Multi-ciphersuite security of the Secure Shell (SSH) protocol

The Secure Shell (SSH) protocol is widely used to provide secure remote access to servers, making it among the most important security protocols on the Internet. We show that the signed-Diffie--Hellman SSH ciphersuites of the SSH protocol are secure: each is a secure authenticated and confidential channel establishment (ACCE) protocol, the same security definition now used to describe the security of Transport Layer Security (TLS) ciphersuites. While the ACCE definition suffices to describe the security of individual ciphersuites, it does not cover the case where parties use the same long-term key with many different ciphersuites: it is common in practice for the server to use the same signing key with both finite field and elliptic curve Diffie--Hellman, for example. While TLS is vulnerable to attack in this case, we show that SSH is secure even when the same signing key is used across multiple ciphersuites. We introduce a new generic multi-ciphersuite composition framework to achieve this result in a black-box way.

Elliptic curve algorithm integration in the secure shell transport layer

This document describes algorithms based on Elliptic Cryptography (ECC) for use within the Secure Shell (SSH) transport protocol. In particular, it specifies Elliptic Curve Diffie-Hellman (ECDH) key agreement, Elliptic Curve Menezes-Qu-Vanstone (ECMQV) key agreement, and Elliptic Curve Digital Signature Algorithm (ECDSA) for use in the SSH Transport Layer protocol.

Culture independent analysis of greyback canegrub-associated microflora and microbial community comparison using subtractive hybridisation

Greyback canegrubs cost the Australian sugarcane industry around $13 million per annum in damage and control. A novel and cost effective biocontrol bacterium could play an important role in the integrated pest management program currently in place to reduce damage and control associated costs. During the course of this project, terminal restriction fragment length polymorphism (TRFLP), 16-S rDNA cloning, suppressive subtractive hybridisation (SSH) and entomopathogen-specific PCR screening were used to investigate the little studied canegrub-associated microflora in an attempt to discover novel pathogens from putatively-diseased specimens. Microflora associated with these soil-dwelling insects was found to be both highly diverse and divergent between individual specimens. Dominant members detected in live specimens were predominantly from taxa of known insect symbionts while dominant sequences amplified from dead grubs were homologous to putativelysaprophytic bacteria and bacteria able to grow during refrigeration. A number of entomopathogenic bacteria were identified such as Photorhabdus luminescens and Pseudomonas fluorescens. Dead canegrubs prior to decomposition need to be analysed if these bacteria are to be isolated. Novel strategies to enrich putative pathogen-associated sequences (SSH and PCR screening) were shown to be promising approaches for pathogen discovery and the investigation of canegrubsassociated microflora. However, due to inter- and intra-grub-associated community diversity, dead grub decomposition and PCR-specific methodological limitations (PCR bias, primer specificity, BLAST database restrictions, 16-S gene copy number and heterogeneity), recommendations have been made to improve the efficiency of such techniques. Improved specimen collection procedures and utilisation of emerging high-throughput sequencing technologies may be required to examine these complex communities in more detail. This is the first study to perform a whole-grub analysis and comparison of greyback canegrub-associated microbial communities. This work also describes the development of a novel V3-PCR based SSH technique. This was the first SSH technique to use V3-PCR products as a starting material and specifically compare bacterial species present in a complex community.

X.509v3 Certificates for Secure Shell authentication

X.509 public key certificates use a signature by a trusted certification authority to bind a given public key to a given digital identity. This document specifies how to use X.509 version 3 public key certificates in public key algorithms in the Secure Shell protocol.

Tracking the magmatic evolution of island arc volcanism : insights from a high-precision Pb isotope record of Montserrat, Lesser Antilles

