开放对等环境下的安全协作关键技术研究

本文以动态开放的对等协作应用环境为背景，围绕实现安全协作存在的公平性、真实性和策略实施一致性安全需求，针对其中的激励机制、声誉系统、索引系统和访问控制授权管理等关键安全机制进行了深入研究，取得了如下研究成果： 第一， 针对P2P文件共享应用环境，提出一种改进的结环交换激励机制，在降低整体开销的同时，通过改变额外开销的分配关系抑制由于激励机制本身漏洞引发的自私行为和恶意攻击。 第二， 分析共享文件应用中服务真实性对声誉和索引数据的真实性的依赖关系，提出刻画服务真实性安全需求的P2P-CW完整性策略模型，用于指导P2P声誉和索引系统中相关安全机制的设计与分析。 第三， 提出在声誉管理系统层次通过保证声誉数据与计算过程的完整性，提高P2P声誉真实性；利用可信计算和虚拟机技术，设计分布式的安全声誉管理系统——可信声誉管理服务架构TRMS，提供更为可信、准确和可用的声誉数值，并兼顾系统整体的低开销、高扩展和强健壮等需求。 第四， 针对分布式结构化索引系统中的索引数据真实性保护问题，提出“安全索引验证机制”的概念；并设计基于数字签名和Bloom Filter的索引验证机制Prosiv，有效遏制索引污染攻击的同时，最小化索引系统的额外开销。 第五， 分析无仲裁者互操作环境下的远程约束实施问题，提出“约束安全互操作”的概念；提出并改进基于冲突闭包的约束冲突检测算法，由只具备局部信息的成员域协作实现职责分离约束的全局一致实施。

水土保持耕作及施肥对盛花期大豆光合生理的影响

依据陕西安塞田间试验,采用LI-6400便携式光合仪,在自然条件下对黄土丘陵区旱作农田传统翻耕化肥(CF)、翻耕有机肥(CM)、翻耕无肥(CN)、免耕化肥(NF)、免耕有机肥(NM)、免耕无肥(NN)等处理下盛花期大豆叶片的净光合速率、气孔导度、水分利用效率及影响因子日变化进行了研究。结果表明:6种不同处理的大豆叶片净光合速率日变化均为双峰曲线,峰值分别在11:30、16:00出现。NM、NF处理对提高大豆净光合速率有明显的促进作用,其中以有机肥(NM)最为显著。气孔导度与蒸腾速率之间达极显著正相关(P<0.01,r=0.9994)。气孔导度日变化也为双峰,峰值分别出现在11:30、16:00。不同处理下,大豆的水分利用效率呈单峰曲线,峰值出现在10:00,低谷出现在13:00以后。其中,NF、NM处理能显著提高大豆盛花期的水分利用效率。相关分析表明:气孔导度、蒸腾速率、叶温、光合有效辐射及基于叶温的蒸汽压亏缺是大豆光合作用的促进因子,而胞间CO_2浓度、空气CO_2浓度、空气相对湿度则为主要的限制因子。CF、NF处理在8:30~10:20和13:00,CM、NN处理在8:30、11:30~13:00、17:...

Spatial variability in water quality and surface sediment diatom assemblages in a complex lake basin,lake of the woods,ontario,canada

Lake of the Woods (LOW) is an international waterbody spanning the Canadian provinces of Ontario and Manitoba, and the U.S. state of Minnesota. In recent years, there has been a perception that water quality has deteriorated in northern regions of the lake, with all increase in the frequency and intensity of toxin-producing cyanobacterial blooms. However, given the lack of long-term data these trends are difficult to verify. As a first step, we examine spatial and seasonal patterns in water quality in this highly complex lake on the Canadian Shield. Further, we examine surface sediment diatom assemblages across multiple sites to determine if they track within-take differences in environmental conditions. Our results show that there are significant spatial patterns in water quality in LOW. Principal Component Analysis divides the lake into three geographic zones based primarily on algal nutrients (i.e., total phosphorus, TP), with the highest concentrations at sites proximal to Rainy River. This variation is closely tracked by sedimentary diatom assemblages, with [TP] explaining 43% of the variation in diatom assemblages across sites. The close correlation between water quality and the surface sediment diatom record indicate that paleoecological models could be used to provide data on the relative importance of natural and anthropogenic sources of nutrients to the lake.

