Publications by authors named "Justin C Fay"

59 Publications

The structure and diversity of strain-level variation in vaginal bacteria.

Microb Genom 2021 Mar 3;7(3). Epub 2021 Mar 3.

Department of Biology, University of Rochester, Rochester, NY 14627, USA.

The vaginal microbiome plays an important role in human health and species of vaginal bacteria have been associated with reproductive disease. Strain-level variation is also thought to be important, but the diversity, structure and evolutionary history of vaginal strains is not as well characterized. We developed and validated an approach to measure strain variation from metagenomic data based on SNPs within the core genomes for six species of vaginal bacteria: , , , , and . Despite inhabiting the same environment, strain diversity and structure varies across species. All species except are characterized by multiple distinct groups of strains. Even so, strain diversity is lower in the species, consistent with a more recent colonization of the human vaginal microbiome. Both strain diversity and the frequency of multi-strain samples is related to species-level diversity of the microbiome in which they occur, suggesting similar ecological factors influencing diversity within the vaginal niche. We conclude that the structure of strain-level variation provides both the motivation and means of testing whether strain-level differences contribute to the function and health consequences of the vaginal microbiome.
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http://dx.doi.org/10.1099/mgen.0.000543DOI Listing
March 2021

High-throughput analysis of adaptation using barcoded strains of .

PeerJ 2020 16;8:e10118. Epub 2020 Oct 16.

Department of Genetics, Washington University in St. Louis, St. Louis, MO, United States of America.

Background: Experimental evolution of microbes can be used to empirically address a wide range of questions about evolution and is increasingly employed to study complex phenomena ranging from genetic evolution to evolutionary rescue. Regardless of experimental aims, fitness assays are a central component of this type of research, and low-throughput often limits the scope and complexity of experimental evolution studies. We created an experimental evolution system in that utilizes genetic barcoding to overcome this challenge.

Results: We first confirm that barcode insertions do not alter fitness and that barcode sequencing can be used to efficiently detect fitness differences via pooled competition-based fitness assays. Next, we examine the effects of ploidy, chemical stress, and population bottleneck size on the evolutionary dynamics and fitness gains (adaptation) in a total of 76 experimentally evolving, asexual populations by conducting 1,216 fitness assays and analyzing 532 longitudinal-evolutionary samples collected from the evolving populations. In our analysis of these data we describe the strengths of this experimental evolution system and explore sources of error in our measurements of fitness and evolutionary dynamics.

Conclusions: Our experimental treatments generated distinct fitness effects and evolutionary dynamics, respectively quantified via multiplexed fitness assays and barcode lineage tracking. These findings demonstrate the utility of this new resource for designing and improving high-throughput studies of experimental evolution. The approach described here provides a framework for future studies employing experimental designs that require high-throughput multiplexed fitness measurements.
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http://dx.doi.org/10.7717/peerj.10118DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7571412PMC
October 2020

Associations between the vaginal microbiome and Candida colonization in women of reproductive age.

Am J Obstet Gynecol 2020 05 22;222(5):471.e1-471.e9. Epub 2019 Oct 22.

Molecular Microbiology and Center for Women's Infectious Disease Research, Washington University School of Medicine, St Louis, MO. Electronic address:

Background: The composition of bacteria within the vaginal microbiome has garnered a lot of recent attention and has been associated with reproductive health and disease. Despite the common occurrence of yeast (primarily Candida) within the vaginal microbiome, there is still an incomplete picture of relationships between yeast and bacteria (especially lactobacilli), as well as how such associations are governed. Such relationships could be important to a more holistic understanding of the vaginal microbiome and its connection to reproductive health.

Objective: The objective of the study was to perform molecular characterization of clinical specimens to define associations between vaginal bacteria (especially Lactobacillus species) and Candida colonization. In vitro studies were conducted to test the 2 most common dominant Lactobacillus species (Lactobacillus crispatus and Lactobacillus iners) in their ability to inhibit Candida growth and to examine the basis for such inhibition.

