Finding More Relevance: Propagating Similarity on Markov Random Field for Image Retrieval

To effectively retrieve objects from large corpus with high accuracy is a challenge task. In this paper, we propose a method that propagates visual feature level similarities on a Markov random field (MRF) to obtain a high level correspondence in image space for image pairs. The proposed correspondence between image pair reflects not only the similarity of low-level visual features but also the relations built through other images in the database and it can be easily integrated into the existing bag-of-visual-words(BoW) based systems to reduce the missing rate. We evaluate our method on the standard Oxford-5K, Oxford-105K and Paris-6K dataset. The experiment results show that the proposed method significantly improves the retrieval accuracy on three datasets and exceeds the current state-of-the-art retrieval performance

Meta-analysis of the effect of expression of MYB transcription factor genes on abiotic stress

Background MYB proteins are a large group of transcription factors. The overexpression of MYB genes has been reported to improve abiotic stress tolerance in plant. However, due to the variety of plant species studied and the types of gene donors/recipients, along with different experimental conditions, it is difficult to interpret the roles of MYB in abiotic stress tolerance from published data. Methods Using meta-analysis approach, we investigated the plant characteristics involved in cold, drought, and salt stress in MYB-overexpressing plants and analyzed the degrees of influence on plant performance by experimental variables. Results The results show that two of the four measured plant parameters in cold-stressed plants, two of the six in drought-stressed, and four of the 13 in salt-stressed were significantly impacted by MYB overexpression by 22% or more, and the treatment medium, donor/recipient species, and donor type significantly influence the effects of MYB-overexpression on drought stress tolerance. Also, the donor/recipient species, donor type, and stress duration all significantly affected the extent of MYB-mediated salt stress tolerance. In summary, this study compiles and analyzes the data across studies to help us understand the complex interactions that dictate the efficacy of heterologous MYB expression designed for improved abiotic stress tolerance in plants

Tobacco OPBP1 Enhances Salt Tolerance and Disease Resistance of Transgenic Rice

Osmotin promoter binding protein 1 (OPBP1), an AP2/ERF transcription factor of tobacco, has been demonstrated to function in disease resistance and salt tolerance in tobacco. To increase stress tolerant capability of rice, we generated rice plants with an OPBP1 overexpressing construct. Salinity shock treatment with 250 mM NaCl indicated that most of the OPBP1 transgenic plants can survive, whereas the control seedlings cannot. Similar recovery was found by using the seedlings grown in 200 mM NaCl for two weeks. The OPBP1 transgenic and control plants were also studied for oxidative stress tolerance by treatment with paraquat, showing the transgenic lines were damaged less in comparison with the control plants. Further, the OPBP1 overexpression lines exhibited enhanced resistance to infections of Magnaporthe oryzae and Rhizoctonia solani pathogens. Gene expressing analysis showed increase in mRNA accumulation of several stress related genes. These results suggest that expression of OPBP1 gene increase the detoxification capability of rice

Deregulation of Sucrose-Controlled Translation of a bZIP-Type Transcription Factor Results in Sucrose Accumulation in Leaves

Sucrose is known to repress the translation of Arabidopsis thaliana AtbZIP11 transcript which encodes a protein belonging to the group of S (S - stands for small) basic region-leucine zipper (bZIP)-type transcription factor. This repression is called sucrose-induced repression of translation (SIRT). It is mediated through the sucrose-controlled upstream open reading frame (SC-uORF) found in the AtbZIP11 transcript. The SIRT is reported for 4 other genes belonging to the group of S bZIP in Arabidopsis. Tobacco tbz17 is phylogenetically closely related to AtbZIP11 and carries a putative SC-uORF in its 5′-leader region. Here we demonstrate that tbz17 exhibits SIRT mediated by its SC-uORF in a manner similar to genes belonging to the S bZIP group of the Arabidopsis genus. Furthermore, constitutive transgenic expression of tbz17 lacking its 5′-leader region containing the SC-uORF leads to production of tobacco plants with thicker leaves composed of enlarged cells with 3–4 times higher sucrose content compared to wild type plants. Our finding provides a novel strategy to generate plants with high sucrose content

