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Two isoforms of human Polycomb-like protein 3 (hPCL3) have been reported as components of the nuclear Polycomb repressive complex 2 (PRC2), with the short isoform (hPCL3s) showing a dominant cytoplasmic localization. The function of cytoplasmic hPCL3s has, however, not been addressed. In this study, we report that hPCL3s is upregulated in clinical hepatocellular carcinoma (HCC) samples and its expression correlated with HCC clinical features. hPCL3s positively regulated the migration, invasion, and metastasis of HCC cells. hPCL3s interacted with components of the cytoplasmic β-catenin destruction complex, inhibited β-catenin degradation, and activated β-catenin/T-cell factor signaling. Downstream of the β-catenin cascade, IL6 mediated the motility-promoting functions of hPCL3s. Forced expression of hPCL3s in the liver of a HCC mouse model promoted tumorigenesis and metastasis. Taken together, these data show that hPCL3s promotes the metastasis of HCC by activating the β-catenin/IL6 pathway.Significance: hPCL3s has an oncogenic role in hepatocellular carcinoma by activating the β-catenin/IL6 signaling axis to promote metastasis. Cancer Res; 78(10); 2536–49. ©2018 AACR.

The supplementary infomation containing Figure legends, five supplemental figures and 3 supplemental tables. Figure S1 The higher expression of hPCL3s correlated with the poor survival of HCC patients. Figure S2 hPCL3s did not promote the tumorigenesis in vivo. Figure S3 The effects of hPCL3s on the growth of Hep3B, Huh7 and PVTT cells in a 48-hour time window were evaluated using MTT assay. Figure S4 Screening the signal pathways affected by hPCL3s. Figure S5 The AAV delivered Flag-hPCL3s was dominantly expressed in the liver. Table S1 Primer sequences. Table S2 The correlation between the expression of hPCL3s and clinical feature (Tissue array 2). Table S3 Microarray data.

Document retrieval is a research hotspot of natural language processing. Compared with short text document which has the characteristics of information diversity and length, in long text retrieval, a query statement is often not related to all sentences in a long text, and strong interference of some highly similar segments will occur. Therefore, the correlation score between a query statement and a document can not be simply calculated based on the similarity between words or strings. Text snippet mechanism (TSM) is proposed for document retrieval. TSM first divides each candidate document into snippets, and then calculates the correlation between query statements and document snippets. The correlation matching scheme used takes into account the semantic and word frequency factors. TSM selects key text snippets and obtains the relevant snippet ratio, and then calculates the correlation score between query and target document based on these information, so as to obtain the Top-K document set. Experimental results show that TSM can improve the performance of information retrieval on IR test collection of Glasgow.

As an irreversible and perennial process, aging is accompanied by functional and morphological declines in organs. Generally, aging liver exhibits a decline in volume and hepatic blood flow. Even with a preeminent regenerative capacity to restore its functions after liver cell loss, its biosynthesis and metabolism abilities decline, and these are difficult to restore to previous standards. Apoptosis is a programmed death process via intrinsic and extrinsic pathways, in which Bcl-2 family proteins and apoptosis-related genes, such as p21 and p53, are involved. Apoptosis inflicts both favorable and adverse influences on liver aging. Apoptosis eliminates transformed abnormal cells but promotes age-related liver diseases, such as nonalcoholic fatty liver disease, liver fibrosis, cirrhosis, and liver cancer. We summarize the roles of apoptosis in liver aging and age-related liver diseases.

The indica ecotypes, IR64, an elite drought-susceptible variety adapted to irrigated ecosystem, and Apo (IR55423-01 or NSIC RC9), a moderate drought-tolerant upland genotype together with their hybrid (IR64 × Apo) were exposed to non- and water-stress conditions. By sequencing (RNA-seq) these genotypes, we were able to map genes diverging in cis and/or trans factors. Under non-stress condition, cis dominantly explains (11.2%) regulatory differences, followed by trans (8.9%). Further analysis showed that water-limiting condition largely affects trans and cis + trans factors. On the molecular level, cis and/or trans regulatory divergence explains their genotypic differences and differential drought response. Between the two parental genotypes, Apo appears to exhibit more photosynthetic efficiency even under water-limiting condition and is ascribed to trans. Statistical analyses showed that regulatory divergence is significantly influenced by environmental conditions. Likewise, the mode of parental expression inheritance which drives heterosis (HET) is significantly affected by environmental conditions indicating the malleability of heterosis to external factors. Further analysis revealed that the HET class, dominance, was significantly enriched under water-stress condition. We also identified allelic imbalance switching in which several genes prefer IR64- (or Apo-) specific allele under non-stress condition but switched to Apo- (or IR64-) specific allele when exposed to water-stress condition.