Study Design: A nested cross-sectional study of reproductive-age women from the Contraceptive CHOICE Project was conducted. Vaginal swabs from 299 women were selected to balance race and bacterial vaginosis status, resulting in a similar representation of black and white women in each of the 3 Nugent score categories (normal [0-3], intermediate [4-6], and bacterial vaginosis [7-10]). Sequencing of the 16S ribosomal gene (V4 region) was used to determine the dominant Lactobacillus species present (primarily Lactobacillus iners and Lactobacillus crispatus), defined as >50% of the community. Subjects without dominance by a single Lactobacillus species were classified as Diverse. A Candida-specific quantitative polymerase chain reaction targeting the internally transcribed spacer 1 was validated using vaginal samples collected from a second cohort of women and used to assess Candida colonization. Two hundred fifty-five nonpregnant women with sufficient bacterial biomass for analysis were included in the final analysis. Generalized linear models were used to evaluate associations between Lactobacillus dominance, sociodemographic and risk characteristics, and vaginal Candida colonization. In separate in vitro studies, the potential of cell-free supernatants from Lactobacillus crispatus and Lactobacillus iners cultures to inhibit Candida growth was evaluated.

Results: Forty-two women (16%) were vaginally colonized with Candida. Microbiomes characterized as Diverse (38%), Lactobacillus iners-dominant (39%), and Lactobacillus crispatus-dominant (20%) were the most common. The microbiome, race, and Candida colonization co-varied with a higher prevalence of Candida among black women and Lactobacillus iners-dominant communities compared with white women and Lactobacillus crispatus-dominant communities. Lactobacillus iners-dominant communities were more likely to harbor Candida than Lactobacillus crispatus-dominant communities (odds ratio, 2.85, 95% confidence interval, 1.03-7.21; Fisher exact test, P = .048). In vitro, Lactobacillus crispatus produced greater concentrations of lactic acid and exhibited significantly more pH-dependent growth inhibition of Candida albicans, suggesting a potential mechanism for the clinical observations.

Conclusion: In nonpregnant women, Lactobacillus iners-dominant communities were significantly more likely to harbor Candida than Lactobacillus crispatus-dominant communities, suggesting that Lactobacillus species have different relationships with Candida. In vitro experiments indicate that Lactobacillus crispatus may impede Candida colonization more effectively than Lactobacillus iners through a greater production of lactic acid.
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http://dx.doi.org/10.1016/j.ajog.2019.10.008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7236091PMC
May 2020

The Fate of Deleterious Variants in a Barley Genomic Prediction Population.

Genetics 2019 12 25;213(4):1531-1544. Epub 2019 Oct 25.

Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108

Targeted identification and purging of deleterious genetic variants has been proposed as a novel approach to animal and plant breeding. This strategy is motivated, in part, by the observation that demographic events and strong selection associated with cultivated species pose a "cost of domestication." This includes an increase in the proportion of genetic variants that are likely to reduce fitness. Recent advances in DNA resequencing and sequence constraint-based approaches to predict the functional impact of a mutation permit the identification of putatively deleterious SNPs (dSNPs) on a genome-wide scale. Using exome capture resequencing of 21 barley lines, we identified 3855 dSNPs among 497,754 total SNPs. We generated whole-genome resequencing data of ssp. as a phylogenetic outgroup to polarize SNPs as ancestral derived. We also observed a higher proportion of dSNPs per synonymous SNPs (sSNPs) in low-recombination regions of the genome. Using 5215 progeny from a genomic prediction experiment, we examined the fate of dSNPs over three breeding cycles. Adjusting for initial frequency, derived alleles at dSNPs reduced in frequency or were lost more often than other classes of SNPs. The highest-yielding lines in the experiment, as chosen by standard genomic prediction approaches, carried fewer homozygous dSNPs than randomly sampled lines from the same progeny cycle. In the final cycle of the experiment, progeny selected by genomic prediction had a mean of 5.6% fewer homozygous dSNPs relative to randomly chosen progeny from the same cycle.
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http://dx.doi.org/10.1534/genetics.119.302733DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6893365PMC
December 2019

Riding the Rhythm of Melatonin Through Pregnancy to Deliver on Time.

Front Endocrinol (Lausanne) 2019 13;10:616. Epub 2019 Sep 13.

Department of Obstetrics and Gynecology, Washington University School of Medicine, St. Louis, MO, United States.

