Overview of genes annotations from <i>Cnaphalocrocis medinalis</i> midgut.

<p>(A) Species distribution of the BLASTX results. (B) GO categories of all unigenes and DEGs. (C) euKaryotic orthologous Groups (KOG) classification.</p

Midgut transcriptomal response of the rice leaffolder, <i>Cnaphalocrocis medinalis</i> (Guenée) to Cry1C toxin

<div><p><i>Cnaphalocrocis medinalis</i> (Guenée) is one of the important insect pests in rice field. Bt agents were recommended in the <i>C</i>. <i>medinalis</i> control and Bt rice is bred as a tactic to control this insect. However, the tolerance or resistance of insect to Bt protein is a main threat to the application of Bt protein. In order to investigate the response of <i>C</i>. <i>medinalis</i> transcriptome in defending a Cry1C toxin, high-through RNA-sequencing was carried in the <i>C</i>. <i>medinalis</i> larvae treated with and without Cry1C toxin. A total of 35,586 high-quality unigenes was annotated in the transcriptome of <i>C</i>. <i>medinalis</i> midgut. The comparative analysis identified 6,966 differently expressed unigenes (DEGs) between the two treatments. GO analysis showed that these genes involved in proteolysis and extracellular region. Among these DEGs, carboxylesterase, glutathione S-transferase and P450 were differently expressed in the treated <i>C</i>. <i>medinalis</i> midgut. Furthermore, trypsin, chymotrypsin, and carboxypeptidase were identified in DEGs, and most of them up-regulated. In addition, thirteen ABC transporters were downregulated and three upregulated in Cry1C-treated <i>C</i>. <i>medinalis</i> midgut. Based on the pathway analysis, antigen processing and presentation pathway, and chronic myeloid leukemia pathway were significant in <i>C</i>. <i>medinalis</i> treated with Cry1C toxin. These results indicated that serine protease, detoxification enzymes and ABC transporter, antigen processing and presentation pathway, and chronic myeloid leukemia pathway may involved in the response of <i>C</i>. <i>medinalis</i> to Cry1C toxin. This study provides a transcriptomal foundation for the identification and functional characterization of genes involved in the toxicity of Bt Cry protein against <i>C</i>. <i>medinalis</i>, and provides potential clues to the studies on the tolerance or resistance of an agriculturally important insect pest <i>C</i>. <i>medinalis</i> to Cry1C toxin.</p></div

Differently expressed unigenes potentially involved in <i>Cnaphalocrocis medinalis</i> response to Cry1C toxin.

<p>Differently expressed unigenes potentially involved in <i>Cnaphalocrocis medinalis</i> response to Cry1C toxin.</p

Trypsin genes of <i>Cnaphalocrocis medinalis</i> midgut in response to the ingestion of Cry1C toxin.

<p>Trypsin genes of <i>Cnaphalocrocis medinalis</i> midgut in response to the ingestion of Cry1C toxin.</p

ABC transporters differently expressed in <i>Cnaphalocrocis medinalis</i> larvae treated with Cry1C toxin.

<p>ABC transporters differently expressed in <i>Cnaphalocrocis medinalis</i> larvae treated with Cry1C toxin.</p

Carboxypeptidase genes of <i>Cnaphalocrocis medinalis</i> midgut in response to the ingestion of Cry1C toxin.

<p>Carboxypeptidase genes of <i>Cnaphalocrocis medinalis</i> midgut in response to the ingestion of Cry1C toxin.</p

Differentially expressed unigenes (DEGs) in the midgut of <i>Cnaphalocrocis medinalis</i> larvae fed with Cry1C toxin.

<p>(A) Number of DEGs. (B) Volcano plot to show the fold change and error rates. The non-DEGs are indicated by black dots, the DEGs up-regulated are indicated by red dots, and the DEGs down-regulated are indicated by blue dots.</p

Enriched pathway of DEGs in <i>Cnaphalocrocis medinalis</i> response to Cry1C toxin (Q-value<0.05).

<p>Enriched pathway of DEGs in <i>Cnaphalocrocis medinalis</i> response to Cry1C toxin (Q-value<0.05).</p

Statistic of GO enrichments of DGEs.

<p>(A) Histogram. (B) Scatter plot.</p

A Prognosis Classifier for Breast Cancer Based on Conserved Gene Regulation between Mammary Gland Development and Tumorigenesis: A Multiscale Statistical Model

<div><p>Identification of novel cancer genes for molecular therapy and diagnosis is a current focus of breast cancer research. Although a few small gene sets were identified as prognosis classifiers, more powerful models are still needed for the definition of effective gene sets for the diagnosis and treatment guidance in breast cancer. In the present study, we have developed a novel statistical approach for systematic analysis of intrinsic correlations of gene expression between development and tumorigenesis in mammary gland. Based on this analysis, we constructed a predictive model for prognosis in breast cancer that may be useful for therapy decisions. We first defined developmentally associated genes from a mouse mammary gland epithelial gene expression database. Then, we found that the cancer modulated genes were enriched in this developmentally associated genes list. Furthermore, the developmentally associated genes had a specific expression profile, which associated with the molecular characteristics and histological grade of the tumor. These result suggested that the processes of mammary gland development and tumorigenesis share gene regulatory mechanisms. Then, the list of regulatory genes both on the developmental and tumorigenesis process was defined an 835-member prognosis classifier, which showed an exciting ability to predict clinical outcome of three groups of breast cancer patients (the predictive accuracy 64∼72%) with a robust prognosis prediction (hazard ratio 3.3∼3.8, higher than that of other clinical risk factors (around 2.0–2.8)). In conclusion, our results identified the conserved molecular mechanisms between mammary gland development and neoplasia, and provided a unique potential model for mining unknown cancer genes and predicting the clinical status of breast tumors. These findings also suggested that developmental roles of genes may be important criteria for selecting genes for prognosis prediction in breast cancer.</p> </div