Identification of core genes and outcomes in hepatocellular carcinoma by bioinformatics analysis

Hepatocellular carcinoma (HCC) is the most common malignant liver disease in the world. However, the mechanistic relationships among various genes and signaling pathways are still largely unclear. In this study, we aimed to elucidate potential core candidate genes and pathways in HCC. The expression profiles GSE14520, GSE25097, GSE29721, and GSE62232, which cover 606 tumor and 550 nontumour samples, were downloaded from the Gene Expression Omnibus (GEO) database. Furthermore, HCC RNA-seq datasets were also downloaded from the Cancer Genome Atlas (TCGA) database. The differentially expressed genes (DEGs) were filtered using R software, and we performed gene ontology (GO) and Kyoto Encyclopedia of Gene and Genome (KEGG) pathway analysis using the online databases DAVID 6.8 and KOBAS 3.0. Furthermore, the protein-protein interaction (PPI) network complex of these DEGs was constructed by Cytoscape software, the molecular complex detection (MCODE) plug-in and the online database STRING. First, a total of 173 DEGs (41 upregulated and 132 downregulated) were identified that were aberrantly expressed in both the GEO and TCGA datasets. Second, GO analysis revealed that most of the DEGs were significantly enriched in extracellular exosomes, cytosol, extracellular region, and extracellular space. Signaling pathway analysis indicated that the DEGs had common pathways in metabolism-related pathways, cell cycle, and biological oxidations. Third, 146 nodes were identified from the DEG PPI network complex, and two important modules with a high degree were detected using the MCODE plug-in. In addition, 10 core genes were identified, TOP2A, NDC80, FOXM1, HMMR, KNTC1, PTTG1, FEN1, RFC4, SMC4, and PRC1. Finally, Kaplan-Meier analysis of overall survival and correlation analysis were applied to these genes. The abovementioned findings indicate that the identified core genes and pathways in this bioinformatics analysis could significantly enrich our understanding of the development and recurrence of HCC; furthermore, these candidate genes and pathways could be therapeutic targets for HCC treatment.     

蜜蜂表皮蛋白apidermin (apd)基因家族3个新成员的特性鉴定及昆虫APD家族序列特征的分析

Apidermin (APD)蛋白家族是一个新的昆虫结构性表皮蛋白家族。本研究结合生物信息学和RT-PCR扩增, 对意大利蜜蜂Apis mellifera ligustica（简称“意蜂”）的apd-1-like, apd-3-like和中华蜜蜂Apis cerena cerena（简称“中蜂”）的apd-2 等3个新的apd基因的结构特征和表达进行了分析, 并分析了昆虫APD蛋白家族的序列特征。结果显示, 在西方蜜蜂Apis mellifera（简称“西蜂”）中, apd基因家族的6个成员串联排列在基因组序列第4号连锁群上, 它们在A. m. ligustica雄蜂头部中的转录水平差异明显, 且其启动子序列所含顺式元件也不同。中蜂apd-2和意蜂apd-1-like都含有3个外显子和2个内含子, 而意蜂apd-3-like则由4个外显子和3个内含子组成。蛋白序列分析结果显示, 目前已知的10条APD蛋白序列N末端均具有相似的信号肽序列, 其成熟蛋白分子量为6.0~37.0 kD, pI为6.2~10.8。其中西蜂的APD1-3、APD-like和东方蜜蜂Apis cerena的APD-2等5条较短的多肽中疏水氨基酸残基达52%~67%, 且Ala含量最为丰富（占25%~34%）; 而丽蝇蛹集金小蜂Nasonia vitripennis的APD 1-3和西蜂APD-1-like, APD-3-like等另外5条APD多肽富含Gly（21%~30%）, 其序列中疏水氨基酸残基含量为35%~41%。多肽序列多重比对和系统进化分析结果显示, APD家族可划分为2个亚家族。亚家族Ⅰ含有西蜂APD 1-3和东方蜜蜂APD-2等4条较短的多肽序列, 其N末端为一个长33 aa的保守基序; 亚家族Ⅱ由另外6条相对较长的多肽序列组成, 其N末端保守基序长50 aa, C末端保守基序长16 aa。本文所描述的APD蛋白家族序列特征有助于以后从其他昆虫中鉴定新的apd基因。     

