Establishment of the model system between phytochemicals and gene expression profiles in Macrosclereid cells of Medicago truncatula

Macrosclereid cells, which are a layer in the seed coat of Medicago truncatula, accumulate large amounts of phytochemicals during their development. But little is known about the complex and dynamic changes during macrosclereid cell development. To characterize the phytochemicals and the related gene expression during the development of M. truncatula macrosclereid cells, a high performance liquid chromatography-mass spectrometry (HPLC-MS) assay and microarray study were conducted on transcriptome changes from macrosclereid cell during seed development. A total of 16 flavonoids by HPLC-MS and 4861 genes exhibited significant differences at transcript levels by microarray analysis were identified for macrosclerid cells at six different time points during seed development. 815 abiotic and biotic stress genes, 223 transcriptional factors (TFs), and 155 annotated transporter proteins exhibited differential expression during the development of macrosclereid cells. A total of 102 genes were identified as involved in flavonoid biosynthesis, phenypropanoid biosynthesis, and flavone and flavonol biosynthesis. We performed a weighted gene co-regulatory network (WGCNA) to analyze the gene-flavonoid association and rebuilt the gene regulatory network during macrosclereid cell development. Our studies revealed that macrosclereid cells are, beside as the first barrier of defense against diseases, an excellent model system to investigate the regulatory network that governs flavonoid biosynthesis

Extensive tRNA gene changes in synthetic Brassica napus

Allopolyploidization, where two species come together to form a new species, plays a major role in speciation and genome evolution. Transfer RNAs (abbreviated tRNA) are typically 73-94 nucleotides in length, and are indispensable in protein synthesis, transferring amino acids to the cell protein synthesis machinery (ribosome). To date, the regularity and function of tRNA gene sequence variation during the process of allopolyploidization have not been well understood. In this study, the inter-tRNA gene corresponding to tRNA amplification polymorphism method was used to detect changes in tRNA gene sequences in the progeny of interspecific hybrids between Brassica rapa and B. oleracea, mimicking the original B. napus (canola) species formation event. Cluster analysis showed that tRNA gene variation during allopolyploidization did not appear to have a genotypic basis. Significant variation occurred in the early generations of synthetic B. napus (F and F generations), but fewer alterations were observed in the later generation (F). The variation-prone tRNA genes tended to be located in AT-rich regions. BlastN analysis of novel tRNA gene variants against a Brassica genome sequence database showed that the variation of these tRNA-gene-associated sequences in allopolyploidization might result in variation of gene structure and function, e.g., metabolic process and transport

COMPARATIVE STUDY ON FREQUENCY DOMAIN FATIGUE ANALYSIS METHODS FOR HALF AXLE OF COMBINE HARVESTER

The calculation models of frequency domain fatigue analysis method are various and their accuracy is different. In order to solve the above problems, based on the time domain analysis results of the half axle, the accuracy comparison of frequency domain fatigue analysis methods is carried out. Firstly, the load signals of the half axle under different working conditions are obtained, and the stationarity, Gaussianity and bandwidth were investigated to obtain the basic properties of the load signal. Secondly, the static analysis of the half axle was carried out, and the transfer coefficients of stress and torque at the dangerous node of the walking half axle were obtained. Meanwhile, the stress time histories of the dangerous node of the half axle under various working conditions were obtained. Based on the above stress time histories, the comparative study of fatigue life in time-frequency domain was carried out, in which the average stress and non-Gaussian correction model were introduced to modify the traditional frequency domain method. The results showed that the accuracy of the modified frequency domain method was significantly better than that of the traditional frequency domain method. In the modified frequency domain method, TB2ms+nG and DKms+nG had the highest accuracy. When the above two methods were applied to the stationary load signals, the reliability was high. Nevertheless, when they were applied to the non-stationary load signals, the reliability was low

An Improved VMD-Based Denoising Method for Time Domain Load Signal Combining Wavelet with Singular Spectrum Analysis

Measured load data play a crucial role in the fatigue durability analysis of mechanical structures. However, in the process of signal acquisition, time domain load signals are easily contaminated by noise. In this paper, a signal denoising method based on variational mode decomposition (VMD), wavelet threshold denoising (WTD), and singular spectrum analysis (SSA) is proposed. Firstly, a simple criterion based on mutual information entropy (MIE) is designed to select the proper mode number for VMD. Detrended fluctuation analysis (DFA) is adopted to obtain the noise level of the noisy signal, which can optimize the selection of MIE threshold. Meanwhile, the noisy signal is adaptively decomposed into band-limited intrinsic mode functions (BLIMFs) by using VMD. In addition, weighted-permutation entropy (WPE) is applied to divide the BLIMFs into signal-dominant BLIMFs and noise-dominant BLIMFs. Then, the signal-dominant BLIMFs are reconstructed with the noise-dominant BLIMFs processed by WTD. Finally, SSA is implemented for the reconstructed signal. Experimental results of synthetic signals demonstrate that the presented method outperforms the conventional digital signal denoising methods and the related methods proposed recently. Effectiveness of the proposed method is verified through experiments of the measured load signals

Additional file 3: Figure S2. of Genome-wide systematic characterization of the bZIP transcriptional factor family in tomato (Solanum lycopersicum L.)

Phylogenetic relationship among the tomato, Arabidopsis and rice bZIP proteins. The unrooted tree was generated using neighbor-joining method by MEGA6.06. Bootstrap values from 1000 replicates are indicated at each node. Protein names of already characterized bZIP proteins have been indicated. (JPEG 8739 kb

Additional file 1: Table S1. of Genome-wide systematic characterization of the bZIP transcriptional factor family in tomato (Solanum lycopersicum L.)

The identified tomato bZIP proteins and their related information. (DOC 166 kb

Additional file 12: Table S7. of Genome-wide systematic characterization of the bZIP transcriptional factor family in tomato (Solanum lycopersicum L.)

Primers used in this study. (DOC 132 kb

CYCLIN-DEPENDENT KINASE8 Differentially Regulates Plant Immunity to Fungal Pathogens through Kinase-Dependent and -Independent Functions in ArabidopsisC

CYCLIN-DEPENDENT KINASE8 (CDK8) is a widely studied component of eukaryotic Mediator complexes. However, the biological and molecular functions of plant CDK8 are not well understood. Here, we provide evidence for regulatory functions of Arabidopsis thaliana CDK8 in defense and demonstrate its functional and molecular interactions with other Mediator and non-Mediator subunits. The cdk8 mutant exhibits enhanced resistance to Botrytis cinerea but susceptibility to Alternaria brassicicola. The contributions of CDK8 to the transcriptional activation of defensin gene PDF1.2 and its interaction with MEDIATOR COMPLEX SUBUNIT25 (MED25) implicate CDK8 in jasmonate-mediated defense. Moreover, CDK8 associates with the promoter of AGMATINE COUMAROYLTRANSFERASE to promote its transcription and regulate the biosynthesis of the defense-active secondary metabolites hydroxycinnamic acid amides. CDK8 also interacts with the transcription factor WAX INDUCER1, implying its additional role in cuticle development. In addition, overlapping functions of CDK8 with MED12 and MED13 and interactions between CDK8 and C-type cyclins suggest the conserved configuration of the plant Mediator kinase module. In summary, while CDK8’s positive transcriptional regulation of target genes and its phosphorylation activities underpin its defense functions, the impaired defense responses in the mutant are masked by its altered cuticle, resulting in specific resistance to B. cinerea