Effects of inoculated Microcoleus vaginatus on the structure and function of biological soil crusts of desert

Microcoleus vaginatus Gom., the dominant species in biological soil crusts (BSCs) in desert regions, plays a significant role in maintaining the BSC structure and function. The BSC quality is commonly assessed by the chlorophyll a content, thickness, and compressive strength. Here, we have studied the effect of different proportions of M. vaginatus, collected from the Gurbantunggut Desert in northwestern China, on the BSC structure and function under laboratory conditions. We found that when M. vaginatus was absent in the BSC, the BSC coverage, quantified by the percentage of BSC area to total land surface area, was low with a chlorophyll a content of 4.77 x 10(-2) mg g(-1) dry soil, a thickness of 0.86 mm, and a compressive strength of 12.21 Pa. By increasing the percentage of M. vaginatus in the BSC, the BSC coverage, chlorophyll a content, crust thickness, and compressive strength all significantly increased (P < 0.01). The maximum chlorophyll a content (13.12 mg g(-1)dry soil), the highest crust thickness, and the compressive strength (1.48 mm and 36.60 Pa, respectively) occurred when the percentage of inoculated M. vaginatus reached 80% with a complex network of filaments under scanning electron microscope. The BSC quality indicated by the above variables, however, declined when the BSC was composed of pure M. vaginatus (monoculture). In addition, we found that secretion of filaments and polymer, which stick sands together in the BSC, increased remarkably with the increase of the dominant species until the percentage of M. vaginatus reached 80%. Our results suggest that not only the dominant species but also the accompanying taxa are critical for maintaining the structure and functions of the BSC and thus the stability of the BSC ecosystems.

Ulva diversity in the Yellow Sea during the large-scale green algal blooms in 2008-2009

P>In the Yellow Sea of China, large-scale green tides have broken out for three consecutive years from 2007 to 2009. As part of the efforts to localize the algal source, two cruises were conducted in the early stage and the outbreak stage of the bloom in 2009. We analyzed the morphological and genetic diversity of drifting Ulva specimens and culture-derived isolates from seawater sampled in different localities. For phylogenetic analyses, the nuclear encoded ribosomal DNA internal transcribed spacer region (ITS nrDNA) and the plastid encoded large subunit of ribulose-1, 5-bisphosphate carboxylase/oxgenase gene (rbcL) were used. Our molecular and morphological data indicate that the dominant free-floating Ulva species in 2008 and 2009 possibly belonged to a single strain of the U. linza-procera-prolifera (LPP) clade. The ITS sequences from bloom-forming algal samples with dense branches were identical to those from U. linza-like specimens without branches derived from the Yellow Sea. Microscopic individuals of the dominant Ulva strain were detected in eight stations, revealing that spore dispersal in the water helped to enlarge biomass in the water during the outbreak stage of green tide in the Yellow Sea.

Genome-wide survey of putative serine/threonine protein kinases in cyanobacteria

Background: Serine/threonine kinases (STKs) have been found in an increasing number of prokaryotes, showing important roles in signal transduction that supplement the well known role of two-component system. Cyanobacteria are photoautotrophic prokaryotes able to grow in a wide range of ecological environments, and their signal transduction systems are important in adaptation to the environment. Sequence information from several cyanobacterial genomes offers a unique opportunity to conduct a comprehensive comparative analysis of this kinase family. In this study, we extracted information regarding Ser/Thr kinases from 21 species of sequenced cyanobacteria and investigated their diversity, conservation, domain structure, and evolution. Results: 286 putative STK homologues were identified. STKs are absent in four Prochlorococcus strains and one marine Synechococcus strain and abundant in filamentous nitrogen-fixing cyanobacteria. Motifs and invariant amino acids typical in eukaryotic STKs were conserved well in these proteins, and six more cyanobacteria- or bacteria-specific conserved residues were found. These STK proteins were classified into three major families according to their domain structures. Fourteen types and a total of 131 additional domains were identified, some of which are reported to participate in the recognition of signals or substrates. Cyanobacterial STKs show rather complicated phylogenetic relationships that correspond poorly with phylogenies based on 16S rRNA and those based on additional domains. Conclusion: The number of STK genes in different cyanobacteria is the result of the genome size, ecophysiology, and physiological properties of the organism. Similar conserved motifs and amino acids indicate that cyanobacterial STKs make use of a similar catalytic mechanism as eukaryotic STKs. Gene gain-and-loss is significant during STK evolution, along with domain shuffling and insertion. This study has established an overall framework of sequence-structure-function interactions for the STK gene family, which may facilitate further studies of the role of STKs in various organisms.