Targeted color-dots with varying shapes and sizes in images are first exhaustively identified, and then their multiscale 2D geometric patterns are extracted for testing spatial uniformness in a progressive fashion. Based on color theory in physics, we develop a new color-identification algorithm relying on highly associative relations among the three color-coordinates: RGB or HSV. Such high associations critically imply low color-complexity of a color image, and renders potentials of exhaustive identification of targeted color-dots of all shapes and sizes. Via heterogeneous shaded regions and lighting conditions, our algorithm is shown being robust, practical and efficient comparing with the popular Contour and OpenCV approaches. Upon all identified color-pixels, we form color-dots as individually connected networks with shapes and sizes. We construct minimum spanning trees (MST) as spatial geometries of dot-collectives of various size-scales. Given a size-scale, the distribution of distances between immediate neighbors in the observed MST is extracted, so do many simulated MSTs under the spatial uniformness assumption. We devise a new algorithm for testing 2D spatial uniformness based on a Hierarchical clustering tree upon all involving MSTs. Our developments are illustrated on images obtained by mimicking chemical spraying via drone in Precision Agriculture., 21 pages, 21 figures

Key message The homologous genes OsbHLH068 and AtbHLH112 have partially redundant functions in the regulation of the salt stress response but opposite functions to control flowering in Arabidopsis. Abstract The transcription factor (TF) basic/Helix-Loop-Helix (bHLH) is important for plant growth, development, and stress responses. OsbHLH068, which is a homologous gene of AtbHLH112 that is up-regulated under drought and salt stresses, as indicated by previous microarray data analysis. However, the intrinsic function of OsbHLH068 remains unknown. In the present study, we characterized the function and compared the role of OsbHLH068 with that of its homolog, AtbHLH112. Histochemical GUS staining indicated that OsbHLH068 and AtbHLH112 share a similar expression pattern in transgenic Arabidopsis during the juvenile-to-adult phase transition. Heterologous overexpression of OsbHLH068 in Arabidopsis delays seed germination, decreases salt-induced H2O2 accumulation, and promotes root elongation, whereas AtbHLH112 knock-out mutant displays an opposite phenotype. Both OsbHLH068-overexpressing transgenic Arabidopsis seedlings and the Atbhlh112 mutant display a late-flowering phenotype. Moreover, the expression of OsbHLH068-GFP driven by an AtbHLH112 promoter can compensate for the germination deficiency in the Atbhlh112 mutant, but the delayed-flowering phenotype tends to be more severe. Further analysis by microarray and qPCR indicated that the expression of FT is down-regulated in both OsbHLH068-overexpressing Arabidopsis plants and Atbhlh112 mutant plants, whereas SOC1 but not FT is highly expressed in AtbHLH112-overexpressing Arabidopsis plants. A comparative transcriptomic analysis also showed that several stress-responsive genes, such as AtERF15 and AtPUB23, were affected in both OsbHLH068- and AtbHLH112-overexpressing transgenic Arabidopsis plants. Thus, we propose that OsbHLH068 and AtbHLH112 share partially redundant functions in the regulation of abiotic stress responses but have opposite functions to control flowering in Arabidopsis, presumably due to the evolutionary functional divergence of homolog-encoded proteins. Electronic supplementary material The online version of this article (doi:10.1007/s11103-017-0624-6) contains supplementary material, which is available to authorized users.

