Identifying core gene modules in glioblastoma based on multilayer factor-mediated dysfunctional regulatory networks through integrating multi-dimensional genomic data

The driver genetic aberrations collectively regulate core cellular processes underlying cancer development. However, identifying the modules of driver genetic alterations and characterizing their functional mechanisms are still major challenges for cancer studies. Here, we developed an integrative multi-omics method CMDD to identify the driver modules and their affecting dysregulated genes through characterizing genetic alteration-induced dysregulated networks. Applied to glioblastoma (GBM), the CMDD identified a core gene module of 17 genes, including seven known GBM drivers, and their dysregulated genes. The module showed significant association with shorter survival of GBM. When classifying driver genes in the module into two gene sets according to their genetic alteration patterns, we found that one gene set directly participated in the glioma pathway, while the other indirectly regulated the glioma pathway, mostly, via their dysregulated genes. Both of the two gene sets were significant contributors to survival and helpful for classifying GBM subtypes, suggesting their critical roles in GBM pathogenesis. Also, by applying the CMDD to other six cancers, we identified some novel core modules associated with overall survival of patients. Together, these results demonstrate integrative multi-omics data can identify driver modules and uncover their dysregulated genes, which is useful for interpreting cancer genome.     

Accumulation of d-Glucose from Pentoses by Metabolically Engineered Escherichia coli

Escherichia coli that is unable to metabolize d-glucose (with knockouts in ptsG, manZ, and glk) accumulates a small amount of d-glucose (yield of about 0.01 g/g) during growth on the pentoses d-xylose or l-arabinose as a sole carbon source. Additional knockouts in the zwf and pfkA genes, encoding, respectively, d-glucose-6-phosphate 1-dehydrogenase and 6-phosphofructokinase I (E. coli MEC143), increased accumulation to greater than 1 g/liter d-glucose and 100 mg/liter d-mannose from 5 g/liter d-xylose or l-arabinose. Knockouts of other genes associated with interconversions of d-glucose-phosphates demonstrate that d-glucose is formed primarily by the dephosphorylation of d-glucose-6-phosphate. Under controlled batch conditions with 20 g/liter d-xylose, MEC143 generated 4.4 g/liter d-glucose and 0.6 g/liter d-mannose. The results establish a direct link between pentoses and hexoses and provide a novel strategy to increase carbon backbone length from five to six carbons by directing flux through the pentose phosphate pathway.     

Vaccinium damingshanense sp. nov. (Ericaceae) from Guangxi,China

Vaccinium damingshanense (Ericaceae), a new species from Daming Mountain, Guangxi Zhuang Autonomous Region, China is described, illustrated and placed in a new key for the identification of species of V. sect. Eococcus Sleumer in China. The new species is similar to V. carlesii Dunn, but differs in leaf shape, leaf margin character and details of anther thecae. Information on its distribution and ecology is also provided.     

陕西汉阴发现朱鹮新分布

中国朱鹮就地保护和易地保护取得的成果使朱鹮分布区的扩大成为可能。2013年6月3日,在陕西汉阴县龙垭镇凤柳村(32°58′N,108°31′E,海拔526 m)发现一对朱鹮(H12♀和B747♂)营巢繁殖,成功出飞3只幼鸟。2014年1月12日,我们又在该地的青泥河畔发现8只朱鹮的越冬觅食群体。其中包括上述繁殖配对及其3只后代、1只来自洋县野生种群的个体(J41)以及2只无法识别身份的个体。同年5月该繁殖配对成功出飞幼鸟4只。自2011年之后,宁陕朱鹮再引入种群的个体与洋县野生个体形成配对,说明两个种群之间存在基因交流。汉阴朱鹮新分布的发现表明,陕西宁陕朱鹮再引入项目的实施增加了朱鹮野生种群(源种群)向秦岭东部地区扩散的速度,还将有利于朱鹮再引入种群(卫星种群)的建立。     

Genetic Diversities of Cymbidium mosaic virus and Odontoglossum ringspot virus Isolates Based on the Coat Protein Genes from Orchids in Guangdong Province,China

Orchids are some of the most important ornamental flowers. Cymbidium mosaic virus (CymMV) and Odontoglossum ringspot virus (ORSV) are the most prevalent and economically important viruses affecting orchids in China. In this study, 20 CymMV and 28 ORSV isolates were selected for genetic diversity analysis. The CymMV isolates shared 84.6–100% and 89.5–100% identities of coat protein (CP) at the nucleotide (nt) and amino acid (aa) levels, respectively. The identities of ORSV isolates were 96.4–100% (nt) and 92.5–99.4% (aa). The CP genes of CymMV were found to have genetic diversity, and the CP genes of ORSV were genetically conservative. These results can aid in designing effective disease‐control strategies.     

First Report of Myrothecium roridum Causing Leaf Spot on Anthurium andraeanum in China

A new severe disease on Anthurium andraeanum Lind. was observed in the summer of 2011 in Beijing, China. The fungus was isolated from symptomatic leaves, and its pathogenicity was confirmed. Based on the morphological characteristics and molecular analysis, the pathogen was identified as Myrothecium roridum Tode ex Fr. This is the first report of M. roridum causing leaf spot on A. andraeanum in China.