A BitTorrent-based peer-to-peer database server

Database systems have traditionally used a Client-Server architecture, where clients send queries to a database server. If the data proves popular, the server may become overloaded, leading to clients experiencing an increase in query response time. In the domain of file-sharing, the problem of server overloading has been successfully addressed by the use of Peer-to-Peer (P2P) techniques in which users (peers) supply files – or pieces of files – to each other. This thesis will examine whether P2P techniques can be applied successfully in a database environment. It will introduce the Wigan Peer-to-Peer Database System, a P2P database system based on the popular BitTorrent file-sharing protocol. The potential benefits of a P2P database system include performance and scalability; allowing peers to answer each others’ queries will reduce the load on the database server and so could overcome the problem of a busy server becoming overloaded. Other potential benefits are fault tolerance and cost reduction. The Wigan architecture is introduced in this thesis, firstly by describing the BitTorrent algorithms and then by discussing how these algorithms must be modified for use in a database system. Experiments carried out on a simulator of Wigan are analysed in order to determine factors which affect its performance. These allow the identification of scenarios where Wigan could outperform a traditional database server. Further extensions to the Wigan architecture are discussed in this thesis, including possible means of handling data updates.EThOS - Electronic Theses Online ServiceGBUnited Kingdo

Multi-locus variable-number tandem-repeat analysis of the fish-pathogenic bacterium Yersinia ruckeri by multiplex PCR and capillary electrophoresis

Under embargo until 17.06.2021.Yersinia ruckeri is an important pathogen of farmed salmonids worldwide, but simple tools suitable for epizootiological investigations (infection tracing, etc.) of this bacterium have been lacking. A Multi-Locus Variable-number tandem-repeat Analysis (MLVA) assay was therefore developed as an easily accessible and unambiguous tool for high-resolution genotyping of recovered isolates. For the MLVA assay presented here, DNA is extracted from cultured Y. ruckeri samples by boiling bacterial cells in water, followed by use of supernatant as template for PCR. Primer-pairs targeting ten Variable-number tandem-repeat (VNTR) loci, interspersed throughout the Y. ruckeri genome, are distributed equally amongst two five-plex PCR reactions running under identical cycling conditions. Forward primers are labelled with either of three fluorescent dyes. Following amplicon confirmation by gel electrophoresis, PCR products are diluted and subjected to capillary electrophoresis. From the resulting electropherogram profiles, peaks representing each of the VNTR loci are size-called and employed for calculating VNTR repeat counts in silico. Resulting ten-digit MLVA profiles are then used to generate Minimum spanning trees enabling epizootiological evaluation by cluster analysis. The highly portable output data, in the form of numerical MLVA profiles, can rapidly be compared across labs and placed in a spatiotemporal context. The entire procedure from cultured colony to epizootiological evaluation may be completed for up to 48 Y. ruckeri isolates within a single working day. The video component of this article can be found at https://www.jove.com/video/59455/.publishedVersio

Biotyping reveals loss of motility in two distinct Yersinia ruckeri lineages exclusive to Norwegian aquaculture

Non-motile strains of Yersinia ruckeri, known as Y. ruckeri biotype 2, now dominate amongst clinical isolates retrieved from rainbow trout internationally. Due to an acute increase in the number of yersiniosis cases in Norway in recent years, followed by introduction of widespread intraperitoneal vaccination against the disease, an investigation on the prevalence of Y. ruckeri biotype 2 in Norwegian aquaculture was conducted. We biotyped 263 Y. ruckeri isolates recovered from diseased salmonids in Norway between 1985 and 2020. A total of seven biotype 2 isolates were identified, four of which were collected between 1985 and 1987, and three of which belong to the current epizootic clone, isolated from two different sea-farms in 2017. Whole-genome sequencing revealed single non-synonymous nucleotide polymorphisms in the flagellar genes flhC in isolates from the 1980s, and in fliP in isolates from 2017. In both variants, motility was restored both by complementation with wild-type alleles in trans and via spontaneous mutation-driven reversion following prolonged incubation on motility agar. While biotype 2 strains do not yet seem to have become broadly established in Norwegian aquaculture, the seven isolates described here serve to document a further two independent cases of Y. ruckeri biotype 2 emergence in salmonid aquaculture.publishedVersio

Studies of the hormonal regulation of leaf senescence

This thesis describes an investigation into the role of abscisic acid (ABA) in the regulation of foliar senescence in radish and bean. The effect of ABA on the decline of protein and RNA pre-labelled with radioactive precursors, and on the loss of chlorophyll during the senescence of leaf discs of radish (Raphanus sativus L.) were studied. ABA stimulated the decline of chlorophyll during the early period of incubation, but subsequent loss of chlorophyll was retarded by ABA. ABA also enhanced the loss of protein and RNA from the leaf discs. Moreover, since the level of radioactive protein or RNA was normally lower in ABA-treated discs than in water-treated discs, it is possible that ABA was acting to stimulate protein and RNA degradation. On the other hand, the data indicate that ABA might act by limiting synthesis of radioactive protein or RNA in the post-labelling period. Thus, protein and RNA synthesis inhibitors were used in order to limit this period of incorporation. The limitations and possible disadvantages of the use of such inhibitors are discussed. The uptake of [14]C-ABA by radish leaf discs was highest 1 to 2 days after excision and then declined to 6 days. This pattern of uptake was not mirrored by uptake of [14]C-sucrose. The uptake of [14]C-ABA and [14]C-sucrose was substantially reduced by anaerobic conditions. Radioactive ABA is metabolised to 2 other major radioactive products by radish leaf discs, even after 6 days of pre-ageing in water. A similar pattern of metabolism for [14]C-ABA was observed in whole leaves of radish. Metabolism of [14]C-ABA in leaf discs was largely dependent on aerobic metabolism and was not affected by the addition of antibiotics to control any microbial contamination. Studies were also made on the pattern of metabolism during a 24 hour time-course and on the fate of partially purified metabolites re-supplied to radish leaf discs. The extraction and identification of the metabolic products of ABA has been attempted. The presence of endogenous ABA in primary leaves of bean (Phaseolus vulgaris L.) has been demonstrated. Using circular dichroism procedures, quantitative determinations of ABA in bean leaves at various stages of development indicated little consistent change in the amount of ABA with the onset and progress of senescence. ABA levels in extracts of wilted and non-wilted leaves of bean were compared in a preliminary experiment. In ultrastructural studies of radish leaf tissue, differences in the pattern of senescence-associated changes in cellular organelles were noted between leaf tissue aged in water, tissue aged in ABA and naturally senescent leaf material. The problems resulting from the possible variation in leaf material and to the asynchronous nature of senescence are discussed. The benefits and disadvantages associated with the use of leaf discs as an assay system for leaf senescence are also discussed

