一种基于氨基酸物理化学性质上的DNA序列图形表示及相似性分析

基于氨基酸的物理化学性质,将氨基酸分为4类,疏水,带电荷,有极性,甘氨酸,在此基础上给出DNA序列一种新的图形表示方法:将1列DNA序列表示为二维空间中的3条特征曲线,利用计算C(i,j)矩阵的主特征值,给出DNA序列的3维特征向量,得到相似距离矩阵.最后计算10种不同物种β-球蛋白第一段外显子的欧式空间距离矩阵D(i,j),并利用UPGMA算法给出了这10种不同物种基于这种相似关系的系统发生树.     

Phaeocystis globosa与Phaeocystis antarctica叶绿体psbA基因的比较

测定了2株球形棕囊藻Phaeocystis globosa P1、P2的psbA基因序列。发现得到的2个序列完全相同。以P2序列对比分析了P．globosa和P．antarctica的psbA基因在DNA序列、氮基酸序列和RNA二级结构上的差异性，发现2种棕囊藻psbA基因DNA序列和氨基酸序列非常保守，无插入／缺失，其核苷酸和氨基酸变异率分别为1．88％和1．13％。与核基因核苷酸的碱基替换不同，psbA基因核苷酸的碱基替换主要发生在密码子的第1位上。且不引起氨基酸的变化，引起氨基酸变化的碱基替换都发生在密码子的第2位和第3位上。在RNA二级结构上两序列的1～4茎环结构完全相同，表现出明显的棕囊藻属的特异性，其它结构区域差异较大。种间差异表现明显。由于psbA基因DNA序列和氨基酸序列非常保守，可能不适宜棕囊藻属的系统发育分析。但其RNA二级结构可能对于棕囊藻的分子分类有一定的参考价值。     

基于DNA序列四维图形表示的相似性分析

最近提出的DNA四维图形表示是以4种碱基A,T,G,C的3种分类为基础的,这种表示方法给出了DNA序列的几何中心.在几何中心的基础上,通过把不同遗传密码序列划分成具有相同长度的片断,构建1种新的相似性分析方法.对表1所列的11种不同物种的第一类β球蛋白基因序列构建的相似性分析表,阐述这种方法的应用.     

栉孔扇贝Fosmid文库的构建及基因组结构特征分析

研究构建第一个栉孔扇贝的fosmid基因组文库,该文库包含133 851个克隆,插入片断平均长度为40 kb,覆盖栉孔扇贝基因组的4.3倍.栉孔扇贝DNA在fosmid传代中表现得较为稳定,没有发现插入片段的丢失或重排.所有的克隆进行了超级池和二级池的构建,并筛选了2个基因和7个微卫星,结果阳性克隆数介于2到8之间.由此可见,该文库可以很好的用于目的基因或标记的筛选,将有利于物理作图和基因的图位克隆研究.2 016个克隆进行双末端测序,获得3 646 条序列.序列总长2 286 986 bp,大约占栉孔扇贝基因组的1.84‰.共得到2 500条串连重复序列,其中微卫星序列371条,小卫星序列1 816条,卫星序列313条.共得到317条散布重复序列,总长97 412 bp,占测序总长的4.26%.查找到的散布重复序列共有4种类型:DNA 转座子、LTR 反转座子、LINE反转座子和滚环转座子,其中LINE反转座子的数目最多.BLAST比对共有1 383条序列与数据库现有的序列有明显的相似性(E＜e-5),占测序总数的37.93%.BLASTN比对有明显相似性的1 036条序列中,与nr数据库序列相似的有113条,与EST数据库序列相似的有923条.BLASTX比对有明显相似性的序列有347条,占序列总数的9.52%.     