BackgroundThe coconut rhinoceros beetle,Oryctes rhinoceros, is a major pest of palm crops in tropical Asia and the Pacific Islands. Little molecular data exists for this pest, impeding our ability to develop effective countermeasures and deal with the species’ growing resistance to viral biocontrols. We present the first molecular biology analyses of this species, including a metagenomic assay to understand the microbiome of different sections of its digestive tract, and a transcriptomics assay to complement the microbiome data and to shed light on genes of interest like plant cell wall degrading enzymes and immunity and xenobiotic resistance genes.ResultsThe gut microbiota ofOryctes rhinoceroslarvae is quite similar to that of the termite gut, as both species feed on decaying wood. We found the first evidence for endogenous beta-1,4-endoglucanase in the beetle, plus evidence for microbial cellobiase, suggesting the beetle can degrade cellulose together with its gut microfauna. A number of antimicrobial peptides are expressed, particularly by the fat body but also by the midgut and hindgut.ConclusionsThis transcriptome provides a wealth of data about the species’ defense against chemical and biological threats, has uncovered several potentially new species of microbial symbionts, and significantly expands our knowledge about this pest.

Abstract cis and/or trans regulatory divergence within or between related taxa on a genome-wide scale has been largely unexamined in crops, more so, the effect of stress on cis/trans architecture. In this study, the indica genotypes IR64, an elite drought-susceptible lowland variety, and Apo (IR55423-01 or NSIC RC9), a moderate drought-tolerant upland genotype together with their hybrid (IR64 × Apo) were exposed to non- and water-stress conditions. Evidence of cis and/or trans regulatory differences was tested between these two indica rice genotypes. By sequencing (RNA-seq) the parents and their hybrid, we are able to map genes diverging in cis and/or trans factors between the two genotypes. Under non-stress conditions, cis dominantly explains (11.2%) regulatory differences, followed by trans (8.9%). Further analysis showed that water-limiting conditions largely affect trans and cis + trans factors. Between the two inbred lines, Apo appears to exhibit higher expression fold change of genes enriched in “response to stress” and “photosynthesis” under non- and water-stress conditions. On the molecular level, cis and/or trans regulatory divergence explains their genotypic differences and differential drought response. Parent–hybrid RNA-seq has the potential to identify genes diverging in cis and/or trans factors even between intra-sub-specifically related genotypes. By comparing cis/trans landscape under stressed and unstressed conditions, this approach has the ability to assess the impact of drought on gene expression. Computational analysis and association of several drought-yield QTL markers with cis-diverging genes provide converging evidences suggestive of a potential approach to identify trait-associated candidate genes using hybrids and their parents alone.Key Messagecis dominantly explains divergence of two indica rice genotypes, IR64 and Apo under normal conditions while trans and cis + trans regulatory factors are largely affected by drought

Two indica inbred rice lines, IR64, a drought-sensitive, and Apo, a moderately drought-tolerant genotype, were exposed to non- (control or unstressed) and water-stress treatments. Leaf samples collected at an early flowering stage were sequenced by RNA-seq. Reads generated were analyzed for differential expression (DE) implementing various models in baySeq to capture differences in genome-wide transcriptional response under contrasting water regimes. IR64, the drought-sensitive variety consistently exhibited a broader transcriptional response while Apo showed relatively modest transcriptional changes under water-stress conditions across all models implemented. Gene ontology (GO) and KEGG pathway analyses of genes revealed that IR64 showed enhancement of functions associated with signal transduction, protein binding and receptor activity. Apo uniquely showed significant enrichment of genes associated with an oxygen binding function and peroxisome pathway. In general, IR64 exhibited more extensive molecular re-programming, presumably, a highly energy-demanding route to deal with the abiotic stress. Several of these differentially expressed genes (DEGs) were found to co-localize with QTL marker regions previously identified to be associated with drought-yield response, thus, are the most promising candidate genes for further studies.

