Genome-wide analysis of restriction-modification system in unicellular and filamentous cyanobacteria

Cyanobacteria are an ancient group of gram-negative bacteria with strong genome size variation ranging from 1.6 to 9.1 Mb. Here, we first retrieved all the putative restriction-modification (RM) genes in the draft genome of Spirulina and then performed a range of comparative and bioinformatic analyses on RM genes from unicellular and filamentous cyanobacterial genomes. We have identified 6 gene clusters containing putative Type I RMs and 11 putative Type II RMs or the solitary methyltransferases (MTases). RT-PCR analysis reveals that 6 of 18 MTases are not expressed in Spirulina, whereas one hsdM gene, with a mutated cognate hsdS, was detected to be expressed. Our results indicate that the number of RM genes in filamentous cyanobacteria is significantly higher than in unicellular species, and this expansion of RM systems in filamentous cyanobacteria may be related to their wide range of ecological tolerance. Furthermore, a coevolutionary pattern is found between hsdM and hsdR, with a large number of site pairs positively or negatively correlated, indicating the functional importance of these pairing interactions between their tertiary structures. No evidence for positive selection is found for the majority of RMs, e. g., hsdM, hsdS, hsdR, and Type II restriction endonuclease gene families, while a group of MTases exhibit a remarkable signature of adaptive evolution. Sites and genes identified here to have been under positive selection would provide targets for further research on their structural and functional evaluations.

Transformation of accommodation space of the Cretaceous Qingshankou Formation, the Songliao Basin, NE China

Analysis of accommodation space variation during deposition of the Cretaceous Qingshankou Formation in the Songliao Basin, NE China, indicates that accommodation space changed both through time and across the basin as a seesaw movement. The mid-upper Qingshankou Formation is divided into three units. In each unit, changes of accommodation space differ in the southern and northern part of the basin. Increasing accommodation in the southern part is accompanied by a decrease in the northern part, and vice versa. Between the northern and southern basin, there was a neutral belt that is like a fulcrum, called the transformation belt here, where the accommodation did not change to any significant degree. We call this response 'accommodation transformation', whose characteristics are defined by tectonic subsidence analysis, palaeontological and sedimentary analyses. The accommodation increasing belt, decreasing belt, transformation belt and accommodation transformation boundary together constitute the accommodation transformation system. The recognition of accommodation transformation in the Songliao Basin provides a new insight into sequence stratigraphy and might be widely applicable.

