Genome-wide identification, structural characterization and gene expression analysis of the WRKY transcription factor family in pea (Pisum sativum L.).

BACKGROUND: The WRKY gene family is one of the largest families of transcription factors in higher plants, and WRKY transcription factors play important roles in plant growth and development as well as in response to abiotic stresses; however, the WRKY gene family in pea has not been systematically reported. RESULTS: In this study, 89 pea WRKY genes were identified and named according to the random distribution of PsWRKY genes on seven chromosomes. The gene family was found to have nine pairs of tandem duplicates and 19 pairs of segment duplicates. Phylogenetic analyses of the PsWRKY and 60 Arabidopsis WRKY proteins were performed to determine their homology, and the PsWRKYs were classified into seven subfamilies. Analysis of the physicochemical properties, motif composition, and gene structure of pea WRKYs revealed significant differences in the physicochemical properties within the PsWRKY family; however, their gene structure and protein-conserved motifs were highly conserved among the subfamilies. To further investigate the evolutionary relationships of the PsWRKY family, we constructed comparative syntenic maps of pea with representative monocotyledonous and dicotyledonous plants and found that it was most recently homologous to the dicotyledonous WRKY gene families. Cis-acting element analysis of PsWRKY genes revealed that this gene family can respond to hormones, such as abscisic acid (ABA), indole-3-acetic acid (IAA), gibberellin (GA), methyl jasmonate (MeJA), and salicylic acid (SA). Further analysis of the expression of 14 PsWRKY genes from different subfamilies in different tissues and fruit developmental stages, as well as under five different hormone treatments, revealed differences in their expression patterns in the different tissues and fruit developmental stages, as well as under hormone treatments, suggesting that PsWRKY genes may have different physiological functions and respond to hormones. CONCLUSIONS: In this study, we systematically identified WRKY genes in pea for the first time and further investigated their physicochemical properties, evolution, and expression patterns, providing a theoretical basis for future studies on the functional characterization of pea WRKY genes during plant growth and development.

Predicting IDH Mutation Status in Low-Grade Gliomas Based on Optimal Radiomic Features Combined with Multi-Sequence Magnetic Resonance Imaging.

The IDH somatic mutation status is an important basis for the diagnosis and classification of gliomas. We proposed a "6-Step" general radiomics model to noninvasively predict the IDH mutation status by simultaneously tuning combined multi-sequence MRI and optimizing the full radiomics processing pipeline. Radiomic features (n = 3776) were extracted from multi-sequence MRI (T1, T2, FLAIR, and T1Gd) in low-grade gliomas (LGGs), and a total of 45,360 radiomics pipeline were investigated according to different settings. The predictive ability of the general radiomics model was evaluated with regards to accuracy, stability, and efficiency. Based on numerous experiments, we finally reached an optimal pipeline for classifying IDH mutation status, namely the T2+FLAIR combined multi-sequence with the wavelet image filter, mean data normalization, PCC dimension reduction, RFE feature selection, and SVM classifier. The mean and standard deviation of AUC, accuracy, sensitivity, and specificity were 0.873 ± 0.05, 0.876 ± 0.09, 0.875 ± 0.11, and 0.877 ± 0.15, respectively. Furthermore, 14 radiomic features that best distinguished the IDH mutation status of the T2+FLAIR multi-sequence were analyzed, and the gray level co-occurrence matrix (GLCM) features were shown to be of high importance. Apart from the promising prediction of the molecular subtypes, this study also provided a general tool for radiomics investigation.

Genome-Wide Identification, Evolution, and Expression Pattern Analysis of the GATA Gene Family in Tartary Buckwheat (Fagopyrum tataricum).

GATA is a transcription factor that exerts a vital function in plant growth and development, physiological metabolism, and environmental responses. However, the GATA gene family has rarely been studied in Tartary buckwheat since the completion of its genome. This study used bioinformatics methods to identify GATA genes of Tartary buckwheat and to analyze their subfamily classification, structural composition, and developmental evolution, as well as to discuss the expression patterns of FtGATA genes in different subfamilies. The twenty-eight identified FtGATA genes in the Tartary buckwheat genome were divided into four subfamilies and distributed on eight chromosomes. One pair of tandem repeat genes and eight pairs of fragments were found in chromosome mapping. Spatiotemporal expression patterns of eight FtGATA genes in different subfamilies indicated that the FtGATA gene family has regulatory roles in tissue specificity, fruit development, abiotic stress, and hormonal responses. This study creates a theoretical and scientific foundation for further research on the evolutionary relationship and biological function of FtGATA.

