Recombination detection results of (A) SPLCV and (B) TYCCNV.

<p>The schematic representations based on alignments of Sweet potato leaf curl virus (SPLCV) isolates (A) and Tomato leaf curl China virus (TYCCNV) components (B) are shown at the top of the figure, which indicates recombination events detected by RDP4 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0071565#pone.0071565-Martin4" target="_blank">[29]</a>. Each sequence is represented by an open rectangle and colored differently from the other sequences. The details of the recombination breakpoint detected by RDP4 are shown. The motifs detected by MEME in the genome of SPLCV and TYCCNV are shown at (C) and (D), respectively, and the same motifs are in the same color. Identical motifs in the TYLCCNV genomes are indicated by open rectangles.</p

The motif distribution of begomovirus with genome rearrangement.

<p>(A) The distribution of motifs in the genomes of DNA-A and DNA-B components of Potato yellow mosaic Panama virus (PYMPV), <i>Gossypium punctatum</i> mild leaf curl virus (GPMLCuV), Tomato leaf curl Hsinchu virus (ToLCHsV) and Tomato yellow leaf curl Kanchanaburi virus (TYLCKaV), detected by MEME <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0071565#pone.0071565-Bailey2" target="_blank">[31]</a>. (B) Schematic representation of the locations of high-confidence motifs. The genome sequences are represented by gray lines. The colored rectangles on the genomes represent the identified motifs, and arrows indicate that the motif is reversed. The motifs belonging to the same set in the same genome are indicated in the same color. Potential recombinant regions are indicated by red open rectangles, and the <i>H_d</i> of each motif set in the regions is listed.</p

The distribution of the motifs in the genomes of Faba bean necrotic yellows virus (FBNYV).

<p>(A) Schematic representation of the Faba bean necrotic yellows virus (FBNYV) genome. (B) The distribution of common motifs in the genomes of BBTV detected by MEME. The solid lines represent the sequences of each FBNYV genome component: DNA-R, -U1, -U2, -U4, -S, -M, -C and -N. The stem-loop region of all components is marked at the top of figure. Three conserved regions, the CR-M-U2, CR-C-U1 and CR-N-U4 regions, shared only by certain components of FBNYV are also indicated. The colored rectangles represent the high-confidence motifs (see text) that are shared by genome components, and the motifs with similar sequences are indicated in the same color; an arrow on a rectangle indicates that the motif is reversed.</p

The distribution and evaluation of common motifs in the Banana bunchy top virus genome.

<p>(A) Schematic representation of the Banana bunchy top virus (BBTV) genome and the distribution of common motifs in the genomes of BBTV, detected by MEME <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0071565#pone.0071565-Bailey2" target="_blank">[31]</a>. The genome sequences of BBTV are represented by gray lines. The rectangles on the genomes represent the identified motifs. The motifs belonging to the same set are indicated in the same color. (B) The evaluation of the motifs by IC is represented on the <i>y</i>-axis. The <i>x</i>-axis represents the rank of the motif among all of the motifs identified. The red line represents the motif sets detected in the BBTV whole-genome sequences, and the green line and blue line represent the motif sets detected by the simulation of the BBTV-genome coding region mimic sequence set and the BBTV-genome random mimic sequence set, respectively. The yellow line represents the IC values that were derived from six identical sequences. (C) The distribution of the percentage of the motif sets detected from BBTV-genome mimic sequences is shown. The <i>x</i>-axis represents the mean pairwise distance (<i>D_h</i>). The <i>y</i>-axis represents the percentage of motif sets with a certain <i>D_h</i> value. The green line and blue line represent the distribution of the percentage of the motif sets detected by the simulation of the BBTV-genome coding region mimic sequence set and the BBTV-genome random mimic sequence set, respectively. The black rectangle represents the <i>D_h</i> of the motif sets detected within the BBTV genome sequences. (D) The percentage of motifs detected by MEME from motifs inserted in randomly generated sequences. The <i>x</i>-axis represents the <i>D_h</i> of artificial motifs that were generated and inserted randomly in begomovirus-genome mimic sequences The <i>y</i>-axis represents the coverage rate <i>C_r</i> of detected motifs compared with the initially inserted artificial motifs. Only the result of the BBTV Taiwan Type I isolate is shown.</p

The information content (IC) values of the top 25 motifs detected by MEME in the BBTV genomes; only the motifs detected from the Taiwan Type I isolate are shown.

