Identification of miRNAs and their targets by high-throughput sequencing and degradome analysis in cytoplasmic male-sterile line NJCMS1A and its maintainer NJCMS1B of soybean

Table S1. Summary of small RNA annotations from NJCMS1A and NJCMS1B. Table S2. Known miRNAs identified in NJCMS1A and NJCMS1B. Table S3. Family member distribution in conserved miRNA families. Table S4. Summary of miRNA families found in NJCMS1A and NJCMS1B. Table S5. Novel miRNAs on the other arm of known pre-miRNAs. Table S6. Novel miRNAs identified in NJCMS1A and NJCMS1B. Table S7-1. High-confidence known miRNAs identified in NJCMS1A and NJCMS1B. Table S7-2. High-confidence novel miRNAs identified in NJCMS1A and NJCMS1B. Table S8-1. The up-regulated miRNAs identified in NJCMS1A and NJCMS1B. Table S8-2. The down-regulated miRNAs identified in NJCMS1A and NJCMS1B. Table S9. The targets of miRNAs identified in NJCMS1A and NJCMS1B. Table S10. Targets of novel miRNAs in NJCMS1A and NJCMS1B. Table S11. Primers used in this study. (ZIP 637 kb

Vertically scanned laser sheet microscopy

Laser sheet microscopy is a widely used imaging technique for imaging the three-dimensional distribution of a fluorescence signal in fixed tissue or small organisms. In laser sheet microscopy, the stripe artifacts caused by high absorption or high scattering structures are very common, greatly affecting image quality. To solve this problem, we report here a two-step procedure which consists of continuously acquiring laser sheet images while vertically displacing the sample, and then using the variational stationary noise remover (VSNR) method to further reduce the remaining stripes. Images from a cleared murine colon acquired with a vertical scan are compared with common stitching procedures demonstrating that vertically scanned light sheet microscopy greatly improves the performance of current light sheet microscopy approaches without the need for complex changes to the imaging setup and allows imaging of elongated samples, extending the field of view in the vertical direction.This work was supported in part by the Bill and Melinda Gates Foundation, the National Basic Research Program of China (973 Program) under Grant No. 2011CB707700, the National Natural Science Foundation of China under Grant No. 81227901, 81027002, 61231004, and 81101095, the Fellowship for Young International Scientists of the Chinese Academy of Sciences under Grant No. 2010Y2GA03, and the Instrument Developing Project of the Chinese Academy of Sciences under Grant No. YZ201164. A. Arranz acknowledges support from the Marie Curie Intra-European Fellowship program IEF-2010-275137. J.R. acknowledges support from EC FP7 IMI project PREDICT-TB, the EC FP7 CIG grant HIGHTHROUGHPUT TOMO, and the Spanish MINECO project grant FIS2013-41802-R MESO-IMAGING

Genome-Wide Identification and Characterization of TALE Superfamily Genes in Soybean (Glycine max L.)

The three-amino-acid-loop-extension (TALE) superfamily genes broadly existed in plants, which played important roles in plant growth, development and abiotic stress responses. In this study, we identified 68 Glycine max TALE (GmTALE) superfamily members. Phylogenetic analysis divided the GmTALE superfamily into the BEL1-like (BLH/BELL homeodomain) and the KNOX (KNOTTED-like homeodomain) subfamilies. Moreover, the KNOX subfamily could be further categorized into three clades (KNOX Class I, KNOX Class II and KNOX Class III). The GmTALE genes showed similarities in the gene structures in the same subfamily or clade, whose coding proteins exhibited analogous motif and conserved domain compositions. Besides, synteny analyses and evolutionary constraint evaluations of the TALE members among soybean and different species provided more clues for GmTALE superfamily evolution. The cis-element analyses in gene promoter regions and relevant gene expression profiling revealed different regulating roles of GmTALE genes during soybean plant development, saline and dehydration stresses. Genome-wide characterization, evolution, and expression profile analyses of GmTALE genes can pave the way for future gene functional research and facilitate their roles for applications in genetic improvement on soybean in saline and dehydration stresses

