Gene coexpression network analysis of fruit transcriptomes uncovers a possible mechanistically distinct class of sugar/acid ratio-associated genes in sweet orange

Background: The ratio of sugars to organic acids, two of the major metabolites in fleshy fruits, has been considered the most important contributor to fruit sweetness. Although accumulation of sugars and acids have been extensively studied, whether plants evolve a mechanism to maintain, sense or respond to the fruit sugar/acid ratio remains a mystery. In a prior study, we used an integrated systems biology tool to identify a group of 39 acid-associated genes from the fruit transcriptomes in four sweet orange varieties (Citrus sinensis L. Osbeck) with varying fruit acidity, Succari (acidless), Bingtang (low acid), and Newhall and Xinhui (normal acid). Results: We reanalyzed the prior sweet orange fruit transcriptome data, leading to the identification of 72 genes highly correlated with the fruit sugar/acid ratio. The majority of these sugar/acid ratio-related genes are predicted to be involved in regulatory functions such as transport, signaling and transcription or encode enzymes involved in metabolism. Surprisingly, only three of these sugar/acid ratio-correlated genes are weakly correlated with sugar level and none of them overlaps with the acid-associated genes. Weighted Gene Coexpression Network Analysis (WGCNA) has revealed that these genes belong to four modules, Blue, Grey, Brown and Turquoise, with the former two modules being unique to the sugar/acid ratio control. Conclusion: Our results indicate that orange fruits contain a possible mechanistically distinct class of genes that may potentially be involved in maintaining fruit sugar/acid ratios and/or responding to the cellular sugar/acid ratio status. Therefore, our analysis of orange transcriptomes provides an intriguing insight into the potentially novel genetic or molecular mechanisms controlling the sugar/acid ratio in fruits

Transcriptome comparison and gene coexpression network analysis provide a systems view of citrus response to ‘Candidatus Liberibacter asiaticus’ infection

Background: Huanglongbing (HLB) is arguably the most destructive disease for the citrus industry. HLB is caused by infection of the bacterium, Candidatus Liberibacter spp. Several citrus GeneChip studies have revealed thousands of genes that are up- or down-regulated by infection with Ca. Liberibacter asiaticus. However, whether and how these host genes act to protect against HLB remains poorly understood. Results: As a first step towards a mechanistic view of citrus in response to the HLB bacterial infection, we performed a comparative transcriptome analysis and found that a total of 21 Probesets are commonly up-regulated by the HLB bacterial infection. In addition, a number of genes are likely regulated specifically at early, late or very late stages of the infection. Furthermore, using Pearson correlation coefficient-based gene coexpression analysis, we constructed a citrus HLB response network consisting of 3,507 Probesets and 56,287 interactions. Genes involved in carbohydrate and nitrogen metabolic processes, transport, defense, signaling and hormone response were overrepresented in the HLB response network and the subnetworks for these processes were constructed. Analysis of the defense and hormone response subnetworks indicates that hormone response is interconnected with defense response. In addition, mapping the commonly up-regulated HLB responsive genes into the HLB response network resulted in a core subnetwork where transport plays a key role in the citrus response to the HLB bacterial infection. Moreover, analysis of a phloem protein subnetwork indicates a role for this protein and zinc transporters or zinc-binding proteins in the citrus HLB defense response. Conclusion: Through integrating transcriptome comparison and gene coexpression network analysis, we have provided for the first time a systems view of citrus in response to the Ca. Liberibacter spp. infection causing HLB

Integrated Systems Biology Analysis of Transcriptomes Reveals Candidate Genes for Acidity Control in Developing Fruits of Sweet Orange (Citrus sinensis L. Osbeck)

Organic acids, such as citrate and malate, are important contributors for the sensory traits of fleshy fruits. Although their biosynthesis has been illustrated, regulatory mechanisms of acid accumulation remain to be dissected. To provide transcriptional architecture and identify candidate genes for citrate accumulation in fruits, we have selected for transcriptome analysis four varieties of sweet orange (Citrus sinensis L. Osbeck) with varying fruit acidity, Succari (acidless), Bingtang (low acid), and Newhall and Xinhui (normal acid). Fruits of these varieties at 45 days post anthesis (DPA), which corresponds to Stage I (cell division), had similar acidity, but they displayed differential acid accumulation at 142 DPA (Stage II, cell expansion). Transcriptomes of fruits at 45 and 142 DPA were profiled using RNA sequencing and analyzed with three different algorithms (Pearson correlation, gene coexpression network and surrogate variable analysis). Our network analysis shows that the acid-correlated genes belong to three distinct network modules. Several of these candidate fruit acidity genes encode regulatory proteins involved in transport (such as AHA10), degradation (such as APD2) and transcription (such as AIL6) and act as hubs in the citrate accumulation gene networks. Taken together, our integrated systems biology analysis has provided new insights into the fruit citrate accumulation gene network and led to the identification of candidate genes likely associated with the fruit acidity control