The volcanic succession on Montserrat provides an opportunity to examine the magmatic evolution of island arc volcanism over a ∼2.5 Ma period, extending from the andesites of the Silver Hills center, to the currently active Soufrière Hills volcano (February 2010). Here we present high-precision double-spike Pb isotope data, combined with trace element and Sr-Nd isotope data throughout this period of Montserrat's volcanic evolution. We demonstrate that each volcanic center; South Soufrière Hills, Soufrière Hills, Centre Hills and Silver Hills, can be clearly discriminated using trace element and isotopic parameters. Variations in these parameters suggest there have been systematic and episodic changes in the subduction input. The SSH center, in particular, has a greater slab fluid signature, as indicated by low Ce/Pb, but less sediment addition than the other volcanic centers, which have higher Th/Ce. Pb isotope data from Montserrat fall along two trends, the Silver Hills, Centre Hills and Soufrière Hills lie on a general trend of the Lesser Antilles volcanics, whereas SSH volcanics define a separate trend. The Soufrière Hills and SSH volcanic centers were erupted at approximately the same time, but retain distinctive isotopic signatures, suggesting that the SSH magmas have a different source to the other volcanic centers. We hypothesize that this rapid magmatic source change is controlled by the regional transtensional regime, which allowed the SSH magma to be extracted from a shallower source. The Pb isotopes indicate an interplay between subduction derived components and a MORB-like mantle wedge influenced by a Galapagos plume-like source.

Multi-stage collapse events in the South Soufrière Hills, Montserrat as recorded in marine sediment cores

We present new evidence for sector collapses of the South Soufrière Hills (SSH) edifice, Montserrat during the mid-Pleistocene. High-resolution geophysical data provide evidence for sector collapse, producing an approximately 1 km3 submarine collapse deposit to the south of SSH. Sedimentological and geochemical analyses of submarine deposits sampled by sediment cores suggest that they were formed by large multi-stage flank failures of the subaerial SSH edifice into the sea. This work identifies two distinct geochemical suites within the SSH succession on the basis of trace-element and Pb-isotope compositions. Volcaniclastic turbidites in the cores preserve these chemically heterogeneous rock suites. However, the subaerial chemostratigraphy is reversed within the submarine sediment cores. Sedimentological analysis suggests that the edifice failures produced high-concentration turbidites and that the collapses occurred in multiple stages, with an interval of at least 2 ka between the first and second failure. Detailed field and petrographical observations, coupled with SEM image analysis, shows that the SSH volcanic products preserve a complex record of magmatic activity. This activity consisted of episodic explosive eruptions of andesitic pumice, probably triggered by mafic magmatic pulses and followed by eruptions of poorly vesiculated basaltic scoria, and basaltic lava flows.

DArT markers: Diversity analyses and mapping in Sorghum bicolor

The sequential nature of gel-based marker systems entails low throughput and high costs per assay. Commonly used marker systems such as SSR and SNP are also dependent on sequence information. These limitations result in high cost per data point and significantly limit the capacity of breeding programs to obtain sufficient return on investment to justify the routine use of marker-assisted breeding for many traits and particularly quantitative traits. Diversity Arrays Technology (DArT™) is a cost effective hybridisation-based marker technology that offers a high multiplexing level while being independent of sequence information. This technology offers sorghum breeding programs an alternative approach to whole-genome profiling. We report on the development, application, mapping and utility of DArT™ markers for sorghum germplasm. Results: A genotyping array was developed representing approximately 12,000 genomic clones using PstI+BanII complexity with a subset of clones obtained through the suppression subtractive hybridisation (SSH) method. The genotyping array was used to analyse a diverse set of sorghum genotypes and screening a Recombinant Inbred Lines (RIL) mapping population. Over 500 markers detected variation among 90 accessions used in a diversity analysis. Cluster analysis discriminated well between all 90 genotypes. To confirm that the sorghum DArT markers behave in a Mendelian manner, we constructed a genetic linkage map for a cross between R931945-2-2 and IS 8525 integrating DArT and other marker types. In total, 596 markers could be placed on the integrated linkage map, which spanned 1431.6 cM. The genetic linkage map had an average marker density of 1/2.39 cM, with an average DArT marker density of 1/3.9 cM. Conclusion: We have successfully developed DArT markers for Sorghum bicolor and have demonstrated that DArT provides high quality markers that can be used for diversity analyses and to construct medium-density genetic linkage maps. The high number of DArT markers generated in a single assay not only provides a precise estimate of genetic relationships among genotypes, but also their even distribution over the genome offers real advantages for a range of molecular breeding and genomics applications.

Identification of putative virulence-associated genes of Haemophilus parasuis through suppression subtractive hybridization.

