细胞因子人MK基因的克隆及在大肠杆菌中的高效表达(简报)

细胞因子Midkine(简称MK)是新发现的一类肝素结合因子家族中的一员。1988年,Kadamatsu等利用差异杂交法在经维甲酸诱导分化的小鼠畸胎瘤细胞株HM-1中首先克隆到小鼠MK基因。人MK基因则最早是从λgt10人胚肾(20-24周)cDNA库和EMBL-3人胎盘基因组库获得。成熟     

An Ensemble Method for Predicting Subnuclear Localizations from Primary Protein Structures

Background

Predicting protein subnuclear localization is a challenging problem. Some previous works based on non-sequence information including Gene Ontology annotations and kernel fusion have respective limitations. The aim of this work is twofold: one is to propose a novel individual feature extraction method; another is to develop an ensemble method to improve prediction performance using comprehensive information represented in the form of high dimensional feature vector obtained by 11 feature extraction methods.

Methodology/Principal Findings

A novel two-stage multiclass support vector machine is proposed to predict protein subnuclear localizations. It only considers those feature extraction methods based on amino acid classifications and physicochemical properties. In order to speed up our system, an automatic search method for the kernel parameter is used. The prediction performance of our method is evaluated on four datasets: Lei dataset, multi-localization dataset, SNL9 dataset and a new independent dataset. The overall accuracy of prediction for 6 localizations on Lei dataset is 75.2% and that for 9 localizations on SNL9 dataset is 72.1% in the leave-one-out cross validation, 71.7% for the multi-localization dataset and 69.8% for the new independent dataset, respectively. Comparisons with those existing methods show that our method performs better for both single-localization and multi-localization proteins and achieves more balanced sensitivities and specificities on large-size and small-size subcellular localizations. The overall accuracy improvements are 4.0% and 4.7% for single-localization proteins and 6.5% for multi-localization proteins. The reliability and stability of our classification model are further confirmed by permutation analysis.

Conclusions

It can be concluded that our method is effective and valuable for predicting protein subnuclear localizations. A web server has been designed to implement the proposed method. It is freely available at http://bioinformatics.awowshop.com/snlpred_page.php.     

Raman spectroscopy detects phenotypic differences among Escherichia coli enriched for 1‐butanol tolerance using a metagenomic DNA library

Advances in Raman spectroscopy are enabling more comprehensive measurement of microbial cell chemical composition. Advantages include results returned in near real‐time and minimal sample preparation. In this research, Raman spectroscopy is used to analyze E. coli with engineered solvent tolerance, which is a multi‐genic trait associated with complex and uncharacterized phenotypes that are of value to industrial microbiology. To generate solvent tolerant phenotypes, E. coli transformed with DNA libraries are serially enriched in the presence of 0.9% (v/v) and 1.1% (v/v) 1‐butanol. DNA libraries are created using degenerate oligonucleotide primed PCR (DOP‐PCR) from the genomic DNA of E. coli, Clostridium acetobutylicum ATCC 824, and the metagenome of a stream bank soil sample, which contained DNA from 72 different phyla. DOP‐PCR enabled high efficiency library cloning (with no DNA shearing or end‐polishing) and the inclusion un‐culturable organisms. Nine strains with improved tolerance are analyzed by Raman spectroscopy and vastly different solvent‐tolerant phenotypes are characterized. Common among these are improved membrane rigidity from increasing the fraction of unsaturated fatty acids at the expense of cyclopropane fatty acids. Raman spectroscopy offers the ability to monitor cell phenotype changes in near real‐time and is adaptable to high‐throughput screening, making it relevant to metabolic engineering.     

细胞色素P450scc在人早期胎盘中的表达（简报）

人妊娠期间,胎盘合成大量的类固醇激素,与妊娠的启动、维持、分娩以及胎儿的发育均存在密切的关系。阐明胎盘类固醇激素特别是孕酮合成与分泌的调节机制对于寻找理想的生育调控技术和生殖保健方法具有重要的意义。因此,胎盘类固醇激素合成与分泌的调节向来是生殖生物学与妇产科学领域所关注的焦点问题之一,     

Gefitinib Synergizes with Irinotecan to Suppress Hepatocellular Carcinoma via Antagonizing Rad51-Mediated DNA-Repair

Chemotherapy is the only choice for most of the advanced hepatocellular carcinoma (HCC) patients, while few agents were available, making it an urgent need to develop new chemotherapy strategies. A phase II clinical trial suggested that the efficacy of irinotecan in HCC was limited due to dose-dependent toxicities. Here, we found that gefitinib exhibited synergistic activity in combination with SN-38, an active metabolite of irinotecan, in HCC cell lines. And the enhanced apoptosis induced by gefitinib plus SN-38 was a result from caspase pathway activation. Mechanistically, gefitinib dramatically promoted the ubiquitin–proteasome-dependent degradation of Rad51 protein, suppressed the DNA repair, gave rise to more DNA damages, and ultimately resulted in the synergism of these two agents. In addition, the increased antitumor efficacy of gefitinib combined with irinotecan was further validated in a HepG2 xenograft mice model. Taken together, our data demonstrated for the first time that the combination of irinotecan and gefitinib showed potential benefit in HCC, which suggests that Rad51 is a promising target and provides a rationale for clinical trials investigating the efficacy of the combination of topoisomerase I inhibitors and gefitinib in HCC.     

