Transcriptome analysis of stem development in the tumourous stem mustard Brassica juncea var. tumida Tsen et Lee by RNA sequencing

<p>Abstract</p> <p>Background</p> <p>Tumourous stem mustard (<it>Brassica juncea </it>var. <it>tumida </it>Tsen et Lee) is an economically and nutritionally important vegetable crop of the <it>Cruciferae </it>family that also provides the raw material for <it>Fuling </it>mustard. The genetics breeding, physiology, biochemistry and classification of mustards have been extensively studied, but little information is available on tumourous stem mustard at the molecular level. To gain greater insight into the molecular mechanisms underlying stem swelling in this vegetable and to provide additional information for molecular research and breeding, we sequenced the transcriptome of tumourous stem mustard at various stem developmental stages and compared it with that of a mutant variety lacking swollen stems.</p> <p>Results</p> <p>Using Illumina short-read technology with a tag-based digital gene expression (DGE) system, we performed <it>de novo </it>transcriptome assembly and gene expression analysis. In our analysis, we assembled genetic information for tumourous stem mustard at various stem developmental stages. In addition, we constructed five DGE libraries, which covered the strains <it>Yong'an </it>and <it>Dayejie </it>at various development stages. Illumina sequencing identified 146,265 unigenes, including 11,245 clusters and 135,020 singletons. The unigenes were subjected to a BLAST search and annotated using the GO and KO databases. We also compared the gene expression profiles of three swollen stem samples with those of two non-swollen stem samples. A total of 1,042 genes with significantly different expression levels occurring simultaneously in the six comparison groups were screened out. Finally, the altered expression levels of a number of randomly selected genes were confirmed by quantitative real-time PCR.</p> <p>Conclusions</p> <p>Our data provide comprehensive gene expression information at the transcriptional level and the first insight into the understanding of the molecular mechanisms and regulatory pathways of stem swelling and development in this plant, and will help define new mechanisms of stem development in non-model plant organisms.</p

One-dimensional photonic crystals : Fabrication, responsiveness and emerging applications in 3D construction

A one-dimensional photonic crystal (1DPC), which is a periodic nanostructure with a refractive index distribution along one direction, has been widely studied by scientists. In this review, materials and methods for 1DPC fabrication are summarized. Applications are listed, with a special emphasis on sensing platforms and photovoltaic devices together with full color display. After that, some typical 3D ordered structures with stacked layers are highlighted, fabrication methods are also described, and remaining problems are pointed out. Lastly, the possibility of building 3D stacked structures based on 1D layers through chemical routes is discussed; a relatively convenient and flexible method. We believe such a method is a promising way to conduct 3D fabrication

Urban Carbon Stock Estimation Based on Deep Learning and UAV Remote Sensing: A Case Study in Southern China

AbstractAccurate carbon (C) stock estimation is crucial for C sequestration research, environmental protection, and policy formulation related to C management. Although, research on C stock in forests, oceans, soil, and desert has received increasing attention, relatively few studies have focused on urban C stock. Moreover, the current mainstream methods for C stock assessment, including field surveys and satellite mapping, are characterized by notable limitations, including being labor-intensive and having limited real-time data acquisition capabilities. Therefore, this paper aims to assess urban C stock and proposes a novel two-stage estimation model based on deep learning and unmanned aerial vehicle (UAV) remote sensing. The first stage is that tree areas recognition via YOLOv5, and achieved 0.792 precision, 0.814 recall, and 0.805 mAP scores, respectively. In the second stage, a grid generation strategy and a Convolutional Neural Network (CNN) regression model were developed to estimate C stock based on recognized tree areas (R2 = 0.711, RMSE = 26.08 kg). Three regions with a minimum of 300 trees in each area were selected as the validation sets. The experimental results, in terms of R2 and RMSE in kg, were (0.717, 0.711, 0.686) and (27.263, 27.857, 28.945), respectively

From 1D to 3D: A new route to fabricate tridimensional structures via photo-generation of silver networks

A rapid and cost effective method has been developed to fabricate 3 dimensional (3D) ordered structures by photo-generating silver networks inside a 1D layered heterogeneous laminate composed of poly(vinyl alcohol) (PVA) and poly(methyl methacrylate) (PMMA). By designing the photo-mask meticulously, the silver nanoparticles (NPs) produced by UV light aggregate to form frameworks in different forms, which perform as the anisotropic component, i.e. the building blocks, thus converting the 1D structure into 3D. Formation of silver NPs increases the refractive index (RI) of the PVA layers, thus bringing optical change to the 1D laminar structure, which allows us to trace the silver formation process by measuring the change of RI value and reflectance spectra. The 1D layered structure is a good building matrix for 3D construction because the total number of layers and the layer thickness can be finely tuned flexibly which allow us to further study the various properties caused by the structural modulation. By utilizing photo-reactive silver ions, an innovative strategy of fabricating 3D structures through in situ photo-generating silver building blocks inside the laminar matrix is established, which makes it possible to fabricate 3D micro/nano composite materials with potential applications in fields such as sensors and photonic meta-materials

Hierarchical-Multiplex DNA Patterns Mediated by Polymer Brush Nanocone Arrays That Possess Potential Application for Specific DNA Sensing

This paper provides a facile and cost-efficient method to prepare single-strand DNA (ssDNA) nanocone arrays and hierarchical DNA patterns that were mediated by poly­(2-hydroxyethyl methacrylate) (PHEMA) brush. The PHEMA brush nanocone arrays with different morphology and period were fabricated via colloidal lithography. The hierarchical structure was prepared through the combination of colloidal lithography and traditional photolithography. The DNA patterns were easily achieved via grafting the amino group modified ssDNA onto the side chain of polymer brush, and the anchored DNA maintained their reactivity. The as-prepared ssDNA nanocone arrays can be applied for target DNA sensing with the detection limit reaching 1.65 nM. Besides, with the help of introducing microfluidic ideology, the hierarchical-multiplex DNA patterns on the same substrate could be easily achieved with each kind of pattern possessing one kind of ssDNA, which are promising surfaces for the preparation of rapid, visible, and multiplex DNA sensors

Tunable Polymer Brush/Au NPs Hybrid Plasmonic Arrays Based on Host–guest Interaction

The fabrication of versatile gold nanoparticle (Au NP) arrays with tunable optical properties by a novel host–guest interaction are presented. The gold nanoparticles were incorporated into polymer brushes by host–guest interaction between β-cyclodextrin (β-CD) ligand of gold nanoparticles and dimethylamino group of poly­(2-(dimethylamino)­ethyl methacrylate) (PDMAEMA). The gold nanoparticle arrays were prepared through the template of PDMAEMA brush patterns which were fabricated combining colloidal lithography and surface-initiated atom-transfer radical polymerization (SI-ATRP). The structure parameters of gold nanoparticle patterns mediated by polymer brushes such as height, diameters, periods and distances, could be easily tuned by tailoring the etching time or size of colloidal spheres in the process of colloidal lithography. The change of optical properties induced by different gold nanoparticle structures was demonstrated. The direct utilization of PDMAEMA brushes as guest avoids a series of complicated modification process and the PDMAEMA brushes can be grafted on various substrates, which broaden its applications. The prepared gold naoparticle arrays are promising in applications of nanosensors, memory storage and surface enhanced spectroscopy