Haemophilus parasuis is the causative agent of Glässer's disease. Up to now 15 serovars of H. parasuis have been identified, with significant differences existing in virulence between serovars. In this study, suppression subtractive hybridization (SSH) was used to identify the genetic difference between Nagasaki (H. parasuis serovar 5 reference strain, highly virulent) and SW114 (H. parasuis serovar 3 reference strain, non-virulent). A total of 191 clones were obtained from the SSH library. Using dot hybridization and PCR, 15 clones were identified containing fragments that were present in the Nagasaki genome while absent in the SW114 genome. Among these 15 fragments, three fragments (ssh1, ssh13, ssh15) encode cell surface-associated components; three fragments (ssh2, ssh5, ssh9) are associated with metabolism and stress response; one fragment (ssh8) is involved in assembly of fimbria and one fragment (ssh6) is a phage phi-105 ORF25-like protein. The remaining seven fragments are hypothetical proteins or unknown. Based on PCR analysis of the 15 serovar reference strains, eight fragments (ssh1, ssh2, ssh3, ssh6, ssh8, ssh10, ssh11 and ssh12) were found in three to five of most virulent serovars (1, 5, 10, 12, 13 and 14), zero to two in three moderately virulent serovars (2, 4 and 15), but absent in the low virulent serovar (8) and non-virulent serovars (3, 6, 7, 9 and 11). In vivo transcription fragments ssh1, ssh2, ssh8 and ssh12 were identified in total RNA samples extracted from experimental infected pig lung by RT-PCR. This study has provided some evidence of genetic differences between H. parasuis strains of different virulence.

Rhipicephalus microplus serine protease inhibitor family: annotation, expression and functional characterisation assessment

Background: Rhipicephalus (Boophilus) microplus evades the host's haemostatic system through a complex protein array secreted into tick saliva. Serine protease inhibitors (serpins) conform an important component of saliva which are represented by a large protease inhibitor family in Ixodidae. These secreted and non-secreted inhibitors modulate diverse and essential proteases involved in different physiological processes. Methods: The identification of R. microplus serpin sequences was performed through a web-based bioinformatics environment called Yabi. The database search was conducted on BmiGi V1, BmiGi V2.1, five SSH libraries, Australian tick transcriptome libraries and RmiTR V1 using bioinformatics methods. Semi quantitative PCR was carried out using different adult tissues and tick development stages. The cDNA of four identified R. microplus serpins were cloned and expressed in Pichia pastoris in order to determine biological targets of these serpins utilising protease inhibition assays. Results: A total of four out of twenty-two serpins identified in our analysis are new R. microplus serpins which were named as RmS-19 to RmS-22. The analyses of DNA and predicted amino acid sequences showed high conservation of the R. microplus serpin sequences. The expression data suggested ubiquitous expression of RmS except for RmS-6 and RmS-14 that were expressed only in nymphs and adult female ovaries, respectively. RmS-19, and -20 were expressed in all tissues samples analysed showing their important role in both parasitic and non-parasitic stages of R. microplus development. RmS-21 was not detected in ovaries and RmS-22 was not identified in ovary and nymph samples but were expressed in the rest of the samples analysed. A total of four expressed recombinant serpins showed protease specific inhibition for Chymotrypsin (RmS-1 and RmS-6), Chymotrypsin / Elastase (RmS-3) and Thrombin (RmS-15). Conclusion: This study constitutes an important contribution and improvement to the knowledge about the physiologic role of R. microplus serpins during the host-tick interaction.

在激波波面中氧分子的非平衡离解

对强激波作用下双原子分子振动与离解耦合的非平衡离解过程进行了理论计算.本工作的特点是将计算起点建立在分子基本参数上,采用主方程理论处理振动与离解的耦合,振动跃迁几率用SSH理论计算,在离解限附近考虑多量子数跃迁并计及原子复合的影响.对O2-Ar体系,计算给出了在正激波后O2分子振动能级分布、振动弛豫时间、离解孕育时间、离解产物浓度、离解速率系数等物理量随时间的演化.计算结果分别与Camac和Wray的实验相符.计算显示,在激波作用的后期,有准稳态的振动能级布居分布.计算结果显示,Park模型低估了非平衡离解速率系数,Hansen模型则高估了非平衡离解速率系数.

