Emilyclare Baker

• Doctor of Philosophy
• PostDoc Position at KU Leuven

Stable adherence to epithelial surfaces is required for colonization by diverse host-associated microbes. Successful attachment of pathogenic microbes to host cells via adhesin molecules is also the first step in many devastating infections. Despite the primacy of epithelial adherence in establishing host-microbe associations, the evolutionary proc...

Stable adherence to epithelial surfaces is required for colonization by diverse host-associated microbes. Successful attachment of pathogenic microbes via surface adhesin molecules is also the first step in many devastating infections. Despite the primacy of epithelial adherence in establishing host-microbe associations, the evolutionary processes...

The human genome encodes an arsenal of proteins that protect us against deadly viruses. Could microbes provide clues regarding the origin of these pathogen defenses? In a recent study published in Nature, Bernheim et al. demonstrate that the mammalian antiviral protein viperin is far more ancient and conserved than previously appreciated.

The most common fermented beverage, lager beer, is produced by interspecies hybrids of the brewing yeast Saccharomyces cerevisiae and its wild relative S. eubayanus. Lager-brewing yeasts are not the only example of hybrid vigour or heterosis in yeasts, but the full breadth of interspecies hybrids associated with human fermentations has received les...

At the molecular level, the evolution of new traits can be broadly divided between changes in gene expression and changes in protein-coding sequence. For proteins, the evolution of novel functions is generally thought to proceed through sequential point mutations or recombination of whole functional units. In Saccharomyces, the uptake of the sugar...

Protein structural alignment between Malt3, Malt4, Malt434, scAgt1, and lgAgt1. Protein structural alignment between Malt3, Malt4, Malt434, scAgt1, and lgAgt1. The purple blocks represent predicted alpha helices, and the orange lines represent predicted beta strands. Red ticks mark predicted maltose-binding sites. Blue ticks mark residues found to...

Oligonucleotides used in this work. (XLSX)

Raw data for S2 Table. (XLSX)

Mutation prediction analyses. Results of mutation prediction analyses for E18V, the sole amino acid substitution in the lgAgt1 protein sequence, relative to tbAgt1. (XLSX)

Maltotriose growth assay. Growth on maltotriose of single-colony isolates from adaptive evolution experiments. Strains were evolved with either maltotriose or maltose as the primary carbon source (2%) with 0.1% added glucose. N = 3. * Control grown in SC + 0.04% glucose to reflect the approximate amount of growth expected from contamination with ot...

Strains and plasmids used in this work. (XLSX)

Maltose growth assay. Growth on maltose of single-colony isolates. Isolated from adaptive evolution of yHRVM108 on 2% maltose + 0.1% glucose. N = 3. * Control grown in SC + 0.04% glucose to reflect the approximate amount of growth expected from contamination with other carbon sources when using 98% pure maltotriose. (XLSX)

Raw data for S3 Table. (XLSX)

A growing body of research suggests that the mitochondrial genome (mtDNA) is important for temperature adaptation. In the yeast genus Saccharomyces , species have diverged in temperature tolerance, driving their use in high- or low-temperature fermentations. Here, we experimentally test the role of mtDNA in temperature tolerance in synthetic and in...

At the molecular level, the evolution of new traits can be broadly divided between changes in gene expression and changes in protein structure. For proteins, the evolution of novel functions is generally thought to proceed through sequential point mutations or recombination of whole functional units. In Saccharomyces , the uptake of the sugar malto...

A growing body of research suggests that the mitochondrial genome (mtDNA) is important for temperature adaptation. In the yeast genus Saccharomyces , species have diverged in temperature tolerance, driving their use in high or low temperature fermentations. Here we experimentally test the role of mtDNA in temperature tolerance in synthetic and indu...

Background Lignocellulosic biomass is a common resource across the globe, and its fermentation offers a promising option for generating renewable liquid transportation fuels. The deconstruction of lignocellulosic biomass releases sugars that can be fermented by microbes, but these processes also produce fermentation inhibitors, such as aromatic aci...

Transposable elements (TEs) comprise large fractions of many eukaryotic genomes and imperil host genome integrity. The host genome combats these challenges by encoding proteins that silence TE activity. Both the introduction of new TEs via horizontal transfer and TE sequence evolution requires constant innovation of host-encoded TE silencing machin...

Essential genes and species incompatibilities Crosses between two fruit fly species, Drosophila melanogaster and D. simulans , result in hybrid progeny that are all female. Although some of the genes responsible for this species barrier are known, the full complement of molecular determinants that lead to inviable males has remained mysterious. Pha...

The dramatic phenotypic changes that occur in organisms during domestication leave indelible imprints on their genomes. Although many domesticated plants and animals have been systematically compared to their wild genetic stocks, the molecular and genomic processes underlying fungal domestication have received less attention. Here we present a near...