Pregnancy is influenced by the circadian ("circa" or approximately; diēm or day) system, which coordinates physiology and behavior with predictable daily changes in the environment such as light/dark cycles. For example, most species deliver around a particular time of day. In mammals, circadian rhythms are controlled by the master circadian pacemaker, the suprachiasmatic nucleus. One key way that the suprachiasmatic nucleus coordinates circadian rhythms throughout the body is by regulating production of the sleep-promoting hormone melatonin. Serum melatonin concentration, which peaks at night and is suppressed during the day, is one of the best biological indicators of circadian timing. Circadian misalignment causes maternal disturbances in the temporal organization of many physiological processes including melatonin synthesis, and these disturbances of the circadian system have been linked to an increased risk for pregnancy complications. Here, we review evidence that melatonin helps regulate the maternal and fetal circadian systems and the timing of birth. Finally, we discuss the potential for melatonin-based therapeutic strategies to alleviate poor pregnancy outcomes such as preeclampsia and preterm birth.
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http://dx.doi.org/10.3389/fendo.2019.00616DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6753220PMC
September 2019

Multiple Changes Underlie Allelic Divergence of Between Species.

G3 (Bethesda) 2019 11 5;9(11):3595-3600. Epub 2019 Nov 5.

Department of Genetics, and.

Under the model of micromutationism, phenotypic divergence between species is caused by accumulation of many small-effect changes. While mapping the causal changes to single nucleotide resolution could be difficult for diverged species, genetic dissection via chimeric constructs allows us to evaluate whether a large-effect gene is composed of many small-effect nucleotide changes. In a previously described non-complementation screen, we found an allele difference of , a copper-binding transcription factor, underlies divergence in copper resistance between and Here, we tested whether the allele effect of was caused by multiple nucleotide changes. By analyzing chimeric constructs containing four separate regions in the gene, including its distal promoter, proximal promoter, DNA binding domain and transcriptional activation domain, we found that all four regions of the allele conferred copper resistance, with the proximal promoter showing the largest effect, and that both additive and epistatic effects are likely involved. These findings support a model of multiple changes underlying evolution and suggest an important role of both protein coding and -regulatory changes in evolution.
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http://dx.doi.org/10.1534/g3.119.400616DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6829129PMC
November 2019

A polyploid admixed origin of beer yeasts derived from European and Asian wine populations.

PLoS Biol 2019 03 5;17(3):e3000147. Epub 2019 Mar 5.

Pacific Northwest Research Institute, Seattle, Washington, United States of America.

Strains of Saccharomyces cerevisiae used to make beer, bread, and wine are genetically and phenotypically distinct from wild populations associated with trees. The origins of these domesticated populations are not always clear; human-associated migration and admixture with wild populations have had a strong impact on S. cerevisiae population structure. We examined the population genetic history of beer strains and found that ale strains and the S. cerevisiae portion of allotetraploid lager strains were derived from admixture between populations closely related to European grape wine strains and Asian rice wine strains. Similar to both lager and baking strains, ale strains are polyploid, providing them with a passive means of remaining isolated from other populations and providing us with a living relic of their ancestral hybridization. To reconstruct their polyploid origin, we phased the genomes of two ale strains and found ale haplotypes to both be recombinants between European and Asian alleles and to also contain novel alleles derived from extinct or as yet uncharacterized populations. We conclude that modern beer strains are the product of a historical melting pot of fermentation technology.
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http://dx.doi.org/10.1371/journal.pbio.3000147DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6400334PMC
March 2019

Mitochondrial DNA and temperature tolerance in lager yeasts.

Sci Adv 2019 01 30;5(1):eaav1869. Epub 2019 Jan 30.

Laboratory of Genetics, Genome Center of Wisconsin, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI, USA.

A growing body of research suggests that the mitochondrial genome (mtDNA) is important for temperature adaptation. In the yeast genus , 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 industrial hybrids ( × or ), which cold-brew lager beer. We find that the relative temperature tolerances of hybrids correspond to the parent donating mtDNA, allowing us to modulate lager strain temperature preferences. The strong influence of mitotype on the temperature tolerance of otherwise identical hybrid strains provides support for the mitochondrial climactic adaptation hypothesis in yeasts and demonstrates how mitotype has influenced the world's most commonly fermented beverage.
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http://dx.doi.org/10.1126/sciadv.aav1869DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6353617PMC
January 2019

Mitochondria-encoded genes contribute to evolution of heat and cold tolerance in yeast.

