Generative Adversarial Mapping Networks

Generative Adversarial Networks (GANs) have shown impressive performance in generating photo-realistic images. They fit generative models by minimizing certain distance measure between the real image distribution and the generated data distribution. Several distance measures have been used, such as Jensen-Shannon divergence, $f$-divergence, and Wasserstein distance, and choosing an appropriate distance measure is very important for training the generative network. In this paper, we choose to use the maximum mean discrepancy (MMD) as the distance metric, which has several nice theoretical guarantees. In fact, generative moment matching network (GMMN) (Li, Swersky, and Zemel 2015) is such a generative model which contains only one generator network $G$ trained by directly minimizing MMD between the real and generated distributions. However, it fails to generate meaningful samples on challenging benchmark datasets, such as CIFAR-10 and LSUN. To improve on GMMN, we propose to add an extra network $F$, called mapper. $F$ maps both real data distribution and generated data distribution from the original data space to a feature representation space $\mathcal{R}$, and it is trained to maximize MMD between the two mapped distributions in $\mathcal{R}$, while the generator $G$ tries to minimize the MMD. We call the new model generative adversarial mapping networks (GAMNs). We demonstrate that the adversarial mapper $F$ can help $G$ to better capture the underlying data distribution. We also show that GAMN significantly outperforms GMMN, and is also superior to or comparable with other state-of-the-art GAN based methods on MNIST, CIFAR-10 and LSUN-Bedrooms datasets.Comment: 9 pages, 7 figure

Preliminary Characterization of Underground Hydrological Processes under Multiple Rainfall Conditions and Rocky Desertification Degrees in Karst Regions of Southwest China

Karst regions are widely distributed in Southwest China and due to the complexity of their geologic structure, it is very challenging to collect data useful to provide a better understanding of surface, underground and fissure flows, needed to calibrate and validate numerical models. Without characterizing these features, it is very problematic to fully establish rainfall–runoff processes associated with soil loss in karst landscapes. Water infiltrated rapidly to the underground in rocky desertification areas. To fill this gap, this experimental work was completed to preliminarily determine the output characteristics of subsurface and underground fissure flows and their relationships with rainfall intensities (30 mm h−1, 60 mm h−1 and 90 mm h−1) and bedrock degrees (30%, 40% and 50%), as well as the role of underground fissure flow in the near-surface rainfall–runoff process. Results indicated that under light rainfall conditions (30 mm h−1), the hydrological processes observed were typical of Dunne overland flows; however, under moderate (60 mm h−1) and high rainfall conditions (90 mm h−1), hydrological processes were typical of Horton overland flows. Furthermore, results confirmed that the generation of underground runoff for moderate rocky desertification (MRD) and severe rocky desertification (SRD) happened 18.18% and 45.45% later than the timing recorded for the light rocky desertification (LRD) scenario. Additionally, results established that the maximum rate of underground runoff increased with the increase of bedrock degrees and the amount of cumulative underground runoff measured under different rocky desertification was SRD > MRD > LRD. In terms of flow characterization, for the LRD configuration under light rainfall intensity the underground runoff was mainly associated with soil water, which was accounting for about 85%–95%. However, under moderate and high rainfall intensities, the underground flow was mainly generated from fissure flow

Genome-wide identification and expression pattern analysis of the SABATH gene family in Neolamarckia cadamba

Plant SABATH methyltransferases are a class of enzymes that catalyze the transfer of the methyl group from S-adenosyl-L-methionine (SAM) to the carboxyl group or the nitrogen group of the substrate to form small molecule methyl esters or N-methylated compounds, which are involved in various secondary metabolite biosynthesis and have important impacts on plant growth, development, and defense reactions. We previously reported the monoterpenoid indole alkaloids (MIAs) cadambine biosynthetic pathway in Neolamarckia cadamba, a woody tree species that provides an important traditional medicine widely used to treat diseases such as diabetes, leprosy, and cancer in Southeast Asia. However, the functions of NcSABATHs in cadambine biosynthesis remain unclear. In this study, 23 NcSABATHs were identified and found to be distributed on 12 of the total 22 chromosomes. Gene structure, conserved motifs, and phylogenetic analysis showed that NcSABATHs could be divided into three groups. According to cis-element analysis, the NcSABATH promoters contained a large number of elements involved in light, plant hormone, and environmental stress responses, as well as binding sites for the BBR-BPC, DOF, and MYB transcription factor families. Based on RNA-seq data and qRT-PCR analysis, the NcSABATH genes exhibited diverse tissue expression patterns. Furthermore, NcSABATH7/22, which clustered with LAMT in the same clade, were both up-regulated under MeJA treatment. The correlation analysis between gene expression and cadambine content showed that NcSABATH7 potentially participated in cadambine biosynthesis. Taken together, our study not only enhanced our understanding of SABATH in N. cadamba but also identified potential candidate genes involved in cadambine biosynthesis