Letters to the Editor

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/65900/1/j.1752-7325.1989.tb02048.x.pd

Expression Analysis of Moritella viscosa-Challenged Atlantic Salmon Identifies Disease-Responding Genes, MicroRNAs and Their Predicted Target Genes and Pathways

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Tenacibaculosis in Norwegian Atlantic salmon (Salmo salar) cage-farmed in cold sea water is primarily associated with Tenacibaculum finnmarkense genomovar finnmarkense

Skin conditions associated with Tenacibaculum spp. constitute a significant threat to the health and welfare of sea-farmed Atlantic salmon (Salmo salar L.) in Norway. Fifteen presumptive tenacibaculosis outbreaks distributed along the Norwegian coast during the late winter and spring of 2018 were investigated. Bacteriological culture confirmed the presence of Tenacibaculum spp. Seventy-six isolates cultured from individual fish were selected and subjected to whole-genome sequencing and MALDI-TOF MS analysis. Average nucleotide identity and MALDI-TOF analyses confirmed the presence of T. finnmarkense and T. dicentrarchi, with further division of T. finnmarkense into genomovars (gv.) finnmarkense and ulcerans. Core genome multilocus sequence typing (cgMLST) and single-nucleotide polymorphism (SNP) analyses identified the presence of a genetically conserved cluster of gv. finnmarkense isolates against a background of relatively genetically diverse gv. finnmarkense and gv. ulcerans isolates in 13 of the 15 studied cases. This clustering strongly suggests a link between T. finnmarkense gv. finnmarkense and development of clinical tenacibaculosis in sea-farmed Norwegian salmon in the late winter and spring. Analysis of 25 Tenacibaculum isolates collected during the spring of 2019 from similar cases identified a similar distribution of genotypes. Low water temperatures were common to all cases, and most incidences involved relatively small fish shortly after sea transfer, suggesting that these fish are particularly predisposed to Tenacibaculum infection.publishedVersio

qPCR screening for Yersinia ruckeri clonal complex 1 against a background of putatively avirulent strains in Norwegian aquaculture

Although a number of genetically diverse Yersinia ruckeri strains are present in Norwegian aquaculture environments, most if not all outbreaks of yersiniosis in Atlantic salmon in Norway are associated with a single specific genetic lineage of serotype O1, termed clonal complex 1. To investigate the presence and spread of virulent and putatively avirulent strains in Norwegian salmon farms, PCR assays specific for Y. ruckeri (species level) and Y. ruckeri clonal complex 1 were developed. Following extensive screening of water and biofilm, the widespread prevalence of putatively avirulent Y. ruckeri strains was confirmed in freshwater salmon hatcheries, while Y. ruckeri clonal complex 1 was found in fewer farms. The formalin-killed bacterin yersiniosis vaccine was detected in environmental samples by both PCR assays for several weeks post-vaccination. It is thus important to interpret results from recently vaccinated fish with great care. Moreover, field studies and laboratory trials confirmed that stressful management procedures may result in increased shedding of Y. ruckeri by sub-clinically infected fish. Analysis of sea water sampled throughout thermal delousing procedures proved effective for detection of Y. ruckeri in sub-clinically infected populations.publishedVersio

MLVA genotyping of Moritella viscosa reveals serial emergence of novel, host-specific clonal complexes in Norwegian salmon farming

A Multi-Locus Variable number of tandem repeat Analysis (MLVA) genotyping scheme was developed for the epidemiological study of Moritella viscosa, which causes ‘winter ulcer’ predominantly in sea-reared Atlantic salmon (Salmo salar L.). The assay involves multiplex PCR amplification of six Variable Number of Tandem Repeat (VNTR) loci, followed by capillary electrophoresis and data interpretation. A collection of 747 spatiotemporally diverse M. viscosa isolates from nine fish species was analysed, the majority from farmed Norwegian salmon. MLVA distributed 76% of the isolates across three major clonal complexes (CC1, CC2 and CC3), with the remaining forming minor clusters and singletons. While 90% of the salmon isolates belong to either CC1, CC2 or CC3, only 20% of the isolates recovered from other fish species do so, indicating a considerable degree of host specificity. We further highlight a series of ‘clonal shifts’ amongst Norwegian salmon isolates over the 35-year sampling period, with CC1 showing exclusive predominance prior to the emergence of CC2, which was later supplanted by CC3, before the recent re-emergence of CC1. Apparently, these shifts have rapidly swept the entire Norwegian coastline and conceivably, as suggested by typing of a small number of non-Norwegian isolates, the Northeast Atlantic region as a whole.publishedVersio