Plasmonic Nano-Oven by Concatenation of Multishell Photothermal Enhancement

Metallodielectric multishell nanoparticles are capable of hosting collective plasmon oscillations distributed among different metallic layers, which result in large near-field enhancement at specific regions of the structure, where light absorption is maximized. We exploit this capability of multishell nanoparticles, combined with thermal boundary resistances and spatial tailoring of the optical near fields, to design plasmonic nano-ovens capable of achieving high temperatures at the core region using moderate illumination intensities. We find a large optical intensity enhancement of ∼10⁴ over a relatively broad core region with a simple design consisting of three metal layers. This provides an unusual thermal environment, which together with the high pressures of ∼10⁵ atm produced by concatenated curved layers holds great potential for exploring physical and chemical processes under extreme optical/thermal/pressure conditions in confined nanoscale spaces, while the outer surface of the nano-oven is close to ambient conditions

Additional file 1 of High-yield production of protopanaxadiol from sugarcane molasses by metabolically engineered Saccharomyces cerevisiae

Additional file 1: Table S1. PPD production of engineering Saccharomyces cerevisiae. Table S2. Plasmids used in this study. Table S3. Primers used in this study. Table S4. Primers used for RT-PCR in this study. Table S5. gRNA target sequences used in this study. Figure S1. High-throughput screening of PPD-producing strains. Figure S2. RT-qPCR of PPD-producing strains. Figure S3. PPD production of strain BY-V with glucose/molasses feeding. Figure S4. Construction of Cas9 expression plasmid. Figure S5. PPD production in a 5-L bioreactor. Supplementary Sequences

Additional file 1 of Ten-eleven translocation-2-mediated macrophage activation promotes liver regeneration

Additional file 1: Supplemental Figure 1. (A) Gene Ontology (GO) enrichment scatterplot of the top 20 pathways of macrophages at 0 and 24 h after PHx. (B) Mice mRNA levels of Tet2 in whole liver tissue 0, 24, and 48 h were detected using qPCR after PHx. The genes were normalized to GAPDH mRNA levels in each sample. (C) Kaplan–Meier analysis was used to determine the survival rate of mice after PHx with BC339 treatment. (A and B,n=3, C, n=10, p <0.05.)

Additional file 1 of Genome-wide identification and analysis of WD40 proteins reveal that NtTTG1 enhances drought tolerance in tobacco (Nicotiana tabacum)

Additional file 1

Table_1_Analysis of herbivore-responsive long noncoding ribonucleic acids reveals a subset of small peptide-coding transcripts in Nicotiana tabacum.XLSX

Long non-coding RNAs (lncRNAs) regulate many biological processes in plants, including defense against pathogens and herbivores. Recently, many small ORFs embedded in lncRNAs have been identified to encode biologically functional peptides (small ORF-encoded peptides [SEPs]) in many species. However, it is unknown whether lncRNAs mediate defense against herbivore attack and whether there are novel functional SEPs for these lncRNAs. By sequencing Spodoptera litura-treated leaves at six time-points in Nicotiana tabacum, 22,436 lncRNAs were identified, of which 787 were differentially expressed. Using a comprehensive mass spectrometry (MS) pipeline, 302 novel SEPs derived from 115 tobacco lncRNAs were identified. Moreover, 61 SEPs showed differential expression after S. litura attack. Importantly, several of these peptides were characterized through 3D structure prediction, subcellular localization validation by laser confocal microscopy, and western blotting. Subsequent bioinformatic analysis revealed some specific chemical and physical properties of these novel SEPs, which probably represent the largest number of SEPs identified in plants to date. Our study not only identifies potential lncRNA regulators of plant response to herbivore attack but also serves as a valuable resource for the functional characterization of SEP-encoding lncRNAs.</p

Image_2_Analysis of herbivore-responsive long noncoding ribonucleic acids reveals a subset of small peptide-coding transcripts in Nicotiana tabacum.TIF

Long non-coding RNAs (lncRNAs) regulate many biological processes in plants, including defense against pathogens and herbivores. Recently, many small ORFs embedded in lncRNAs have been identified to encode biologically functional peptides (small ORF-encoded peptides [SEPs]) in many species. However, it is unknown whether lncRNAs mediate defense against herbivore attack and whether there are novel functional SEPs for these lncRNAs. By sequencing Spodoptera litura-treated leaves at six time-points in Nicotiana tabacum, 22,436 lncRNAs were identified, of which 787 were differentially expressed. Using a comprehensive mass spectrometry (MS) pipeline, 302 novel SEPs derived from 115 tobacco lncRNAs were identified. Moreover, 61 SEPs showed differential expression after S. litura attack. Importantly, several of these peptides were characterized through 3D structure prediction, subcellular localization validation by laser confocal microscopy, and western blotting. Subsequent bioinformatic analysis revealed some specific chemical and physical properties of these novel SEPs, which probably represent the largest number of SEPs identified in plants to date. Our study not only identifies potential lncRNA regulators of plant response to herbivore attack but also serves as a valuable resource for the functional characterization of SEP-encoding lncRNAs.</p