三疣梭子蟹线粒体DNA 16S rRNA和COI基因片段序列的比较研究

本文采用 PCR扩增和序列测定等技术 ,对三疣梭子蟹 (Portunustrituberculatus)线粒体DNA1 6Sr RNA和 COI基因片段进行了初步研究。经 PCR扩增和序列测定 ,分别得到 1 6Sr RNA和 COI2个基因片段的碱基序列 ,其中 1 6Sr RNA基因片段的大小为 566bp,碱基 A,T,G,C的含量分别为 35.1 6% ,34.45% ,1 2 .37%和 1 8.0 2 % ;COI基因片段的大小为 658bp,碱基 A,T,G,C的含量分别为 36.63% ,2 6.44% ,2 0 .52 %和 1 6.41 %。在 2种基因片段中 ,AT含量均明显高于 GC含量 ,这与果蝇、虾类、蟹类等无脊椎动物的 1 6Sr RNA和 COI基因片段研究结果相似。通过对三疣梭子蟹 1 6S r RNA和 COI2个基因片段遗传特征的研究 ,发现其种内变异较低 ,在 3个样本中 1 6Sr RNA基因片段序列完全一样 ,COI基因片段中也只有 2个 T/ C位点转换。另外 ,比较本研究所得序列与 Gen Bank中梭子蟹科 5个属的 1 6Sr RNA基因片段序列后 ,发现其聚类结果与传统分类相一致。     

碱蓬PEPCase基因的克隆与分析

采用cDNA末端快速扩增(RACE)技术首次获得碱蓬(Suaeda glauca)中含PEPCase基因完整编码区的cDNA序列,长度为3 038 bp.获得的序列采用生物信息学方法和系统进化方法进行分析.结果表明,获得的cDNA序列包含2 898 bp的完整开放阅读框,编码的966个氨基酸序列含有两个PEPCase活性位点以及6种其他的活性位点;预测蛋白质的相对分子质量为109 785.3,等电点为5.51,属于不稳定的亲水性蛋白;含量相对较多的氨基酸是Leu、Glu、Arg、Asp、Ser,不含Pyl和Sec;不包含跨膜结构和信号肽序列,推断为非分泌性蛋白;二级结构以α螺旋为主,三级结构为紧密球状结构;分析结果还表明获得的碱蓬PEPCase基因应该属于C3型.通过对碱蓬PEPCase基因的克隆及序列分析从而为后期碱蓬PEPCase蛋白表达的研究及获得高油量的转基因碱蓬植株奠定了基础.     

日本(虫寻)和底栖短桨蟹线粒体DNA 12SrRNA基因序列的初步研究

以相应引物对日本和底栖短桨蟹的线粒体 DNA1 2 S r RNA基因片段进行了 PCR扩增和序列测定 ,分析比较了 2种间序列差异。结果表明 :日本 1 2 S r RNA基因片段长度为 41 4 bp,底栖短桨蟹为 41 5bp,2种的 A,T,G,C含量分别为 1 51 bp(36.47% ) ,1 53bp(36.96% ) ,43bp(1 0 .39% ) ,67bp(1 6.1 8% )和 1 50 bp(36.1 4 % ) ,1 55bp(37.35% ) ,44bp(1 0 .60 % ) ,66bp(1 5.90 % )。 2种间共出现了 3个碱基的缺失 /插入和 38bp的序列差异 ,其碱基转换与碱基颠换比约为 2 .1 7。     

3种鲍16S rRNA基因片段序列的初步研究

本文对引自日本的盘鲍 (H aliotisdiscusdiscus)、皱纹盘鲍 (H.discushannai)和大鲍 (H.gi-gantiea) 3个自然群体的线粒体 DNA 1 6S r RNA基因片段进行了扩增和测序 ,分析了 52 8bp的碱基序列 ,结果显示 :3种鲍的基因序列中 A+T含量为 56.74%～ 57.1 2 %。 3个自然群体间碱基片段序列差异不显著 ,盘鲍与皱纹盘鲍、大鲍彼此均仅有 1处核苷酸检测到变异 ,皆为碱基转换 ,同源性为99.81 % ;皱纹盘鲍与大鲍有 2处碱基转换 ,同源性为 99.61 %。 1 6Sr RNA基因在鲍属内表现出很高的保守性。     

用16S rDNA序列初步探讨部分真虾类的系统发育关系

利用DNA序列测定技术测定了真虾下目7科8个种的线粒体16S rDNA部分序列,与从GenBank检索得到的12个相关种的16S rDNA部分序列进行同源性比对,探讨其系统发育关系及16S rDNA在真虾类系统发育研究中的应用。比对序列长353bp,其中变异位点221个、简约信息位点180个。碱基转换替代速度比颊换替代速度慢。以螯虾下目的Austropotamobius pallipes为外群构建了这20种真虾的系统发育关系分支图,结果展示：（1）长臂虾科隐虾亚科的Awhistus custos远离长臂虾亚科分支。而且它的16S rDNA序列在Genbank中,首先与六足纲（Hexapoda）的昆虫比对上。（2）长臂虾科长臂虾亚科的两个近缘属Palaemon和Palaemonetes问的4个种混合相聚,说明传统形态分类中以大颚有无触须作为这两个属的属级形态鉴定特征尚需进一步审定。（3）鼓虾总科藻虾科的Exhippolysmata ensirostris与褐虾总科褐虾科的Crangon affinis处在同一分支,而没与鼓虾科的种类形成姐妹群。研究结果表明,16S rDNA片段的序列很适合研究真虾类的属间系统发育关系,而在研究属上高级阶元或种下阶元间的系统发生关系时较不敏感,因其变异对于种级水平显得过于保守,而对于科级以上阶元又显得太快。     