Sci Adv 2019 01 30;5(1):eaav1848. Epub 2019 Jan 30.

Department of Genetics, Washington University, St. Louis, MO 63110, USA.

Genetic analysis of phenotypic differences between species is typically limited to interfertile species. Here, we conducted a genome-wide noncomplementation screen to identify genes that contribute to a major difference in thermal growth profile between two reproductively isolated yeast species, and . The screen identified only a single nuclear-encoded gene with a moderate effect on heat tolerance, but, in contrast, revealed a large effect of mitochondrial DNA (mitotype) on both heat and cold tolerance. Recombinant mitotypes indicate that multiple genes contribute to thermal divergence, and we show that protein divergence in affects both heat and cold tolerance. Our results point to the yeast mitochondrial genome as an evolutionary hotspot for thermal divergence.
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http://dx.doi.org/10.1126/sciadv.aav1848DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6353624PMC
January 2019

Genetic Basis of Variation in Heat and Ethanol Tolerance in .

G3 (Bethesda) 2019 01 9;9(1):179-188. Epub 2019 Jan 9.

Department of Genetics, Washington University, St. Louis, MO 63110

has the capability of fermenting sugar to produce concentrations of ethanol that are toxic to most organisms. Other species also have a strong fermentative capacity, but some are specialized to low temperatures, whereas is the most thermotolerant. Although has been extensively used to study the genetic basis of ethanol tolerance, much less is known about temperature dependent ethanol tolerance. In this study, we examined the genetic basis of ethanol tolerance at high temperature among strains of We identified two amino acid polymorphisms in that cause strong sensitivity to ethanol at high temperature and more limited sensitivity to temperature in the absence of ethanol. We also identified a single amino acid polymorphism in that causes sensitivity to high temperature in a strain dependent fashion. The genes we identified provide further insight into genetic variation in ethanol and temperature tolerance and the interdependent nature of these two traits in .
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http://dx.doi.org/10.1534/g3.118.200566DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6325899PMC
January 2019

Chronodisruption: An untimely cause of preterm birth?

Best Pract Res Clin Obstet Gynaecol 2018 Oct 20;52:60-67. Epub 2018 Aug 20.

Department of Obstetrics and Gynecology, Washington University in St. Louis, MO, USA. Electronic address:

Circadian rhythms, endogenous and entrainable adaptations to 24-hour cycles of light and dark, influence almost all physiologic functions. Emerging evidence suggests that the disruption of normal circadian rhythms, termed chronodisruption, could affect a wide range of disease-related processes. In this review, we describe the molecular generation of circadian rhythms, the effects of chronodisruption on human health, the circadian timing of birth in multiple species, the possible effects of chronodisruption on preterm birth, and some of the open questions in this field.
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http://dx.doi.org/10.1016/j.bpobgyn.2018.08.001DOI Listing
October 2018

Comparative Genomics Approaches Accurately Predict Deleterious Variants in Plants.

G3 (Bethesda) 2018 10 3;8(10):3321-3329. Epub 2018 Oct 3.

Department of Genetics, Washington University, St. Louis, MO 63110

Recent advances in genome resequencing have led to increased interest in prediction of the functional consequences of genetic variants. Variants at phylogenetically conserved sites are of particular interest, because they are more likely than variants at phylogenetically variable sites to have deleterious effects on fitness and contribute to phenotypic variation. Numerous comparative genomic approaches have been developed to predict deleterious variants, but the approaches are nearly always assessed based on their ability to identify known disease-causing mutations in humans. Determining the accuracy of deleterious variant predictions in nonhuman species is important to understanding evolution, domestication, and potentially to improving crop quality and yield. To examine our ability to predict deleterious variants in plants we generated a curated database of 2,910 mutants with known phenotypes. We evaluated seven approaches and found that while all performed well, their relative ranking differed from prior benchmarks in humans. We conclude that deleterious mutations can be reliably predicted in and likely other plant species, but that the relative performance of various approaches does not necessarily translate from one species to another.
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http://dx.doi.org/10.1534/g3.118.200563DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6169392PMC
October 2018

Mouse models of preterm birth: suggested assessment and reporting guidelines.