Genome-wide survey of putative serine/threonine protein kinases in cyanobacteria

Background: Serine/threonine kinases (STKs) have been found in an increasing number of prokaryotes, showing important roles in signal transduction that supplement the well known role of two-component system. Cyanobacteria are photoautotrophic prokaryotes able to grow in a wide range of ecological environments, and their signal transduction systems are important in adaptation to the environment. Sequence information from several cyanobacterial genomes offers a unique opportunity to conduct a comprehensive comparative analysis of this kinase family. In this study, we extracted information regarding Ser/Thr kinases from 21 species of sequenced cyanobacteria and investigated their diversity, conservation, domain structure, and evolution. Results: 286 putative STK homologues were identified. STKs are absent in four Prochlorococcus strains and one marine Synechococcus strain and abundant in filamentous nitrogen-fixing cyanobacteria. Motifs and invariant amino acids typical in eukaryotic STKs were conserved well in these proteins, and six more cyanobacteria- or bacteria-specific conserved residues were found. These STK proteins were classified into three major families according to their domain structures. Fourteen types and a total of 131 additional domains were identified, some of which are reported to participate in the recognition of signals or substrates. Cyanobacterial STKs show rather complicated phylogenetic relationships that correspond poorly with phylogenies based on 16S rRNA and those based on additional domains. Conclusion: The number of STK genes in different cyanobacteria is the result of the genome size, ecophysiology, and physiological properties of the organism. Similar conserved motifs and amino acids indicate that cyanobacterial STKs make use of a similar catalytic mechanism as eukaryotic STKs. Gene gain-and-loss is significant during STK evolution, along with domain shuffling and insertion. This study has established an overall framework of sequence-structure-function interactions for the STK gene family, which may facilitate further studies of the role of STKs in various organisms.

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.

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.

Construction of shuttle, expression vector of human tumor necrosis factor alpha (hTNF-alpha) gene and its expression in a cyanobacterium, Anabaena sp. PCC 7120

The construction of the shuttle, expression vector of human tumor necrosis factor alpha (hTNF-alpha) gene and its expression in a cyanobacterium Anabaena sp. PCC 7120 was reported. The 700-bp hTNF cDNA fragments have been recovered from plasmid pRL-rhTNF, then inserted downstream of the promoter PpsbA in the plasmid pRL439. The resultant intermediary plasmid pRL-TC has further been combined with the shuttle vector pDC-8 to get the shuttle, expression vector pDC-TNF. The expression of the rhTNF gene in Escherichia coil has been analyzed by SDS-PAGE and thin-layer scanning, and the results show that the expressed TNF protein with these two vectors is 16.9 percent (pRL-TC) and 15.0 percent (pDC-TNF) of the total proteins in the cells, respectively, while the expression level of TNF gene in plasmid pRL-rhTNF is only 11.8 percent. Combined with the participation of the conjugal and helper plasmids, pDC-TNF has been introduced into Anabaena sg PCC 7120 by triparental conjugative transfer, and the stable transgenic strains have been obtained. The existence of the introduced plasmid pDC-TNF in recombinant cyanobacterial cells has been demonstrated by the results of the agarose electrophoresis with the extracted plasmid samples and Southern blotting with alpha-(32)p labeled hTNF cDNA probes, while the expression of the hTNF gene in Anabaena sp. PCC 7120 has been confirmed by the results of Western blotting with extracted protein samples and human TNF-alpha monoclonal antibodies. The cytotoxicity assays using the mouse cancer cell line L929 proved the cytotoxicity of the TNF in the crude extracts from the transgenic cyanobacterium Anabaena sp. PCC 7120.

