Inhibition of flowering by gibberellins in the woody plant Jatropha curcas is restored by overexpression of JcFT.

Jatropha curcas (J. curcas) is a perennial oil-seed plant with vigorous vegetative growth but relatively poor reproductive growth and low seed yield. Gibberellins (GAs) promotes flowering in most annual plants but inhibits flowering in many woody plants, including J. curcas. However, the underlying mechanisms of GA inhibits flowering in perennial woody plants remain unclear. Here, we found that overexpression of the GA biosynthesis gene JcGA20ox1 inhibits flowering in J. curcas and in J. curcas × J. integerrima hybrids. Consistent with this finding, overexpression of the GA catabolic gene JcGA2ox6 promotes flowering in J. curcas. qRTPCR revealed that inhibits floral transition by overexpressing JcGA20ox1 resulted from a decrease in the expression of JcFT and other flowering-related genes, which was restored by overexpressing JcFT in J. curcas. Overexpression of JcGA20ox1 or JcGA2ox6 reduced seed yield, but overexpression of JcFT significantly increased seed yield. Furthermore, hybridization experiments showed that the reduction in seed yield caused by overexpression of JcGA20ox1 or JcGA2ox6 was partially restored by the overexpression of JcFT. In addition, JcGA20ox1, JcGA2ox6 and JcFT were also found to be involved in the regulation of seed oil content and endosperm development. In conclusion, our study revealed that the inhibitory effect of GA on flowering is mediated through JcFT and demonstrated the effects of JcGA20ox1, JcGA2ox6 and JcFT on agronomic traits in J. curcas. This study also indicates the potential value of GA metabolism genes and JcFT in the breeding of new varieties of woody oil-seed plants.

Integrative transcriptome and metabolome analysis reveals the mechanisms of light-induced pigmentation in purple waxy maize.

Introduction: Waxy maize, mainly consumed at the immature stage, is a staple and vegetable food in Asia. The pigmentation in the kernel of purple waxy maize enhances its nutritional and market values. Light, a critical environmental factor, affects anthocyanin biosynthesis and results in pigmentation in different parts of plants, including in the kernel. SWL502 is a light-sensitive waxy maize inbred line with purple kernel color, but the regulatory mechanism of pigmentation in the kernel resulting in purple color is still unknown. Methods: In this study, cyanidin, peonidin, and pelargonidin were identified as the main anthocyanin components in SWL502, evaluated by the ultra-performance liquid chromatography (UPLC) method. Investigation of pigment accumulation in the kernel of SWL502 was performed at 12, 17, and 22 days after pollination (DAP) under both dark and light treatment conditions via transcriptome and metabolome analyses. Results: Dark treatment affected genes and metabolites associated with metabolic pathways of amino acid, carbohydrate, lipid, and galactose, biosynthesis of phenylpropanoid and terpenoid backbone, and ABC transporters. The expression of anthocyanin biosynthesis genes, such as 4CL2, CHS, F3H, and UGT, was reduced under dark treatment. Dynamic changes were identified in genes and metabolites by time-series analysis. The genes and metabolites involved in photosynthesis and purine metabolism were altered in light treatment, and the expression of genes and metabolites associated with carotenoid biosynthesis, sphingolipid metabolism, MAPK signaling pathway, and plant hormone signal transduction pathway were induced by dark treatment. Light treatment increased the expression level of major transcription factors such as LRL1, myc7, bHLH125, PIF1, BH093, PIL5, MYBS1, and BH074 in purple waxy maize kernels, while dark treatment greatly promoted the expression level of transcription factors RVE6, MYB4, MY1R1, and MYB145. Discussion: This study is the first report to investigate the effects of light on waxy maize kernel pigmentation and the underlying mechanism at both transcriptome and metabolome levels, and the results from this study are valuable for future research to better understand the effects of light on the regulation of plant growth.

The dynamic transcriptome of waxy maize (Zea mays L. sinensis Kulesh) during seed development.