Controllable Antibacterial Activity through Acid-Triggered Molecular Cage Release of Stored Ag+

Aiming for solving the emergence of drug-resistant bacteria worldwide, the construction of novel supramolecular self-assembly systems with antibacterial functions is attracting growing research attention. Herein, using dynamically reversible Schiff-base imine bonds as the assembly strategy, a three-dimensional pure organic cage, namely 4-cage, was obtained in high yield. By taking advantage of the bidentate chelating capability of its imine-based skeleton, 4-cage was demonstrated to serve as an Ag+-carrier. Owing to the acid-induced decomposition of this skeleton, the Ag+-loaded 4-cage can controllably release Ag+ through pH regulation, hence, as a proof-of-concept, it is proved to be applicable as a controllable release antibacterial reagent. Such pH-responsive Ag+-carried supramolecular architecture may shed light on the molecule design strategies for bacterial elimination in different environments, or for controllable functions in various other fields

Genome-Wide Comparison of Structural Variations and Transposon Alterations in Soybean Cultivars Induced by Spaceflight

Space mutation causes genetic and phenotypic changes in biological materials. Transposon activation is an adaptive mechanism for organisms to cope with changes in the external environment, such as space mutation. Although transposon alterations have been widely reported in diverse plant species, few studies have assessed the global transposon alterations in plants exposed to the space environment. In this study, for the first time, the effects of transposon alterations in soybean caused by space mutation were considered. A new vegetable soybean variety, ‘Zhexian 9’ (Z9), derived from space mutation treatment of ‘Taiwan 75’ (T75), was genetically analyzed. Comparative analyses of these two soybean genomes uncovered surprising structural differences, especially with respect to translocation breakends, deletions, and inversions. In total, 12,028 structural variations (SVs) and 29,063 transposable elements (TEs) between T75 and Z9 were detected. In addition, 1336 potential genes were variable between T75 and Z9 in terms of SVs and TEs. These differential genes were enriched in functions such as defense response, cell wall-related processes, epigenetics, auxin metabolism and transport, signal transduction, and especially methylation, which implied that regulation of epigenetic mechanisms and TE activity are important in the space environment. These results are helpful for understanding the role of TEs in response to the space environment and provide a theoretical basis for the selection of wild plant materials suitable for space breeding

Identification of testicular cancer immune infiltrates and novel immune cell subtypes

Testicular germ cell tumors (TGCT) are the most common type of testicular cancer, comprising 90–95% of cases and representing the most prevalent solid malignancy in young adult men. Immune infiltrates play important regulatory roles in tumors, but their role in TGCT remains unclear. Molecular subtyping is a promising way to provide precisely personalized treatment and avoid unnecessary toxicities. This study investigated immune infiltrates, key biomarkers, and immune subtyping of TGCT. In GSE3218, 24 differentially expressed immune genes (immDEGs) were identified. A new risk signature consisting of six immDEGs was developed using these genes. Individuals in the high‐risk group had poor overall survival (OS; hazard ratio of 4.61 and P‐value < 0.001). We validated the six‐immDEGs risk signature in pure seminoma and mixed TGCT types. Two distinct immune patterns (Cluster 1 and Cluster 2) were identified using the consensusclusterplus, and Cluster 1 possessed an unfavorable OS compared with Cluster 2 (hazard ratio, 2.56; P < 0.001). Cluster 1 patients had significantly lower naive B cells, memory B cells, plasma cells, naive CD4 T cells, gamma delta T cells, and activated dendritic cells than Cluster 2 patients. Genes relating to the WNT signaling pathway, TGF‐β signaling pathway, antigen processing and presentation, and NK cell‐mediated cytotoxicity were associated with TGCT. STC1 was elevated in TGCT tissues, and its high expression showed advanced clinicopathological characteristics and poor prognosis of TGCT. Our findings may contribute to an increased understanding of the onset and progression of TGCT

CsICE1 Functions in Cold Tolerance by Regulating Polyamine levels May through Interacting with Arginine Decarboxylase in the Tea Tree