低温胁迫下红榄李(Lumnitzera littorea)DEAD-box RNA解旋酶基因的表达分析

转录组分析发现DEAD-box RNA解旋酶家族参与红榄李(Lumnitzera littorea)对低温胁迫的响应。本文对4个低温显著差异表达基因LlDEAD12,LlDEAD32,LlDEAD43和LlDEAD65的生物信息学特性、组织特异性以及在不同温度处理下的红榄李幼苗中的差异表达进行研究。结果表明,LlDEAD12、LlDEAD32、LlDEAD43和LlDEAD65均属于疏水性蛋白,二级结构均由α-螺旋、β-转角、延伸链和无规则卷曲组成,具有多个糖基化位点和磷酸化位点,且不含有跨膜结构域和信号肽。亚细胞定位分析表明,LlDEAD12和LlDEAD32分别定位于细胞质和细胞核,而LlDEAD43和LlDEAD65则定位于线粒体上。通过蛋白质氨基酸序列的比对分析发现LlDEAD12、LlDEAD32和LlDEAD43分别与马尾松(Pinus massoniana)、巨桉(Eucalyptus grandis)和石榴(Punica granatum)的DEAD-box RNA解旋酶有较近的亲缘关系。荧光定量PCR技术分析发现,LlDEAD12和LlDEAD32在叶中高表达,LlD...     

The phase difference effects on 3-D structure of wave pressure acting on a composite breakwater

In designing the coastal structures, the accurate estimation of the wave forces on them is of great importance. In this paper, the influences of the phase difference on wave pressure acting on a composite breakwater installed in the three-dimensional (3-D) wave field are studied numerically. We extend the earlier model [Hur, D.S., Mizutani, N., 2003. Coastal Engineering 47, 329–345] to simulate 3-D wave fields by introducing 3-D Navier–Stokes solver with the Smagorinsky's sub-grid scale (SGS) model. For the validation of the model, the wave field around a 3-D asymmetrical structure installed on a submerged breakwater, in which the complex wave deformations generate, is simulated, and the numerical solutions are compared to the experimental data reported by Hur, Mizutani, Kim [2004. Coastal Engineering (51, 407–420)]. The model is then adopted to investigate 3-D characteristics of wave pressure and force on a caisson of composite breakwater, and the numerical solutions were discussed with respect to the phase difference between harbor and seaward sides induced by the transmitted wave through the rubble mound or the diffraction. The numerical results reveal that wave forces acting on the composite breakwater are significantly different at each cross-section under influence of wave diffraction that is important parameter on 3-D wave interaction with coastal structures.     

2-D and 3-D modelling of wide-angle seismic data: an example from the Vøring volcanic passive margin

This study presents the modelling of 2-D and 3-D wide-angle seismic data acquired on the complex, volcanic passive margin of the Vøring Plateau, off Norway. Three wide-angle seismic profiles were shot and recorded simultaneously by 21 Ocean Bottom Seismometers, yielding a comprehensive 3-D data set, in addition to the three in-line profiles. Coincident multi-channel seismic profiles are used to better constrain the modelling, but the Mesozoic and deeper structures are poorly imaged due to the presence of flood basalts and sills. Velocity modelling reveals an unexpectedly large 30 km basement high hidden below the flood basalt. When interpreted as a 2-D structure, this basement high produces a modelled gravity anomaly in disagreement with the observed gravity. However, both the gravity and the seismic data suggest that the structure varies in all three directions. The modelling of the entire 3-D set of travel times leads to a coherent velocity structure that confirms the basement high; it also shows that the abrupt transition to the slower Cretaceous basin coincides in position and orientation with the fault system forming the Rån Ridge. The positive gravity anomaly over the Rån Ridge originates from the focussed and coincident elevation of the high velocity lower crust and pre-Cretaceous basement. Although the Moho is not constrained by the seismic data, the gravity modelled from the 3-D velocity model shows a better fit along the profiles. This study illustrates the interest of a 3-D acquisition of wide-angle seismic over complex structures and the benefit of the subsequent integrated interpretation of the seismic and gravity data.     