A 12-bit 30 MS/s Successive Approximation-Register Analog-to-Digital Converter with Foreground Digital Calibration Algorithm

This paper presents a foreground digital calibration algorithm based on a dynamic comparator that aims to reduce comparator offset and capacitor mismatch, as well as improve the performance of the successive approximation analog-to-digital converter (SARADC). The dynamic comparator is designed with two preamplifiers and one latch to facilitate high speed, high precision, and low noise. The foreground digital calibration algorithm provides high speed with minimal area consumption. This design is implemented on a 12-bit 30 MS/s SARADC with a standard 0.13 μm Complementary Metal Oxide Semiconductor (CMOS) process. The simulation Nyquist 68.56 dB signal-to-noise-and-distortion ratio (SNDR) and 84.45 dBc spurious free dynamic range (SFDR) at 30 MS/s, differential nonlinearity (DNL) and integral nonlinearity (INL) are within 0.64 Least Significant Bits (LSB) and 1.3 LSB, respectively. The ADC achieves an effective number of bits (ENOB) of 11.08 and a figure-of-merit (FoM) of 39.45 fJ/conv.-step

Image Restoration for Fluorescence Planar Imaging with Diffusion Model

Fluorescence planar imaging (FPI) is failure to capture high resolution images of deep fluorochromes due to photon diffusion. This paper presents an image restoration method to deal with this kind of blurring. The scheme of this method is conceived based on a reconstruction method in fluorescence molecular tomography (FMT) with diffusion model. A new unknown parameter is defined through introducing the first mean value theorem for definite integrals. System matrix converting this unknown parameter to the blurry image is constructed with the elements of depth conversion matrices related to a chosen plane named focal plane. Results of phantom and mouse experiments show that the proposed method is capable of reducing the blurring of FPI image caused by photon diffusion when the depth of focal plane is chosen within a proper interval around the true depth of fluorochrome. This method will be helpful to the estimation of the size of deep fluorochrome

Size Transformation of the Au22(SG)18 Nanocluster and Its Surface-Sensitive Kinetics.

For many applications of well-defined gold nanoclusters, it is desirable to understand their structural evolution behavior under working conditions with molecular precision. Here we report the first systematic investigation of the size transformation products of the Au22(SG)18 nanocluster under representative working conditions and highlight the surface effect on the transformation kinetics. Under thermal and aerobic conditions, the consecutive and pH-dependent transformation from Au22 to both well-defined clusters and small Au(I)SR species was identified by ESI-MS and UV-vis spectroscopy. By introducing a perturbation onto the Au22 surface, significant changes in the activation parameters were determined from the kinetic study of the Au22 transformation. This indicates the sensitivity of the nanocluster transformation pathway to the cluster surface. The systematic study of cluster transformation and the sensitivity of cluster transformation to the surface revealed herein has significant implications for future attempts to design gold nanoparticles with adaptation to the working environment and the regeneration of active nanoparticles

Heat-Responsive miRNAs Participate in the Regulation of Male Fertility Stability in Soybean CMS-Based F₁ under High Temperature Stress

MicroRNAs (miRNAs), a class of noncoding small RNAs (sRNAs), are widely involved in the response to high temperature (HT) stress at both the seedling and flowering stages. To dissect the roles of miRNAs in regulating male fertility in soybean cytoplasmic male sterility (CMS)-based F1 under HT, sRNA sequencing was performed using flower buds from HT-tolerant and HT-sensitive CMS-based F1 combinations (NF1 and YF1, respectively). A total of 554 known miRNAs, 59 new members of known miRNAs, 712 novel miRNAs, and 1145 target genes of 580 differentially expressed miRNAs (DEMs) were identified under normal temperature and HT conditions. Further integrated analysis of sRNA and transcriptome sequencing found that 21 DEMs and 15 differentially expressed target genes, such as gma-miR397a/Laccase 2, gma-miR399a/Inorganic phosphate transporter 1-4, and gma-miR4413a/PPR proteins, mitochondrial-like, were negatively regulated under HT stress. Furthermore, all members of the gma-miR156 family were suppressed by HT stress in both NF1 and YF1, but were highly expressed in YF1 under HT condition. The negative correlation between gma-miR156b and its target gene squamosa promoter-binding protein-like 2b was confirmed by expression analysis, and overexpression of gma-miR156b in Arabidopsis led to male sterility under HT stress. With these results, we proposed that miRNAs play an important role in the regulation of male fertility stability in soybean CMS-based F1 under HT stress