Digital Gene Expression Tag Profiling Analysis of the Gene Expression Patterns Regulating the Early Stage of Mouse Spermatogenesis

<div><p>Detailed characterization of the gene expression patterns in spermatogonia and primary spermatocytes is critical to understand the processes which occur prior to meiosis during normal spermatogenesis. The genome-wide expression profiles of mouse type B spermatogonia and primary spermatocytes were investigated using the Solexa/Illumina digital gene expression (DGE) system, a tag based high-throughput transcriptome sequencing method, and the developmental processes which occur during early spermatogenesis were systematically analyzed. Gene expression patterns vary significantly between mouse type B spermatogonia and primary spermatocytes. The functional analysis revealed that genes related to junction assembly, regulation of the actin cytoskeleton and pluripotency were most significantly differently expressed. Pathway analysis indicated that the Wnt non-canonical signaling pathway played a central role and interacted with the actin filament organization pathway during the development of spermatogonia. This study provides a foundation for further analysis of the gene expression patterns and signaling pathways which regulate the molecular mechanisms of early spermatogenesis.</p> </div

Data_Sheet_1_Analysis of herbivore-responsive long noncoding ribonucleic acids reveals a subset of small peptide-coding transcripts in Nicotiana tabacum.docx

Long non-coding RNAs (lncRNAs) regulate many biological processes in plants, including defense against pathogens and herbivores. Recently, many small ORFs embedded in lncRNAs have been identified to encode biologically functional peptides (small ORF-encoded peptides [SEPs]) in many species. However, it is unknown whether lncRNAs mediate defense against herbivore attack and whether there are novel functional SEPs for these lncRNAs. By sequencing Spodoptera litura-treated leaves at six time-points in Nicotiana tabacum, 22,436 lncRNAs were identified, of which 787 were differentially expressed. Using a comprehensive mass spectrometry (MS) pipeline, 302 novel SEPs derived from 115 tobacco lncRNAs were identified. Moreover, 61 SEPs showed differential expression after S. litura attack. Importantly, several of these peptides were characterized through 3D structure prediction, subcellular localization validation by laser confocal microscopy, and western blotting. Subsequent bioinformatic analysis revealed some specific chemical and physical properties of these novel SEPs, which probably represent the largest number of SEPs identified in plants to date. Our study not only identifies potential lncRNA regulators of plant response to herbivore attack but also serves as a valuable resource for the functional characterization of SEP-encoding lncRNAs.</p

Image_1_Analysis of herbivore-responsive long noncoding ribonucleic acids reveals a subset of small peptide-coding transcripts in Nicotiana tabacum.TIF

Long non-coding RNAs (lncRNAs) regulate many biological processes in plants, including defense against pathogens and herbivores. Recently, many small ORFs embedded in lncRNAs have been identified to encode biologically functional peptides (small ORF-encoded peptides [SEPs]) in many species. However, it is unknown whether lncRNAs mediate defense against herbivore attack and whether there are novel functional SEPs for these lncRNAs. By sequencing Spodoptera litura-treated leaves at six time-points in Nicotiana tabacum, 22,436 lncRNAs were identified, of which 787 were differentially expressed. Using a comprehensive mass spectrometry (MS) pipeline, 302 novel SEPs derived from 115 tobacco lncRNAs were identified. Moreover, 61 SEPs showed differential expression after S. litura attack. Importantly, several of these peptides were characterized through 3D structure prediction, subcellular localization validation by laser confocal microscopy, and western blotting. Subsequent bioinformatic analysis revealed some specific chemical and physical properties of these novel SEPs, which probably represent the largest number of SEPs identified in plants to date. Our study not only identifies potential lncRNA regulators of plant response to herbivore attack but also serves as a valuable resource for the functional characterization of SEP-encoding lncRNAs.</p

Protein levels of FGF13, SFRP2, RAC, WNT10A and FGF7.

<p>(A) Protein levels of FGF13, SFRP2 and RAC in GC-1spg and GC-2spd (ts) cells were detected by western blotting respectively. β-Actin were used to normalize the individual expression levels. (B) Protein level of WNT10A and FGF7 in the medium supernatants from GC-1spg and GC-2spd (ts) cells were determined by ELISA. The data are presented as the mean plus SEM from a representative of three independent experiments, with each performed in triplicate. Statistically significant differences between GC-1spg and GC-2spd (ts) cells are indicated above the bars: * means P<0.05.</p