Arabidopsis sucrose transporter 4 (AtSUC4) is involved in high sucrose-mediated inhibition of root elongation

AbstractSucrose transporters (SUCs/SUTs) play crucial roles in apoplast transport and long-distance distribution of sucrose throughout the whole plant. However, whether and how the Arabidopsis AtSUC4 modulates sucrose import from apoplast to cytosol remains unclear. In the present study, we found that AtSUC4 protein was localized to the plasma membrane in the root. Expression of AtSUC4 in roots was gradually induced with the increasing sucrose concentrations (0%, 2%, 4% and 6%). When feeding high concentrations (4% and 6%) of sucrose, the primary root growth of seedling was inhibited. Interestingly, atsuc4 mutants exhibited longer primary root than the wild type under these conditions, indicating that atsuc4 mutants were less sensitive to excess sucrose. Moreover, the root of atsuc4 mutants accumulated less sucrose and abscisic acid (ABA) and more indole-3-acetic acid (IAA) on 4% and 6% sucrose supplementation. Transcriptomic analysis revealed that numerous genes associated with sugar transport and metabolism, as well as ABA signalling were down-regulated, whereas many IAA signaling-related genes were up-regulated in mutant plants relative to the wild type under 6% sucrose treatment. Collectively, our finding demonstrated that the deficiency of AtSUC4 reduced the inhibition of primary root growth under high sucrose condition, probably through reducing the sucrose transportation and metabolism, and subsequent alteration in IAA and ABA signalling

Genome-wide organization and expression profiling of the R2R3-MYB transcription factor family in pineapple (Ananas comosus)

Abstract Background The MYB proteins comprise one of the largest families of plant transcription factors, which are involved in various plant physiological and biochemical processes. Pineapple (Ananas comosus) is one of three most important tropical fruits worldwide. The completion of pineapple genome sequencing provides a great opportunity to investigate the organization and evolutionary traits of pineapple MYB genes at the genome-wide level. Results In the present study, a total of 94 pineapple R2R3-MYB genes were identified and further phylogenetically classified into 26 subfamilies, as supported by the conserved gene structures and motif composition. Collinearity analysis indicated that the segmental duplication events played a crucial role in the expansion of pineapple MYB gene family. Further comparative phylogenetic analysis suggested that there have been functional divergences of MYB gene family during plant evolution. RNA-seq data from different tissues and developmental stages revealed distinct temporal and spatial expression profiles of the AcMYB genes. Further quantitative expression analysis showed the specific expression patterns of the selected putative stress-related AcMYB genes in response to distinct abiotic stress and hormonal treatments. The comprehensive expression analysis of the pineapple MYB genes, especially the tissue-preferential and stress-responsive genes, could provide valuable clues for further function characterization. Conclusions In this work, we systematically identified AcMYB genes by analyzing the pineapple genome sequence using a set of bioinformatics approaches. Our findings provide a global insight into the organization, phylogeny and expression patterns of the pineapple R2R3-MYB genes, and hence contribute to the greater understanding of their biological roles in pineapple

Genome-Wide Identification and Expression Analysis of WRKY Gene Family in <i>Neolamarckia cadamba</i>