Cross-protection triggered by a mild strain of virus acts as a prophylaxis to prevent subsequent infections by related viruses in plants; however, the underling mechanisms are not fully understood. Through mutagenesis, we isolated a mutant strain of Turnip mosaic virus (TuMV), named Tu-GK, that contains an Arg182Lys substitution in helper component-proteinase (HC-ProK) that confers complete cross-protection against infection by a severe strain of TuMV in Nicotiana benthamiana, Arabidopsis thaliana Col-0, and the Arabidopsis dcl2-4/dcl4-1 double mutant defective in DICER-like ribonuclease (DCL)2/DCL4-mediated silencing. Our analyses showed that HC-ProK loses the ability to interfere with microRNA pathways, although it retains a partial capability for RNA silencing suppression triggered by DCL. We further showed that Tu-GK infection triggers strong salicylic acid (SA)-dependent and SA-independent innate immunity responses. Our data suggest that DCL2/4-dependent and –independent RNA silencing pathways are involved, and may crosstalk with basal innate immunity pathways, in host defense and in cross-protection.

Two isoforms of human Polycomb-like protein 3 (hPCL3) have been reported as components of the nuclear Polycomb repressive complex 2 (PRC2), with the short isoform (hPCL3s) showing a dominant cytoplasmic localization. The function of cytoplasmic hPCL3s has, however, not been addressed. In this study, we report that hPCL3s is upregulated in clinical hepatocellular carcinoma (HCC) samples and its expression correlated with HCC clinical features. hPCL3s positively regulated the migration, invasion, and metastasis of HCC cells. hPCL3s interacted with components of the cytoplasmic β-catenin destruction complex, inhibited β-catenin degradation, and activated β-catenin/T-cell factor signaling. Downstream of the β-catenin cascade, IL6 mediated the motility-promoting functions of hPCL3s. Forced expression of hPCL3s in the liver of a HCC mouse model promoted tumorigenesis and metastasis. Taken together, these data show that hPCL3s promotes the metastasis of HCC by activating the β-catenin/IL6 pathway. Significance: hPCL3s has an oncogenic role in hepatocellular carcinoma by activating the β-catenin/IL6 signaling axis to promote metastasis. Cancer Res; 78(10); 2536–49. ©2018 AACR.

The solid electrolyte Li 0.5 La 0.5 TiO 3 (LLTO) with high lithium ion conductivity was prepared by the conventional solid-state reaction method, and those LLTO powders were mixed with inactive second phase (Al 2 O 3 , MgO, SiO 2 ) to give composites. The microstructure and conductivity properties of the composite are investigated by using X-ray diffraction, scanning electron microscope and AC impedance method. Those prepared LLTO is cubic crystal with superstructure. All conductivities of LLTO-based composites decrease with the addition of Al 2 O 3 or MgO, but the grain boundary conductivity increases with the addition of SiO 2 .

Pineapple (Ananas comosus (L.) Merr.) is the most economically valuable crop possessing crassulacean acid metabolism (CAM), a photosynthetic carbon assimilation pathway with high water use efficiency, and the second most important tropical fruit after banana in terms of international trade. We sequenced the genomes of pineapple varieties ‘F153’ and ‘MD2’, and a wild pineapple relative A. bracteatus accession CB5. The pineapple genome has one fewer ancient whole genome duplications than sequenced grass genomes and, therefore, provides an important reference for elucidating gene content and structure in the last common ancestor of extant members of the grass family (Poaceae). Pineapple has a conserved karyotype with seven pre rho duplication chromosomes that are ancestral to extant grass karyotypes. The pineapple lineage has transitioned from C3 photosynthesis to CAM with CAM-related genes exhibiting a diel expression pattern in photosynthetic tissues using beta-carbonic anhydrase (βCA) for initial capture of CO2. Promoter regions of all three βCA genes contain a CCA1 binding site that can bind circadian core oscillators. CAM pathway genes were enriched with cis-regulatory elements including the morning (CCACAC) and evening (AAAATATC) elements associated with regulation of circadian-clock genes, providing the first link between CAM and the circadian clock regulation. Gene-interaction network analysis revealed both activation and repression of regulatory elements that control key enzymes in CAM photosynthesis, indicating that CAM evolved by reconfiguration of pathways preexisting in C3 plants. Pineapple CAM photosynthesis is the result of regulatory neofunctionalization of preexisting gene copies and not acquisition of neofunctionalized genes via whole genome or tandem gene duplication.