Discriminative Feature Learning with Foreground Attention for Person Re-Identification

The performance of person re-identification (Re-ID) has been seriously effected by the large cross-view appearance variations caused by mutual occlusions and background clutters. Hence learning a feature representation that can adaptively emphasize the foreground persons becomes very critical to solve the person Re-ID problem. In this paper, we propose a simple yet effective foreground attentive neural network (FANN) to learn a discriminative feature representation for person Re-ID, which can adaptively enhance the positive side of foreground and weaken the negative side of background. Specifically, a novel foreground attentive subnetwork is designed to drive the network's attention, in which a decoder network is used to reconstruct the binary mask by using a novel local regression loss function, and an encoder network is regularized by the decoder network to focus its attention on the foreground persons. The resulting feature maps of encoder network are further fed into the body part subnetwork and feature fusion subnetwork to learn discriminative features. Besides, a novel symmetric triplet loss function is introduced to supervise feature learning, in which the intra-class distance is minimized and the inter-class distance is maximized in each triplet unit, simultaneously. Training our FANN in a multi-task learning framework, a discriminative feature representation can be learned to find out the matched reference to each probe among various candidates in the gallery. Extensive experimental results on several public benchmark datasets are evaluated, which have shown clear improvements of our method over the state-of-the-art approaches

MicroRNA-9-5p functions as a tumor suppressor in prostate cancer via targeting UTRN

Accumulating evidence indicates that miR-9-5p plays an important role in several diseases, especially tumor progression. In this study, we investigated the clinical significance and biological function of miR-9-5p in prostate cancer (PCa). Using quantitative real time PCR (qRT-PCR) analysis, we found miR-9-5p level was significantly down-regulated in PCa tissues and cell lines. The decreased miR-9-5p expression was associated with tumor size, preoperative PSA, Gleason score and lymph node metastasis. Kaplan-Meier survival analysis showed patients with low level of miR-9-5p had significantly decreased rates of overall survival (OS). Multivariate analyses showed that miR-9-5p was an independent predictor of PCa patients’ prognosis. Through CCK-8 and Transwell assays, miR-9-5p overexpression by miR-9-5p mimics transfection was demonstrated to suppress the proliferation, migration and invasion of PCa cells. Mechanistically, luciferase reporter assay, qRT-PCR and Western blot demonstrated that Utrophin (UTRN) is a direct target of miR-9-5p in PCa cells. The status of UTRN protein in PCa tissues was much higher than that in adjacent tissues by immunohistochemical staining and its mRNA levels were inversely correlated with miR-9-5p in PCa tissues. Importantly, UTRN knockdown by siUTRN imitated the suppressive effects of miR-9-5p on cell proliferation, migration and invasion in PCa. In summary, miR-9-5p might novel prognostic biomarker in and targeting UTRN by miR-9-5p could be potential therapeutic candidates for PCa

Integrating Semi-supervised and Supervised Learning Methods for Label Fusion in Multi-Atlas Based Image Segmentation

A novel label fusion method for multi-atlas based image segmentation method is developed by integrating semi-supervised and supervised machine learning techniques. Particularly, our method is developed in a pattern recognition based multi-atlas label fusion framework. We build random forests classification models for each image voxel to be segmented based on its corresponding image patches of atlas images that have been registered to the image to be segmented. The voxelwise random forests classification models are then applied to the image to be segmented to obtain a probabilistic segmentation map. Finally, a semi-supervised label propagation method is adapted to refine the probabilistic segmentation map by propagating its reliable voxelwise segmentation labels, taking into consideration consistency of local and global image appearance of the image to be segmented. The proposed method has been evaluated for segmenting the hippocampus in MR images and compared with alternative machine learning based multi-atlas based image segmentation methods. The experiment results have demonstrated that our method could obtain competitive segmentation performance (average Dice index > 0.88), compared with alternative multi-atlas based image segmentation methods under comparison. Source codes of the methods under comparison are publicly available at www.nitrc.org/frs/?group_id=1242