DIPOS: database of interacting proteins in Oryza sativa

Rice is an important crop throughout the world and is the staple food for about half the world's population. For better breeding and improved production, we need to know the function of rice molecules which facilitate their function through interactions with each other. The database of interacting proteins in Oryza sativa (DIPOS) provides comprehensive information of interacting proteins in rice, where the interactions are predicted using two computational methods, i.e., interologs and domain based methods. DIPOS contains 14?614?067 pairwise interactions among 27?746 proteins, covering about 41% of the whole Oryaza sativa proteome. Furthermore, each interaction is assigned a confidence score which further enables biologists to sort out the important proteins. Biological explanations of pathways and interactions are also provided based on the database. Public access to the DIPOS is available at and .     

SLiCE: a novel bacterial cell extract-based DNA cloning method

We describe a novel cloning method termed SLiCE (Seamless Ligation Cloning Extract) that utilizes easy to generate bacterial cell extracts to assemble multiple DNA fragments into recombinant DNA molecules in a single in vitro recombination reaction. SLiCE overcomes the sequence limitations of traditional cloning methods, facilitates seamless cloning by recombining short end homologies (≥15 bp) with or without flanking heterologous sequences and provides an effective strategy for directional subcloning of DNA fragments from Bacteria Artificial Chromosomes (BACs) or other sources. SLiCE is highly cost effective as a number of standard laboratory bacterial strains can serve as sources for SLiCE extract. In addition, the cloning efficiencies and capabilities of these strains can be greatly improved by simple genetic modifications. As an example, we modified the DH10B Escherichia coli strain to express an optimized λ prophage Red recombination system. This strain, termed PPY, facilitates SLiCE with very high efficiencies and demonstrates the versatility of the method.     

The optimization of regeneration tissue culture system of three chilli peppers cultivars based on the uniform design and the mathematical model equation

Using uniform random design optimization and the mathematical model equation we optimized the regeneration tissue culture system of the chilli pepper. An efficient and detailed plant reproducible protocol in vitro has been established using different explants and induction media for three chilli pepper cultivars. The result displayed that the seedlings at the curved hypocotyl stage were the best choice to prepare for explants, the genotype of explants affected shoot buds induction frequency and number of shoot buds per explant, and the cotyledon explant was more responsive than hypocotyl explant. The optimal media for maximum shoot initiation and regeneration and the optimal elongation medium were obtained. For Capsicum annuum var. annuum (cv. Xinsu), Capsicum annuum var. annuum (cv. Neimengchifeng) and Capsicum frutescens (cv. Xingfu), the induction rates were 99.17%, 97.50 and 96.11%, respectively; the elongation rates of shoot buds were 86.67%, 85.19% and 82.96%, respectively. The MS medium with 0.57 μM IAA and 0.69 μM NAA is the best choice for root induction. The frequency of their root emergence was 95.00-98.33%. Regenerated chilli peppers were successfully acclimatized and cultivated with 100% survival. This work will help to improve multiplication process and the genotype of chilli pepper, and may have commercial impact.     

利用基因芯片对一高保守基因进行肿瘤相关分析

本对大规模人类cDNA测序过程中获得的一条高保守基因进行了初步功能研究,生物信息学研究发现该基因在人类、小鼠、果蝇、拟南芥和裂殖酶母中都有很高的保守性,其他分析预测该基因可能具有肿瘤相关性。RT－PCR分析表明,该基因在成人和胎儿组织中广泛谱表达。利用基因芯片分析该基因在7例肝癌、5例胰腺癌、2例喉癌和2例肺癌中表达情况,结果证实了该基因的肿瘤相关性,并且提示该基因在不同类型中可能处于不同的地位。     

Cathelicidin LL37 promotes epithelial and smooth-muscle-like differentiation of adipose-derived stem cells through the Wnt/β-catenin and NF-κB pathways

Ureter reconstruction is a difficult procedure in urology. Adipose-derived stem cells (ADSCs), along with multipotency and self-renewal capacity, are a preferred choice for tissue engineering-based ureteral reconstruction. We explored the synergic role of cathelicidin LL37 (LL37) in epithelial and smooth-muscle-like differentiation. ADSCs were separated from adipose tissues of mouse and characterized by flow cytometry. The ADSCs were then stably transfected with pGC-FU-GFP (pGC) or pGC containing full-length LL37 (pGC-LL37), respectively. Cell viability and apoptosis were respectively estimated in the stably transfected cells and non-transfected cells. Then, qRT-PCR and Western blot analysis were used for determinations of epithelial marker expressions after induction by all-trans retinoic acid as well as smooth-muscle-like marker expressions after induction by transforming growth factor-β1. Then, possibly involved signaling pathways and extracellular expression of LL37 were detected. Cell viability and apoptosis were not changed after LL37 overexpression. Expression levels of epithelial and smooth-muscle-like markers were significantly upregulated by LL37 overexpression. Moreover, expressions of key kinases involved in the Wnt/β-catenin pathway as well as epithelial marker were upregulated by the LL37 overexpression, while it was reversed by Wnt/β-catenin inhibitor. Likewise, expressions of key kinases involved in the nuclear factor κB (NF-κB) pathway as well as smooth-muscle-like markers were upregulated by LL37 overexpression, which was reversed by NF-κB inhibitor. LL37 was found in the culture medium. LL37, which could be released into the medium, had no impact on cell proliferation and apoptosis of ADSCs. However, LL37 promoted epithelial and smooth-muscle-like differentiation through activating the Wnt/β-catenin and NF-κB pathways, respectively.     