The transport of exogenous surfactant in an axisymmetric pulmonary airway lining is analyzed using the model based on lubrication theory to understand the parameters involved in surfactant replacement therapy for neonatal respiratory distress syndrome, including the ratio of film thickness-to-airway radius e , and the initial exogenous and endogenous surfactant distributions. Numerical simulation of the model indicates that the film disturbance induced by Marangoni flow in low generation airways (small e , such as trachea) would be more significant than that in high generation airways (large e , such as bronchioles) for the same amount of instilled surfactant. The non-dimensional transport properties of the exogenous surfactant, however, are virtually identical in various airway generations considered. Increasing the initial local exogenous concentration enhances the surfactant transport and also intensifies the film disturbance. The presence of endogenous surfactant tends to moderate the shock-like film disturbance and also prolongs the extent of surfactant monolayer front. This, however, does not mean that the spread of exogenous surfactant is enhanced with the presence of endogenous surfactant. The extended monolayer is attributed to the compression of endogenous surfactant concentration in regions ahead of the advancing exogenous surfactant front.

Background The in vivo infectious clone of Turnip mosaic virus (TuMV), p35S-TuMV, was used on plant pathology research for many years. To activate p35S-TuMV, the plasmid was mechanically introduced to the local lesion host Chenopodium quinoa. However, low infectivity occurred when the TuMV from C. quinoa was transferred to the systemic host Nicotiana benthamiana. Results To increase the efficiency of initial infectivity on N. benthamiana, the expression of the TuMV infectious clone by a binary vector that directly activates viral RNA through agro-infiltration is considered to be a good alternative. The size of the binary vector by agro-infiltration is usually large and its backbone has numerous restriction sites that increase difficulty for construction. In this study, we attempted to construct a mini binary vector (pBD003) with less restriction sites. The full-length cDNA of TuMV genome, with or without green fluorescence protein, was inserted in pBD003 to generate pBD-TuMV constructs, which were then individually introduced to N. benthamiana plants by agro-infiltration. Symptom development and ELISA positivity with TuMV antiserum indicated that the pBD-TuMV constructs are infectious. Moreover, the initial infectivity of a mild strain TuMV-GK, which contains an R182K mutation on HC-Pro, constructed in the pBD003 vector was significantly increased by agro-infiltration. Conclusion Thus, we concluded that the newly constructed mini binary vector provides a more feasible tool for TuMV researches in areas, such as creating a mild strain for cross-protection, or a viral vector for foreign gene expression. In addition, the multiple cloning sites will be further cloned in pBD003 for convenience in constructing other viral infectious clones. Electronic supplementary material The online version of this article (doi:10.1186/1999-3110-54-22) contains supplementary material, which is available to authorized users.

This study presents a similarity-determining method for measuring regulatory relationships between pairs of genes from microarray time series data. The proposed similarity metrics are based on a new method to measure structural similarity to compare the quality of images. We make use of the Dual-Tree Wavelet Transform (DTWT) since it provides approximate shift invariance and maintain the structures between pairs of regulation related time series expression data. Despite the simplicity of the presented method, experimental results demonstrate that it enhances the similarity index when tested on known transcriptional regulatory genes.

The authors sought to evaluate the treatment outcome of children with medulloblastoma at a single institution. Forty-two children were analyzed. Eighty-six percent of the children who received chemotherapy were treated with cisplatin-based chemotherapy. No factors were found to affect outcome significantly. Compared with children treated before 1994 at the same institution, the median survival time was significantly longer (40 vs. 25 months, p = .0003). The authors conclude that some improvement of treatment outcome for children with medulloblastoma seemed to be achieved.

