Analysis of synonymous codon usage in H5N1 virus and other influenza A viruses

In this study, we calculated the codon usage bias in H5N1 virus and performed a comparative analysis of synonymous codon usage patterns in H5N1 virus, five other evolutionary related influenza A viruses and a influenza B virus. Codon usage bias in H5N1 genome is a little slight, which is mainly determined by the base compositions on the third codon position. By comparing synonymous codon usage patterns in different viruses, we observed that the codon usage pattern of H5N1 virus is similar with other influenza A viruses, but not influenza B virus, and the synonymous codon usage in influenza A virus genes is phylogenetically conservative, but not strain-specific. Synonymous codon usage in genes encoded by different influenza A viruses is genus conservative. Compositional constraints could explain most of the variation of synonymous codon usage among these virus genes, while gene function is also correlated to synonymous codon usages to a certain extent. However, translational selection and gene length have no effect on the variations of synonymous codon usage in these virus genes.     

怒江河谷入侵植物与乡土植物丰富度的分布格局与影响因子

外来物种入侵严重威胁着乡土植物多样性并削弱了生态系统服务功能。本文基于滇西北怒江河谷植被调查的样方数据, 从群落水平研究了乡土和入侵植物多样性的空间分布格局, 以及地形、气候、人类干扰等因子对两种格局的影响。本研究共记录到外来入侵植物26种, 隶属于13科21属; 乡土植物1,145种, 分属于158科628属。沿着怒江河谷, 入侵植物物种丰富度随纬度与海拔的增加而减少; 乡土物种丰富度则随纬度增加而增加, 并在海拔梯度上呈单峰格局。运用广义线性模型分析公路边缘效应(反映生境干扰)、气候、地形和土壤等环境因素对物种丰富度分布格局的影响。等级方差分离的结果显示, 公路两侧的生境干扰对入侵种和乡土种的丰富度格局均具有首要影响。在自然环境因子中, 降水量是入侵植物丰富度的主要限制因子, 而乡土物种丰富度则主要受到地形因子尤其是坡向的影响。结构方程模型的分析结果也表明, 乡土植物和入侵植物丰富度之间的负相关关系反映了二者对环境响应的差异。本文结果支持物种入侵的资源可利用性限制假说, 并强调了人类活动对生物多样性的负面影响; 乡土植物或已较好地适应了干旱河谷气候, 但并没有显示出对外来物种入侵的抵抗作用。     

DNA存储中的编码技术

脱氧核糖核酸(Deoxyribonucleic Acid, DNA)是一种天然的信息存储介质,具有存储密度高、存储时间长、损耗率低等特点。在传统存储方式不能满足信息增长的需求时,DNA数据存储技术逐渐成为研究热点。DNA编码是用尽可能少的碱基序列无错的存储数据信息,包括压缩(尽可能少的占用空间)、纠错(无错存储)和转换(数字信息转为碱基序列)3部分。DNA编码是DNA存储中的关键技术,它的结果直接影响存储性能的优劣和数据读写的完整。本文首先介绍DNA存储的发展历史,然后介绍DNA存储的框架,其中重点介绍DNA编码技术,最后对DNA存储中的编解码技术的未来发展方向进行讨论。     

环状RNA计算预测方法的研究进展

环状RNA(circular RNA,circRNA)是一类具有重要生物作用的内源性RNA,大多在可变剪接过程中通过5'端和3'端反向共价连接形成闭合环状结构.目前,环状RNA的识别策略主要分为两大类:一类方法从高通量测序(RNA-seq)数据中检测反向剪接位点,另一类直接从RNA序列中检测成环特征.由于数据本身和识别...     

Functional Mechanism of Antimicrobial Peptide Bomidin and Its Safety for Macrobrachium rosenbergii

Macrobrachium rosenbergii is an economically important source of crustacean seafood worldwide. Vibrio parahaemolyticus is an important aquatic pathogen that causes epidemics of acute hepatopancreatic necrosis in shrimp populations, which results in significant economic losses to aquaculture farmers. To prevent the antibiotics abuse, which has become a serious threat to human health, novel anti-infective strategies are urgently required to control V. parahaemolyticus. Antimicrobial peptides, which exhibit favourable germicidal activity compared to traditional antibiotics, can be used as a key method to prevent and treat bacterial diseases. Herein, an antimicrobial peptide, bomidin, was expressed through genetic engineering technology. The minimum inhibitory concentration (MIC) of bomidin showed a significant inhibitory effect on V. parahaemolyticus that was equivalent to that of ampicillin. Subsequently, the mechanism of action of recombinant bomidin was explored using PNP and ONPG assays to investigate the effects on membrane permeability. These assays indicated that bomidin penetrated the germ membrane and induced the release of cytoplasmic contents and ultimately interacted with DNA to form a bomidin–DNA complex that inhibits bacterial survival. Transmission electron microscopy and scanning electron microscopy revealed that bomidin could cause damage and dysfunction to the cell wall and membrane. Bomidin was nontoxic to mouse red blood cells within a concentration range that was much larger than the MIC. Toxicity assays revealed that 0.02 mg/mL bomidin was safe for use with juvenile freshwater prawns of M. rosenbergii and significantly inhibited the growth of V. parahaemolyticus in cultured water. These results demonstrated that synthetic peptide bomidin had great antibacterial effect against V. parahaemolyticus and therefore a therapeutic potential in aquaculture.

