miRConnect: identifying effector genes of miRNAs and miRNA families in cancer cells

micro(mi)RNAs are small non-coding RNAs that negatively regulate expression of most mRNAs. They are powerful regulators of various differentiation stages, and the expression of genes that either negatively or positively correlate with expressed miRNAs is expected to hold information on the biological state of the cell and, hence, of the function of the expressed miRNAs. We have compared the large amount of available gene array data on the steady state system of the NCI60 cell lines to two different data sets containing information on the expression of 583 individual miRNAs. In addition, we have generated custom data sets containing expression information of 54 miRNA families sharing the same seed match. We have developed a novel strategy for correlating miRNAs with individual genes based on a summed Pearson Correlation Coefficient (sPCC) that mimics an in silico titration experiment. By focusing on the genes that correlate with the expression of miRNAs without necessarily being direct targets of miRNAs, we have clustered miRNAs into different functional groups. This has resulted in the identification of three novel miRNAs that are linked to the epithelial-to-mesenchymal transition (EMT) in addition to the known EMT regulators of the miR-200 miRNA family. In addition, an analysis of gene signatures associated with EMT, c-MYC activity, and ribosomal protein gene expression allowed us to assign different activities to each of the functional clusters of miRNAs. All correlation data are available via a web interface that allows investigators to identify genes whose expression correlates with the expression of single miRNAs or entire miRNA families. miRConnect.org will aid in identifying pathways regulated by miRNAs without requiring specific knowledge of miRNA targets.     

中国"三江并流"纵谷地蚤类丰富度与区系沿纬度梯度的水平分布格局

为探讨横断山区蚤类物种丰富度与区系沿纬度梯度变化的基本规律以及影响它们分布的主要生态因子,作者就云南西部横断山区21o-28oN的8个纬度梯度带目前所知分布的9科45属153种(亚种)蚤类的水平分布资料进行了综合整理和统计分析。结果表明:(1)这一区域蚤类科、属、种丰富度,特有种丰富度和特有度,以及东洋界和古北界区系成分物种丰富度沿纬度梯度的变化,都呈现了随纬度增加先增高后降低的单峰分布格局,最大峰值出现在25o-27oN之间,研究认为,形成物种密度高峰的主要因素是两大区系分界线和交错区的边缘效应;(2)东洋和古北两大区系成分构成比的水平分布格局截然不同,前者随纬度的增加递减,后者则随纬度的增加呈递增的趋势,两区系成分过渡或交错区的跨度在23o-29oN之间,并在25o-27oN形成交汇和分异的中心;(3)聚类分析结果表明,横断山8个纬度梯度带的蚤类总体上归为3个主要地域区系类型,反映出纬度、地理气候环境等因素对蚤类区系及物种分布的影响,以及蚤类区系和物种组成沿纬度梯度的水平分布格局与地理和气候环境的统一性;(4)蚤类的属、种β多样性沿纬度梯度的水平分布基本呈现双峰格局,峰值反映出蚤类的组成及分布在不同纬度梯度、气候带之间的过渡与转变,说明β多样性的水平分布格局与纬度梯度的气候、环境变化程度的关系密切,以及过渡区的边缘效应对两区系物种丰富度高峰的形成具有重要影响;(5)横断山区蚤类物种丰富度与区系的水平分布与垂直分布的规律和格局基本相同,显示了具有同源性的水平地带性与垂直地带性对蚤类空间分布格局所产生的类似影响,证实了横断山区蚤类物种丰富度与区系的水平分布格局理应出现近似于它们垂直分布的一般规律与格局的推论;(6)横断山25o-27oN的区域形成了两大区系物种交汇和分异的中心,由于边缘效应和复杂的地理景观,这里蚤类科、属、种、特有种都具有较高多样性,据此作者推断,这里可能是我国横断山区多物种保存、分布和分化的核心区。     

滇西北藏区草地管理方式对草地昆虫群落多样性的影响

采用野外样地生态方法研究了4种不同管理草地的昆虫群落的多样性。结果表明,草地昆虫群落优势类群为叶蝉总科、盲蝽科、蝇科、瘿蚊科等;刈草草地、种植草地、自由放牧草地和灌丛草地拥有的昆虫的科数分别为40、44、35和36,个体数分别为1869、1510、997和848;刈草草地昆虫群落多样性指数相对较高。用Jaccard相似性系数(ISJ)判别发现,4种管理方式草地昆虫群落处于中等相似水平。因此,不同管理方式对昆虫群落的多样性有影响,传统管理的刈草草地有利于维持草地昆虫的多样性。     

Biochemical basis for the requirement of kinase activity for Cbl-dependent ubiquitinylation and degradation of a target tyrosine kinase