基于Matlab的TEQC在GPS数据预处理中的应用

利用Matlab二次开发编制teqcplot程序模块,实现质量检查结果的图形显示和可视化查询,将GPS观测数据中存在的电离层延迟和多路径效应的影响定量地表示出来,提高了数据处理的工作效率。并用实测数据进行验算,根据检查结果对GPS观测数据进行相应的处理,通过对比分析结果表明,经TEQC预处理后的观测数据,有效地提高了GPS基线解算的质量。     

Comparison of hydroelastic computer codes based on the ISSC VLFS benchmark

There has been substantial development in computer codes for linear hydroelasticity in recent years, driven in part by the motivation to investigate the wave-induced response of very large floating structures (VLFSs). A recent International Ship and Offshore Structures Congress (ISSC) state-of-the-art report on VLFS design and analysis [ISSC, 2006. Report of Specialist Task Committee VI.2, very large floating structures. In: Frieze, P.A., Shenoi, R.A. (eds.), Proceedings of the 16th International Ship and Offshore Structures Congress, Elsevier, Southampton, UK, pp. 397-451] included a brief comparative study of the simulation results from different computer codes for a pontoon (mat-like) VLFS. The codes covered a mix of both fluid models (potential and linear Green-Naghdi) and structural models (3-D grillage, 2-D plate, 3-D shell). A more detailed comparison of the results from a select group of models from that study is provided and discussed herein. The similarities in the results increase the confidence level of the state-of-the-art in predicting the hydroelastic response of such structures, and the differences, including in computational efficiency, lead to an understanding of the significance of specific modeling assumptions and their impact on the predicted response.     

3-D non-breaking regular wave interaction with submerged breakwaters

Modelling of the transformation and interaction of regular wave trains with submerged permeable structures is carried out. The existing literature, is summarized relevant theories presented, and theoretical results are compared with existing laboratory data. Special attention is paid to wave reflection. The influence of wave characteristics including oblique incidence, structure geometry and porous material properties on the kinematics and dynamics over and inside the breakwater is considered. Two different models are presented: an eigenfunction expansion 3-D model and a 2-D model based on a mild-slope equation for porous media to account for breakwater slope.     

Structural stability of detached low crested breakwaters

The aim of the paper is to describe hydraulic stability of rock-armoured low-crested structures on the basis of new experimental tests and prototype observations.Rock armour stability results from earlier model tests under non-depth-limited long-crested head-on waves are reviewed.Results from new 2-D and 3-D model tests, carried out at Aalborg University, are presented. The tests were performed on detached low-crested breakwaters exposed to short-crested head-on and oblique waves, including depth-limited conditions. A formula that corresponds to initiation of hydraulic damage and allows determining armour stone size in shallow water conditions is given together with a rule of thumb for the required stone size in depth-limited design waves.Rock toe stability is discussed on the basis of prototype experience, hard bottom 2-D tests in depth-limited waves and an existing hydraulic stability formula. Toe damage predicted by the formula is in agreement with experimental results. In field sites, damage at the toe induced by scour or by sinking is observed and the volume of the berm is often insufficient to avoid regressive erosion of the armour layer.Stone sinking and settlement in selected sites, for which detailed information is available, are presented and discussed.     

Prototype measurements and small-scale model tests of wave overtopping at shallow rubble-mound breakwaters: the Ostia-Rome yacht harbour case

The paper presents the comparison between the results of small-scale model tests and prototype measurements of wave overtopping at a rubble-mound breakwater. The specific structure investigated is the west breakwater of the yacht harbour of Rome at Ostia (Italy) and is characterized by a gentle seaward slope (1/4) and by a long, shallow foreshore. The laboratory tests firstly aimed at carefully reproducing two measured storms in which overtopping occurred and was measured. The tests have been carried out in two independent laboratories, in a wave flume and in a wave basin, hence using a two-dimensional (2-D) and a three-dimensional (3-D) setup. In the 2-D laboratory tests no overtopping occurred during the storm reproductions; in the 3-D case discharges five to ten times smaller than those observed in prototype have been measured. This indicates the existence of model and scale effects. These effects have been discussed on the basis of the results of several parametric tests, which have been carried out in both laboratories, in addition to the storm reproductions, varying wave and water level characteristics. Final comparison of all the performed tests with 86 prototype measurements still suggests the existence of scale and model effects that induce strong underestimation of overtopping discharge at small scale. The scale reproduction of wave breaking on the foreshore, together with the 3-D features of the prototype conditions and the absence of wind stress in the laboratory measurements, have been individuated as the main sources of scale and model effects. The paper also provides a comparison between the data and a largely used formula for wave overtopping discharges in the presence of structures similar to the one at hand. The suitable value of a roughness factor that appears in that formula is investigated and good agreement is found with other recent researches on rubble-mound breakwaters.     

