Gavin Sherlock
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View article: Adaptive genetics reveals constraints on protein structure/function by evolving E. coli under constant nutrient limitation
Adaptive genetics reveals constraints on protein structure/function by evolving E. coli under constant nutrient limitation Open
Our observations highlight the value of experimental evolution as a proving ground for inferences gathered from traditional molecular genetics. By coupling experimental evolution to whole-genome, whole-population sequencing, adaptive genet…
View article: Correction: Fit-Seq2.0: An Improved Software for High-Throughput Fitness Measurements Using Pooled Competition Assays
Correction: Fit-Seq2.0: An Improved Software for High-Throughput Fitness Measurements Using Pooled Competition Assays Open
View article: Centromeres evolve progressively through selection at the kinetochore interface
Centromeres evolve progressively through selection at the kinetochore interface Open
During mitosis, stable but dynamic interactions between the centromere DNA and kinetochore complex enable accurate and efficient chromosome segregation. Even though many proteins of the kinetochore are highly conserved, centromeres are amo…
View article: A high-resolution two-step evolution experiment in yeast reveals a shift from pleiotropic to modular adaptation
A high-resolution two-step evolution experiment in yeast reveals a shift from pleiotropic to modular adaptation Open
Evolution by natural selection is expected to be a slow and gradual process. In particular, the mutations that drive evolution are predicted to be small and modular, incrementally improving a small number of traits. However, adaptive mutat…
View article: Microbe Profile: Candida glabrata – a master of deception
Microbe Profile: Candida glabrata – a master of deception Open
Graphical abstract Candida glabrata , an opportunistic fungal pathogen. (a) Unable to form hyphae, relies on tissue disruption to invade and disseminate host. (b) Calcofluor-white cells, 60X objective. (c) Colony morphology on YPD.
View article: The<i>Candida</i>Genome Database: Annotation and Visualization Updates
The<i>Candida</i>Genome Database: Annotation and Visualization Updates Open
The Candida Genome Database (CGD; www.candidagenome.org ) is unique in being both a model organism database and a fungal pathogen database. As a fungal pathogen database, CGD hosts locus pages for five species of the best-studied pathogeni…
View article: <i>Saccharomyces</i>Genome Database: Advances in Genome Annotation, Expanded Biochemical Pathways, and Other Key Enhancements
<i>Saccharomyces</i>Genome Database: Advances in Genome Annotation, Expanded Biochemical Pathways, and Other Key Enhancements Open
Budding yeast ( Saccharomyces cerevisiae ) is the most extensively characterized eukaryotic model organism and has long been used to gain insight into the fundamentals of genetics, cellular biology, and the functions of specific genes and …
View article: High-throughput DNA engineering by mating bacteria
High-throughput DNA engineering by mating bacteria Open
To reduce the operational friction and scale DNA engineering, we report here an in vivo DNA assembly technology platform called SCRIVENER ( S equential C onjugation and R ecombination for I n V ivo E longation of N ucleotides with low ER r…
View article: Spindle architecture constrains karyotype evolution
Spindle architecture constrains karyotype evolution Open
View article: A shift from pleiotropic to modular adaptation revealed by a high-resolution two-step adaptive walk
A shift from pleiotropic to modular adaptation revealed by a high-resolution two-step adaptive walk Open
Evolution by natural selection is expected to be a slow and gradual process. In particular, the mutations that drive evolution are predicted to be small and modular, incrementally improving a small number of traits. However, adaptive mutat…
View article: Arrayed <i>in vivo</i> barcoding for multiplexed sequence verification of plasmid DNA and demultiplexing of pooled libraries
Arrayed <i>in vivo</i> barcoding for multiplexed sequence verification of plasmid DNA and demultiplexing of pooled libraries Open
Sequence verification of plasmid DNA is critical for many cloning and molecular biology workflows. To leverage high-throughput sequencing, several methods have been developed that add a unique DNA barcode to individual samples prior to poo…
View article: Updates to the Alliance of Genome Resources central infrastructure
Updates to the Alliance of Genome Resources central infrastructure Open
The Alliance of Genome Resources (Alliance) is an extensible coalition of knowledgebases focused on the genetics and genomics of intensively studied model organisms. The Alliance is organized as individual knowledge centers with strong con…
View article: Analysis and culturing of the prototypic crAssphage reveals a phage-plasmid lifestyle
Analysis and culturing of the prototypic crAssphage reveals a phage-plasmid lifestyle Open
Summary The prototypic crAssphage ( Carjivirus communis ) is one of the most abundant, prevalent, and persistent gut bacteriophages, yet it remains uncultured and its lifestyle uncharacterized. For the last decade, crAssphage has escaped p…
View article: Updates to the Alliance of Genome Resources Central Infrastructure Alliance of Genome Resources Consortium
Updates to the Alliance of Genome Resources Central Infrastructure Alliance of Genome Resources Consortium Open
The Alliance of Genome Resources (Alliance) is an extensible coalition of knowledgebases focused on the genetics and genomics of intensively-studied model organisms. The Alliance is organized as individual knowledge centers with strong con…
View article: Spindle architecture constrains karyotype in budding yeast
Spindle architecture constrains karyotype in budding yeast Open
The eukaryotic cell division machinery must rapidly and reproducibly duplicate and partition the cell’s chromosomes in a carefully coordinated process. However, chromosome number varies dramatically between genomes, even on short evolution…
