Online Forum Thread Retrieval using Pseudo Cluster Selection and Voting Techniques

Online forums facilitate knowledge seeking and sharing on the Web. However, the shared knowledge is not fully utilized due to information overload. Thread retrieval is one method to overcome information overload. In this paper, we propose a model that combines two existing approaches: the Pseudo Cluster Selection and the Voting Techniques. In both, a retrieval system first scores a list of messages and then ranks threads by aggregating their scored messages. They differ on what and how to aggregate. The pseudo cluster selection focuses on input, while voting techniques focus on the aggregation method. Our combined models focus on the input and the aggregation methods. The result shows that some combined models are statistically superior to baseline methods.Comment: The original publication is available at http://www.springerlink.com/. arXiv admin note: substantial text overlap with arXiv:1212.533

Cultivation of hitherto-uncultured bacteria belonging to the Verrucomicrobia subdivision 1 from the potato (Solanum tuberosum L.) rhizosphere

The role of dominant bacterial groups in the plant rhizosphere, e.g., those belonging to the phyla Acidobacteria and Verrucomicrobia, has, so far, not been elucidated, and this is mainly due to the lack of culturable representatives. This study aimed to isolate hitherto-uncultured bacteria from the potato rhizosphere by a combination of cultivation approaches. An agar medium low in carbon availability (oligotrophic agar medium) and either amended with potato root exudates or catalase or left unamended was used with the aim to improve the culturability of bacteria from the potato rhizosphere. The colony forming unit numbers based on colonies and microcolonies were compared with microscopically determined fluorescence-stained cell numbers. Taxonomical diversity of the colonies was compared with that of library clones made from rhizosphere DNA, on the basis of 16S rRNA gene comparisons. The oligotrophic media amended or not with catalase or rhizosphere extract recovered up to 33.6% of the total bacterial numbers, at least seven times more than the recovery observed on R2A. Four hitherto-uncultured Verrucomicrobia subdivision 1 representatives were recovered on agar, but representatives of this group were not found in the clone library. The use of oligotrophic medium and its modifications enabled the growth of colony numbers, exceeding those on classical agar media. Also, it led to the isolation of hitherto-uncultured bacteria from the potato rhizosphere. Further improvement in cultivation will certainly result in the recovery of other as-yet-unexplored bacteria from the rhizosphere, making these groups accessible for further investigation, e.g., with respect to their possible interactions with plants

Assessment of transformability of bacteria associated with tomato and potato plants

Transformation of plant-associated bacteria by plant DNA has never been demonstrated in agricultural fields. In total 552 bacterial isolates from stems of Ralstonia solanacearum-infected and healthy tomato plants and from stems and leaves of healthy potato plants were tested for natural genetic competence using plasmid pSKTG DNA and homologous DNA extracts. Control strain Acinetobacter baylyi ADP1 was transformable with both DNA extracts. No transformable isolates were observed after treatment with plasmid pSKTG DNA. Two isolates, P34, identified as Pseudomonas trivialis and A19, identified as Pseudomonas fragi, were selected on the basis of the consistently higher Rp-resistant CFU numbers after treatment with DNA from Rp-resistant cells than with that from wild-type cells. P34 showed 2.1-fold and A19 1.5-fold higher Rp-resistant CFU numbers after treatment with DNA from homologous Rp-resistant cells versus that from wild-type cells. It is concluded that bacteria capable of in vitro capture and integration of exogenous DNA into their genomes are relatively rare in culturable bacterial communities associated with tomato and potato plants, or that conditions conducive to transformation were not met in transformation assays

Adapting voting techniques for online forum thread retrieval

Online forums or message boards are rich knowledge-based communities. In these communities, thread retrieval is an essential tool facilitating information access. However, the issue on thread search is how to combine evidences from text units(messages) to estimate thread relevance. In this paper, we first rank a list of messages, then score threads by aggregating their ranked messages’ scores. To aggregate the message scores, we adopt several voting techniques that have been applied in ranking aggregates tasks such as blog distillation and expert finding. The experimental result shows that many voting techniques should be preferred over a baseline that treats threads as a concatenation of their messages’ text