Biol Reprod 2018 11;99(5):922-937

Center for Reproductive Health Sciences, Department of Obstetrics and Gynecology, Washington University School of Medicine, St. Louis, Missouri, USA.

Preterm birth affects approximately 1 out of every 10 births in the United States, leading to high rates of mortality and long-term negative health consequences. To investigate the mechanisms leading to preterm birth so as to develop prevention strategies, researchers have developed numerous mouse models of preterm birth. However, the lack of standard definitions for preterm birth in mice limits our field's ability to compare models and make inferences about preterm birth in humans. In this review, we discuss numerous mouse preterm birth models, propose guidelines for experiments and reporting, and suggest markers that can be used to assess whether pups are premature or mature. We argue that adoption of these recommendations will enhance the utility of mice as models for preterm birth.
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http://dx.doi.org/10.1093/biolre/ioy109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6297318PMC
November 2018

A multi-phase approach to select new wine yeast strains with enhanced fermentative fitness and glutathione production.

Appl Microbiol Biotechnol 2018 Mar 22;102(5):2269-2278. Epub 2018 Jan 22.

Department of Life Sciences, University of Modena and Reggio Emilia, Via Amendola 2, 42122, Reggio Emilia, Italy.

The genetic improvement of winemaking yeasts is a virtually infinite process, as the design of new strains must always cope with varied and ever-evolving production contexts. Good wine yeasts must feature both good primary traits, which are related to the overall fermentative fitness of the strain, and secondary traits, which provide accessory features augmenting its technological value. In this context, the superiority of "blind," genetic improvement techniques, as those based on the direct selection of the desired phenotype without prior knowledge of the genotype, was widely proven. Blind techniques such as adaptive evolution strategies were implemented for the enhancement of many traits of interest in the winemaking field. However, these strategies usually focus on single traits: this possibly leads to genetic tradeoff phenomena, where the selection of enhanced secondary traits might lead to sub-optimal primary fermentation traits. To circumvent this phenomenon, we applied a multi-step and strongly directed genetic improvement strategy aimed at combining a strong fermentative aptitude (primary trait) with an enhanced production of glutathione (secondary trait). We exploited the random genetic recombination associated to a library of 69 monosporic clones of strain UMCC 855 (Saccharomyces cerevisiae) to search for new candidates possessing both traits. This was achieved by consecutively applying three directional selective criteria: molybdate resistance (1), fermentative aptitude (2), and glutathione production (3). The strategy brought to the selection of strain 21T2-D58, which produces a high concentration of glutathione, comparable to that of other glutathione high-producers, still with a much greater fermentative aptitude.
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http://dx.doi.org/10.1007/s00253-018-8773-3DOI Listing
March 2018

Genetic variation and expression changes associated with molybdate resistance from a glutathione producing wine strain of Saccharomyces cerevisiae.

PLoS One 2017 6;12(7):e0180814. Epub 2017 Jul 6.

Department of Life Sciences, University of Modena and Reggio Emilia, Reggio Emilia, Italy.

Glutathione (GSH) production during wine fermentation is a desirable trait as it can limit must and wine oxidation and protect various aromatic compounds. UMCC 2581 is a Saccharomyces cerevisiae wine strain with enhanced GSH content at the end of wine fermentation. This strain was previously derived by selection for molybdate resistance following a sexual cycle of UMCC 855 using an evolution-based strategy. In this study, we examined genetic and gene expression changes associated with the derivation of UMCC 2581. For genetic analysis we sporulated the diploid UMCC 855 parental strain and found four phenotype classes of segregants related to molybdate resistance, demonstrating the presence of segregating variation from the parental strain. Using bulk segregant analysis we mapped molybdate traits to two loci. By sequencing both the parental and evolved strain genomes we identified candidate mutations within the two regions as well as an extra copy of chromosome 1 in UMCC 2581. Combining the mapped loci with gene expression profiles of the evolved and parental strains we identified a number of candidate genes with genetic and/or gene expression changes that could underlie molybdate resistance and increased GSH levels. Our results provide insight into the genetic basis of GSH production relevant to winemaking and highlight the value of enhancing wine strains using existing variation present in wine strains.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0180814PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5500363PMC
October 2017

Cis-Regulatory Divergence in Gene Expression between Two Thermally Divergent Yeast Species.