Genome-wide identification and characterization of the SPL gene family and its expression in the various developmental stages and stress conditions in foxtail millet (Setaria italica).

BACKGROUND: Among the major transcription factors, SPL plays a crucial role in plant growth, development, and stress response. Foxtail millet (Setaria italica), as a C4 crop, is rich in nutrients and is beneficial to human health. However, research on the foxtail millet SPL (SQUAMOSA PROMOTER BINDING-LIKE) gene family is limited.  RESULTS: In this study, a total of 18 SPL genes were identified for the comprehensive analysis of the whole genome of foxtail millet. These SiSPL genes were divided into seven subfamilies (I, II, III, V, VI, VII, and VIII) according to the classification of the Arabidopsis thaliana SPL gene family. Structural analysis of the SiSPL genes showed that the number of introns in subfamilies I and II were much larger than others, and the promoter regions of SiSPL genes were rich in different cis-acting elements. Among the 18 SiSPL genes, nine genes had putative binding sites with foxtail millet miR156. No tandem duplication events were found between the SiSPL genes, but four pairs of segmental duplications were detected. The SiSPL genes expression were detected in different tissues, which was generally highly expressed in seeds development process, especially SiSPL6 and SiSPL16, which deserve further study. The results of the expression levels of SiSPL genes under eight types of abiotic stresses showed that many stress responsive genes, especially SiSPL9, SiSPL10, and SiSPL16, were highly expressed under multiple stresses, which deserves further attention. CONCLUSIONS: In this research, 18 SPL genes were identified in foxtail millet, and their phylogenetic relationships, gene structural features, duplication events, gene expression and potential roles in foxtail millet development were studied. The findings provide a new perspective for the mining of the excellent SiSPL gene and the molecular breeding of foxtail millet.

Genome-wide identification, phylogenetic and expression pattern analysis of MADS-box family genes in foxtail millet (Setaria italica).

Foxtail millet (Setaria italica) is rich in nutrients and extremely beneficial to human health. We identified and comprehensively analyzed 89 MADS-box genes in the foxtail millet genome. According to the classification of MADS-box genes in Arabidopsis thaliana and rice, the SiMADS-box genes were divided into M-type (37) and MIKC-type (52). During evolution, the differentiation of MIKC-type MADS-box genes occurred before that of monocotyledons and dicotyledons. The SiMADS-box gene structure has undergone much differentiation, and the number of introns in the MIKC-type subfamily is much greater than that in the M-type subfamily. Analysis of gene duplication events revealed that MIKC-type MADS-box gene segmental duplication accounted for the vast majority of gene duplication events, and MIKC-type MADS-box genes played a major role in the amplification of SiMADS-box genes. Collinearity analysis showed highest collinearity between foxtail millet and maize MADS-box genes. Analysis of tissue-specific expression showed that SiMADS-box genes are highly expressed throughout the grain-filling process. Expression analysis of SiMADS-box genes under eight different abiotic stresses revealed many stress-tolerant genes, with induced expression of SiMADS33 and SiMADS78 under various stresses warranting further attention. Further, some SiMADS-box proteins may interact under external stress. This study provides insights for MADS-box gene mining and molecular breeding of foxtail millet in the future.

Genome-wide identification and expression analysis of the bHLH transcription factor family and its response to abiotic stress in foxtail millet (Setaria italica L.).