广藿香八氢番茄红素合成酶PcPSY1基因克隆和序列分析

根据已获得的广藿香转录组数据中的PSY转录本序列,利用Primer 3在线设计基因全长扩增引物,采用RT-PCR方法获得广藿香的八氢番茄红素合成酶(phytoene synthase,PSY)基因。并利用在线分析平台和生物软件对该其因进行生物信息学分析。获得的广藿香PSY1基因长1 550 bp,编码439个氨基酸,命名为PcPSY1,GenBank登录号为KC862310; 预测了PcPSY1 编码蛋白的结构与功能,且基于PSY基因利用NJ法构建了与21个不同物种间的进化树,进化树表明广藿香PcPSY1基因与桂花的PSY序列亲缘关系最近。成功克隆并分析广藿香PcPSY1基因的全长序列,为进一步阐明广藿香萜类代谢途径奠定基础。     

家蝇新型抗菌肽Muscin的基因克隆、表达模式及抑菌活性

【目的】鉴定家蝇 Musca domestica (Linnaeus)中一种新型抗菌肽(Muscin)基因,并分析其功能。【方法】通过数字基因表达谱和生物信息学分析,在家蝇转录组中筛选得到一条抗菌肽基因,命名为 muscin。以实时荧光定量PCR技术研究该基因的组织分布以及用大肠杆菌Escherichia coli和金黄色葡萄球菌Staphylococcus aureus混合细菌刺激后的表达量变化。并对合成肽Muscin进行抑菌活性检测及溶血率测定。【结果】muscin基因cDNA序列全长379 bp,包含完整的开放阅读框153 bp。推导Muscin多肽序列由50个氨基酸残基组成,N端含有由25个氨基酸残基组成的信号肽。成熟肽中富含疏水性氨基酸残基和带正电荷的氨基酸残基,理论等电点为9.39。基因定量结果显示 muscin 基因在血细胞和脂肪体中表达量最高。通过细菌刺激进行免疫诱导后,幼虫体内该基因的表达水平明显上调,并在6 h达到高峰。抑菌和溶血实验显示c-Muscin对革兰氏阳性菌和革兰氏阴性菌具有广谱抑菌活性,且溶血活性较低。【结论】Muscin是一种新型的广谱抗菌肽,可能参与家蝇抗菌免疫反应,且具有一定药物开发潜质。     

亚洲玉米螟幼虫酚氧化酶原基因序列的生物信息学分析

酚氧化酶原PPO是昆虫免疫的关键酶, 本文从生物信息学角度对亚洲玉米螟Ostrinia furnacalis Guenée幼虫PPO进行分析, 为进一步研究其高级结构与功能的关系提供理论依据。利用我们已提交到GenBank的数据, 采用在线分析及MEGA4和RasMol软件对亚洲玉米螟酚氧化酶原（Of-PPO）的核苷酸和氨基酸序列、系统发生关系和蛋白质三级结构进行分析。结果表明: Of-PPO全长cDNA序列有2 686 bp, 包含一个2 079 bp的开放阅读框, 其推导的693个氨基酸序列中包含6个组氨酸残基构成的2个铜离子结合位点, 以及保守的硫羟酸酯区域。Of-PPO属于PPO2类群, 其N端不含信号肽, 无跨膜结构域区域, 无糖基化位点, 44个磷酸化位点均匀分布于整个多肽链中, 有2段序列可能形成卷曲螺旋, 有5个区域的氨基酸具较强疏水性, 其二级结构中α-螺旋占22.54%, 随机卷曲占56.79%。同源建模显示其三级结构为“α/β型”中的“滚筒结构”, 存在一个明显的空位, 可能与该酶催化活性有关。本文可为Of-PPO的实验研究和应用开发提供有价值的信息。     

