BreakTrans: uncovering the genomic architecture of gene fusions

Producing gene fusions through genomic structural rearrangements is a major mechanism for tumor evolution. Therefore, accurately detecting gene fusions and the originating rearrangements is of great importance for personalized cancer diagnosis and targeted therapy. We present a tool, BreakTrans, that systematically maps predicted gene fusions to structural rearrangements. Thus, BreakTrans not only validates both types of predictions, but also provides mechanistic interpretations. BreakTrans effectively validates known fusions and discovers novel events in a breast cancer cell line. Applying BreakTrans to 43 breast cancer samples in The Cancer Genome Atlas identifies 90 genomically validated gene fusions. BreakTrans is available at http://bioinformatics.mdanderson.org/main/BreakTrans     

ES5 is involved in the regulation of phosphatidylserine synthesis and impacts on early senescence in rice (Oryza sativa L.)

Leaf senescence, which affects plant growth and yield in rice, is an ideal target for crop improvement and remarkable advances have been made to identify the mechanism underlying this process. We have characterized an early senile mutant es5 (early leaf senescence 5) in rice exhibiting leaf yellowing phenotype after the 4-leaf stage. This phenotype was confirmed by the higher accumulation of reactive oxygen species (ROS) and malondialdehyde (MDA), the disintegration of chloroplasts, reduction in chlorophyll content and photosynthetic rate and up-regulation of senescence-associated genes (SAGs) like Osh36, OsI57, and OsI85. Positional cloning revealed that the es5 phenotype is the result of one base substitution in ES5, encoding phosphatidylserine synthase (PSS) family protein, which is involved in the base-exchange type reaction to synthesize the minor membrane phospholipid phosphatidylserine. Functional complementation of ES5 in the es5 plants completely restored the wild-type phenotype. Ultra-high-performance liquid chromatography (UHPLC) analysis showed that es5 plants had increased levels of phosphatidylserine (PS) and decreased level of phosphatidylcholine (PC). These results provide evidence about the role of PS in rice leaf senescence.

     

Cyclin D1 Induction by Benzo[a]pyrene-7,8-diol-9,10-epoxide via the Phosphatidylinositol 3-Kinase/Akt/MAPK- and p70s6k-dependent Pathway Promotes Cell Transformation and Tumorigenesis

Benzo[a]pyrene-7,8-diol-9,10-epoxide (B[a]PDE), the major metabolite of B[a]P, has been well recognized as one ubiquitous carcinogen, but the molecular mechanism involved in its carcinogenic effect remains obscure. In the present study, we found that bronchial epithelial cells (Beas-2B) and hepatocytes treated with B[a]PDE presented a significant increase of cyclin D1 expression. Moreover, Akt, p70^s6k, and MAPKs including JNK, Erks, and p38 were notably activated in B[a]PDE-treated Beas-2B cells, whereas NF-κB, NFAT, and Egr-1 were not. Our results demonstrated that JNK and Erks were required in B[a]PDE-induced cyclin D1 expression because the inhibition of JNK or Erks by a selective chemical inhibitor or dominant negative mutant robustly impaired the cyclin D1 induction by B[a]PDE. Furthermore, we found that overexpression of the dominant negative mutant of p85 (regulatory subunit of phosphatidylinositol 3-kinase) or Akt dramatically suppressed B[a]PDE-induced JNK and Erk activation as well as cyclin D1 expression, suggesting that cyclin D1 induction by B[a]PDE is via the phosphatidylinositol 3-kinase/Akt/MAPK-dependent pathway. In addition, we clarified that p70^s6k is also involved in B[a]PDE-induced cyclin D1 expression because rampamycin pretreatment dramatically reduced cyclin D1 induction by B[a]PDE. More importantly, we demonstrated that up-regulated cyclin D1 by B[a]PDE plays a critical role in oncogenic transformation and tumorigenesis of Beas-2B cells. These results not only broaden our knowledge of the molecular mechanism of B[a]PDE carcinogenicity but also lead to the further study of chemoprevention of B[a]PDE-associated human cancers.     

Artificial and natural duplicates in pyrosequencing reads of metagenomic data

Background  

Artificial duplicates from pyrosequencing reads may lead to incorrect interpretation of the abundance of species and genes in metagenomic studies. Duplicated reads were filtered out in many metagenomic projects. However, since the duplicated reads observed in a pyrosequencing run also include natural (non-artificial) duplicates, simply removing all duplicates may also cause underestimation of abundance associated with natural duplicates.     

MiR-21 Simultaneously Regulates ERK1 Signaling in HSC Activation and Hepatocyte EMT in Hepatic Fibrosis

Background

MicroRNA-21 (miR-21) plays an important role in the pathogenesis and progression of liver fibrosis. Here, we determined the serum and hepatic content of miR-21 in patients with liver cirrhosis and rats with dimethylnitrosamine-induced hepatic cirrhosis and examined the effects of miR-21 on SPRY2 and HNF4α in modulating ERK1 signaling in hepatic stellate cells (HSCs) and epithelial-mesenchymal transition (EMT) of hepatocytes.

