positive designation. The plasmid used to generate the colonies is indicated above each histogram.</p

Effect of GGT insertion on GFP expression in pooled cultures of G418-resistant colonies^a.

a<p>Colonies (collected from three plates per plasmid) in pooled cultures were harvested and analyzed by flow cytometry as described in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0015704#s4" target="_blank">Materials and Methods</a>.</p>b<p>percentage of cells in the population with FL1-H>10^1.1.</p>c<p>per cell.</p>d<p>not done.</p

Read-through activation in Neo-GFP cell lines.

<p>A. Nuclear RNA prepared from pooled cultures of cell lines isolated after electroporation with 1 µg of DNA was assayed by hybridization and protection from nuclease S1 digestion. Expression of <i>E1a-neo,</i> read-through transcription (RT), and <i>E1b-gfp</i> produced the specific protected bands indicated in the diagram below the autoradiographic data. The arrows indicate the relative positions of the transcripts in the template (the uncertain end of the read-through transcript is indicated by the dashed line). The probe is indicated by a line with the position of the 5′-end label shown as an asterisk. The region of the probe protected by each transcript is indicated as double-stranded (DNA-RNA hybrid). The position of divergence of the sequence of the probe for read-through transcription from the read-through RNA product is shown by the loss of DNA-RNA hybrid formation. Variation in migration of the RT and E1a-GFP products probably was caused by sequence differences at the junction site produced during plasmid construction. Lane designations: 1: HeLa cells; 2: culture derived from pNeoE1bGFP; 3: culture derived from pNeoGGTE1bGFP; 4: culture derived from pNeoDPME1bGFP. The positions of size markers (not shown) are indicated on the left of the autoradiograms. B. <i>E1b-GFP</i> RNA levels from two experiments (Expt 1 is shown in A) were quantified and normalized to the quantity of <i>E1a-Neo</i> RNA. The results are expressed relative to the pNeoE1bGFP value (1.00).</p

Integrated NeoGGTE1bGFP sequences in stable cell lines.

<p>DNA was extracted from G418-resistant stable cell lines established with the plasmid pNeoGGTE1bGFP (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0015704#pone-0015704-g001" target="_blank">Fig. 1b</a>). Blots were prepared and probed as described in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0015704#s4" target="_blank">Materials and Methods</a>. Lane designations: M, size markers derived from an <i>Eco</i>RI/<i>Psh</i>A1 digest of the plasmid (sizes shown on the left); 2, reconstruction with 2 copies of <i>Sph</i>I-digested (linear) plasmid (7.2 kbp), based on quasi-tetraploid human DNA content; 20, reconstruction with 20 copies of plasmid; A+, GFP-expressing cell line 1 isolated after electroporation of 1 µg of DNA; A−, GFP-negative cell line from the same experiment as A+; B+, GFP-expressing cell line isolated in a second experiment after electroporation of 1 µg of DNA; B−, GFP-negative cell line from the same experiment as B+; C+, GFP-expressing cell line isolated after lipofection with 1 µg of DNA; C−, GFP-negative cell line 2 from the same experiment as C+. An irrelevant lane was removed from between lanes 20 and A+. The diagram below shows the results expected from a single (top) or tandem (bottom) integration of the complete plasmid sequence (open box). For the former, the sizes of the two junction DNA fragments that hybridize to the probe (shaded box) will depend on the site of insertion. For the latter, in addition to the junction fragments, a unit length band (7.2 kbp) will be generated and its intensity will depend on the number of copies in the tandem array. There is a single site for <i>Sph</i>I (S) cleavage in the plasmid <i>neo</i> gene.</p

Effect of <i>GGT</i> insertion on the expression of a downstream <i>gfp</i> reporter in G418-resistant cell lines.

a<p>difference from GGT, p<0.0003, paired t-test.</p>b<p>difference from GGT, p<0.0003, paired t-test.</p

Insight into the Structures and Properties of Morphology-Controlled Legs of Tetrapod-Like ZnO Nanostructures

The fine structure characterization of individual legs is essential for understanding the detailed formation mechanism and the origin of the unique properties of tetrapod-like ZnO nanostructures. We have synthesized tetrapod-like ZnO nanostructures with thin needle (TN-ZnO), uniform hexagonal prism (TU-ZnO), and hierarchical hexagonal prism (TH-ZnO) legs through oxidization of zinc vapor followed by ZnO condensation at relatively lower temperatures. The individual legs of as-synthesized ZnO nanotetrapods were characterized complementarily by scanning electron microscopy (SEM), transmission electron microscopy (TEM), electron dispersive spectrum (EDS), and cathodoluminescence (CL). We demonstrated that the legs have wurtzite structure and prefer to grow along the [0001] direction. We found that all legs grew from similar ZnOx nuclei, where x is about 0.3, and all of them showed a strong visible luminescent property. EDS and CL spectra obtained from different regions in an individual leg illustrated that the strong visible luminescence resulted from their surface states rather than the heavy oxygen vacancy. The possible nucleation and growth mechanisms of the legs with different morphologies are discussed

Effects of Heteroatoms of Tetracene and Pentacene Derivatives on Their Stability and Singlet Fission

The effects of the introduction of an sp²-hybridized nitrogen atom (N) and thiophene ring on the structure geometries, frontier molecular orbital energies, and excited state energies related to singlet fission (SF) for some tetracene and pentacene derivatives were theoretically investigated by quantum chemical methods. The introduction of a nitrogen atom significantly decreases the energies of frontier molecular orbitals and hence improves their stabilities in air and light illumination. More importantly, it is helpful for reducing the energy loss of the exothermic singlet fission of pentacene derivatives. For fused benzene-thiophene structures, the (α, β) connection pattern could stabilize the frontier molecular orbitals, while the (β, β) connection pattern can promote the thermodynamic driving force of singlet fission. These facts provide a theoretical ground for rational design of SF materials

Read-through activation in Neo-Luc cell lines.

<p>Total RNA prepared from individual cell lines isolated after electroporation with 1 µg of DNA was assayed by hybridization and protection from nuclease S1 digestion. Expression of <i>E1a-neo,</i> read-through transcription (RT), and <i>E1b-luc</i> produced the specific protected bands indicated in the diagram below the autoradiographic data. The diagram is laid out as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0015704#pone-0015704-g004" target="_blank">Fig. 4</a>. Each lane represents a different cell line. He: Hela cells; DPM: cell lines derived from pNeoDPME1bLuc; GGT: cell lines derived from pNeoGGTE1bLuc; M: size standards.</p