David S. Milner
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View article: <i>De Novo</i> Genome Sequence Assembly of the RNAi-Tractable <i>Paramecium bursaria</i> 186b: An Endosymbiotic Model System
<i>De Novo</i> Genome Sequence Assembly of the RNAi-Tractable <i>Paramecium bursaria</i> 186b: An Endosymbiotic Model System Open
How two species engage in stable endosymbiosis is a biological quandary. The study of facultative endosymbiotic interactions has emerged as a useful approach to understand how endosymbiotic functions can arise. The ciliate protist Parameci…
View article: Permeability selection of biologically relevant membranes matches the stereochemistry of life on Earth
Permeability selection of biologically relevant membranes matches the stereochemistry of life on Earth Open
Early in the evolution of life, a proto-metabolic network was encapsulated within a membrane compartment. The permeability characteristics of the membrane determined several key functions of this network by determining which compounds coul…
View article: Immune-like glycan-sensing and horizontally-acquired glycan-processing orchestrate host control in a microbial endosymbiosis
Immune-like glycan-sensing and horizontally-acquired glycan-processing orchestrate host control in a microbial endosymbiosis Open
Endosymbiosis was a key factor in the evolution of eukaryotic cellular complexity. Yet the mechanisms that allow host regulation of intracellular symbionts, a pre-requisite for stable endosymbiosis and subsequent organelle evolution, are l…
View article: <i>De novo</i>genome sequence assembly of the RNAi-tractable endosymbiosis model system<i>Paramecium bursaria</i>186b reveals factors shaping intron repertoire
<i>De novo</i>genome sequence assembly of the RNAi-tractable endosymbiosis model system<i>Paramecium bursaria</i>186b reveals factors shaping intron repertoire Open
How two species engage in stable endosymbiosis is a biological quandary. The study of facultative endosymbiotic interactions has emerged as a useful approach to understand how endosymbiotic functions can arise. The ciliate protist Parameci…
View article: Duplication and neofunctionalization of a horizontally transferred xyloglucanase as a facet of the Red Queen coevolutionary dynamic
Duplication and neofunctionalization of a horizontally transferred xyloglucanase as a facet of the Red Queen coevolutionary dynamic Open
Oomycete protists share phenotypic similarities with fungi, including the ability to cause plant diseases, but branch in a distant region of the tree of life. It has been suggested that multiple horizontal gene transfers (HGTs) from fungi-…
View article: Membrane permeability selection drove the stereochemistry of life
Membrane permeability selection drove the stereochemistry of life Open
Early in the evolution of life a proto-metabolic network was encapsulated within a membrane compartment. The permeability characteristics of the membrane determined several key functions of this network by determining which compounds could…
View article: Duplication and neofunctionalization of a horizontally-transferred xyloglucanase as a facet of the red queen co-evolutionary dynamic
Duplication and neofunctionalization of a horizontally-transferred xyloglucanase as a facet of the red queen co-evolutionary dynamic Open
Oomycetes are heterotrophic protists that share phenotypic similarities with fungi, including the ability to cause plant diseases, but branch in a separate and distant region of the eukaryotic tree of life. It has been suggested that multi…
View article: Systematic comparison of unilamellar vesicles reveals that archaeal core lipid membranes are more permeable than bacterial membranes
Systematic comparison of unilamellar vesicles reveals that archaeal core lipid membranes are more permeable than bacterial membranes Open
One of the deepest branches in the tree of life separates the Archaea from the Bacteria. These prokaryotic groups have distinct cellular systems including fundamentally different phospholipid membrane bilayers. This dichotomy has been term…
View article: Transporter Proteins as Ecological Assets and Features of Microbial Eukaryotic Pangenomes
Transporter Proteins as Ecological Assets and Features of Microbial Eukaryotic Pangenomes Open
Here we review two connected themes in evolutionary microbiology: ( a) the nature of gene repertoire variation within species groups (pangenomes) and ( b) the concept of metabolite transporters as accessory proteins capable of providing ni…
View article: A Genome Sequence Assembly of the Phototactic and Optogenetic Model Fungus <i>Blastocladiella emersonii</i> Reveals a Diversified Nucleotide-Cyclase Repertoire
A Genome Sequence Assembly of the Phototactic and Optogenetic Model Fungus <i>Blastocladiella emersonii</i> Reveals a Diversified Nucleotide-Cyclase Repertoire Open
The chytrid fungus Blastocladiella emersonii produces spores with swimming tails (zoospores); these cells can sense and swim toward light. Interest in this species stems from ongoing efforts to develop B. emersonii as a model for understan…
View article: Paramecium bursaria immunofluorescence protocol v1
Paramecium bursaria immunofluorescence protocol v1 Open
This protocol has been developed for immunofluorescent localisation of host proteins in Paramecium bursaria 186b.