Nonlinear responses of productivity and diversity of alpine meadow communities to degradation北大核心CSCD

Aims The alpine meadow degradation could have profound effects on the grassland productivity. The aim of our study is to clarify the dynamic response of community productivity and species diversity in the process of alpine meadow degradation. Methods In the Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Northern Tibetan Grassland Ecosystem Research Station (Nagqu station), we conducted stages experiments with multiple degradation levels: control, mild degraded meadow, moderate degraded meadow, severe degraded meadow and serious sandy meadow. Important findings The response of aboveground biomass to alpine meadow degradation showed a linear or nonlinear increased response patterns, but the belowground biomass and total biomass decreased nonlinearly. As observed in measurement of aboveground biomass, Margalef index, Simpson index, Shannon-Wiener index and Pielou evenness index also exhibit a nonlinear increased response to degradation. The results of structural equation models showed that belowground biomass has a positive relationship with soil carbon content (p < 0.05) and volume water content (p < 0.1). However, soil nutrient and soil physical properties had no significant impact on aboveground biomass (p < 0.1). Compared with soil physical properties, soil nutrition is an important factor influencing the diversity index. In our study, the nonlinear responses of productivity and diversity of alpine meadow were described by using the multiple levels of degradation in space. The results suggested that aboveground productivity cannot interpret the degree of degradation of alpine meadow, and by contrast, alpine meadow degradation should be measured by the change of plant functional groups, such as edible grasses and poisonous forbs. © 2018 Editorial Office of Chinese Journal of Plant Ecology. All rights reserved.     

Self‐Powered Wireless Sensor Node Enabled by a Duck‐Shaped Triboelectric Nanogenerator for Harvesting Water Wave Energy

This paper presents a fully enclosed duck‐shaped triboelectric nanogenerator (TENG) for effectively scavenging energy from random and low‐frequency water waves. The design of the TENG incorporates the freestanding rolling mode and the pitch motion of a duck‐shaped structure generated by incident waves. By investigating the material and structural features, a unit of the TENG device is successfully designed. Furthermore, a hybrid system is constructed using three units of the TENG device. The hybrid system achieves an instantaneous peak current of 65.5 µA with an instantaneous output power density of up to 1.366 W m^?2. Following the design, a fluid–solid interaction analysis is carried out on one duck‐shaped TENG to understand the dynamic behavior, mechanical efficiency, and stability of the device under various water wave conditions. In addition, the hybrid system is experimentally tested to enable a commercial wireless temperature sensor node. In summary, the unique duck‐shaped TENG shows a simple, cost‐effective, environmentally friendly, light‐weight, and highly stable system. The newly designed TENG is promising for building a network of generators to harvest existing blue energy in oceans, lakes, and rivers.     

假苍耳的生活史进程中几种生理生化指标的变化

本文试图从生理生化的角度对假苍耳(Iva xanthifolia)生活史进程中可溶性糖类、赤霉素、单宁以及黄酮的变化进行探讨。通过对假苍耳在生长发育期间几种生理生化指标的测定,结果表明,在假苍耳生活史进程的不同阶段,其体内各种代谢产物的含量基本都在种子或芽阶段具有最高含量。此外,不同发育阶段可溶性还原糖含量的变化规律相似：芽＞花序＞苗＞成株＞种子。除在花序和苗阶段没有测到海藻糖,其他各阶段海藻糖的含量变化如下：芽＞成株＞种子。另外,只有在种子阶段检测到棉子糖,其含量为15.43 mg·g~(-1)。赤霉素含量的变化规律如下：种子＞芽≈苗≈花序＞成株。单宁含量的变化趋势：种子＞成株＞苗＞芽＞花序。黄酮含量的变化趋势：种子＞芽＞成株≈花序＞苗。值得注意的是,当单宁/黄酮的比值接近1时,植物体内需要的单宁和黄酮的含量则相对较低;相反,当单宁/黄酮的比值接近0时,植物体内需要的单宁和黄酮的含量则较高。     

表达O型口蹄疫病毒VPl基因的重组病毒BHV-1的构建与鉴定

[目的]为了构建表达口蹄疫病毒(O/china/99)VP1基因的牛疱疹病毒1型,将人工合成的口蹄疫病毒VP1基因插入到巨细胞病毒(CMV)启动子之下构建gE基因缺失转移载体.[方法]利用磷酸钙介导转染法将该转移载体与亲本病毒BHV-1/gE-/LacZ+的基因组DNA共转染牛鼻甲细胞后收获增殖的病毒.通过筛选白色病毒蚀斑,得到重组病毒BHV-1/gE-/VP1.[结果]PCR检测结果表明VP1基因已经插入到了重组病毒BHV-1/gE-的基因组中,间接免疫荧光试验和Westem blot证实了BHV-1/gE-/VP1中的VP1基因在感染的细胞中获得了表达.[结论]本研究成功地构建了表达口蹄疫病毒VP1基因的重组病毒BHV-1/gE-/VP1,为研制口蹄疫及其他重要牛传染病的BHV-1病毒载体疫苗奠定了基础.