BACKGROUND: Waxy maize (Zea mays L. sinensis Kulesh) is a mutant of maize (Zea mays L.) with a mutation at Waxy1 (Wx1) gene locus. The seed of waxy maize has higher viscosity compared to regular maize. By now, we know little about the expression patterns of genes that involved in the seed development of waxy maize. OBJECTIVE: By analyzing the transcriptome data during waxy maize seed development, we attempt to dig out the genes that may influence the seed development of waxy maize. METHODS: The seeds of waxy maize inbred line SWL01 from six phases after pollination were used to do RNA-seq. Bioinformatics methods were used to analyze the expression patterns of the expressed genes, to identify the genes involved in waxy maize seed development. RESULTS: A total of 24,546 genes including 1611 transcription factors (TFs) were detected during waxy maize seed development. Coexpression analysis of expressed genes revealed the dynamic processes of waxy maize seed development. Particularly, 2457 genes including 177 TFs were specially expressed in waxy maize seed, some of which mainly involved in the process of seed dormancy and maturation. In addition, 2681, 5686, 4491, 4386, 3669 and 4624 genes were identified to be differential expressed genes (DEGs) at six phases compared to regular maize B73, and 113 DEGs among them may be key genes that lead the difference of seed development between waxy and regular maizes in milk stage. CONCLUSION: In summary, we elucidated the expression patterns of expressed genes during waxy maize seed development globally. A series of genes that associated with seed development were identified in our research, which may provide an important resource for functional study of waxy maize seed development to help molecular assisted breeding.

Progress of ethylene action mechanism and its application on plant type formation in crops.

The plant hormone ethylene exerts a huge influence in the whole life cycle of plants, especially stress-resistance responses. With the development of functional genomics, that the action mechanism of ethylene takes part in mediated plant architecture has been clarified gradually, such as plant roots, stems, leaves, fiber elongation and so on. Accordingly, the application of ethylene on crops chemical control and genetic improvement is greatly expanded. From the view of ethylene mediated plant architecture in crops, here reviewed advances in ethylene biosynthesis and signal transduction pathway, stress-resistance responses and the yield potential enhance of crops in recently 20 years. On these grounds, the objectives of this paper were to provide scientific reference and a useful clue for the crop creation of ideal plant type.

Overexpression of Jatropha Gibberellin 2-oxidase 6 (JcGA2ox6) Induces Dwarfism and Smaller Leaves, Flowers and Fruits in Arabidopsis and Jatropha.

Gibberellins (GAs) are plant hormones that play fundamental roles in plant growth and development. Gibberellin 2-oxidase (GA2ox) plays a direct role in determining the levels of bioactive GAs by catalyzing bioactive GAs or their immediate precursors to inactive forms. In this study, a GA2ox gene, designated JcGA2ox6, was isolated from Jatropha curcas. JcGA2ox6 is expressed in all tissues of adult Jatropha, with the highest expression level in male flowers and the lowest expression level in young leaves. Overexpression of JcGA2ox6 in Arabidopsis resulted in a typical dwarf phenotype, along with late flowering, smaller leaves and flowers, shorter siliques and smaller seeds. Similarly, when JcGA2ox6 was overexpressed in Jatropha, the transgenic plants exhibited a dwarf phenotype with dark-green leaves and smaller inflorescences, flowers, fruits and seeds. However, the flowering time of Jatropha was not affected by overexpression of JcGA2ox6, unlike that in the transgenic Arabidopsis. Moreover, the number of flowers per inflorescence, the weight of 10 seeds and the seed oil content were significantly decreased in transgenic Jatropha. The results indicated that overexpression of JcGA2ox6 had a great impact on the vegetative and reproductive growth of transgenic Jatropha. Furthermore, we found that the dwarf phenotype of transgenic Jatropha was caused by a decrease in endogenous bioactive GA4, which was correlated with the degree of dwarfism.

Studies on quantitative analysis and automatic recognition of cell types of lung cancer.