Members of the Cbl family of ubiquitin ligases have emerged as crucial negative regulators of tyrosine kinase signaling. These proteins preferentially interact with and target activated tyrosine kinases for ubiquitinylation, thereby facilitating the lysosomal sorting of receptor tyrosine kinases or proteasomal degradation of nonreceptor tyrosine kinases. Recent work has indicated a crucial role of the target kinase activity in Cbl-dependent ubiquitinylation and degradation, but the biochemical basis for this requirement is not understood. Here, we have used the Src-family kinase Fyn, a well characterized Cbl target, to address this issue. Using defined Fyn mutants, we demonstrate that the kinase activity of Fyn is crucial for its Cbl-dependent ubiquitinylation and degradation, but a low level of ubiquitinylation and degradation of kinase-inactive Fyn mutants was consistently observed. Mutational induction of an open conformation enhanced the susceptibility of kinase-active Fyn to Cbl but was insufficient to promote the ubiquitinylation and degradation of kinase-inactive Fyn. Notably, the Cbl-dependent degradation of Fyn did not require the Fyn-mediated phosphorylation of Cbl. Finally, we show that the major determinant of the susceptibility of Fyn protein to Cbl-dependent ubiquitinylation and degradation is the extent to which it physically associates with Cbl; kinase activity of Fyn serves as a critical determinant to promote its association with Cbl, which we demonstrate is mediated by multiple protein-protein interactions. Our results strongly suggest that promotion of association with Cbl is the primary mechanism by which the kinase activity of the targets of Cbl contributes to their susceptibility to Cbl.     

Small molecules blocking the entry of severe acute respiratory syndrome coronavirus into host cells

Severe acute respiratory syndrome coronavirus (SARS-CoV) is the pathogen of SARS, which caused a global panic in 2003. We describe here the screening of Chinese herbal medicine-based, novel small molecules that bind avidly with the surface spike protein of SARS-CoV and thus can interfere with the entry of the virus to its host cells. We achieved this by using a two-step screening method consisting of frontal affinity chromatography-mass spectrometry coupled with a viral infection assay based on a human immunodeficiency virus (HIV)-luc/SARS pseudotyped virus. Two small molecules, tetra-O-galloyl-beta-D-glucose (TGG) and luteolin, were identified, whose anti-SARS-CoV activities were confirmed by using a wild-type SARS-CoV infection system. TGG exhibits prominent anti-SARS-CoV activity with a 50% effective concentration of 4.5 microM and a selective index of 240.0. The two-step screening method described here yielded several small molecules that can be used for developing new classes of anti-SARS-CoV drugs and is potentially useful for the high-throughput screening of drugs inhibiting the entry of HIV, hepatitis C virus, and other insidious viruses into their host cells.     

Accumulation of ions during seed development under controlled saline conditions of two Suaeda salsa populations is related to their adaptation to saline environments

Controlled conditions were used to investigate the relationship between ion distribution in developing seeds of two Suaeda salsa populations and seed germination and seedling emergence. Seeds were harvested from S. salsa plants that had been treated with 1 or 400 mM NaCl for 122 (saline inland population) or 135 days (intertidal zone population) in a glasshouse. Germination and seedling emergence were evaluated under salinity. In both populations, more ions were accumulated in the pericarps of plants cultured in 400 mM NaCl than in 1 mM NaCl. Pericarps accumulated much higher ion concentrations in the intertidal zone population than in the saline inland population, while the opposite trend occurred for ion accumulation in the embryos. Seeds of plants from the intertidal zone population germinated more rapidly than those from plants of the saline inland population, regardless of the NaCl concentration during seed germination. However, seedling emergence under high salinity was lower with seeds from the intertidal zone population than with seeds from the saline inland population. In conclusion, S. salsa in the intertidal zone employs superior control of ion compartmentalization in the pericarps to tolerate salinity but requires a minimal level of ions in embryos to ensure seedling establishment in highly saline environments. This indicates that euhalophytes require salts during the mature seed stage to maintain seed viability and to ensure seedling emergence and population establishment.     

Intein-Mediated Protein trans-Splicing of the Recombinant Streptavidin on Magnetosomes

Molecular Biology - When expressing streptavidin recombinant polypeptide on magnetosomes (called bacterial magnetic nanoparticles, or BMPs), the presence of endogenous bacterial biotin might be...     

A novel domain-duplicated SlitFAR3 gene involved in sex pheromone biosynthesis in Spodoptera litura

Fatty acyl reductases (FARs) are key enzymes that participate in sex pheromone biosynthesis by reducing fatty acids to fatty alcohols. Lepidoptera typically harbor numerous FAR gene family members. Although FAR genes are involved in the biosynthesis of sex pheromones in moths, the key FAR gene of Spodoptera litura remains unclear. In this work, we predicted 30 FAR genes from the S. litura genome and identified a domain duplication within gene SlitFAR3, which exhibited high and preferential expression in the sexually mature female pheromone glands (PGs) and a rhythmic expression pattern during the scotophase of sex pheromone production. The molecular docking of SlitFAR3, as predicted using a 3D model, revealed a co-factor NADPH binding cavity and 2 substrate binding cavities. Functional expression in yeast cells combined with comprehensive gas chromatography indicated that the SlitFAR3 gene could produce fatty alcohol products. This study is the first to focus on the special phenomenon of FAR domain duplication, which will advance our understanding of biosynthesis-related genes from the perspective of evolutionary biology.