View article: Evolution of haploid and diploid populations reveals common, strong, and variable pleiotropic effects in non-home environments
Evolution of haploid and diploid populations reveals common, strong, and variable pleiotropic effects in non-home environments Open
Adaptation is driven by the selection for beneficial mutations that provide a fitness advantage in the specific environment in which a population is evolving. However, environments are rarely constant or predictable. When an organism well …
View article: Arrayed<i>in vivo</i>barcoding for multiplexed sequence verification of plasmid DNA and demultiplexing of pooled libraries
Arrayed<i>in vivo</i>barcoding for multiplexed sequence verification of plasmid DNA and demultiplexing of pooled libraries Open
Sequence verification of plasmid DNA is critical for many cloning and molecular biology workflows. To leverage high-throughput sequencing, several methods have been developed that add a unique DNA barcode to individual samples prior to poo…
View article: Author response: Evolution of haploid and diploid populations reveals common, strong, and variable pleiotropic effects in non-home environments
Author response: Evolution of haploid and diploid populations reveals common, strong, and variable pleiotropic effects in non-home environments Open
View article: Improved Sugarcane-Based Fermentation Processes by an Industrial Fuel-Ethanol Yeast Strain
Improved Sugarcane-Based Fermentation Processes by an Industrial Fuel-Ethanol Yeast Strain Open
In Brazil, sucrose-rich broths (cane juice and/or molasses) are used to produce billions of liters of both fuel ethanol and cachaça per year using selected Saccharomyces cerevisiae industrial strains. Considering the important role of feed…
View article: Comparative Genomic Analysis and Phenotypic Characterization of <em>Saccharomyces cerevisiae</em> Strains used in Sugarcane-based Fermentation Processes to Improve Sucrose Fermentation by an Industrial Fuel-ethanol Yeast Strain
Comparative Genomic Analysis and Phenotypic Characterization of <em>Saccharomyces cerevisiae</em> Strains used in Sugarcane-based Fermentation Processes to Improve Sucrose Fermentation by an Industrial Fuel-ethanol Yeast Strain Open
In Brazil, sucrose-rich broths (cane juice and/or molasses) are used to produce billions of liters of both fuel ethanol and cachaça per year using selected Saccharomyces cerevisiae industrial strains. Aiming to improve this disaccha…
View article: Paths to adaptation under fluctuating nitrogen starvation: The spectrum of adaptive mutations in Saccharomyces cerevisiae is shaped by retrotransposons and microhomology-mediated recombination
Paths to adaptation under fluctuating nitrogen starvation: The spectrum of adaptive mutations in Saccharomyces cerevisiae is shaped by retrotransposons and microhomology-mediated recombination Open
There are many mechanisms that give rise to genomic change: while point mutations are often emphasized in genomic analyses, evolution acts upon many other types of genetic changes that can result in less subtle perturbations. Changes in ch…
View article: Experimental evolution for cell biology
Experimental evolution for cell biology Open
View article: An improved algorithm for inferring mutational parameters from bar-seq evolution experiments
An improved algorithm for inferring mutational parameters from bar-seq evolution experiments Open
View article: Insufficient evidence for non-neutrality of synonymous mutations
Insufficient evidence for non-neutrality of synonymous mutations Open
View article: Fit-Seq2.0: An Improved Software for High-Throughput Fitness Measurements Using Pooled Competition Assays
Fit-Seq2.0: An Improved Software for High-Throughput Fitness Measurements Using Pooled Competition Assays Open
The fitness of a genotype is defined as its lifetime reproductive success, with fitness itself being a composite trait likely dependent on many underlying phenotypes. Measuring fitness is important for understanding how alteration of diffe…
View article: Far From Home: Evolution of haploid and diploid populations reveals common, strong, and variable pleiotropic effects in non-home environments
Far From Home: Evolution of haploid and diploid populations reveals common, strong, and variable pleiotropic effects in non-home environments Open
Adaptation is driven by the selection for beneficial mutations that provide a fitness advantage in the specific environment in which a population is evolving. However, environments are rarely constant or predictable. When an organism well …
View article: Yca1 metacaspase: diverse functions determine how yeast live and let die
Yca1 metacaspase: diverse functions determine how yeast live and let die Open
The Yca1 metacaspase was discovered due to its role in the regulation of apoptosis in Saccharomyces cerevisiae. However, the mechanisms that drive apoptosis in yeast remain poorly understood. Additionally, Yca1 and other metacaspase protei…
View article: An Improved Algorithm for Inferring Mutational Parameters from Bar-Seq Evolution Experiments
An Improved Algorithm for Inferring Mutational Parameters from Bar-Seq Evolution Experiments Open
Genetic barcoding provides a high-throughput way to simultaneously track the frequencies of large numbers of competing and evolving microbial lineages. However making inferences about the character of the evolution that is taking place rem…
View article: No evidence that synonymous mutations in yeast genes are mostly deleterious
No evidence that synonymous mutations in yeast genes are mostly deleterious Open
In a recent paper 1 , Shen et al . reported that most mutations in the coding regions of 21 yeast genes were strongly deleterious, and that the distributions of fitness effects were similar for synonymous and nonsynonymous mutations. Taken…
View article: S. cerevisiae Cells Can Grow without the Pds5 Cohesin Subunit
S. cerevisiae Cells Can Grow without the Pds5 Cohesin Subunit Open
Sister chromatid cohesion is vital for faithful chromosome segregation, chromosome folding into loops, and gene expression. A multisubunit protein complex known as cohesin holds the sister chromatids from S phase until the anaphase stage.