16 Works

Additional file 6 of The Venturia inaequalis effector repertoire is dominated by expanded families with predicted structural similarity, but unrelated sequence, to avirulence proteins from other plant-pathogenic fungi

Mercedes Rocafort, Joanna K. Bowen, Berit Hassing, Murray P. Cox, Brogan McGreal, Silvia de la Rosa, Kim M. Plummer, Rosie E. Bradshaw & Carl H. Mesarich
Additional file 6: List of protein tertiary structures from Venturia inaequalis with a confident AlphaFold2 prediction and list of predicted SCOPe folds.

Additional file 7 of The Venturia inaequalis effector repertoire is dominated by expanded families with predicted structural similarity, but unrelated sequence, to avirulence proteins from other plant-pathogenic fungi

Mercedes Rocafort, Joanna K. Bowen, Berit Hassing, Murray P. Cox, Brogan McGreal, Silvia de la Rosa, Kim M. Plummer, Rosie E. Bradshaw & Carl H. Mesarich
Additional file 7: Matrix amino acid identity of the effector candidate (EC) structural families (MAX, ToxA, LARS, FOLD).

Data from: A clockwork fish. Age-prediction using DNA methylation-based biomarkers in the European seabass

Dafni Anastasiadi & Francesc Piferrer
Age-related changes in DNA methylation do occur. Taking advantage of this, mammalian and avian epigenetic clocks have been constructed to predict age. In fish, studies on age-related DNA methylation changes are scarce and no epigenetic clocks are available. However, in fisheries and population studies there is a need for accurate estimation of age, something that is often impossible for some economically important species with the currently available methods. Here, we used the European sea bass,...

Data from: Analysis of the genome of the New Zealand giant collembolan (Holacanthella duospinosa) sheds light on hexapod evolution

Chen Wu, Melissa D. Jordan, Richard D. Newcomb, Neil J. Gemmell, Sarah Bank, Karen Meusemann, Peter K. Dearden, Elizabeth J. Duncan, Sefanie Grosser, Kim Rutherford, Paul P. Gardner, Ross N. Crowhurst, Bernd Steinwender, Leah K. Tooman, Mark I. Stevens & Thomas R. Buckley
Background: The New Zealand collembolan genus Holacanthella contains the largest species of springtails (Collembola) in the world. Using Illumina technology we have sequenced and assembled a draft genome and transcriptome from Holacanthella duospinosa (Salmon). We have used this annotated assembly to investigate the genetic basis of a range of traits critical to the evolution of the Hexapoda, the phylogenetic position of H. duospinosa and potential horizontal gene transfer events. Results: Our genome assembly was ~375...

Additional file 4 of The Venturia inaequalis effector repertoire is dominated by expanded families with predicted structural similarity, but unrelated sequence, to avirulence proteins from other plant-pathogenic fungi

Mercedes Rocafort, Joanna K. Bowen, Berit Hassing, Murray P. Cox, Brogan McGreal, Silvia de la Rosa, Kim M. Plummer, Rosie E. Bradshaw & Carl H. Mesarich
Additional file 4: List of Pfam domains in proteins encoded by genes of the five distinct temporal expression waves of Venturia inaequalis that are upregulated during colonization of susceptible apple cultivar ‘Royal Gala’, when compared to growth of the fungus in culture on the surface of cellophane membranes overlying potato dextrose agar.

Additional file 7 of The Venturia inaequalis effector repertoire is dominated by expanded families with predicted structural similarity, but unrelated sequence, to avirulence proteins from other plant-pathogenic fungi

Mercedes Rocafort, Joanna K. Bowen, Berit Hassing, Murray P. Cox, Brogan McGreal, Silvia de la Rosa, Kim M. Plummer, Rosie E. Bradshaw & Carl H. Mesarich
Additional file 7: Matrix amino acid identity of the effector candidate (EC) structural families (MAX, ToxA, LARS, FOLD).

Data from: Disruption of foraging by a dominant invasive species to decrease its competitive ability

Fabian Ludwig Westermann, David Maxwell Suckling & Philip John Lester
Invasive species are a major threat to biodiversity when dominant within their newly established habitat. The globally distributed Argentine ant Linepithema humile has been reported to break the trade-off between interference and exploitative competition, achieve high population densities, and overpower nests of many endemic ant species. We have used the sensitivity of the Argentine ant to the synthetic trail pheromone (Z)-9-hexadecanal to investigate species interactions for the first time. We predicted that disrupting Argentine ant...

Novel insight into the effects of CPXR on Salmonella enteritidis cells during the chlorhexidine treatment and non-stressful growing conditions

Sinisa Vidovic
The emergence and spread of antimicrobial resistance is a significant global challenge. To solve this emerging problem, the discovery of novel bacterial cellular targets and the critical pathways associated with antimicrobial resistance is urgently needed. In this study, we investigated the role of the two most critical extracytoplasmic stress response regulators, RpoE and CpxR, on the physiology and susceptibility of growing Salmonella enterica serovar Enteritidis cells using the polycationic antimicrobial agent, chlorhexidine (CHX). We showed...