Development of rRNA and rDNA-targeted probes for fluorescence in situ hybridization to detect Heterosigma akashiwo (Raphidophyceae)

Heterosigma akashiwo (Hada) is a fragile, fish-killing alga. Efforts to understand and prevent blooms due to this harmful species to mitigate the impact on aquaculture require the development of methods for rapid and precise identification and quantification, so that adequate warning of a harmful algal bloom may be given. Here, we report the development and application of rRNA and rDNA-targeted oligonucleotide probes for fluorescence in situ hybridization (FISH) to aid in the detection and enumeration of H. akashiwo. The designed probes were species specific, showing no cross-reactivity with four common HAB causative species: Prorocentrum micans Ehrenberg, P. minimum (Pavillard) Schiller, Alexandrium tarmarense (Lebour) Balech, and Skeletonema costatum (Greville) Cleve, or with four other microalgae, including Gymnodinium sp. Stein, Platy-monas cordiformis (Karter) Korsch, Skeletonema sp.1 Greville and Skeletonema sp.2. The rRNA-targeted probe hybridized to cytoplasmic rRNA, showing strong green fluorescence throughout the whole cell, while cells labeled by rDNA-targeted probe exhibited exclusively fluorescent nucleus. The detection protocols were optimized and could be completed within an hour. For rRNA and rDNA probes, about a corresponding 80% and 70% of targeted cells could be identified and quantified during the whole growth circle, despite the inapparent variability in the average probe reactivity. The established FISH was proved promising for specific, rapid, precise, and quantitative detection of H. akashiwo. (C) 2008 Elsevier B.V. All rights reserved.

Morphological and phylogenetic analysis of a Gymnodinium-like species from the Chinese Coast

A Gymnodinium-like species was studied with light microscopy (LM) and scanning electron microscopy (SEM). Also, the internal transcribed spacers (containing 5.8S rDNA) and large ribosomal subunit DNA (D1-D2) sequences were obtained by PCR amplification, and then sequenced to explore the relationships within our isolate, Gymnodinium and other Gymnodinium-like species, including Karenia, Gyrodinium, Karlodinium and Symbiodinium. The LM observation showed that the species was characterized by moving in a levorotatory direction, visible hypocone, epicone and transverse groove, all of which are typical for Gymnodinium. In addition, two flagella could be found under SEM. The phylogenetic analysis revealed that the isolate grouped with Symbiodium, rather than other relevant dinoflagellates. All results showed our isolate belongs to Symbiodium. The strain was isolated from a red tide water sample, denoting that Symbiodium may be causative species for algal bloom.

Lineage-specific domain fusion in the evolution of purine nucleotide cyclases in cyanobacteria

Cyclic nucleotides (both cAMP and cGMP) play extremely important roles in cyanobacteria, such as regulating heterocyst formation, respiration, or gliding. Catalyzing the formation of cAMP and cGMP from ATP and GTP is a group of functionally important enzymes named adenylate cyclases and guanylate cyclases, respectively. To understand their evolutionary patterns, in this study, we presented a systematic analysis of all the cyclases in cyanobacterial genomes. We found that different cyanobacteria had various numbers of cyclases in view of their remarkable diversities in genome size and physiology. Most of these cyclases exhibited distinct domain architectures, which implies the versatile functions of cyanobacterial cyclases. Mapping the whole set of cyclase domain architectures from diverse prokaryotic organisms to their phylogenetic tree and detailed phylogenetic analysis of cyclase catalytic domains revealed that lineage-specific domain recruitment appeared to be the most prevailing pattern contributing to the great variability of cyanobacterial cyclase domain architectures. However, other scenarios, such as gene duplication, also occurred during the evolution of cyanobacterial cyclases. Sequence divergence seemed to contribute to the origin of putative guanylate cyclases which were found only in cyanobacteria. In conclusion, the comprehensive survey of cyclases in cyanobacteria provides novel insight into their potential evolutionary mechanisms and further functional implications.

Vast laminated diatom mat deposits from the west low-latitude Pacific Ocean in the last glacial period

Diatoms are one of the predominant contributors to global carbon fixation by accounting for over 40% of total oceanic primary production and dominate export production. They play a significant role in marine biogeochemistry cycle. The diatom mat deposits are results of vast diatoms bloom. By analysis of diatom mats in 136 degrees 00'-140 degrees 00'E, 15 degrees 00'-21 degrees 00'N, Eastern Philippines Sea, we identified the species of the diatoms as giant Ethmodiscus rex (Wallich) Hendey. AMS C-14 dating shows that the sediments rich in diatom mats occurred during 16000-28600 a B.P., which means the bloom mainly occurred during the last glacial period, while there are no diatom mat deposits in other layers. Preliminary analysis indicates that Antarctic Intermediate Water (AAIW) expanded northward and brought silicate-rich water into the area, namely, silicon leakage processes caused the bloom of diatoms. In addition, the increase of iron input is one of the main reasons for the diatom bloom.