     

脑脊液蛋白质组技术及临床应用研究进展

脑脊液(CSF)围绕并支持中枢神经系统(CNS),包括脑室和蛛网膜下腔,由于脑脊液与中枢神经系统直接接触,所以其是寻找中枢神经系统疾病生物标记物的重要来源。国内外学者开展了大量CSF蛋白质组学的研究工作,并取得了较大进展。文中综述了近年来CSF蛋白质组学技术及临床应用研究进展。     

甘蓝型油菜线粒体功能未知基因 ORF 117的载体构建与转化

本研究克隆了甘蓝型油菜线粒体功能未知基因 ORF 117,构建了带有线粒体转运信号肽序列（TP ）的植物过表达载体35S ∷TP-ORF117、35S ∷TP-EGFP 和35S ∷TP-ORF117-EGFP ,转化野生型拟南芥并进行抗除草剂筛选,共获得纯合的转基因拟南芥株系62个。qPCR 表明,ORF 117在转基因材料中得到高效过表达。用转35S ∷TP-EGFP 、35S ∷TP-ORF117-EGFP 拟南芥制备原生质体,经线粒体特异染料染色,在激光共聚焦显微镜下做线粒体、GFP 共定位检测,GFP 蛋白和 ORF117-EGFP 融合蛋白被准确定位到了线粒体。     

Complete Genome Sequence of Duck Tembusu Virus,Isolated from Muscovy Ducks in Southern China

We report here the complete genomic sequence of the duck Tembusu virus (DTMUV) WJ-1 strain, isolated from Muscovy ducks. This is the first complete genome sequence of DTMUV reported in southern China. Compared with the other strains (TA, GH-2, YY5, and ZJ-407) that were previously found in eastern China, WJ-1 bears a few differences in the nucleotide and amino acid sequences. We found that there are 47 mutations of amino acids encoded by the whole open reading frame (ORF) among these five strains. The whole-genome sequence of DTMUV will help in understanding the epidemiology and molecular characteristics of duck Tembusu virus in southern China.     

陕西榆林发现巨嘴沙雀

<正>笔者于2010年2月22日在陕西省榆林地区调查陕北冬季鸟类时,在榆林市农业生态示范园(N38°15′06.9″,E109°44′39.0″,海拔1072m)发现10余只集小群活动的巨嘴沙雀(Rhodopechys obsoleta)并拍到照片(图1)。此处     

台湾维管束植物物种丰富度和种域宽度的海拔格局及对Rapoport法则的检验

物种丰富度和种域(即物种分布范围)沿环境梯度的变化是生物地理学和生物多样性研究的核心问题.岛屿由于受到地理隔离的作用.其物种分布、多样性格局及其成因的特殊性对于发展和检验生物地理学的假说具有重要意义.Rapoport法则提出,生物种域存在着随海拔上升而增大的趋势.台湾地区具有显著的海拔梯度和典型的岛屿环境,其植物区系丰富而独特.我们首次对台湾维管束植物的海拔分布进行研究,包括不同类群植物的物种丰富度和种域的海拔梯度格局,并检验了Rapoport法则的适用性.综合相关信息得到台湾维管束植物区系包含241科1,466属4,751种(含种下单位),对其中具有海拔分布范围信息的3,330种植物进行统计,结果表明:(1)台湾维管束植物科、属、种的丰富度总体上随海拔上升而减小,入侵植物丰富度具有类似格局,而台湾特有植物呈现明显的单峰格局;按照分类群计,蕨类植物和裸子植物为单峰格局,被子植物的3个生态类群均为单调递减格局.(2)物种种域海拔宽度与海拔的关系随不同类群和分析方法而异.其中,入侵植物的种域宽度和中点海拔具有显著的正相关关系,支持Rapoport法则,而全部植物和特有植物不支持;蕨类植物的海拔分布支持Rapopott法则,裸子植物不支持,其他分类群因方法不同而结果之间不一致.我们还比较了台湾和周边大陆和岛屿山地的物种丰富度海拔格局,认为它们物种丰富度海拔梯度模式的不同可能与降水海拔格局的差异有关;而关于Rapoport法则的检验表明,即使在同一山体,不同类群植物分布范围的海拔模式也可能取决于不同的因素和作用机制.