MOESM1 of Label-free visualization of fruit lignification: Raman molecular imaging of loquat lignified cells

Additional file 1: Figure S1. A to F, Repetitions of bright field, fluorescence and lignin staining microscopic analysis of the loquat flesh. Scale bar = 20 μm. Figure S2. A to C, Three-dimensional spatial concentration distribution of lignin, cellulose and pectin in the lignified cell of loquat fruit. Scale bar = 10 μm. Figure S3. Baseline correction using adaptive iteratively reweighted penalized least squares (airPLS). A, Original Raman spectra; B, Raman spectra pre-processed by airPLS. Figure S4. Raman intensity variations of lignin (1603 cm−1, black line) and cellulose (1383 cm−1, red line) along selected y-segment. The y-sampling was conducted in 1-μm steps

Effects of pHE DNA addition on PCR efficiency.

a<p>A two-copy transgenic T₀ tomato plant was used;</p>b<p>The concentration was 10.20 ng µl⁻¹, containing 10,000 <i>ELIP</i> and 10,000 <i>HPT</i> molecules µl⁻¹;</p>c<p>The concentration was 0.051 pg µl⁻¹, containing 10,000 <i>ELIP</i> and 10,000 <i>HPT</i> molecules µl⁻¹.</p

Determination of transgene copy number of six transgenic tomato plants by standard addition qPCR (SAQPCR).

<p>A quantified amount of 10.20 ng of tomato genomic DNA, which contains around 10,000 molecules of <i>ELIP</i>, was included in each PCR reaction.</p>a<p>Refers to the copy number per diploid genome.</p

Construction of recombinant plasmid pHE.

<p>pELIP: plasmid harboring tomato <i>ELIP</i> gene; pHPT: plasmid harboring <i>Escherichia coli HPT</i> gene; pHE: plasmid harboring both tomato <i>ELIP</i> and <i>E. coli HPT</i> gene.</p

Southern blot analysis of six transgenic tomato T₀ lines.

<p>A) <i>Hind</i> III digestion; B) <i>BamH</i> I digestion. M, λDNA/<i>Hind</i> III marker; L1-L6, transgenic tomato T₀ lines, were the same as those appeared in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0053489#pone-0053489-g003" target="_blank">Figure 3</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0053489#pone-0053489-t003" target="_blank">Table 3</a>; P, positive control (plasmid); WT, negative control (wild type).</p

Effects of standard DNA addition on fluorescence intensity and C_t.

<p>Oblique lines: exponential amplification phases suggested by LinRegPCR; Sample A: with 1 µl of tomato genomic DNA (10.20 ng µl⁻¹, containing 10,000 <i>ELIP</i> molecules µl⁻¹) as PCR template; Sample B: with 1 µl tomato genomic DNA plus 1 µl of pHE (0.051 pg µl⁻¹, containing 10,000 <i>ELIP</i> molecules µl⁻¹) as PCR template; Sample C: with 1 µl tomato genomic DNA plus 3 µl of pHE as PCR template.</p

Transcript expressions of genes related to citrate degradation and transport as measured by RNA-Seq and qRT-PCR.

<p>Lines represent expression determined by RNA-Seq in RPKM value (right axis), while histograms represent transcript expression determined by qRT-PCR (left axis). The error bars represent the standard errors.</p

Calculation of N_0ELIP when taking a C_b within I_b −10 to I_b +5.

<p>The values above/beneath the arrows indicate the coefficient of variation. Line 1-Line 6 (L1-L6) were the six transgenic T₀ tomato lines; I_b was set as the integer part for C_tb; C_b indicated cycles in the exponential amplification phase of sample B.</p

HPLC (280 nm) analysis of HPCE and its different fractions.

<p>A: HPCE; B: The fraction eluted with 40% methanol, F5; C: The fraction eluted with 50% methanol, F6; D: The fraction eluted with 60% methanol, F7; E: The fraction eluted with 100% methanol, F8.</p

Direct infusion ESI-MS spectrum of Hemaoli pulp crude extracts (HPCE) in the negative mode.

<p>Direct infusion ESI-MS spectrum of Hemaoli pulp crude extracts (HPCE) in the negative mode.</p