Phylogenetic relationships and gene structure of soybean <i>Dof</i> genes.

<p>(A) The phylogenetic tree of soybean Dof proteins constructed from a complete alignment of 78 GmDof proteins using MEGA 4.0 by the neighbor-joining method with 1,000 bootstrap replicates. Percentage bootstrap scores >50% are indicated on the nodes. The nine major phylogenetic subgroups designated I to IX are indicated. (B) Exon/intron structures of <i>Dof</i> genes from soybean. Exons are represented by green boxes and introns by black lines. The sizes of exons and introns can be estimated using the scale below.</p

Phylogenetic tree of all Dof domain containing proteins from soybean, <i>Arabidopsis</i>, and rice.

<p>The deduced full-length amino-acid sequences of 78 soybean, 36 <i>Arabidopsis</i> and 30 rice <i>Dof</i> genes were aligned by Clustal X 1.83 and the phylogenetic tree was constructed using MEGA 4.0 by the neighbor-joining method with 1,000 bootstrap replicates. Each Dof subgroup is indicated by a specific color.</p

Schematic distributions of the conserved motifs among defined gene clusters.

<p>Motifs were identified by means of MEME software using the deduced amino-acid sequences of the 78 GmDofs. The relative position of each identified motif in all Dof proteins is shown. Multilevel consensus sequences for the MEME defined motifs are listed in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0076809#pone.0076809.s004" target="_blank">Table S4</a>.</p

Chromosomal locations, region duplications, and predicted clusters for soybean <i>Dof</i> genes.

<p>The schematic diagram of genome-wide chromosome organization and segmental duplication arising from the genome duplication event in soybean was derived from the CViT genome search and synteny viewer at the Legume Information System (<a href="http://comparative-legumes.org" target="_blank">http://comparative-legumes.org</a>). Colored blocks to the left of each chromosome show duplications with chromosomes of the same color. For example, the gray blocks at the bottom of Gm10 correspond with regions on the brown Gm20, and <i>vice </i><i>versa</i>. The chromosomal positions of all <i>Dof</i> genes in soybean were mapped on each chromosome. The locations of centromeric repeats are shown as black rectangles over the chromosomes. The chromosome numbers are indicated at the top of each bar and sizes of chromosomes are represented by the vertical scale.</p

Dof domains are highly conserved across all Dof proteins in soybean.

<p>The sequence logos are based on alignments of all soybean Dof domains. Multiple alignment analysis of 78 typical soybean Dof domains was performed with ClustalW. The bit score indicates the information content for each position in the sequence. Asterisks indicate the conserved cysteine residues (Cys) in the Dof domain.</p

The linear regression plots of the content percentage (<i>P</i>_i%) of the marker compounds vs. the linear quantitative similarity (<i>b</i>).

<p>(A) for MT, (B) for SPR, (C) for OMT, (D) for <b><i>P</i></b>_3C%, (E) for <b><i>R</i></b>%, (F) for all the marker compounds, <b><i>P</i></b>_3C% and <b><i>R</i></b>%.</p

Linear Quantitative Profiling Method Fast Monitors Alkaloids of Sophora Flavescens That Was Verified by Tri-Marker Analyses

<div><p>The present study demonstrated the use of the Linear Quantitative Profiling Method (LQPM) to evaluate the quality of Alkaloids of Sophora flavescens (ASF) based on chromatographic fingerprints in an accurate, economical and fast way. Both linear qualitative and quantitative similarities were calculated in order to monitor the consistency of the samples. The results indicate that the linear qualitative similarity (LQLS) is not sufficiently discriminating due to the predominant presence of three alkaloid compounds (matrine, sophoridine and oxymatrine) in the test samples; however, the linear quantitative similarity (LQTS) was shown to be able to obviously identify the samples based on the difference in the quantitative content of all the chemical components. In addition, the fingerprint analysis was also supported by the quantitative analysis of three marker compounds. The LQTS was found to be highly correlated to the contents of the marker compounds, indicating that quantitative analysis of the marker compounds may be substituted with the LQPM based on the chromatographic fingerprints for the purpose of quantifying all chemicals of a complex sample system. Furthermore, once reference fingerprint (RFP) developed from a standard preparation in an immediate detection way and the composition similarities calculated out, LQPM could employ the classical mathematical model to effectively quantify the multiple components of ASF samples without any chemical standard.</p></div

The HPLC fingerprints of 27 batches of the ASF samples, the reference fingerprint (RFP), and the reference sample (RS) detected at 210 nm.

<p>(A) Normal HPLC fingerprints (B) the relative characteristic profilings referenced by peak MT.</p

The PCA loading plot (A) and scores scatter plot (B) for all the ASF samples.

<p>The PCA loading plot (A) and scores scatter plot (B) for all the ASF samples.</p

The results of the quantitative analysis for the tri-marker compounds and the fingerprint analysis assessed by LQPM.

<p>The results of the quantitative analysis for the tri-marker compounds and the fingerprint analysis assessed by LQPM.</p