*<p>A consensus sequence of a motif set is a pseudo sequence that has a minimal average distance to every motif in the set.</p

Phylogenetic analysis of a Banana bunchy top virus Taiwan isolate using motifs detected by MEME.

<p>(A) The NJ trees supported the grouping of Banana bunchy top virus (BBTV) component; only the bootstrap values above 75% were counted. (B) The distance matrix calculated by SPRING <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0071565#pone.0071565-Lin2" target="_blank">[43]</a> represents the recombination steps that are necessary for changing the motif order from that of one genome to that of another. (C) The neighbor-joining tree constructed from the distance matrix calculated in (B). (D) The index of specifically shared motifs. The number represents the number of motifs that were shared specifically by partial components. We applied these methods to all of the BBTV isolates (Australia, India, Egypt, Taiwan, China and Tonga) (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0071565#pone-0071565-t003" target="_blank">Table 3</a>). The results derived from all of the BBTV isolates are similar, although the rearrangement distance (B) and the number of motifs that were shared specifically by subsets of components (D) varied between BBTV isolates (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0071565#pone.0071565.s003" target="_blank">Figure S3</a>). Only the result derived from the BBTV Taiwan Type I isolate is shown here.</p

The distribution of the motifs in the genomes of five Banana bunchy top virus isolates.

<p>The solid lines represent the sequences of each Banana bunchy top virus (BBTV) genome component derived from the different isolates (Aus, Australia; Ind, India; Egy, Egypt; Tai, Taiwan, Chi, China; Tog, Tonga). All of the BBTV genome components, DNA-R (A), -U3 (B), -S (C), -M (D), -C (E), and -N (F), which were derived from different isolates, are aligned separately. The dotted lines represented gapped regions (only the gapped lengths longer than 10 are shown). The two conserved regions, the stem-loop (SL) and the major (CR-M) common region, are marked above the alignment. The colored rectangles represent the high-confidence motifs (see text) that are shared by all of the genome components of the isolates, and the motifs with similar sequences are indicated in the same color; an arrow on a rectangle indicates that the motif is reversed; a star on a rectangle indicates a high-confidence motif that is shared only by a subset of the genome components of an isolate.</p

The variables used in MEME to detect motifs.

<p>The variables used in MEME to detect motifs.</p

Schematic representation of the possible outcomes of genomic recombination in organisms with frequent recombination.

<p>(A) Conserved sequences (represented by dark rectangles) in the offspring genomes are separated by foreign segments (represented by empty blocks) as a result of multiple insertion events. (B) Recombination and inversion might occur in the offspring genomes and lead to positional and directional rearrangement of the conserved region (represented by dark arrows; the arrowhead indicates the direction). (C) Progeny genomes can share similar genome organization, but certain distinctive segments (represented by gray rectangles) within these regions can be shared only by a subset of the progeny.</p

Continuous Microwave-Assisted Gas–Liquid Segmented Flow Reactor for Controlled Nucleation and Growth of Nanocrystals

Hot-injection techniques are currently the state-of-the-art method for the synthesis of high-quality colloidal nanocrystals (NCs) but have typically been limited to small batch reactors. The nature of this method leads to local fluctuations in temperature and concentration where inhomogeneity due to mixing makes precise control of reaction conditions very challenging at a large scale. Therefore, development of methods to produce high-quality colloidal NCs with high-throughput is necessary for many technological applications. Herein, we report a high-quality and high-throughput NC synthesis method via a continuous microwave-assisted flow reactor where separation of nucleation and growth is demonstrated. A significant issue of microwave heating in a single-phase continuous flow microwave reactor is the deposition of in situ generated NCs on the inner wall of the reactor in the microwave zone. This deposited material leads to significantly enhanced microwave absorption and rapid heating and can result in sparking in the reactor. A gas–liquid segmented flow is used to avoid this problem and also results in improved residence time distributions. The use of this system allows for finely tuned parameters to achieve a high level of control over the reaction by separating the nucleation and growth stages