The Effect of CuO/CeO

In this paper, the porous CeO2 flowerlike spheres support and a series of CuO/CeO2 prepared by different methods were synthesized. The SEM, XRD, BET, H2-TPR and FT-IR characterization were conducted to probe the physicochemical properties of the samples. To evaluate the HCN catalytic removal efficiency over the prepared samples, the breakthrough time of HCN over different samples were investigated. The results implied the CuO/CeO2 prepared by precipitation method (donated as Ce-5) showed highest catalytic activity, the breakthrough time of which was more than 70 min at 30 °C. It was proved the dispersion of CuO phase on the support, the redox properties and the interaction between CuO and CeO2 support over CuO/CeO2 played an important role in the HCN catalytic removal process. FT-IR analysis demonstrated the CuCN was generated due to the chemisorption of CuO and HCN

Heat-Responsive miRNAs Participate in the Regulation of Male Fertility Stability in Soybean CMS-Based F1 under High Temperature Stress

MicroRNAs (miRNAs), a class of noncoding small RNAs (sRNAs), are widely involved in the response to high temperature (HT) stress at both the seedling and flowering stages. To dissect the roles of miRNAs in regulating male fertility in soybean cytoplasmic male sterility (CMS)-based F1 under HT, sRNA sequencing was performed using flower buds from HT-tolerant and HT-sensitive CMS-based F1 combinations (NF1 and YF1, respectively). A total of 554 known miRNAs, 59 new members of known miRNAs, 712 novel miRNAs, and 1145 target genes of 580 differentially expressed miRNAs (DEMs) were identified under normal temperature and HT conditions. Further integrated analysis of sRNA and transcriptome sequencing found that 21 DEMs and 15 differentially expressed target genes, such as gma-miR397a/Laccase 2, gma-miR399a/Inorganic phosphate transporter 1-4, and gma-miR4413a/PPR proteins, mitochondrial-like, were negatively regulated under HT stress. Furthermore, all members of the gma-miR156 family were suppressed by HT stress in both NF1 and YF1, but were highly expressed in YF1 under HT condition. The negative correlation between gma-miR156b and its target gene squamosa promoter-binding protein-like 2b was confirmed by expression analysis, and overexpression of gma-miR156b in Arabidopsis led to male sterility under HT stress. With these results, we proposed that miRNAs play an important role in the regulation of male fertility stability in soybean CMS-based F1 under HT stress

Metabolomics Studies on Cytoplasmic Male Sterility during Flower Bud Development in Soybean

Abnormal reactive oxygen species (ROS) may mediate cytoplasmic male sterility (CMS). To observe the effect of ROS on soybean CMS, metabolite content and antioxidant enzyme activity in the flower buds between soybean N8855-derived CMS line and its maintainer were compared. Of the 612 metabolites identified, a total of 74 metabolites were significantly differentiated in flower buds between CMS line and its maintainer. The differential metabolites involved 32 differential flavonoids, 13 differential phenolamides, and 1 differential oxidized glutathione (GSSG) belonging to a non-enzymatic ROS scavenging system. We observed lower levels of flavonoids and antioxidant enzyme activities in flower buds of the CMS line than in its maintainer. Our results suggest that deficiencies of enzymatic and non-enzymatic ROS scavenging systems in soybean CMS line cannot eliminate ROS in anthers effectively, excessive accumulation of ROS triggered programmed cell death and ultimately resulted in pollen abortion of soybean CMS line