Congenital development disorders with variable severity occur in trisomy 21. However, how these phenotypic abnormalities develop with variations remains elusive. We hypothesize that the differences in euploid gene expression variation among trisomy 21 tissues are caused by the presence of an extra copy of chromosome 21 and may contribute to the phenotypic variations in Down syndrome. We used DNA microarray to measure the differences in gene expression variance between four human trisomy 21 and six euploid amniocytes. The three publicly available data sets of fetal brains, adult brains, and fetal hearts were also analyzed. The numbers of euploid genes with greater variance were significantly higher in all four kinds of trisomy 21 tissues (p < 0.01) than in the corresponding euploid tissues. Seventeen euploid genes with significantly different variance between trisomy 21 and euploid amniocytes were found using the F test. In summary, there is a set of euploid genes that shows greater variance of expression in human trisomy 21 tissues than in euploid tissues. This change may contribute to producing the variable phenotypic abnormalities observed in Down syndrome.

Cold stress affects rice growth, quality and yield. The investigation of genome-wide gene expression is important for understanding cold stress tolerance in rice. We performed comparative transcriptome analysis of the shoots and roots of 2 rice seedlings (TNG67, cold-tolerant; and TCN1, cold-sensitive) in response to low temperatures and restoration of normal temperatures following cold exposure. TNG67 tolerated cold stress via rapid alterations in gene expression and the re-establishment of homeostasis, whereas the opposite was observed in TCN1, especially after subsequent recovery. Gene ontology and pathway analyses revealed that cold stress substantially regulated the expression of genes involved in protein metabolism, modification, translation, stress responses, and cell death. TNG67 takes advantage of energy-saving and recycling resources to more efficiently synthesize metabolites compared with TCN1 during adjustment to cold stress. During recovery, expression of OsRR4 type-A response regulators was upregulated in TNG67 shoots, whereas that of genes involved in oxidative stress, chemical stimuli and carbohydrate metabolic processes was downregulated in TCN1. Expression of genes related to protein metabolism, modification, folding and defense responses was upregulated in TNG67 but not in TCN1 roots. In addition, abscisic acid (ABA)-, polyamine-, auxin- and jasmonic acid (JA)-related genes were preferentially regulated in TNG67 shoots and roots and were closely associated with cold stress tolerance. The TFs AP2/ERF were predominantly expressed in the shoots and roots of both TNG67 and TCN1. The TNG67-preferred TFs which express in shoot or root, such as OsIAA23, SNAC2, OsWRKY1v2, 24, 53, 71, HMGB, OsbHLH and OsMyb, may be good candidates for cold stress tolerance-related genes in rice. Our findings highlight important alterations in the expression of cold-tolerant genes, metabolic pathways, and hormone-related and TF-encoding genes in TNG67 rice during cold stress and recovery. The cross-talk of hormones may play an essential role in the ability of rice plants to cope with cold stress.

Objective: G-protein-coupled receptor 30 (GPR30) has been reported to be a novel estrogen receptor a (ERa) in vitro. Therefore, the interactions among GPR30, ERa, progesterone receptor (PR) and human epidermal growth factor receptor-2 (HER-2/neu), and their prognostic utilities in the infiltrating ductal carcinoma (IDC) of the breast were evaluated. Materials and Methods: Messenger RNA (mRNA) levels of GPR30, ERa, PR and HER-2/neu in the tumor samples of 118 Taiwanese IDC patients and 27 non-tumor mammary tissues were measured via quantitative polymerase chain reaction analyses. The correlations of GPR30 mRNA levels with clinical parameters, i.e. tumor/non-tumor, ERa, PR, HER-2/neu, age, lymph node metastasis, lymph–vascular invasion, grade, stage and patient survival, were assessed by using appropriate statistical analyses. Results: GPR30 expression was observed to be lower in IDC (p < 0.001) than in non-tumor mammary tissues. Importantly, GPR30 mRNA level was positively correlated with that of ERa (p = 0.001) and PR (p = 0.001) but not correlated with that of HER-2/neu when they were analyzed as continuous variables. However, lower GPR30 was noticed in tumors with HER-2/neu protein overexpression. GPR30 expression was not correlated with age, lymph node metastasis, lymph–vascular invasion, grade and stage in IDC. GPR30 expression was not an independent prognostic factor for patient survival. Conclusion: GPR30 expression is downregulated in IDC. GPR30 is preferentially co-expressed with ER and/or PR but is lowly expressed in HER-2/neu(+) tumors. The correlation of GPR30 expression with clinical parameters, including patient survival, was not evident in this cohort.