Genome Biol Evol 2017 05;9(5):1120-1129

Department of Genetics, Washington University, St. Louis, MO.

Gene regulation is a ubiquitous mechanism by which organisms respond to their environment. While organisms are often found to be adapted to the environments they experience, the role of gene regulation in environmental adaptation is not often known. In this study, we examine divergence in cis-regulatory effects between two Saccharomycesspecies, S. cerevisiaeand S. uvarum, that have substantially diverged in their thermal growth profile. We measured allele specific expression (ASE) in the species' hybrid at three temperatures, the highest of which is lethal to S. uvarumbut not the hybrid or S. cerevisiae. We find that S. uvarumalleles can be expressed at the same level as S. cerevisiaealleles at high temperature and most cis-acting differences in gene expression are not dependent on temperature. While a small set of 136 genes show temperature-dependent ASE, we find no indication that signatures of directional cis-regulatory evolution are associated with temperature. Within promoter regions we find binding sites enriched upstream of temperature responsive genes, but only weak correlations between binding site and expression divergence. Our results indicate that temperature divergence between S. cerevisiaeand S. uvarumhas not caused widespread divergence in cis-regulatory activity, but point to a small subset of genes where the species' alleles show differences in magnitude or opposite responses to temperature. The difficulty of explaining divergence in cis-regulatory sequences with models of transcription factor binding sites and nucleosome positioning highlights the importance of identifying mutations that underlie cis-regulatory divergence between species.
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http://dx.doi.org/10.1093/gbe/evx072DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5554586PMC
May 2017

Hybridization and adaptive evolution of diverse species for cellulosic biofuel production.

Biotechnol Biofuels 2017 27;10:78. Epub 2017 Mar 27.

Laboratory of Genetics, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI USA.

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 acids and aldehydes. Several research projects have investigated lignocellulosic biomass fermentation by the baker's yeast . Most projects have taken synthetic biological approaches or have explored naturally occurring diversity in to enhance stress tolerance, xylose consumption, or ethanol production. Despite these efforts, improved strains with new properties are needed. In other industrial processes, such as wine and beer fermentation, interspecies hybrids have combined important traits from multiple species, suggesting that interspecies hybridization may also offer potential for biofuel research.

Results: To investigate the efficacy of this approach for traits relevant to lignocellulosic biofuel production, we generated synthetic hybrids by crossing engineered xylose-fermenting strains of with wild strains from various species. These interspecies hybrids retained important parental traits, such as xylose consumption and stress tolerance, while displaying intermediate kinetic parameters and, in some cases, heterosis (hybrid vigor). Next, we exposed them to adaptive evolution in ammonia fiber expansion-pretreated corn stover hydrolysate and recovered strains with improved fermentative traits. Genome sequencing showed that the genomes of these evolved synthetic hybrids underwent rearrangements, duplications, and deletions. To determine whether the genus contains additional untapped potential, we screened a genetically diverse collection of more than 500 wild, non-engineered isolates and uncovered a wide range of capabilities for traits relevant to cellulosic biofuel production. Notably, strains have high innate tolerance to hydrolysate toxins, while some species have a robust native capacity to consume xylose.

Conclusions: This research demonstrates that hybridization is a viable method to combine industrially relevant traits from diverse yeast species and that members of the genus beyond may offer advantageous genes and traits of interest to the lignocellulosic biofuel industry.
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http://dx.doi.org/10.1186/s13068-017-0763-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5369230PMC
March 2017

The Role of Deleterious Substitutions in Crop Genomes.

Mol Biol Evol 2016 09 14;33(9):2307-17. Epub 2016 Jun 14.