家蚕精巢蛋白质的双向电泳及质谱分析

精巢是雄性家蚕Bombyx mori的生殖腺,它的主要功能是产生精子,全面检测和鉴定精巢器官的蛋白分布将为分析家蚕雄性个体的发育和繁殖奠定基础。本研究利用双向聚丙烯酰胺凝胶电泳和蛋白硝酸银染色技术对家蚕5龄第5天幼虫的精巢组织进行了蛋白检测,利用基质辅助激光解析质量飞行时间质谱（MALDI-TOF-MS）对表达量较高的蛋白点进行了肽质量指纹图谱鉴定。结果表明：家蚕精巢蛋白质可以检测出1 000个以上的蛋白点,这些蛋白点主要集中在分子量为15～90 kD区域,等电点3.5～9之间,其中60个蛋白点得到了成功鉴定,按照已知或推测的蛋白功能,将其分为8类,包括：细胞骨架和细胞结构蛋白,膜蛋白或信号相关蛋白,大量应激反应蛋白（伴侣蛋白）,线粒体和能量产生相关蛋白,转录调控和翻译及DNA/RNA结合相关蛋白,酶和少量血液组成蛋白。其中很多蛋白可能在鞭毛形成、能量代谢及减数分裂过程中有重要作用。这些结果为进一步认识家蚕精子形成过程提供了重要的生物学信息。     

Optimization of 3D Poisson–Nernst‐Planck model for fast evaluation of diverse protein channels

We show the accuracy and applicability of our fast algorithmic implementation of a three‐dimensional Poisson–Nernst–Planck (3D‐PNP) flow model for characterizing different protein channels. Due to its high computational efficiency, our model can predict the full current‐voltage characteristics of a channel within minutes, based on the experimental 3D structure of the channel or its computational model structure. Compared with other methods, such as Brownian dynamics, which currently needs a few weeks of the computational time, or even much more demanding molecular dynamics modeling, 3D‐PNP is the only available method for a function‐based evaluation of very numerous tentative structural channel models. Flow model tests of our algorithm and its optimal parametrization are provided for five native channels whose experimental structures are available in the protein data bank (PDB) in an open conductive state, and whose experimental current‐voltage characteristics have been published. The channels represent very different geometric and structural properties, which makes it the widest test to date of the accuracy of 3D‐PNP on real channels. We test whether the channel conductance, rectification, and charge selectivity obtained from the flow model, could be sufficiently sensitive to single‐point mutations, related to unsignificant changes in the channel structure. Our results show that the classical 3D‐PNP model, under proper parametrization, is able to achieve a qualitative agreement with experimental data for a majority of the tested characteristics and channels, including channels with narrow and irregular conductivity pores. We propose that although the standard PNP model cannot provide insight into complex physical phenomena due to its intrinsic limitations, its semiquantitative agreement is achievable for rectification and selectivity at a level sufficient for the bioinformatical purpose of selecting the best structural models with a great advantage of a very short computational time. Proteins 2013; 81:1802–1822. © 2013 Wiley Periodicals, Inc.     

东亚飞蝗fem-1基因的克隆与表达分析

秀丽隐杆线虫Caenorhabditis elegans fem-1基因是性别决定的关键基因。本研究基于生物信息学方法从东亚飞蝗Locusta migratoria manilensis的转录组数据库中克隆出了线虫fem-1的3个同源基因, 将其分别命名为Lmfem-1a, Lmfem-1b和Lmfem-1c (GenBank登录号分别为AB698670, AB698671和AB698672)。其cDNA序列长度分别为2 233, 2 625和2 142 bp, 分别编码662, 642和638个氨基酸。生物信息学分析显示, Lmfem-1a, Lmfem-1b和Lmfem-1c分别含有6, 8和8个典型的锚蛋白重复序列模体。组织表达谱分析发现, Lmfem-1a, Lmfem-1b和Lmfem-1c基因在检测的所有组织中都有表达, 但均在精巢中的表达水平最高, 说明Lmfem-1a, Lmfem-1b和Lmfem-1c基因可能参与东亚飞蝗的多种生理过程, 并受到严格的表达调控。而且, 随着精巢的发育, Lmfem-1a, Lmfem-1b和Lmfem-1c的表达均逐渐增强, 可能与东亚飞蝗的精子形成有关, 但这3个基因是否参与东亚飞蝗的性别决定还有待进一步研究。     

我国生物信息产业的现状及问题分析

针对我国生物信息产业的现状及存在的问题进行分析,介绍了生物信息学以及生物芯片研究的现状和新技术、生物信息产业的发展,并对生物信息产业的知识产权保护问题进行了分析和讨论。对于今后如何发展我国生物信息产业以及如何采取策略和措施提供参考。