MicroRNA-294 promotes cellular proliferation and motility through the PI3K/AKT and JAK/STAT pathways by upregulation of NRAS in bladder cancer

In our study we examined the role of microRNA-294 (miR-294) in bladder cancer and related mechanisms. Realtime polymerase chain reaction (RT-PCR) was performed to determine the expression level of miR-294. Western blot was used to determine the expression of NRAS, mainly factors in the PI3K/AKT and JAK/STAT pathways. Cell counting kit8 assay, clonogenic assay, wound-healing assay, transwell and flow cytometry were used to explore, respectively, cell proliferation, survival, migration, invasion, and apoptosis of bladder cancer cell line T24. The expressions of miR-294 in bladder cancer cells including J82, HT1376, T24, and SW780 were significantly increased compared to those in human bladder epithelium cells (both HCV29 and SV-HUC-1). The proliferation rate, surviving fraction, migration, and invasion of T24 cells in miR-294 mimetic transfected group were significantly increased, while they were significantly decreased by miR294 inhibitor transfection. Moreover, miR-294 suppression could increase the apoptotic rate of T24 cells. In addition, drug resistance of T24 cells to cisplatin was increased in miR-294 mimetic-treated group, while it was decreased by miR-294 inhibitor compared to empty control. Overexpression of miR-294 could upregulate NRAS expression in T24 cells and activate PI3K/AKT and JAK/STAT pathways. We found that miR-294 expression was positively related with proliferation and motility of T24 cells. Moreover, miR-294 suppression could promote the sensitivity of T24 cells to cisplatin. We also found miR-294 could upregulate NRAS and activate the PI3K/AKT and JAK/STAT pathways in T24 cells.     

Management Practices of <Emphasis Type="Italic">Miscanthus</Emphasis> × <Emphasis Type="Italic">giganteus</Emphasis> Strongly Influence Soil Properties and N<Subscript>2</Subscript>O Emissions Over the Long Term

Cropping practices of Miscanthus × giganteus, a promising energy crop, can influence C and N cycles and therefore potentially affect N₂O emissions. They may vary in harvesting date, either early (EH) or late harvest (LH), and the fertiliser form (NH₄ or NO₃). In this study, we combined a long-term field experiment and simulations with the STICS model to investigate the effect of these practices on soil parameters, N₂O emissions and the contribution of nitrification and denitrification. Daily N₂O fluxes and soil parameters were measured during the 4-month period following fertilisation in 2014 and 2015. Mean cumulative N₂O emissions were markedly higher in LH than EH (4.21 vs. 0.89 kg N₂O–N ha^?1 year^?1) but did not differ significantly between fertiliser forms or years. The difference was mainly attributed to the higher soil water-filled pore space (WFPS) observed in LH (80 vs. 56 % in EH) which resulted itself from the leaf mulch present in LH and not in EH. WFPS explained 67 % of the variance of N₂O emissions. The large decrease in pH observed after NH₄ fertilisation stimulated N₂O emissions probably through less-efficient reduction of N₂O to N₂ as simulated by STICS. Model outputs suggest a large contribution of nitrification in EH and a dominant contribution of denitrification in LH. Our study highlights the crucial impact of management practises on N₂O emissions in Miscanthus crops through changes in physico-chemical parameters and soil processes on the short and long term and brings knowledge required to maximise the benefits of bioenergy crops.     

一个由HSVⅠ诱导的类SR蛋白新基因的克隆

 根据mRNA差异显示分析 ,由单纯疱疹病毒 (HSV)Ⅰ型结合人成纤维细胞膜受体后 2h诱导产生的早期基因cDNA库中 ,分离到一个编码具有SR蛋白结构特征的新基因 ,该基因长 90 4bp .编码产生的蛋白含 12 1个氨基酸残基 ,分子量 14 9kD ,具有RS重复区和PPLP结构域 ,但不具备SR蛋白家族所特有的RNA识别区域 (RRM) .主要分布于细胞质内 ,仅在细胞膜相应受体与HSVⅠ结合后特异产生