Department of Agronomy and Plant Genetics, University of Minnesota

Populations continually incur new mutations with fitness effects ranging from lethal to adaptive. While the distribution of fitness effects of new mutations is not directly observable, many mutations likely either have no effect on organismal fitness or are deleterious. Historically, it has been hypothesized that a population may carry many mildly deleterious variants as segregating variation, which reduces the mean absolute fitness of the population. Recent advances in sequencing technology and sequence conservation-based metrics for inferring the functional effect of a variant permit examination of the persistence of deleterious variants in populations. The issue of segregating deleterious variation is particularly important for crop improvement, because the demographic history of domestication and breeding allows deleterious variants to persist and reach moderate frequency, potentially reducing crop productivity. In this study, we use exome resequencing of 15 barley accessions and genome resequencing of 8 soybean accessions to investigate the prevalence of deleterious single nucleotide polymorphisms (SNPs) in the protein-coding regions of the genomes of two crops. We conclude that individual cultivars carry hundreds of deleterious SNPs on average, and that nonsense variants make up a minority of deleterious SNPs. Our approach identifies known phenotype-altering variants as deleterious more frequently than the genome-wide average, suggesting that putatively deleterious variants are likely to affect phenotypic variation. We also report the implementation of a SNP annotation tool BAD_Mutations that makes use of a likelihood ratio test based on alignment of all currently publicly available Angiosperm genomes.
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http://dx.doi.org/10.1093/molbev/msw102DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4989107PMC
September 2016

Independent Origins of Yeast Associated with Coffee and Cacao Fermentation.

Curr Biol 2016 Apr 24;26(7):965-71. Epub 2016 Mar 24.

Pacific Northwest Diabetes Research Institute, Seattle, WA 98122, USA; Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA. Electronic address:

Modern transportation networks have facilitated the migration and mingling of previously isolated populations of plants, animals, and insects. Human activities can also influence the global distribution of microorganisms. The best-understood example is yeasts associated with winemaking. Humans began making wine in the Middle East over 9,000 years ago [1, 2]. Selecting favorable fermentation products created specialized strains of Saccharomyces cerevisiae [3, 4] that were transported along with grapevines. Today, S. cerevisiae strains residing in vineyards around the world are genetically similar, and their population structure suggests a common origin that followed the path of human migration [3-7]. Like wine, coffee and cacao depend on microbial fermentation [8, 9] and have been globally dispersed by humans. Theobroma cacao originated in the Amazon and Orinoco basins of Colombia and Venezuela [10], was cultivated in Central America by Mesoamerican peoples, and was introduced to Europeans by Hernán Cortés in 1530 [11]. Coffea, native to Ethiopia, was disseminated by Arab traders throughout the Middle East and North Africa in the 6(th) century and was introduced to European consumers in the 17(th) century [12]. Here, we tested whether the yeasts associated with coffee and cacao are genetically similar, crop-specific populations or genetically diverse, geography-specific populations. Our results uncovered populations that, while defined by niche and geography, also bear signatures of admixture between major populations in events independent of the transport of the plants. Thus, human-associated fermentation and migration may have affected the distribution of yeast involved in the production of coffee and chocolate.
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http://dx.doi.org/10.1016/j.cub.2016.02.012DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4821677PMC
April 2016

Selective photonic disinfection of cell culture using a visible ultrashort pulsed laser.

IEEE J Sel Top Quantum Electron 2016 May-Jun;22(3). Epub 2015 Nov 9.

Department of Physics and Center for Biophysics, Arizona State University, Tempe, AZ 85287-1504.

Microbial contamination of cell culture is a major problem encountered both in academic labs and in the biotechnology/pharmaceutical industries. A broad spectrum of microbes including mycoplasma, bacteria, fungi, and viruses are the causative agents of cell culture contamination. Unfortunately, the existing disinfection techniques lack selectivity and/or lead to the development of drug-resistance, and more importantly there is no universal method to address all microbes. Here, we report a novel, chemical-free visible ultrashort pulsed laser method for cell culture disinfection. The ultrashort pulsed laser technology inactivates pathogens with mechanical means, a paradigm shift from the traditional pharmaceutical and chemical approaches. We demonstrate that ultrashort pulsed laser treatment can efficiently inactivate mycoplasma, bacteria, yeast, and viruses with good preservation of mammalian cell viability. Our results indicate that this ultrashort pulsed laser technology has the potential to serve as a universal method for the disinfection of cell culture.
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http://dx.doi.org/10.1109/JSTQE.2015.2498920DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4800335PMC
November 2015

Changes in the Relative Abundance of Two Saccharomyces Species from Oak Forests to Wine Fermentations.