黄东海胶质浮游动物水母类研究

近年来，胶质类浮游动物尤其是水母类在近岸高生产力的海洋生态系统中的作用越来越受到全球科学家们的关注。这种关注很大程度上是由于近年来很多海域或海湾出现水母类大量繁殖的现象而引起的，这种现象与过度捕捞、气候变化、富营养化以及生物入侵等因素有着内在的联系，给人们带来经济，社会和生态等各方面的损失。这种损失包括：当水母大量出现时，由于它们与鱼类存在食物和捕食竞争，使渔业资源和渔业生产锐减；由于它们会堵塞和撕破渔业生产网，干扰了人们的渔业生产活动；另外水母增多增加了海滨游泳爱好者被蛰伤甚至死亡事件发生的频率，对旅游者们的娱乐行为造成不便。到目前为止全球范围内报道了许多水母大量繁殖并对经济社会或海洋生态系统造成负面影响的事件。在北海水母数量爆发的频率与气候相关的事实表明了该海域将要面临一个更多的胶质类浮游动物的未来。所有这些都表明海洋中水母的生态学问题仍旧是全球的一个研究热点。到目前为止，在世界上许多海湾和海区有关水母生态学问题的研究上，均已取得方方面面有意义的进展。但在我国，由于对水母功能群的研究缺乏足够的重视，对于大型水母来讲它们被认为是渔业生产的副产品或者‘垃圾’，在渔业拖网捕获后把它们直接扔入海中并不去研究；对于小型水母来讲，因为它们为非饵料生物，并且有易碎，粘糊糊等难操作的特点，对浮游生物网同步采集到的水母的研究力度远不如对其他浮游动物类群的研究力度，因此我国对水母功能群生态学的研究基础相当薄弱。 本论文基于以上背景对黄东海大型和小型水母类的生物地理分布格局进行了研究，对其生物量或丰度等生态学指标进行了定量研究。（1）利用浮游生物网样品对黄海小型水母类的种类组成及其丰度的时空变化进行了研究，表明黄海测区内小型水母整体丰度很低，且主要分布在50 m等深线以浅海域，各水母类群以及优势种类的季节更替非常明显。比较不同海区的小型水母的丰度水平及其占浮游动物丰度的比例，发现黄海的小型水母丰度水平最低，为0.8（0.04–1.3）ind. m-3，只占浮游动物丰度的 < 0.5 %，表明小型水母在黄海海域并非占优势的功能群。（2）在中国黄东海采集的沙海蜇和在日本采集的越前水母的COI基因序列差异（0.2%）处于种内水平，从分子水平上证明两者为同一个种类，基于形态学和分子生物学的证据，我国大型水母沙海蜇的分类地位可初步订正为：Nemopilema nomurai Kishinouye, 1922（Scyphozoa：Rhizostomeae：Rhizostomatidae）。（3）利用渔业底层拖网的方法对黄东海大型水母的种类组成，总生物量及各优势种类生物量的时空分布进行了半定量研究。结果共鉴定到11个种（类），其中沙海蜇（Nemopilema nomurai），洋须水母（Ulmaridae genus sp.）以及多管水母（Aequorea spp.）为黄海的优势种（类），沙海蜇（只在东海北部）和霞水母（Cyanea spp.）为东海的优势种（类）；这四个种（类）的湿重随着伞径的增大成冪增长的方式。大型水母平均总生物量的季节变化模式为：3月份水母总生物量最低，为4.6 ± 9.4 kg km–2，春夏季随着海水表层温度的升高，大型水母的生物量逐渐增加，9月初水母的总生物量达到最高值，为22891 ± 25888 kg km–2，随后随着海水的温度下降，生物量也逐渐下降。洋须水母的生物量在10月份达到最高值（2780 ind. km–2，1807 kg km–2），主要在黄海中部出现。多管水母在5月份丰度最高，为8262 kg km–2，且主要分布在30N以北海域。 聚焦大量爆发的水母种（类）沙海蜇和霞水母，基于实测的拖网资料，提供了该种可见的浮游阶段1周年的地理发生和生物量数据；结果表明，这两个种（类）表现了不同的季节出现和生物量格局：首先是黄海出现的沙海蜇（5–12月在黄海出现），5月份少量幼水母体在黄东海的交界处出现，6月它们的分布范围在南黄海扩大，到8月末及9月初沙海蜇几乎遍布黄海，其生物量和丰度以压倒其他大型水母类的优势形成“bloom”（生物量占所有大型水母的96.7%，丰度占93%，在南黄海平均生物量20446 kg km-2，平均占渔获物生物量的86.1 %），10月份至12月，沙海蜇的生物量逐渐减少甚至为零，其分布区域也向北回缩。其次为东海出现的霞水母（5月–10月）：霞水母在5月初达到生物量的高值（平均生物量为380 kg km-2），其伞径随纬度的升高而变小，8月至10月其生物量骤然下降。这两个种类的生物量高值分布在温度或潮汐锋区。结合水文条件及沙海蜇和霞水母关键的生活史策略推测了黄东海该种浮游阶段的生活史模型。 最后，通过对黄海8、9月份沙海蜇生物量的最高峰或暴发时期的呼吸率，摄食率进行估算，获得其每天对浮游动物现存量及生产力的潜在摄食压力，结果表明2006年9月在对沙海蜇最大捕获率的情况下，沙海蜇的摄食率为8.37（0.12–37.83）mg C m-2d-1，假设都以浮游动物为食，这时每天对浮游动物现存量及生产力的摄食压力分别为11.2%（0.17–50.6%），134.1%（1.98–605.7%）。因此在沙海蜇暴发期间对浮游动物的潜在的消耗非常大，甚至为毁灭性的。

