AIM2 promotes non-small-cell lung cancer cell growth through inflammasome-dependent pathway

The human absent in melanoma 2 (AIM2) is considered as a DNA recognizer. AIM2 has been described as a tumor suppressor gene in the early years. But recent studies suggested that it functions as an oncogene in several cancers. However, its roles in non-small-cell lung cancer (NSCLC) remain unclear. Here we reported that AIM2 highly expressed in NSCLC cells and exhibited a tumor-promoting property both in vitro and in vivo. Besides, AIM2 short hairpin RNA (shRNA)-mediated suppression of cell proliferation was triggered by the accumulation of cells at the G2/M phase. Knockdown of AIM2 reduced the inflammasome formation, while overexpression of AIM2 or stimulation by poly(dA:dT) induced the inflammasome formation. Interestingly, blockade of the inflammasome by caspase-1 inhibitor VX-765 or ASC small interfering RNA (siRNA) abolished the effects brought by AIM2 shRNA and AIM2 plasmid. In summary, our results revealed that AIM2 functioned as an oncogene in NSCLC in an inflammasome-dependent way.     

PCAS – a precomputed proteome annotation database resource

Background  

Many model proteomes or "complete" sets of proteins of given organisms are now publicly available. Much effort has been invested in computational annotation of those "draft" proteomes. Motif or domain based algorithms play a pivotal role in functional classification of proteins. Employing most available computational algorithms, mainly motif or domain recognition algorithms, we set up to develop an online proteome annotation system with integrated proteome annotation data to complement existing resources.     

Secreted protein prediction system combining CJ-SPHMM,TMHMM, and PSORT

To increase the coverage of secreted protein prediction, we describe a combination strategy. Instead of using a single method, we combine Hidden Markov Model (HMM)-based methods CJ-SPHMM and TMHMM with PSORT in secreted protein prediction. CJ-SPHMM is an HMM-based signal peptide prediction method, while TMHMM is an HMM-based transmembrane (TM) protein prediction algorithm. With CJ-SPHMM and TMHMM, proteins with predicted signal peptide and without predicted TM regions are taken as putative secreted proteins. This HMM-based approach predicts secreted protein with Ac (Accuracy) at 0.82 and Cc (Correlation coefficient) at 0.75, which are similar to PSORT with Ac at 0.82 and Cc at 0.76. When we further complement the HMM-based method, i.e., CJ-SPHMM + TMHMM with PSORT in secreted protein prediction, the Ac value is increased to 0.86 and the Cc value is increased to 0.81. Taking this combination strategy to search putative secreted proteins from the International Protein Index (IPI) maintained at the European Bioinformatics Institute (EBI), we constructed a putative human secretome with 5235 proteins. The prediction system described here can also be applied to predicting secreted proteins from other vertebrate proteomes. Availability: The CJ-SPHMM and predicted secreted proteins are available at: ftp://ftp.cbi.pku.edu.cn/pub/secreted-protein/     

Domain selection combined with improved cloning strategy for high throughput expression of higher eukaryotic proteins

Background  

Expression of higher eukaryotic genes as soluble, stable recombinant proteins is still a bottleneck step in biochemical and structural studies of novel proteins today. Correct identification of stable domains/fragments within the open reading frame (ORF), combined with proper cloning strategies, can greatly enhance the success rate when higher eukaryotic proteins are expressed as these domains/fragments. Furthermore, a HTP cloning pipeline incorporated with bioinformatics domain/fragment selection methods will be beneficial to studies of structure and function genomics/proteomics.     

Systematic high-yield production of human secreted proteins in Escherichia coli

Human secreted proteins play a very important role in signal transduction. In order to study all potential secreted proteins identified from the human genome sequence, systematic production of large amounts of biologically active secreted proteins is a prerequisite. We selected 25 novel genes as a trial case for establishing a reliable expression system to produce active human secreted proteins in Escherichia coli. Expression of proteins with or without signal peptides was examined and compared in E. coli strains. The results indicated that deletion of signal peptides, to a certain extent, can improve the expression of these proteins and their solubilities. More importantly, under expression conditions such as induction temperature, N-terminus fusion peptides need to be optimized in order to express adequate amounts of soluble proteins. These recombinant proteins were characterized as well-folded proteins. This system enables us to rapidly obtain soluble and highly purified human secreted proteins for further functional studies.     