BACKGROUND: Members of the basic helix-loop-helix (bHLH) transcription factor family perform indispensable functions in various biological processes, such as plant growth, seed maturation, and abiotic stress responses. However, the bHLH family in foxtail millet (Setaria italica), an important food and feed crop, has not been thoroughly studied. RESULTS: In this study, 187 bHLH genes of foxtail millet (SibHLHs) were identified and renamed according to the chromosomal distribution of the SibHLH genes. Based on the number of conserved domains and gene structure, the SibHLH genes were divided into 21 subfamilies and two orphan genes via phylogenetic tree analysis. According to the phylogenetic tree, the subfamilies 15 and 18 may have experienced stronger expansion in the process of evolution. Then, the motif compositions, gene structures, chromosomal spread, and gene duplication events were discussed in detail. A total of sixteen tandem repeat events and thirty-eight pairs of segment duplications were identified in bHLH family of foxtail millet. To further investigate the evolutionary relationship in the SibHLH family, we constructed the comparative syntenic maps of foxtail millet associated with representative monocotyledons and dicotyledons species. Finally, the gene expression response characteristics of 15 typical SibHLH genes in different tissues and fruit development stages, and eight different abiotic stresses were analysed. The results showed that there were significant differences in the transcription levels of some SibHLH members in different tissues and fruit development stages, and different abiotic stresses, implying that SibHLH members might have different physiological functions. CONCLUSIONS: In this study, we identified 187 SibHLH genes in foxtail millet and further analysed the evolution and expression patterns of the encoded proteins. The findings provide a comprehensive understanding of the bHLH family in foxtail millet, which will inform further studies on the functional characteristics of SibHLH genes.

Genome-wide identification, expression analysis, and functional study of the GRAS transcription factor family and its response to abiotic stress in sorghum [Sorghum bicolor (L.) Moench].

BACKGROUND: GRAS, an important family of transcription factors, have played pivotal roles in regulating numerous intriguing biological processes in plant development and abiotic stress responses. Since the sequencing of the sorghum genome, a plethora of genetic studies were mainly focused on the genomic information. The indepth identification or genome-wide analysis of GRAS family genes, especially in Sorghum bicolor, have rarely been studied. RESULTS: A total of 81 SbGRAS genes were identified based on the S. bicolor genome. They were named SbGRAS01 to SbGRAS81 and grouped into 13 subfamilies (LISCL, DLT, OS19, SCL4/7, PAT1, SHR, SCL3, HAM-1, SCR, DELLA, HAM-2, LAS and OS4). SbGRAS genes are not evenly distributed on the chromosomes. According to the results of the gene and motif composition, SbGRAS members located in the same group contained analogous intron/exon and motif organizations. We found that the contribution of tandem repeats to the increase in sorghum GRAS members was slightly greater than that of fragment repeats. By quantitative (q) RT-PCR, the expression of 13 SbGRAS members in different plant tissues and in plants exposed to six abiotic stresses at the seedling stage were quantified. We further investigated the relationship between DELLA genes, GAs and grain development in S. bicolor. The paclobutrazol treatment significantly increased grain weight, and affected the expression levels of all DELLA subfamily genes. SbGRAS03 is the most sensitive to paclobutrazol treatment, but also has a high response to abiotic stresses. CONCLUSIONS: Collectively, SbGRAs play an important role in plant development and response to abiotic stress. This systematic analysis lays the foundation for further study of the functional characteristics of GRAS genes of S. bicolor.

Genome-wide identification and expression analysis of the bHLH transcription factor family and its response to abiotic stress in sorghum [Sorghum bicolor (L.) Moench].

BACKGROUND: Basic helix-loop-helix (bHLH) is a superfamily of transcription factors that is widely found in plants and animals, and is the second largest transcription factor family in eukaryotes after MYB. They have been shown to be important regulatory components in tissue development and many different biological processes. However, no systemic analysis of the bHLH transcription factor family has yet been reported in Sorghum bicolor. RESULTS: We conducted the first genome-wide analysis of the bHLH transcription factor family of Sorghum bicolor and identified 174 SbbHLH genes. Phylogenetic analysis of SbbHLH proteins and 158 Arabidopsis thaliana bHLH proteins was performed to determine their homology. In addition, conserved motifs, gene structure, chromosomal spread, and gene duplication of SbbHLH genes were studied in depth. To further infer the phylogenetic mechanisms in the SbbHLH family, we constructed six comparative syntenic maps of S. bicolor associated with six representative species. Finally, we analyzed the gene-expression response and tissue-development characteristics of 12 typical SbbHLH genes in plants subjected to six different abiotic stresses. Gene expression during flower and fruit development was also examined. CONCLUSIONS: This study is of great significance for functional identification and confirmation of the S. bicolor bHLH superfamily and for our understanding of the bHLH superfamily in higher plants.

Adding NBPT to urea increases N use efficiency of maize and decreases the abundance of N-cycling soil microbes under reduced fertilizer-N rate on the North China Plain.