Partial characterization of the hemolytic activity of the nematocyst venom from the jellyfish Cyanea nozakii Kishinouye

Using a recently developed technique to extract jellyfish venom from nematocysts, the present study investigated the hemolytic activity of Cyanea nozakii Kishinouye nematocyst venom on chicken erythrocytes. Venom extract caused a significant concentration-dependent hemolytic effect. The extract could retain its activity at -80 degrees C but was unstable when kept at 4 degrees C and -20 degrees C for 2 days. The hemolytic activity was inhibited by heating within the range of 37-100 degrees C. The extract was active over a pH range of 5.0-8.63 and the pH optima for the extract was 7.8. Incubation of the venom with sphingomyelin specially inhibited hemolytic activity by up to 70%. Cu2+ and Mn2+ greatly reduced the hemolytic activity while Mg2+, Sr2+ and Ba2+ produced a relatively low inhibiting effect on the hemolytic activity. Treatment with Ca2+ induced a concentration-dependent increase in the hemolytic activity. In the presence of 5 mM EDTA, all the hemolytic activity was lost, however, the venom containing 1.5 mM EDTA was stable in the long-term storage. PLA(2) activity was also found in the nematocyst venom of C. nozakii. These characteristics provide us a fundamental knowledge in the C. nozakii nematocyst venom which would benefit future research. (C) 2010 Published by Elsevier Ltd.

CIM-OSA的思想及其应用

计算机集成制造系统开放式体系结构 CIM-OSA 是欧共体 ESPRIT 计划的 AMICE 协作体的研究成果,本文系统地介绍了 CIM-OSA 的内容及特点,并对 CIM-OSA 思想的应用实例 IMPACS(集成制造计划和控制系统)和 IBM 的 CIM 结构做了详细分析和阐述.