Methods

Quantitative RT-PCR was used to determine miR-21 and the expression of SPRY2, HNF4α and other genes. Immunoblotting assay was carried out to examine the expression of relevant proteins. Luciferase reporter assay was performed to assess the effects of miR-21 on its predicted target genes SPRY2 and HNF4α. Primary HSCs and hepatocytes were treated with miR-21 mimics/inhibitors or appropriate adenoviral vectors to examine the relation between miR-21 and SPRY2 or HNF4α.

Results

The serum and hepatic content of miR-21 was significantly higher in cirrhotic patients and rats. SPRY2 and HNF4α mRNA levels were markedly lower in the cirrhotic liver. MiR-21 overexpression was associated with enhanced ERK1 signaling and EMT in liver fibrosis. Luciferase assay revealed suppressed SPRY2 and HNF4α expression by miR-21. Ectopic miR-21 stimulated ERK1 signaling in HSCs and induced hepatocyte EMT by targeting SPRY2 or HNF4α. Downregulating miR-21 suppressed ERK1 signaling, inhibited HSC activation, and blocked EMT in TGFβ1-treated hepatocytes.

Conclusions

MiR-21 modulates ERK1 signaling and EMT in liver fibrosis by regulating SPRY2 and HNF4α expression. MiR-21 may serve as a potentially biomarker as well as intervention target for hepatic cirrhosis.     

Meta-analysis of the Association Between DCDC2 Polymorphisms and Risk of Dyslexia

Developmental dyslexia (DD) is a highly heritable neurological disorder that is prevalent in school-aged children. The dyslexia-associated gene DCDC2 is a member of the DCX family of genes known to play roles in neurogenesis, neuronal migration, and differentiation. However, the associations between DCDC2 genetic variations and dyslexia have yielded inconclusive results. Clarifying the effects of DCDC2 polymorphisms on dyslexia risk will advance not only elucidation of the role of DCDC2 in the brain development but also development of possible therapeutic approach for dyslexia. In this review, we summarized the ongoing association studies concerning DCDC2 polymorphisms and dyslexia risk by using meta-analysis and revealed that DCDC2 rs807701 might contribute significantly to dyslexia risk.     

Light Spatial Distribution in the Canopy and Crop Development in Cotton

The partitioning of light is very difficult to assess, especially in discontinuous or irregular canopies. The aim of the present study was to analyze the spatial distribution of photosynthetically active radiation (PAR) in a heterogeneous cotton canopy based on a geo-statistical sampling method. Field experiments were conducted in 2011 and 2012 in Anyang, Henan, China. Field plots were arranged in a randomized block design with the main plot factor representing the plant density. There were 3 replications and 6 densities used in every replicate. The six plant density treatments were 15,000, 33,000, 51,000, 69,000, 87,000 and 105,000 plants ha⁻¹. The following results were observed: 1) transmission within the canopy decreased with increasing density and significantly decreased from the top to the bottom of the canopy, but the greatest decreases were observed in the middle layers of the canopy on the vertical axis and closing to the rows along the horizontal axis; 2) the transmitted PAR (TPAR) of 6 different cotton populations decreased slowly and then increased slightly as the leaves matured, the TPAR values were approximately 52.6–84.9% (2011) and 42.7–78.8% (2012) during the early cotton developmental stage, and were 33.9–60.0% (2011) and 34.5–61.8% (2012) during the flowering stage; 3) the Leaf area index (LAI) was highly significant exponentially correlated (R² = 0.90 in 2011, R² = 0.91 in 2012) with the intercepted PAR (IPAR) within the canopy; 4) and a highly significant linear correlation (R² = 0.92 in 2011, R² = 0.96 in 2012) was observed between the accumulated IPAR and the biomass. Our findings will aid researchers to improve radiation-use efficiency by optimizing the ideotype for cotton canopy architecture based on light spatial distribution characteristics.     

酸枝木类原植物分类学概述

酸枝木类为《红木》国家标准中最大的一类,原植物皆隶属于豆科(Leguminosae)黄檀属(Dalbergia).为准确鉴定红木酸枝木市场的树种,回顾了豆科黄檀属分类学历史,对13种酸枝木的原植物进行了分类学文献考证研究并提供了详细的形态描述.     

FR-HIT, a very fast program to recruit metagenomic reads to homologous reference genomes

SUMMARY: Fragment recruitment, a process of aligning sequencing reads to reference genomes, is a crucial step in metagenomic data analysis. The available sequence alignment programs are either slow or insufficient for recruiting metagenomic reads. We implemented an efficient algorithm, FR-HIT, for fragment recruitment. We applied FR-HIT and several other tools including BLASTN, MegaBLAST, BLAT, LAST, SSAHA2, SOAP2, BWA and BWA-SW to recruit four metagenomic datasets from different type of sequencers. On average, FR-HIT and BLASTN recruited significantly more reads than other programs, while FR-HIT is about two orders of magnitude faster than BLASTN. FR-HIT is slower than the fastest SOAP2, BWA and BWA-SW, but it recruited 1-5 times more reads. AVAILABILITY: http://weizhongli-lab.org/frhit.