The WRKY transcription factor family plays important regulatory roles in multiple biological processes in higher plants. They have been identified and functionally characterized in a number of plant species, but very little is known in Neolamarckia cadamba, a ‘miracle tree’ for its fast growth and potential medicinal resource in Southeast Asia. In this study, a total of 85 WRKY genes were identified in the genome of N. cadamba. They were divided into three groups according to their phylogenetic features, with the support of the characteristics of gene structures and conserved motifs of protein. The NcWRKY genes were unevenly distributed on 22 chromosomes, and there were two pairs of segmentally duplicated events. In addition, a number of putative cis-elements were identified in the promoter regions, of which hormone- and stress-related elements were shared in many NcWRKYs. The transcript levels of NcWRKY were analyzed using the RNA-seq data, revealing distinct expression patterns in various tissues and at different stages of vascular development. Furthermore, 16 and 12 NcWRKY genes were confirmed to respond to various hormone treatments and two different abiotic stress treatments, respectively. Moreover, the content of cadambine, the active metabolite used for the various pharmacological activities found in N. cadamba, significantly increased after Methyl jasmonate treatment. In addition, expression of NcWRKY64/74 was obviously upregulated, suggesting that they may have a potential function of regulating the biosynthesis of cadambine in response to MeJA. Taken together, this study provides clues into the regulatory roles of the WRKY gene family in N. cadamba

Loss of Wnt16 Leads to Skeletal Deformities and Downregulation of Bone Developmental Pathway in Zebrafish

Wingless-type MMTV integration site family, member 16 (wnt16), is a wnt ligand that participates in the regulation of vertebrate skeletal development. Studies have shown that wnt16 can regulate bone metabolism, but its molecular mechanism remains largely undefined. We obtained the wnt16−/− zebrafish model using the CRISPR-Cas9-mediated gene knockout screen with 11 bp deletion in wnt16, which led to the premature termination of amino acid translation and significantly reduced wnt16 expression, thus obtaining the wnt16−/− zebrafish model. The expression of wnt16 in bone-related parts was detected via in situ hybridization. The head, spine, and tail exhibited significant deformities, and the bone mineral density and trabecular bone decreased in wnt16−/− using light microscopy and micro-CT analysis. RNA sequencing was performed to explore the differentially expressed genes (DEGs). Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis found that the down-regulated DEGs are mainly concentrated in mTOR, FoxO, and VEGF pathways. Protein–protein interaction (PPI) network analysis was performed with the detected DEGs. Eight down-regulated DEGs including akt1, bnip4, ptena, vegfaa, twsg1b, prkab1a, prkab1b, and pla2g4f.2 were validated by qRT-PCR and the results were consistent with the RNA-seq data. Overall, our work provides key insights into the influence of wnt16 gene on skeletal development

<i>Arabidopsis</i> sucrose transporter 4 (AtSUC4) is involved in high sucrose-mediated inhibition of root elongation

Sucrose transporters (SUCs/SUTs) play crucial roles in apoplast transport and long-distance distribution of sucrose throughout the whole plant. However, whether and how the Arabidopsis AtSUC4 modulates sucrose import from apoplast to cytosol remains unclear. In the present study, we found that AtSUC4 protein was localized to the plasma membrane in the root. Expression of AtSUC4 in roots was gradually induced with the increasing sucrose concentrations (0%, 2%, 4% and 6%). When feeding high concentrations (4% and 6%) of sucrose, the primary root growth of seedling was inhibited. Interestingly, atsuc4 mutants exhibited longer primary root than the wild type under these conditions, indicating that atsuc4 mutants were less sensitive to excess sucrose. Moreover, the root of atsuc4 mutants accumulated less sucrose and abscisic acid (ABA) and more indole-3-acetic acid (IAA) on 4% and 6% sucrose supplementation. Transcriptomic analysis revealed that numerous genes associated with sugar transport and metabolism, as well as ABA signalling were down-regulated, whereas many IAA signaling-related genes were up-regulated in mutant plants relative to the wild type under 6% sucrose treatment. Collectively, our finding demonstrated that the deficiency of AtSUC4 reduced the inhibition of primary root growth under high sucrose condition, probably through reducing the sucrose transportation and metabolism, and subsequent alteration in IAA and ABA signalling.</p

Additional file 9: of Genome-wide organization and expression profiling of the R2R3-MYB transcription factor family in pineapple (Ananas comosus)

The RNA-seq data of AcMYB genes in different tissues and developmental stages. (XLSX 89 kb