Urease inhibitor (UI) and nitrification inhibitor (NI) can reduce N losses from agricultural soils but effects of inhibitors on N cycle are unclear. A field experiment was conducted with maize to test effects of UI (N-(n-Butyl) thiophosphoric, NBPT) and NI (3,4-dimethylepyrazolephosphate, DMPP) on N uptake and N-cycling soil microbes. Five treatments were imposed: no N fertilizer input (CK), conventional fertilization (CF) and 80% of urea input with NBPT (80%U+UI), with DMPP (80%U+NI) and with half NBPT and half DMPP (80%U+1/2(UI+NI)). There were no significant differences in biomass between 80%U+UI, 80%U+NI and CF but harvest index was increased under 80%U+UI and 80%U+NI. Compared to CF, N use efficiency of grain under 80%U+UI was increased by 7.1%, whereas grain yield and N uptake under 80%U+1/2(UI+NI) were decreased by 8.2% and 9.4%, respectively. The peak soil [Formula: see text] content was at about 15 days after fertilization (DAF) under CF but 30 DAF under the inhibitor treatments. In soils of 80%U+UI, the activities of urease and nitrate reductase were decreased between 15-45 DAF and between 5-30 DAF. The abundance of N-cycling soil microbes was affected: 80%U+UI and 80%U+NI reduced the copies of the amoA AOA and nir genes at about 15 days and reduced the copies of the amoA AOB gene at about 30 days. Correlation analysis indicated that there were significant positive relationships between amoA AOB gene and [Formula: see text], as well as between nirK gene and [Formula: see text]. Overall, urea applied with NBPT has greater potential for improving maize N use efficiency and inhibiting nitrification under reduced fertilizer-N applications.

iMAGE cloud: medical image processing as a service for regional healthcare in a hybrid cloud environment.

OBJECTIVES: To handle the emergence of the regional healthcare ecosystem, physicians and surgeons in various departments and healthcare institutions must process medical images securely, conveniently, and efficiently, and must integrate them with electronic medical records (EMRs). In this manuscript, we propose a software as a service (SaaS) cloud called the iMAGE cloud. METHODS: A three-layer hybrid cloud was created to provide medical image processing services in the smart city of Wuxi, China, in April 2015. In the first step, medical images and EMR data were received and integrated via the hybrid regional healthcare network. Then, traditional and advanced image processing functions were proposed and computed in a unified manner in the high-performance cloud units. Finally, the image processing results were delivered to regional users using the virtual desktop infrastructure (VDI) technology. Security infrastructure was also taken into consideration. RESULTS: Integrated information query and many advanced medical image processing functions-such as coronary extraction, pulmonary reconstruction, vascular extraction, intelligent detection of pulmonary nodules, image fusion, and 3D printing-were available to local physicians and surgeons in various departments and healthcare institutions. CONCLUSIONS: Implementation results indicate that the iMAGE cloud can provide convenient, efficient, compatible, and secure medical image processing services in regional healthcare networks. The iMAGE cloud has been proven to be valuable in applications in the regional healthcare system, and it could have a promising future in the healthcare system worldwide.

The promoting effects of alginate oligosaccharides on root development in Oryza sativa L. mediated by auxin signaling.

Alginate oligosaccharides (AOS), which are marine oligosaccharides, are involved in regulating plant root growth, but the promotion mechanism for AOS remains unclear. Here, AOS (10-80 mg/L) induced the expression of auxin-related gene (OsYUCCA1, OsYUCCA5, OsIAA11 and OsPIN1) in rice (Oryza sativa L.) tissues to accelerate auxin biosynthesis and transport, and reduced indole-3-acetic acid (IAA) oxidase activity in rice roots. These changes resulted in the increase of 37.8% in IAA concentration in rice roots, thereby inducing the expression of root development-related genes, promoting root growth in a dose-dependent manner, which were inhibited by auxin transport inhibitor 2,3,5-triiodo benzoic acid (TIBA) and calcium-chelating agent ethylene glycol bis (2-aminoethyl) tetraacetic acid (EGTA). AOS also induced calcium signaling generation in rice roots. Those results indicated that auxin mediated AOS regulation of root development, and calcium signaling may act mainly in the upstream of auxin in the regulation of AOS on rice root development.