Additional file 3 of The Venturia inaequalis effector repertoire is dominated by expanded families with predicted structural similarity, but unrelated sequence, to avirulence proteins from other plant-pathogenic fungi

Mercedes Rocafort, Joanna K. Bowen, Berit Hassing, Murray P. Cox, Brogan McGreal, Silvia de la Rosa, Kim M. Plummer, Rosie E. Bradshaw & Carl H. Mesarich
Additional file 3: Differentially expressed genes of Venturia inaequalis during infection of susceptible apple cultivar ‘Royal Gala’, when compared to growth of the fungus in culture on the surface of cellophane membranes overlying potato dextrose agar.

Additional file 5 of The Venturia inaequalis effector repertoire is dominated by expanded families with predicted structural similarity, but unrelated sequence, to avirulence proteins from other plant-pathogenic fungi

Mercedes Rocafort, Joanna K. Bowen, Berit Hassing, Murray P. Cox, Brogan McGreal, Silvia de la Rosa, Kim M. Plummer, Rosie E. Bradshaw & Carl H. Mesarich
Additional file 5: List of effector candidates (ECs) identified from Venturia inaequalis, their family classification, and indication of whether EC family members cluster in the genome.

Additional file 6 of The Venturia inaequalis effector repertoire is dominated by expanded families with predicted structural similarity, but unrelated sequence, to avirulence proteins from other plant-pathogenic fungi

Mercedes Rocafort, Joanna K. Bowen, Berit Hassing, Murray P. Cox, Brogan McGreal, Silvia de la Rosa, Kim M. Plummer, Rosie E. Bradshaw & Carl H. Mesarich
Additional file 6: List of protein tertiary structures from Venturia inaequalis with a confident AlphaFold2 prediction and list of predicted SCOPe folds.

Data from: A new plant virus discovered by immunocapture of double stranded RNA; assessment of a novel approach for viral metagenomics studies

Arnaud G. Blouin, Howard A. Ross, Jody Hobson-Peters, Caitlin A. O’Brien, Ben Warren, Robin MacDiarmid & Caitlin A. O'Brien
Next-generation sequencing technologies enable the rapid identification of viral infection of diseased organisms. However, despite a consistent decrease in sequencing costs, it is difficult to justify their use in large-scale surveys without a virus sequence enrichment technique. As the majority of plant viruses have an RNA genome, a common approach is to extract the double-stranded RNA (dsRNA) replicative form, to enrich the replicating virus genetic material over the host background. The traditional dsRNA extraction is...

Climate and ice in the last glacial maximum explain patterns of isolation by distance inferred for alpine grasshoppers

David Carmelet-Rescan, Mary Morgan-Richards, Emily Koot & Steven Trewick
Aim: Cold-adapted species are likely to have had widespread ranges with greater connectivity of populations during the last glacial cycle. We sought evidence of this in the level and distribution of variation within one alpine insect species. Location: Southern Alps, New Zealand Taxon: The endemic, wingless, alpine grasshopper Sigaus australis (Orthoptera: Acrididae) Methods: The current fragmented alpine distribution of Sigaus australis was used to estimate its environmental envelope (niche) and this model was then used...

Additional file 3 of The Venturia inaequalis effector repertoire is dominated by expanded families with predicted structural similarity, but unrelated sequence, to avirulence proteins from other plant-pathogenic fungi

Mercedes Rocafort, Joanna K. Bowen, Berit Hassing, Murray P. Cox, Brogan McGreal, Silvia de la Rosa, Kim M. Plummer, Rosie E. Bradshaw & Carl H. Mesarich
Additional file 3: Differentially expressed genes of Venturia inaequalis during infection of susceptible apple cultivar ‘Royal Gala’, when compared to growth of the fungus in culture on the surface of cellophane membranes overlying potato dextrose agar.

Additional file 4 of The Venturia inaequalis effector repertoire is dominated by expanded families with predicted structural similarity, but unrelated sequence, to avirulence proteins from other plant-pathogenic fungi

Mercedes Rocafort, Joanna K. Bowen, Berit Hassing, Murray P. Cox, Brogan McGreal, Silvia de la Rosa, Kim M. Plummer, Rosie E. Bradshaw & Carl H. Mesarich
Additional file 4: List of Pfam domains in proteins encoded by genes of the five distinct temporal expression waves of Venturia inaequalis that are upregulated during colonization of susceptible apple cultivar ‘Royal Gala’, when compared to growth of the fungus in culture on the surface of cellophane membranes overlying potato dextrose agar.

Additional file 5 of The Venturia inaequalis effector repertoire is dominated by expanded families with predicted structural similarity, but unrelated sequence, to avirulence proteins from other plant-pathogenic fungi

Mercedes Rocafort, Joanna K. Bowen, Berit Hassing, Murray P. Cox, Brogan McGreal, Silvia de la Rosa, Kim M. Plummer, Rosie E. Bradshaw & Carl H. Mesarich
Additional file 5: List of effector candidates (ECs) identified from Venturia inaequalis, their family classification, and indication of whether EC family members cluster in the genome.

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