A model for querying semistructured data through the exploitation of regular sub-structures

Much research has been undertaken in order to speed up the processing of semistructured data in general and XML in particular. Many approaches for storage, compression, indexing and querying exist, e.g. [1, 2]. We do not present yet another such algorithm but a unifying model in which these algorithm can be understood. The key idea behind this research is the assumption, that most practical queries are based on a particular pattern of data that can be deduced from the query and which can then be captured using a regular structure amendable to efficient processing techniques

Compact in-memory representation of XML data : design and implementation of a compressed DOM for data-centric documents

Over recent years XML has evolved from a document exchange format to a multi-purpose data storage and retrieval solution. To make use of the full potential of XML in the domain of large, data-centric documents it is necessary to have easy and fast access to individual data elements. We describe an implementation of the Document Object Model (DOM) that is designed with these objectives in mind. It uses compression to allow large documents to be stored in the computer's main memory. Query-relevant DOM methods are optimised to work on top of the created data structure. Measurements indicate that compression up to a factor of 5 is possible without losing the ability to directly address individual elements. No prior decompression is needed to query and locate nodes

The hypersensitivity resistance of european plum to the Plum pox virus and its potential impact on the epidemiology of the virus

Since the detection of the Plum pox virus (PPV) different strategies for Sharka containment were developed. One of the most important one is the breeding of resistant cultivars. Other than in Prunus persica and in Prunus armeniaca, in Prunus domestica a type of natural resistance was detected which seems to be able to prevent the spread of PPV both over long and short distances. Therefore, this type of Sharka resistance which is based on a hypersensitive response and has been stable for more than 20 years is suggested to have the most beneficial impact on the epidemiology of the virus compared to other mechanisms of resistance or tolerance.Keywords: Sharka containment, Prunus domestica, plum breedin

The inheritance of the hypersensitivity resistance of European plum (Prunus domestica L.) against the Plum pox virus

In between 2003 and 2009 more than 500 seedlings have been tested for hypersensitivity resistance against the Plum pox virus (PPV), which causes Sharka disease. The seedlings had at least one hypersensitive parent genotype. They were tested for hypersensitivity resistance by double grafting onto PPV infected interstem in the green house. In crossing combinations with two hypersensitive parents the percentage of hypersensitive seedlings was highest. There is also no equal distribution of the genotypes over the individual hypersensitivity classes (HC) in all crossing combinations. The percentage of hypersensitive seedlings strongly depends on the parentage. Furthermore investigations regarding the origin of the hypersensitivity resistance of the cultivar ‘Jojo’, which is a descendant of a crossing combination from ‘Ortenauer’ × ‘Stanley’, were done. It was shown that the cultivar ‘Ortenauer’ is the donor of the hypersensitivity trait.Keywords: Plum pox virus, hypersensitivity, inheritance, Prunus domestica L., resistanc

Preliminary studies on the use of the Cascade Rolling Circle Amplification technique for Plum pox virus detection

Isothermal techniques for the amplification of nucleic acids have emerged in the last years. In contrast to the Polymerase chain reaction (PCR), the most prevalent method to amplify DNA in vitro, the reactions can be run at constant temperatures. Specificity and sensitivity are at least as high as that obtained by using PCR and the methods are less time consuming. Therefore, the isothermal amplification of nucleic acids provides a powerful tool for the detection of Plum pox virus (PPV), the causal agent of the Sharka disease. The cascade rolling circle amplification (CRCA), first described by Thomas et al. (1999), is based on the rolling circle mechanism that many viruses use to replicate their genome multiplicatively. Circular Probes, also called Padlock probes (PLP), which arise from the ligation of the terminal region of DNA probes upon side by side hybridization to the target serve as template (Nilsson et al. 1994).For detecting PPV by CRCA, RNA was extracted and reverse transcribed to cDNA using a PPV specific primer. Several PLPs with varying lengths and sequences complementary region to the cDNA were designed and tested. Furthermore, different pairs of primers for the subsequent amplification were developed. For specific ligation Ampligase and T4 DNA Ligase were tested. In CRCA, two polymerases with strong strand displacement activity were compared: Phi29 DNA Polymerase and Bst DNA Polymerase. These enzymes differ in their optimal reaction temperature.Ligation as well as amplification do occur, but there is high background amplification also in negative and no template controls. Discrimination was possible after a restriction digestion is carried out. As proven by sequencing of reaction products non-specific signals were a result of primer polymerization. Current work focuses on the reduction of the background amplification and improvement of the sensitivity. Keywords: Cascade Rolling Circle Amplification, CRCA, isothermal amplification of DNA, Plum pox virus, PP

Photounbinding of Calmodulin from a Family of CaM Binding Peptides

Background: Recent studies have shown that fluorescently labeled antibodies can be dissociated from their antigen by illumination with laser light. The mechanism responsible for the photounbinding effect, however, remains elusive. Here, we give important insights into the mechanism of photounbinding and show that the effect is not restricted to antibody/ antigen binding. Methodology/Principal Findings: We present studies of the photounbinding of labeled calmodulin (CaM) from a set of CaM-binding peptides with different affinities to CaM after one- and two-photon excitation. We found that the photounbinding effect becomes stronger with increasing binding affinity. Our observation that photounbinding can be influenced by using free radical scavengers, that it does not occur with either unlabeled protein or non-fluorescent quencher dyes, and that it becomes evident shortly after or with photobleaching suggest that photounbinding and photobleaching are closely linked. Conclusions/Significance: The experimental results exclude surface effects, or heating by laser irradiation as potential causes of photounbinding. Our data suggest that free radicals formed through photobleaching may cause a conformationa

Apoptosis at Inflection Point in Liquid Culture of Budding Yeasts

Budding yeasts are highly suitable for aging studies, because the number of bud scars (stage) proportionally correlates with age. Its maximum stages are known to reach at 20–30 stages on an isolated agar medium. However, their stage dynamics in a liquid culture is virtually unknown. We investigate the population dynamics by counting scars in each cell. Here one cell division produces one new cell and one bud scar. This simple rule leads to a conservation law: “The total number of bud scars is equal to the total number of cells.” We find a large discrepancy: extremely fewer cells with over 5 scars than expected. Almost all cells with 6 or more scars disappear within a short period of time in the late log phase (corresponds to the inflection point). This discrepancy is confirmed directly by the microscopic observations of broken cells. This finding implies apoptosis in older cells (6 scars or more)

Conserved genes underlie phenotypic plasticity in an incipiently social bee

Despite a strong history of theoretical work on the mechanisms of social evolution, relatively little is known of the molecular genetic changes that accompany transitions from solitary to eusocial forms. Here we provide the first genome of an incipiently social bee that shows both solitary and social colony organization in sympatry, the Australian carpenter bee Ceratina australensis. Through comparative analysis, we provide support for the role of conserved genes and cis-regulation of gene expression in the phenotypic plasticity observed in nest-sharing, a rudimentary form of sociality. Additionally, we find that these conserved genes are associated with caste differences in advanced eusocial species, suggesting these types of mechanisms could pave the molecular pathway from solitary to eusocial living. Genes associated with social nesting in this species show signatures of being deeply conserved, in contrast to previous studies in other bees showing novel and faster-evolving genes are associated with derived sociality. Our data provide support for the idea that the earliest social transitions are driven by changes in gene regulation of deeply conserved genes