中国东部上第三系硬粘土的工程地质特性及边坡开挖工程环境效应研究

The engineering geological properties of Neogene hard clays and related engineering problems are frontiers in the fields of Engineering Geology, Soil Mechanics and Rock Mechanics. Recently, it has been recognized that Neogene hard clay is the intermediate type of material between the soil and the rock. Many aspects of them, such as sampling, testing, calculating and engineering process, are special, which could not be researched by means of theories and methods of traditional Soil Mechanics of Rock Mechanics. In order to get real knowledge and instruct the engineering practice, intersect studying of multiple disciplines, including Engineering Geology, Soil Mechanics and Rock Mechanics, etc., is necessary. Neogene hard clay is one of the important study objects of regional problem rocks & soils in our country, which extensively distributed in China, especially in Eastern China. Taking the related areas along the middle line of the Project of Transferring Water from the South to the North (e.g. Nanyang basin, Fangcheng-Baofeng area and Handan-Yongnian area), South-west of Shandong, Xu-Huai area and Beijing area, etc. as main study areas, the paper divided Neogene hard clays into reduction environment dominated origin and oxidation environment dominated origin, which distributed on areas western and eastern to Mount Taihangshan respectively. Intermediate types are also existed in some areas, which mainly distribute near the edges of depositional basins; they are usually of transitions between diluvial and lacustrine deposits. As to Neogene hard clays from Eastern China, the clay particle content is high, and montmorillonite or illite/montmorillonite turbostratic mineral is the dominating clay mineral. The content of effective montmorillonite is very high in each area, which is the basis for the undesirable engineering properties of Neogene hard clays. For hard clays from the same area, the content of effective montmorillonite in gray-greenish hard clay is much higher than that in purple-brownish or brown-yellowish hard clay, which is the reason why the gray-greenish hard clay usually has outstanding expansive property. On the other hand, purple-brownish or brown-yellowish hard clay has relatively less montmorillonite, so its property is better. All of these prove that the composition (clay mineral) of Neogene hard clay is the control factor for the engineering properties. Neogene hard clays have obvious properties such as fissured, overconsolidated and expansive, which are the main reasons that many engineering problems and geological harzards usually occur in Neogene hard clays. The paper systematically elaborates the engineering properties of Neogene hard clays from Eastern China, analyses the relationships between engineering properties and basic indexes. The author introduces the ANN method into the prediction of engineering property indexes of hard clays, which provides a new way for quantitatively assessment and prediction of engineering property indexes. During investigation in the field, the author found that there exists obvious seam-sheared zone between different hard clays in Miocene Xiacaowan formation in Xu-Huai area. Similar phenomenon also exists near the borderline between Neogene hard clays and underlying coal measures in the Southwest of Shandong province, which could be observed in the cores. The discovery of seam-sheard zone has important theoretical and practical significance for engineering stability analysis and revealing the origin of fissures in Neogene hard clays. The macrostructure, medium structure and microstructure together control the engineering properties of hard clays. The author analyses and summarizes the structural effects on hard clays in detail. The complex of the strength property of hard clays is mostly related to the characteristics of fissures, which is one of the main factors that affect the choice of shear strength parameters. So structure-control theory must be inseparably combined with composition-control theory during the engineering geological and rock/soil mechanics research of hard clays. The engineering properties, such as fissured, overconsolidated and expansive, control the instability of engineering behaviors of Neogene hard clays under the condition of excavation, i.e. very sensitive to the change of existence environment. Based on test data analysis, the author elaborates the effects of engineering environment change on the engineering properties. Taking Nanyang basin as example, the author utilizes FEM to study the effects of various factors on stability of cutting canal slopes, than sets forth the characteristics, development laws and formation mechanism of the deformation and failure of hard clay canal slopes, summarizes the protection and reinforcement principles, as well as the protection and remedy steps. On the basis of comparison of engineering properties of domestic and foreign Neogene muddy deposits, in the view of whole globe and associated with the geological characteristics of China, the paper demonstrates that the intermediate type of the material between the soil and the rock, named "hard clay/soft rock", which can not be separated abruptly, really exists in China. The author has given a preliminary classification based on its geological origin and distribution law, which is very significant for promoting the mixture of Engineering Geology, Soil Mechanics and Rock Mechanics. In the course of large scales engineering construction in China, many engineering experiences and testing data are gained, summarizing these testing results and automatically managing them with computer technology are very necessary. The author develops a software named "Hard Clay-Soft Rock Engineering Geological Information Management and Analysis System (HRGIMS)", realizes the automatic and visual management of geo-engineering information, on the basis of information management, the functions of test data analysis and engineering property prediction are strengthened. This system has well merits for practice and popularization.

层控夕卡岩型矿床成矿系统的元素活动性及质量迁移——以铜陵冬瓜山铜矿床为例

应用改善了的质量平衡方程研究冬瓜山层控夕卡岩型铜矿床成矿系统的元素活动性及质量迁移,结果表明:系统中Zr ,Hf ,Y和Nb 为不活动元素,其余均为活动元素。主量元素中仅CaO 为迁出组分,其质量迁移量为84 % ,其余均为带入组分,带入量最大的SiO2 的质量迁移量高达2384 %;稀土元素均为带入组分,其中,中稀土较轻稀土和重稀土的活动性更强;其它微量元素中,带入序列由强到弱为:Cr →Ta →Sn →Th ,迁出序列由强至弱依次为:U →Sb →Ni →Sr →Ba →Rb →Co →W;成矿元素Cu 和Ag 为带入组分,其中Cu 的带入量最大,质量迁移量高达1200 %。本文还得出两点具普适性认识: ①稀土元素较其它微量元素对体系条件的变化更为敏感,且往往表现出明显的规律性变化,能更好地示踪地质地球化学过程。②不同元素在不同体系中的行为特征差异极大,仅凭经验判定某一元素为不活动元素往往不可靠。因此,在开展质量平衡研究时,首先采用适当方法确认体系的不活动元素是一项不可或缺的前提工作。