Eric M. Young
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View article: Oleaginous Yeast Biology Elucidated With Comparative Transcriptomics
Oleaginous Yeast Biology Elucidated With Comparative Transcriptomics Open
Extremophilic yeasts have favorable metabolic and tolerance traits for biomanufacturing‐ like lipid biosynthesis, flavinogenesis, and halotolerance – yet the connection between these favorable phenotypes and strain genotype is not well und…
View article: Ten Years of the Synthetic Biology Summer Course at Cold Spring Harbor Laboratory
Ten Years of the Synthetic Biology Summer Course at Cold Spring Harbor Laboratory Open
The Cold Spring Harbor Laboratory (CSHL) Summer Course on Synthetic Biology, established in 2013, has emerged as a premier platform for immersive education and research in this dynamic field. Rooted in CSHL's rich legacy of biological disc…
View article: A correlative study of the genomic underpinning of virulence traits and drug tolerance of <i>Candida auris</i>
A correlative study of the genomic underpinning of virulence traits and drug tolerance of <i>Candida auris</i> Open
Candida auris is an opportunistic fungal pathogen with high mortality rates which presents a clear threat to public health. The risk of C. auris infection is high because it can colonize the body, resist antifungal treatment, and evade the…
View article: Integration of Yeast Episomal/Integrative Plasmid Causes Genotypic and Phenotypic Diversity and Improved Sesquiterpene Production in Metabolically Engineered <i>Saccharomyces cerevisiae</i>
Integration of Yeast Episomal/Integrative Plasmid Causes Genotypic and Phenotypic Diversity and Improved Sesquiterpene Production in Metabolically Engineered <i>Saccharomyces cerevisiae</i> Open
The variability in phenotypic outcomes among biological replicates in engineered microbial factories presents a captivating mystery. Establishing the association between phenotypic variability and genetic drivers is important to solve this…
View article: Targeted control of supporting pathways in paclitaxel biosynthesis with CRISPR-guided methylation
Targeted control of supporting pathways in paclitaxel biosynthesis with CRISPR-guided methylation Open
Introduction: Plant cell culture biomanufacturing is rapidly becoming an effective strategy for production of high-value plant natural products, such as therapeutic proteins and small molecules, vaccine adjuvants, and nutraceuticals. Many …
View article: Isolation and sequencing of the spoilage yeast <i>Kregervanrija delftensis</i>
Isolation and sequencing of the spoilage yeast <i>Kregervanrija delftensis</i> Open
New sequencing workflows can enable the genomics of microbes isolated from craft beverages. Here, we use hybrid, short, and long-read sequencing to assemble the genome of a yeast isolated from cider, Kregervanrija delftensis NCC-J. The Kre…
View article: Phenotypic and genomic evidence for transparent cellulose, metabolic diversity, and stable cellulose production in the Acetobacteraceae
Phenotypic and genomic evidence for transparent cellulose, metabolic diversity, and stable cellulose production in the Acetobacteraceae Open
The Acetobacteraceae are a family of microbes that use sugars from fruits, beverages and fermented foods to overproduce bacterial nanocellulose (BNC), a living material with broad applications in medicine and industry. Yet, the family has …
View article: Draft genome of the <i>Ogataea polymorpha</i> type strain CBS 4732
Draft genome of the <i>Ogataea polymorpha</i> type strain CBS 4732 Open
The methylotrophic yeast Ogataea polymorpha is of significant biotechnological interest, particularly in high-temperature fermentations and for recombinant protein production. Here, we present a high-quality genome assembly for the O. poly…
View article: Omics driven onboarding of the carotenoid producing red yeast<i>Xanthophyllomyces dendrorhous</i>CBS 6938
Omics driven onboarding of the carotenoid producing red yeast<i>Xanthophyllomyces dendrorhous</i>CBS 6938 Open
Transcriptomics is a powerful approach for functional genomics and systems biology, yet it can also be used for genetic part discovery. Genetic part discovery has never been more necessary, as advances in synthetic biology increase the num…
View article: Systematic Part Transfer by Extending a Modular Toolkit to Diverse Bacteria
Systematic Part Transfer by Extending a Modular Toolkit to Diverse Bacteria Open
It is impractical to develop a new parts collection for every potential host organism. It is well-established that gene expression parts, like genes, are qualitatively transferable, but there is little quantitative information defining tra…
View article: Genetic basis for probiotic yeast phenotypes revealed by nanopore sequencing
Genetic basis for probiotic yeast phenotypes revealed by nanopore sequencing Open
Probiotic yeasts are emerging as preventative and therapeutic solutions for disease. Often ingested via cultured foods and beverages, they can survive the harsh conditions of the gastrointestinal tract and adhere to it, where they provide …
View article: A correlative study of the genomic underpinning of virulence traits and drug tolerance of<i>Candida auris</i>
A correlative study of the genomic underpinning of virulence traits and drug tolerance of<i>Candida auris</i> Open
Candida auris is an opportunistic fungal pathogen with high mortality rates that presents a clear and present threat to public health. The risk of C. auris infection is high because it can colonize the body, resist antifungal treatment, an…
View article: Systematic part transfer by extending a modular toolkit to diverse bacteria
Systematic part transfer by extending a modular toolkit to diverse bacteria Open
It is impractical to develop a new parts collection for every potential host organism. It is well-established that gene expression parts, like genes, are qualitatively transferable, but there is little quantitative information defining tra…
View article: Multicolor plate reader fluorescence calibration
Multicolor plate reader fluorescence calibration Open
Plate readers are commonly used to measure cell growth and fluorescence, yet the utility and reproducibility of plate reader data is limited by the fact that it is typically reported in arbitrary or relative units. We have previously estab…
View article: Verification of genetic engineering in yeasts with nanopore whole genome sequencing
Verification of genetic engineering in yeasts with nanopore whole genome sequencing Open
Yeast genomes can be assembled from sequencing data, but genome integrations and episomal plasmids often fail to be resolved with accuracy, completeness, and contiguity. Resolution of these features is critical for many synthetic biology a…
View article: Synthetic biology for bio-derived structural materials
Synthetic biology for bio-derived structural materials Open
Biologically derived materials have numerous applications in biomedical fields and beyond. Yet, the properties of these materials are difficult to alter because the natural biosynthetic mechanisms are difficult to elucidate, imitate, or ad…
View article: Formation of Nitrogenase NifDK Tetramers in the Mitochondria of <i>Saccharomyces cerevisiae</i>
Formation of Nitrogenase NifDK Tetramers in the Mitochondria of <i>Saccharomyces cerevisiae</i> Open
Transferring the prokaryotic enzyme nitrogenase into a eukaryotic host with the final aim of developing N2 fixing cereal crops would revolutionize agricultural systems worldwide. Targeting it to mitochondria has potential advantages becaus…