库木塔格沙漠地区野骆驼活动节律与家域特征

野生双峰驼(Camelus ferus)生存于中亚沙漠腹地, 是国家I级重点保护野生动物。为探究野骆驼活动节律和家域状况, 了解其时间和空间尺度上的活动模式, 为其有效保护管理提供支持。本研究于2012年5月至2013年7月利用GPS跟踪项圈先后对库木塔格沙漠地区7峰野骆驼进行轨迹跟踪。利用跟踪数据对野骆驼活动节律进行分析, 并采用布朗桥模型对野骆驼家域进行分析。结果表明: (1)野骆驼日活动节律呈现明显双峰模式, 属晨昏活动类型, 活动高峰期主要出现于上午6:00-9:00及下午15:00-20:00。(2)野骆驼晨昏活动高峰存在明显的季节性变动, 双峰从暖季到冷季向中午移动, 按间隔时间长短排序为: 夏季 > 春季 > 秋季 > 冬季。(3)野骆驼日活动强度有明显的季节性差异, 大小关系为: 夏季 > 秋季 > 春季和冬季, 春季和冬季间差异不显著。(4)野骆驼为核心家域利用类型, 且存在多个核心家域, 一些野骆驼家域分布于沙漠南北两侧, 意味着其具有横跨沙漠的运动能力。(5)野骆驼个体间家域面积差异显著, 性别间家域面积差异不显著。季节间家域面积差异显著, 从大到小排序为: 夏季(1,256.27 ± 427.45 km²) > 春季(556.90 ± 259.35 km²) > 秋季(396.77 ± 82.31 km²) > 冬季(250.83 ± 99.64 km²)。     

高效价甘薯羽状斑驳病毒抗血清的制备

用嫁接方法将甘薯羽状斑驳病毒（ＳＰＦＭＶ）接种到Ｉ．ｓｅｔｏｓａ上扩繁,以０．２ｍｏｌ／ＬｐＨ７．２ＰＢＫ缓冲液、垫层差速离心、蔗糖密度梯度离心提取纯化ＳＰＦＭＶ。纯化的ＳＰＦＭＶＯＤ２６０／２８０的比值为１．２５。将纯化的ＳＰＦＭＶ免疫家兔制备抗血清,在环状沉淀和微量沉淀试验中,用提纯病毒测定抗血清的效价均为１：４０９６;以ＳＰＦＭＶ－ＩｇＧ为第一抗体,应用Ｄｏｔ－ＥＬＩＳＡ对甘薯和Ｉ．ｓｅｌｏｓａ叶片中的ＳＰＦＭＶ分别作了测定。     

Scenario-Based Multi-Objective Optimum Allocation Model for Earthquake Emergency Shelters Using a Modified Particle Swarm Optimization Algorithm: A Case Study in Chaoyang District,Beijing, China

The correct location of earthquake emergency shelters and their allocation to residents can effectively reduce the number of casualties by providing safe havens and efficient evacuation routes during the chaotic period of the unfolding disaster. However, diverse and strict constraints and the discrete feasible domain of the required models make the problem of shelter location and allocation more difficult. A number of models have been developed to solve this problem, but there are still large differences between the models and the actual situation because the characteristics of the evacuees and the construction costs of the shelters have been excessively simplified. We report here the development of a multi-objective model for the allocation of residents to earthquake shelters by considering these factors using the Chaoyang district, Beijing, China as a case study. The two objectives of this model were to minimize the total weighted evacuation time from residential areas to a specified shelter and to minimize the total area of all the shelters. The two constraints were the shelter capacity and the service radius. Three scenarios were considered to estimate the number of people who would need to be evacuated. The particle swarm optimization algorithm was first modified by applying the von Neumann structure in former loops and global structure in later loops, and then used to solve this problem. The results show that increasing the shelter area can result in a large decrease in the total weighted evacuation time from scheme 1 to scheme 9 in scenario A, from scheme 1 to scheme 9 in scenario B, from scheme 1 to scheme 19 in scenario C. If the funding were not a limitation, then the final schemes of each scenario are the best solutions, otherwise the earlier schemes are more reasonable. The modified model proved to be useful for the optimization of shelter allocation, and the result can be used as a scientific reference for planning shelters in the Chaoyang district, Beijing.     

TNF receptor-associated factor 5 gene confers genetic predisposition to acute anterior uveitis and pediatric uveitis

Introduction

TNF Receptor-Associated Factor 5 (TRAF5) has been shown to be associated with autoimmune disease. The current study sought to investigate the potential association of TRAF5 with acute anterior uveitis (AAU) and pediatric uveitis in Han Chinese.

Methods

Three TRAF5 SNPs were analyzed in 450 AAU patients with or without ankylosing spondylitis (AS), 458 pediatric uveitis patients, and 1,601 healthy controls by using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) or TaqMan SNP Genotyping Assay. Numerous variables were evaluated, including age, sex distribution, and clinical and laboratory observations.

Results

Two SNPs (rs6540679, rs12569232) of TRAF5 were associated with pediatric uveitis, and rs12569232 also showed a relation with the presence of microvascular leakage. No significant associations were found when patients were subdivided according to their rheumatoid factor (RF) or anti-nuclear antibody (ANA) status or whether they had juvenile idiopathic arthritis (JIA). Rs12569232 predisposed to AAU and its subgroups (with ankylosing spondylitis (AS) or HLA-B27 positive). No association was found between rs10863888 and either pediatric uveitis or AAU.

Conclusion

This study revealed that TRAF5 is involved in the development of AAU and pediatric uveitis. Further stratified analysis according to the clinical and laboratory observations suggested that rs12569232/TRAF5 may play a role in the development of retinal vasculitis.