Recognition of lung cancer cells is very important to the clinical diagnosis of lung cancer. In this paper we present a novel method to extract the structure characteristics of lung cancer cells and automatically recognize their types. Firstly soft mathematical morphology methods are used to enhance the grayscale image, to improve the definition of images, and to eliminate most of disturbance, noise and information of subordinate images, so the contour of target lung cancer cell and biological shape characteristic parameters can be extracted accurately. Then the minimum distance classifier is introduced to realize the automatic recognition of different types of lung cancer cells. A software system named "CANCER.LUNG" is established to demonstrate the efficiency of this method. The clinical experiments show that this method can accurately and objectively recognize the type of lung cancer cells, which can significantly improve the pathology research on the pathological changes of lung cancer and clinical assistant diagnoses.

Mitochondrial genome of silver gudgeon, Squalidus argentatus (Teleostei, Cypriniformes).

In this paper, we first determined the complete mitochondrial genome sequence of Squalidus argentatus, which was 16,607 bp in size and the whole base composition was estimated to be 30.48% A, 25.45% T, 27.36% C, 16.72% G with AT bias of 55.93%. The complete mitogenome comprised 13 protein-coding genes, 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes and 1 control region, with the gene order and content identical to other vertebrate mitogenomes. The complete mitogenome of S. argentatus provides the valuable information for population genetics and phylogeography studies on this species.

Complete mitochondrial genome of the smallscale yellowfin, Plagiognathops microlepis (Teleostei: Cypriniformes: Cyprinidae).

The smallscale yellowfin, Plagiognathops microlepis is the only one species in the genus Plagiognathops. In this study, we sequenced the complete mitochondrial genome of the P. microlepis. The complete mitogenome was 16,623 bp in size, consisting of 13 protein-coding genes, 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes, and 1 control region. It has the typical circular molecule structure of vertebrate's mitochondrial genome. The whole base composition was estimated to be 30.60% A, 25.19% T, 27.32% C and 16.89% G with AT bias of 55.79%. The complete mitogenome of P. microlepis provides the basis for preservation of genetic resources and genetic breeding studies on this species.

Complete mitochondrial genome of the pseudobream, Pseudobrama simoni (Teleostei:Cypriniformes:Cyprinidae).

The Pseudobrama simoni (Bleeker) is the only one species within the genus Pseudobrama of the subfamily Xenocyprinae. In this study, we first determined the complete mitochondrial genome sequence of the P. simoni. The whole mitogenome is 16,618 bp in size, consisting of 13 protein-coding genes, 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes and 1 control region. The gene order and molecule structure are similar to most vertebrates. The complete mitogenome of P. simoni provides the valuable information for the biogeographic and phylogenetic studies on the subfamily Xenocyprinae.

Automatic recognition of small cell carcinoma based on the self-organizing neural network.

In this paper the recognition of Small Cell Carcinoma (SCC) is studied. For each type we select 128 samples for training, and randomly measure 200 cells in each sample. We introduce multi-scale morphology based on centroid coordinates to extract the boundaries of nuclei and obtain feature images of nuclei. The features of lung cancer cells are described by morphological and colorimetrical parameters, which is valuable to recognize SCC. Then the architecture of self-organizing feature mapping (SOFM) neural network is studied for recognition of SCC. The weights of the network are adjusted by self-organizing competition, and finally inputted patterns are classified. This algorithm has the advantage of parallelism and fast-convergence, and may simplify the analysis of SCC. Clinical experiment results show that the correctness ratio of this system may reach 95.3% while recognizing lung cancer cell types. Our work is significant to the pathological researches of lung cancer, assistant clinic diagnosis, and assessment of therapeutic effects. Meanwhile a software system named as SCC. LUNG is established for automatic analysis.

Automatic quantitative analysis of ore content of human tooth enamel based on image processing.

Introducing the theory of fuzzy set, mathematical morphology and computerized mask fast scanning, we developed the TOOTH.SCA software and method to analyze the effect of fluoride (NaF) on ore content of human tooth enamel automatically and quantitatively. And we obtained some characteristic parameters, such as the depth, the type and the demineralized content of every scathing layer of dental caries. The smallest scale of mask scanning is 0.1 microm x 0.1 microm and the time required to analyze a sample is only 12 s. The applied software and method we built play an important role to the research on the mechanism of pathological changes of teeth and preventing dental caries.