FPSO典型焊接接头残余应力释放数值预报

浮式生产储油卸油船(FPSO)经历满载和卸载,油船试验和多变的波浪载荷.此时结构中较高的初始残余应力常常已被释放,很大程度上影响了此类结构疲劳强度估算准确性.应用三维弹塑性有限元方法模拟FPSO典型焊接接头的残余应力释放,并用试验数据进行验证.对结构在变幅循环载荷下的残余应力释放进行研究,得到相关的残余应力释放预报公式.从而为提高FPSO在实际载况下疲劳强度估算准确性提供有价值参考.     

Mud volcanoes in the Mediterranean Sea are hot spots of exclusive meiobenthic species

Mud volcanoes are cold seeps, in which the escape of gas and fluids associated with mud creates 3-D bottom structures that enhance the spatial heterogeneity and potentially alter the functioning of the benthic ecosystems. We investigated a complex system of mud volcanoes of the Mediterranean Sea characterised by the presence of different structures (i.e., isolated domes, domes surrounded by moats, clustered domes, and ridges) displaying different levels of seepage. We hypothesize that the combined effects of seafloor heterogeneity (i.e., different 3-D structures as revealed by detailed topographic analysis), fluid emissions and trophic characteristics of these systems can influence the structural and functional biodiversity of meiofauna (with special focus on the nematodes). We found that sediments affected by intensive seepage displayed the lowest faunal abundances and number of higher taxa. However, mud volcanoes without emissions, but characterized by a high structural complexity (such as the ridges), were associated with the highest meiofaunal abundances and number of higher taxa. Mud volcanoes hosted also a remarkable abundance of rare taxa specifically associated with these structures (e.g., acarians, cumaceans, tanaids, cladocerans and hydroids) and absent in slope sediments (used as a control). Each mud-volcano area displayed a different nematode species composition. Overall 76 nematode species (from a total of 235) were exclusively associated with mud-volcano structures, whilst 29 were exclusively encountered in slope sediments. We conclude that the presence of mud volcanoes, for their contribution to increase spatial heterogeneity and for the extreme conditions associated with gas emissions, promotes higher levels of beta diversity, thus enhancing the regional (gamma) benthic diversity. These findings provide new insights on the factors controlling meiobenthic biodiversity in mud volcanoes and clues for future action of conservation of the biodiversity specifically associated with these habitats.     

Stakeholder priorities for multi-functional coastal defence developments and steps to effective implementation

To fulfil international conservation commitments, governments have begun to recognise the need for more proactive marine planning policies, advocating sensitive engineering design that can deliver secondary benefits above and beyond the primary purpose of developments. In response, there is growing scientific interest in novel multi-functional coastal defence structures with built-in secondary ecological and/or socio-economic benefits. To ensure research efforts are invested effectively, it is first necessary to determine what secondary benefits can potentially be built-in to engineered coastal defence structures, and further, which of these benefits would be most desirable. It is unlikely that secondary benefits are perceived in the same way across different stakeholder groups. Further, their order of priority when evaluating different options is unlikely to be consistent, since each option will present a suite of compromises and trade-offs. The aim of this study was to investigate stakeholder attitudes towards multi-functional coastal defence developments across different sector groups. A preliminary questionnaire indicated unanimous support for implementing multi-functional structures in place of traditional single-purpose ones. This preliminary survey informed the design of a Delphi-like study, which revealed a more nuanced and caveated level of support from a panel of experts and practitioners. The study also elicited a degree of consensus that the most desirable secondary benefits that could be built-in to developments would be ecological ones – prioritised over social, economic and technical benefits. This paper synthesises these findings, discusses the perceived barriers that remain, and proposes a stepwise approach to effective implementation of multi-functional coastal defence developments.