Background: The identification of C-repeat binding factor (CBF), and the characterization as an inducer of CBF Expression 1 (ICE1), and a major activator for C-repeat binding factor, were important breakthroughs in the cold signaling network. Methods: In the present study, the full length cDNA of ICE1 was isolated from the tea tree (Camellia sinensis). CsICE1 protein was located in the cell nucleus as revealed by subcellular localization analysis. To investigate the biological functions of CsICE1, a transgenic line fused with the CsICE1 gene in Arabidopsis thaliana (arabidopsis) was generated by the floral dip method. Results: The CsICE1 was expressed differentially in various tea tree tissues, mostly in buds and leaves, and the transcript level of CsICE1 was increased after 1 h and peaked at 2 h under cold treatment. Transcription activity assay indicated that the spermine synthase (SPMS) and arginine decarboxylase (ADC) genes were possible targets of CsICE1. In addition, the values of net photosynthetic rate, transpiration rate, stomatal conductance in transgenic lines declined by less extent than wild-type plants under low temperatures. Furthermore, transcript levels of ADC genes in the transgenic lines had no apparent alteration under normal growth conditions but substantially increased under cold conditions, consistent of changes in free polyamine levels. Taken together, these results demonstrated that CsICE1 plays a positive role in cold tolerance, which may be due to the modulation of polyamine levels through interacting with CsADC

Gene expression analysis in leaf of Camellia sinensis reveals the response to fluoride

Tea plants (Camellia sinensis (L.) Kuntze) can hyperaccumulate fluoride (F-) without any toxic symptom, especially in mature leaves. However, the molecular mechanism of absorption and hyperaccumulation of F- was poorly understood in C. sinensis. Here, a transcriptomic analysis was performed to compare the responses to fluoride stress of tea leaves to understand F- accumulation and its influence on gene expression in C. sinensis leaves. The results indicated that numerous differentially expressed genes involved in ion absorption and transport exist in the process of F- absorption in C. sinensis leaves. The up-regulated expression of genes associated with uptake and transport of Ca2+ and K+ (CNGC, TPC1, CAX, and VHA) increased the intracellular and vacuole cation concentration during F- accumulation in C. sinensis leaves. We also found that some of AQP (PIPs and TIPs) genes may promote F- into the intracellular spaces and vacuoles in C. sinensis leaves, respectively. In addition, F- induced the expression of differential genes related to plant hormone metabolism and signaling pathways (ABA, auxin, and GA). Subsequently, a lot of transcription factors (WRKY, MYB, NAC, bHLH and AP2/ERF) were activated to respond to F- stress in tea leaves by regulating plant hormone signal transduction and other pathways. And ubiquitin systems were involved in the regulation of proteins homeostasis under F- stress indicating that they are responsible for the response of C. sinensis leaves to F-. Overall, these findings provide a comprehensive understanding of the F- absorption mechanism and its influence on gene expression in tea leaves

Genome-Wide Variation Analysis of Four Vegetable Soybean Cultivars Based on Re-Sequencing

Vegetable soybean is a type of value-added specialty soybean, served as a fresh vegetable or snack in China. Due to the difference from other types, it is important to understand the genetic structure and diversity of vegetable soybean for further utilization in breeding programs. The four vegetable cultivars, Taiwan-75, Zhexiandou No. 8, Zhexian No. 9 and Zhexian No. 10 are popular soybean varieties planted in Zhejiang province, and have large pods and intermediate maturity. The clustering showed a close relationship of these four cultivars in simple sequence repeat analysis. To reveal the genome variation of vegetable soybean, these four improved lines were analyzed by whole-genome re-sequencing. The average sequencing depth was 7X and the coverage ratio of each cultivar was at least more than 94%. Compared with the reference genome, a large number of single-nucleotide polymorphisms, insertion/deletions and structure variations were identified with different chromosome distributions. The average heterozygosity rate of the single-nucleotide polymorphisms was 11.99% of these four cultivars. According to the enrichment analysis, there were 23,371 genes identified with putative modifications, and a total of 282 genes were related to carbohydrate metabolic processes. These results provide useful information for genetic research and future breeding, which can facilitate the selection procedures in vegetable soybean breeding