Browsing by Author "Robinson Z"

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    Avian Influenza Virus Surveillance Across New Zealand and Its Subantarctic Islands Detects H1N9 in Migratory Shorebirds, but Not 2.3.4.4b HPAI H5N1
    (John Wiley and Sons Ltd, 2025-04) Waller SJ; Wierenga JR; Heremia L; Darnley JA; de Vries I; Dubrulle J; Robinson Z; Miller AK; Niebuhr CN; Melville DS; Schuckard R; Battley PF; Wille M; Alai B; Cole R; Cooper J; Ellenberg U; Elliott G; Faulkner J; Fischer JH; Fyfe J; Hay L; Houston D; Keys BC; Long J; Long R; Mattern T; McGovern H; McNutt L; Moore P; Neil O; Osborne J; Pagé A-S; Parker KA; Perry M; Philp B; Reid J; Rexer-Huber K; Russell JC; Sagar R; Ruru TT; Thompson T; Thomson L; Tinnemans J; Uddstrom L; Waipoua TA; Walker K; Whitehead E; Wickes C; Young MJ; McInnes K; Winter D; Geoghegan JL
    Highly pathogenic avian influenza (HPAI) virus subtype H5N1 has never been detected in New Zealand. The potential impact of this virus on New Zealand's wild birds would be catastrophic. To expand our knowledge of avian influenza viruses across New Zealand, we sampled wild aquatic birds from New Zealand, its outer islands and its subantarctic territories. Metatranscriptomic analysis of 700 individuals spanning 33 species revealed no detection of H5N1 during the annual 2023–2024 migration. A single detection of H1N9 in red knots (Calidris canutus) was noted. This study provides a baseline for expanding avian influenza virus monitoring in New Zealand.
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    Genomic and genetic analyses of diversity and plant interactions of Pseudomonas fluorescens
    (BIOMED CENTRAL LTD, 2009) Silby MW; Cerdeno-Tarraga AM; Vernikos GS; Giddens SR; Jackson RW; Preston GM; Zhang XX; Moon CD; Gehrig SM; Godfrey SAC; Knight CG; Malone JG; Robinson Z; Spiers AJ; Harris S; Challis GL; Yaxley AM; Harris D; Seeger K; Murphy L; Rutter S; Squares R; Quail MA; Saunders E; Mavromatis K; Brettin TS; Bentley SD; Hothersall J; Stephens E; Thomas CM; Parkhill J; Levy SB; Rainey PB; Thomson NR
    BACKGROUND: Pseudomonas fluorescens are common soil bacteria that can improve plant health through nutrient cycling, pathogen antagonism and induction of plant defenses. The genome sequences of strains SBW25 and Pf0-1 were determined and compared to each other and with P. fluorescens Pf-5. A functional genomic in vivo expression technology (IVET) screen provided insight into genes used by P. fluorescens in its natural environment and an improved understanding of the ecological significance of diversity within this species. RESULTS: Comparisons of three P. fluorescens genomes (SBW25, Pf0-1, Pf-5) revealed considerable divergence: 61% of genes are shared, the majority located near the replication origin. Phylogenetic and average amino acid identity analyses showed a low overall relationship. A functional screen of SBW25 defined 125 plant-induced genes including a range of functions specific to the plant environment. Orthologues of 83 of these exist in Pf0-1 and Pf-5, with 73 shared by both strains. The P. fluorescens genomes carry numerous complex repetitive DNA sequences, some resembling Miniature Inverted-repeat Transposable Elements (MITEs). In SBW25, repeat density and distribution revealed 'repeat deserts' lacking repeats, covering approximately 40% of the genome. CONCLUSIONS: P. fluorescens genomes are highly diverse. Strain-specific regions around the replication terminus suggest genome compartmentalization. The genomic heterogeneity among the three strains is reminiscent of a species complex rather than a single species. That 42% of plant-inducible genes were not shared by all strains reinforces this conclusion and shows that ecological success requires specialized and core functions. The diversity also indicates the significant size of genetic information within the Pseudomonas pan genome.