植物对重金属砷和镉胁迫适应的分子机理初探

随着现代工业的发展，重金属污染日趋严重。重金属污染引发的环境和健康问题在许多国家都有报道，我国的重金属污染状况也不容乐观。土壤和水体中的重金属污染可以通过食物链进入人体，对人类健康造成很大的危害，如诱发癌症 和畸胎等。 植物修复是一种利用植物对重金属或有机污染物的超富集能力清除或减低污染的环境生物技术。植物修复的生物学机制的研究为这项技术走向实用化奠定了基础。植物修复近期的进展可能来自于可更有效地富集重金属的植物品种的选择、土壤条件的改善等;但长远看来，植物修复技术的巨大进步将取决于新的可更好地抵抗重金属或降解有机毒物的基因的鉴定和克隆，并通过转基因技术创造一批新的植物品种，如可迅速大量富集重金属的高生物量的用作环境净化的植物，以及可排拒重金属吸收的粮食、蔬菜和水果等作物。 本研究针对砷污染的植物修复机制，以超富集砷的凤尾蕨属植物——蜈蚣草为试材取得了如下进展： 1． 以从砷污染地区采集的蜈蚣草（Pteris vittataL．）为植物材料，利用抑制消减杂交(SSH)分离了经砷诱导处理与其对照间表达有差异的cDNA片段，以期得到与砷富集密切相关的基因。其中筛选到的一个cDNA片段与ABC transporter (ATP-binding cassette transporter)有较高的同源性。通过RACE方法对该基因进行了克隆，并进行了初步的结构和功能分析。结果表明所获得的PvABCTl (Accession No. AY496966)为一全长cDNA，长度为2165 bp，其中开读框架为1791 bp，编码597个氨基酸。该基因所编码的蛋白中含有2个ABC transporter特性结构域，1个ATP-binding cassette和2个ATP/GTP结合位点(P-loop)，没有明显的跨膜区。 2． 对蜈蚣草在砷胁迫下PvABCT1基因的表达模式进行了研究。转录水平分析表明PvABCT1的表达受砷的诱导。进一步通过PvABCTl-GFP融合基因在洋葱细胞中的表达进行亚细胞定位，结果显示该基因可能定位于细胞质中。 3． 为了研究所克隆的PvABCT1基因的功能，本研究构建了PvABCT1的酵母表达载体，把该基因转入因ACR3基因缺失而对砷敏感的酵母突变株。酵母功能互补实验表明PvABCT1不仅不能与ACR3基因功能互补，反而使酵母对砷的敏感性增加，同时酵母细胞中的砷含量较未转化的酵母细胞增加。即在转入PvABCT1后，酵母细胞吸收了更多的砷。这暗示该基因与蜈蚣草中砷的高吸收有关。 针对食品重金属污染问题，本研究探讨了减低蔬菜对重金属吸收的方法及其 作用机理，取得了如下进展： 1．研究了钙离子和镧离子对镉离子胁迫下生菜种子萌发和植株生长的影响，结果表明在种子萌发时外施4 mM CaCI2或0.04 mg/L La(N03)3均可提高生菜对重金属镉的抗性。 2．通过检测0.5 mM CdCl2胁迫下生菜植株中的镉含量以及外施钙离子或镧离子后相应的镉含量，发现4 mM CaCl2可以增加镉胁迫下生菜植株中镉的积累;而0.04 mg/L La(N03)3可以降低镉胁迫下生菜植株中镉的积累。 3．对生菜中植物络合素合酶基因进行了克隆，通过RT-PCR分析以及植物络合素( phytochelatins，PCs)的检测，探讨了外施钙离子或镧离子对镉胁迫下生菜植株中植物络合素合酶基因在转录水平的表达量、植物络合素含量以及镉的积累三者之间的关系。结果表明：4 mM CaCl2可以提高镉胁迫下生菜植株中植物络合素合酶基因在转录水平的表达以及植物络合素的含量，增加镉的积累;而0.04 mg/L La(N03)3虽然同样可以提高植物络合素合酶基因在转录水平的表达以及植物络合素的含量，却能降低镉胁迫下生菜植株中镉的积累。这暗示外施钙离子可以促进用于重金属污染环境修复的植物对重金属的吸收，而外施镧离子可以用于降低叶菜类蔬菜中重金属镉的积累。