View article: A diversified and segregated mRNA spliced-leader system in the parasitic Perkinsozoa
A diversified and segregated mRNA spliced-leader system in the parasitic Perkinsozoa Open
Spliced-leader trans -splicing (SLTS) has been described in distantly related eukaryotes and acts to mark mRNAs with a short 5′ exon, giving different mRNAs identical 5′ sequence-signatures. The function of these systems is obscure. Perkin…
View article: A light-sensing system in the common ancestor of the fungi
A light-sensing system in the common ancestor of the fungi Open
Diverse light-sensing organs (i.e., eyes) have evolved across animals. Interestingly, several subcellular analogs have been found in eukaryotic microbes. All of these systems have a common “recipe”: a light occluding or refractory surface …
View article: Nutrient and salt depletion synergistically boosts glucose metabolism in individual bacteria
Nutrient and salt depletion synergistically boosts glucose metabolism in individual bacteria Open
The interaction between a cell and its environment shapes fundamental intracellular processes such as cellular metabolism. In most cases growth rate is treated as a proximal metric for understanding the cellular metabolic status. However, …
View article: Membrane permeability differentiation at the lipid divide
Membrane permeability differentiation at the lipid divide Open
One of the deepest branches in the tree of life separates the Archaea from the Bacteria. These prokaryotic groups have distinct cellular systems including fundamentally different phospholipid membrane bilayers. This dichotomy has been term…
View article: Emergent RNA–RNA interactions can promote stability in a facultative phototrophic endosymbiosis
Emergent RNA–RNA interactions can promote stability in a facultative phototrophic endosymbiosis Open
Significance Stable endosymbiosis between eukaryotic microbes has driven the evolution of further cellular complexity. Yet the mechanisms that can act to stabilize an emergent eukaryote–eukaryote endosymbiosis are unclear. Using the model …
View article: Expanded host and geographic range of tadpole associations with the Severe Perkinsea Infection group
Expanded host and geographic range of tadpole associations with the Severe Perkinsea Infection group Open
Severe Perkinsea infection is an emerging disease of amphibians, specifically tadpoles. Disease presentation correlates with liver infections of a subclade of Perkinsea (Alveolata) protists, named Pathogenic Perkinsea Clade (PPC). Tadpole …
View article: A functional bacteria-derived restriction modification system in the mitochondrion of a heterotrophic protist
A functional bacteria-derived restriction modification system in the mitochondrion of a heterotrophic protist Open
The overarching trend in mitochondrial genome evolution is functional streamlining coupled with gene loss. Therefore, gene acquisition by mitochondria is considered to be exceedingly rare. Selfish elements in the form of self-splicing intr…
View article: Characterization of the RNA-interference pathway as a tool for reverse genetic analysis in the nascent phototrophic endosymbiosis, <i>Paramecium bursaria</i>
Characterization of the RNA-interference pathway as a tool for reverse genetic analysis in the nascent phototrophic endosymbiosis, <i>Paramecium bursaria</i> Open
Endosymbiosis was fundamental for the evolution of eukaryotic complexity. Endosymbiotic interactions can be dissected through forward- and reverse-genetic experiments, such as RNA-interference (RNAi). However, distinguishing small (s)RNA p…
View article: A novel duplex qPCR assay for stepwise detection of multiple Perkinsea protistan infections of amphibian tissues
A novel duplex qPCR assay for stepwise detection of multiple Perkinsea protistan infections of amphibian tissues Open
Alveolate protists within the phylum Perkinsea have been found to infect amphibians across a broad taxonomic and geographic range. Phylogenetic analysis has suggested the existence of two clades of amphibian Perkinsea: a putatively non-pat…
View article: A functional bacterial-derived restriction modification system in the mitochondrion of a heterotrophic protist
A functional bacterial-derived restriction modification system in the mitochondrion of a heterotrophic protist Open
The overarching trend in mitochondrial evolution is functional streamlining coupled with gene loss; therefore, gene acquisition by mitochondria is considered to be exceedingly rare. Selfish elements in the form of self-splicing introns occ…
View article: Fig_2A_S1_HpaII-like_accessions.fa
Fig_2A_S1_HpaII-like_accessions.fa Open
HpaII sequence data for Fig 2A and Fig S1 of 'A functional bacteria-derived restriction modification system in the mitochondrion of a heterotrophic protist'
View article: Fig_S1B_trimmed_alignment.mase
Fig_S1B_trimmed_alignment.mase Open
Alignment data for Fig S1B of 'A functional bacteria-derived restriction modification system in the mitochondrion of a heterotrophic protist'
View article: Fig_2A_trimmed_alignment.mase
Fig_2A_trimmed_alignment.mase Open
Alignment data for Fig 2A of 'A functional bacteria-derived restriction modification system in the mitochondrion of a heterotrophic protist'
View article: Fig_S1B_trimmed_alignment.txt
Fig_S1B_trimmed_alignment.txt Open
Alignment data for Fig S1B of 'A functional bacteria-derived restriction modification system in the mitochondrion of a heterotrophic protist'
View article: Fig_2A_S1_HpaIICM_accessions.fa
Fig_2A_S1_HpaIICM_accessions.fa Open
HpaII-CM sequence data for Fig 2A and Fig S1 of 'A functional bacteria-derived restriction modification system in the mitochondrion of a heterotrophic protist'
View article: Fig_2A_trimmed_alignment.txt
Fig_2A_trimmed_alignment.txt Open
Alignment data for Fig 2A of 'A functional bacteria-derived restriction modification system in the mitochondrion of a heterotrophic protist'
View article: Fig_S1A_trimmed_alignment.mase
Fig_S1A_trimmed_alignment.mase Open
Alignment data for Fig S1A of 'A functional bacteria-derived restriction modification system in the mitochondrion of a heterotrophic protist'