Additional file 5: Figure S4. of Genome-wide identification of grain filling genes regulated by the OsSMF1 transcription factor in rice

The expression patterns of transcription factors as a putative target of OsSMF1 based on the 300 K Rice Genome Microarray ( www.ggbio.com ). The expression was measured in different sized panicles before heading (1, 3, 5, 8, 10, 15, 20, and 22 cm), at the indicated days after pollination (1, 3, 4, 11, and 21 days) and in the leaf, root, germinating seed, callus, and regenerating callus. (PPTX 75 kb

Plasmonic–Photonic Interference Coupling in Submicrometer Amorphous TiO₂–Ag Nanoarchitectures

In this study, we report the crystallinity effects of submicrometer titanium dioxide (TiO₂) nanotube (TNT) incorporated with silver (Ag) nanoparticles (NPs) on surface-enhanced Raman scattering (SERS) sensitivity. Furthermore, we demonstrate the SERS behaviors dependent on the plasmonic–photonic interference coupling (P-PIC) in the TNT-AgNP nanoarchitectures. Amorphous TNTs (A-TNTs) are synthesized through a two-step anodization on titanium (Ti) substrate, and crystalline TNTs (C-TNTs) are then prepared by using thermal annealing process at 500 °C in air. After thermally evaporating 20 nm thick Ag on TNTs, we investigate SERS signals according to the crystallinity and P-PIC on our TNT-AgNP nanostructures. (A-TNTs)-AgNP substrates show dramatically enhanced SERS performance as compared to (C-TNTs)-AgNP substrates. We attribute the high enhancement on (A-TNTs)-AgNP substrates with electron confinement at the interface between A-TNTs and AgNPs as due to the high interfacial barrier resistance caused by band edge positions. Moreover, the TNT length variation in (A-TNTs)-AgNP nanostructures results in different constructive or destructive interference patterns, which in turn affects the P-PIC. Finally, we could understand the significant dependency of SERS intensity on P-PIC in (A-TNTs)-AgNP nanostructures. Our results thus might provide a suitable design for a myriad of applications of enhanced EM on plasmonic-integrated devices

Additional file 1: Figure S1. of Genome-wide identification of grain filling genes regulated by the OsSMF1 transcription factor in rice

Transcript levels of Wsi18, OsSMF1, and OsREM from 300 K Rice Genome Microarray ( www.ggbio.com ). The transcript levels were measured in different sized panicles before heading (1, 3, 5, 8, 10, 15, 20, and 22 cm), at the indicated days after pollination (1, 3, 4, 11, and 21 days) and in the leaf, root, germinating seed, callus, and regenerating callus. (PPTX 70 kb

Additional file 4: Figure S3. of Genome-wide identification of grain filling genes regulated by the OsSMF1 transcription factor in rice

The query gene, OsSMF1, is marked by an asterisk. Each circle indicates a gene, and the lines represent the correlations between the genes. Eighty-five genes were identified as OsSMF1-related genes, with a minimum correlation value of 0.55 and depth of 1. (PPTX 473 kb

Detection of recombinant proteins containing methionine sulfoxide (MetSO) residues by western blotting.

<p>Rubi (Ribulose-bisphosphate carboxylase activase, Os11g0707000), PBGD (Porphobilinogen deaminase, Os02g0168800), and Cys (Cysteine synthase, Os12g0625000) were cloned into the pET-DsRed vector, expressed in <i>E. coli</i>, purified, and treated with 0.3% H₂O₂. These recombinant proteins containing MetSO were detected by western blotting with the methionine sulfoxide polyclonal antibody (Cayman). kDa, molecular mass indicators (in kDa The experiments were representative of three independent experiments.</p

MetSO/Met ratio in individual methionine residues of PBGD.

<p>The gray and black bars represent the Met and MetSO residues, respectively. The MetSO content is expressed as the percent of MetSO in relation to the each Met residues (Met + MetSO). The figures that shown are in the bar graph represent the absolute numbers of Met or MetSO. The results shown are the mean ± SD, n = 3 replicates for each group (*<i>P</i><0.05 compared to PBGD + H₂O₂ + MSRB2 value).</p

Phylogenetic and amino acid comparisons of the MSRBs.

<p>(A) Phylogenetic tree of the MSRBs from <i>Arabidopsis thaliana</i> (AtMSRB1: NP_564640, AtMSRB2: NP_567639, AtMSRB3: NP_567271, AtMSRB4: NP_192390, AtMSRB5: NP_192392, AtMSRB6: NP_192393, AtMSRB7: NP_567637, AtMSRB8: NP_193915, AtMSRB9: NP_567638), Oryza sativa (OsMSRB1.1: AK063588, OsMSRB1.2: AK111486, OsMSRB3: AK071730, OsMSRB5: AK068764), and <i>Capsicum annuum</i> (CaMSRB2: EF144171, CaMSRB1: EF144174, CaMSRB3: EF144173). The phylogenetic tree was constructed by ClustalW and Phylip package (Neighbor-joining method) with full-length sequences including transit peptides and visualized using TreeView. (B) The amino acid sequence alignment of the conserved SelR domain of the MSRBs from <i>Arabidopsis thaliana, Oryza sativa</i>, and <i>Capsicum annuum</i> was constructed using ClustalW (<a href="http://www.ebi.ac.uk/Tools/msa/clustalo/" target="_blank">http://www.ebi.ac.uk/Tools/msa/clustalo/</a>). Four putative MSRB signature motifs are boxed, and two conserved Cys residues are indicated with arrows.</p

Changes in chlorophyll fluorescence during drought stress.

<p>The leaves were detached from four-week-old plants of the transgenic and WT lines and were air-dried at 25°C under continuous light (100 µmol protons m⁻² S⁻¹). The <i>Fv/Fm</i> value was measured by mini PAM according to the time course. The results shown are the mean ± SD, n = 5 replicates for each group. The experiments were representative of three independent experiments.</p

Expression of nine genes in the WT and CaMSRB2-transformed rice as detected by real-time PCR.

<p>The y-axis shows the relative expression level normalized to that of the WT plants that were grown under drought conditions for 2 days. Os04g0414700 (photosystem I PsaO domain-containing protein), Os03g0778100 (photosystem-1 F subunit), Os08g0502700 (pyridoxal phosphate-dependent transferase), Os08g0248800 (aspartate carbamoyltransferase 3), Os04g0644600 (esterases and lipases epoxide hydrolase family protein), Os07g0693800 (fatty acid desaturase), Os07g0412100 (granule-bound starch synthase Ib, chloroplast precursor), Os02g0596000 (rhodanese-like domain-containing protein), Os03g0736400 (methylase putative domain-containing protein), and Os04g0465500 (GCN5-related N-acetyltransferase domain-containing protein). The results shown are the mean ± SD, n = 3 replicates for each group (^***<i>P</i><0.001; **<i>P</i><0.01; and *<i>P</i><0.05 compared to WT). The experiments were representative of two independent experiments.</p

Subcellular Localization of CaMSRB2 by transient expression.

<p>The expression of CaMSRB2 fused in-frame to DsRed was driven by the <i>CaMV</i> 35S promoter in rice protoplasts and examined under a confocal microscope. GFP with an N-terminal chloroplast transit peptide was constructed under the control of the <i>RbcS</i> promoter as a chloroplast marker. White scale bar represents 5 um.</p