Diversity of endophytic bacterial populations and their interaction with Xylella fastidiosa in citrus plants

Citrus variegated chlorosis (CVC) is caused by Xylella fastidiosa, a phytopathogenic bacterium that can infect all Citrus sinensis cultivars. The endophytic bacterial communities of healthy, resistant, and CVC-affected citrus plants were studied by using cultivation as well as cultivation-independent techniques. The endophytic communities were assessed in surface-disinfected citrus branches by plating and denaturing gradient gel electrophoresis (DGGE). Dominant isolates were characterized by fatty-acid methyl ester analysis as Bacillus pumilus, Curtobacterium flaccumfaciens, Enterobacter cloacae, Methylobacterium spp. (including Methylobacterium extorquens, M. fujisawaense, M. mesophilicum, M. radiotolerans, and M. zatmanii), Nocardia sp., Pantoea agglomerans, and Xanthomonas campestris. We observed a relationship between CVC symptoms and the frequency of isolation of species of Methylobacterium, the genus that we most frequently isolated from symptomatic plants. In contrast, we isolated C. flaccumfaciens significantly more frequently from asymptomatic plants than from those with symptoms of CVC while P. agglomerans was frequently isolated from tangerine (Citrus reticulata) and sweet-orange (C. sinensis) plants, irrespective of whether the plants were symptomatic or asymptomatic or showed symptoms of CVC. DGGE analysis of 16S rRNA gene fragments amplified from total plant DNA resulted in several bands that matched those from the bacterial isolates, indicating that DGGE profiles can be used to detect some endophytic bacteria of citrus plants. However, some bands had no match with any isolate, suggesting the occurrence of other, nonculturable or as yet uncultured, endophytic bacteria. A specific band with a high G C ratio was observed only in asymptomatic plants. The higher frequency of C. flaccumfaciens in asymptomatic plants suggests a role for this organism in the resistance of plants to CVC

Impact of transgenic potatoes expressing anti-bacterial agents on bacterial endophytes is comparable with the effects of plant genotype, soil type and pathogen infection

1. Blackleg and soft rot disease of potatoes Solanum tuberosum L., mainly caused by the bacterial pathogen Erwinia carotovora ssp. atrospetica (Eca), lead to enormous yield losses world-wide. Genetically modified (GM) potatoes producing anti-bacterial agents, such as cecropin/attacin and T4 lysozyme, may offer effective future pathogen control strategies. Because of concerns about undesirable ecological side-effects of GM crops, it is important to analyse the potential environmental impact of GM crops carefully. The objective of this study was to investigate the effect of GM potatoes with anti-bacterial activity on the diversity and functional abilities of bacteria colonizing the intercellular spaces and vascular tissues (endosphere) of potato plants. 2. A greenhouse experiment was performed to analyse the effect of GM potatoes expressing either attacin/cecropin or T4 lysozyme on endophytic bacterial communities. Endophytic bacteria colonizing the GM potato lines as well as their nearly isogenic wild types were analysed at two vegetation stages. In order to compare GM-related variations with impacts caused by changing environmental conditions, potatoes were cultivated in two different soil types, and challenged with the pathogen Eca. Endophytic diversity was assessed by 16S rRNA-based terminal-restriction fragment length polymorphism (T-RFLP) analysis. Cultivated community members were identified by 16S rRNA gene analysis and screened for a range of plant growth-promoting and plant pathogen-antagonistic abilities. 3. Both genetic transformation events induced a differentiation in the community structures of associated bacterial populations and in the related functional abilities of cultivated bacterial endophytes. In comparison with the other factors analysed, the impact of both genetic modification types was minor or comparable with the variations caused by plant genotype, vegetation stage, pathogen exposure and soil type. 4. Synthesis and applications. This study has shown that the expression of anti-bacterial proteins may affect bacterial endophytes; however, the impacts were no greater than those of other factors analysed. Future risk assessment studies of GM crops should consider different environmental factors. This study contributes to the ongoing risk assessment of GM crops and provides valuable baseline information for prospective GM crop assays