Front Microbiol 2016 24;7:215. Epub 2016 Feb 24.

Department of Genetics and Center for Genome Sciences and System Biology, Washington University St. Louis, MO, USA.

Saccharomyces cerevisiae and its sibling species Saccharomyces paradoxus are known to inhabit temperate arboreal habitats across the globe. Despite their sympatric distribution in the wild, S. cerevisiae is predominantly associated with human fermentations. The apparent ecological differentiation of these species is particularly striking in Europe where S. paradoxus is abundant in forests and S. cerevisiae is abundant in vineyards. However, ecological differences may be confounded with geographic differences in species abundance. To compare the distribution and abundance of these two species we isolated Saccharomyces strains from over 1200 samples taken from vineyard and forest habitats in Slovenia. We isolated numerous strains of S. cerevisiae and S. paradoxus, as well as a small number of Saccharomyces kudriavzevii strains, from both vineyard and forest environments. We find S. cerevisiae less abundant than S. paradoxus on oak trees both within and outside the vineyard, but more abundant on grapevines and associated substrates. Analysis of the uncultured microbiome shows, that both S. cerevisiae and S. paradoxus are rare species in soil and bark samples, but can be much more common in grape must. In contrast to S. paradoxus, European strains of S. cerevisiae have acquired multiple traits thought to be important for life in the vineyard and dominance of wine fermentations. We conclude, that S. cerevisiae and S. paradoxus currently share both vineyard and non-vineyard habitats in Slovenia and we discuss factors relevant to their global distribution and relative abundance.
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http://dx.doi.org/10.3389/fmicb.2016.00215DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4764737PMC
March 2016

Divergent MLS1 Promoters Lie on a Fitness Plateau for Gene Expression.

Mol Biol Evol 2016 05 18;33(5):1270-9. Epub 2016 Jan 18.

Department of Genetics, Washington University, St. Louis Center for Genome Sciences and Systems Biology, Washington University, St. Louis

Qualitative patterns of gene activation and repression are often conserved despite an abundance of quantitative variation in expression levels within and between species. A major challenge to interpreting patterns of expression divergence is knowing which changes in gene expression affect fitness. To characterize the fitness effects of gene expression divergence, we placed orthologous promoters from eight yeast species upstream of malate synthase (MLS1) in Saccharomyces cerevisiae As expected, we found these promoters varied in their expression level under activated and repressed conditions as well as in their dynamic response following loss of glucose repression. Despite these differences, only a single promoter driving near basal levels of expression caused a detectable loss of fitness. We conclude that the MLS1 promoter lies on a fitness plateau whereby even large changes in gene expression can be tolerated without a substantial loss of fitness.
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http://dx.doi.org/10.1093/molbev/msw010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4839218PMC
May 2016

Patterns of Gene Conversion in Duplicated Yeast Histones Suggest Strong Selection on a Coadapted Macromolecular Complex.

Genome Biol Evol 2015 Nov 11;7(12):3249-58. Epub 2015 Nov 11.

Division of Animal Sciences, University of Missouri, Columbia Informatics Institute, University of Missouri, Columbia

We find evidence for interlocus gene conversion in five duplicated histone genes from six yeast species. The sequences of these duplicated genes, surviving from the ancient genome duplication, show phylogenetic patterns inconsistent with the well-resolved orthology relationships inferred from a likelihood model of gene loss after the genome duplication. Instead, these paralogous genes are more closely related to each other than any is to its nearest ortholog. In addition to simulations supporting gene conversion, we also present evidence for elevated rates of radical amino acid substitutions along the branches implicated in the conversion events. As these patterns are similar to those seen in ribosomal proteins that have undergone gene conversion, we speculate that in cases where duplicated genes code for proteins that are a part of tightly interacting complexes, selection may favor the fixation of gene conversion events in order to maintain high protein identities between duplicated copies.
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http://dx.doi.org/10.1093/gbe/evv216DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4700949PMC
November 2015

Cori meets Dobzhansky: Evolution and Gene Expression in St. Louis: A report on the "Evolution and Core Processes in Gene Regulation" meeting in St. Louis, June 25-28, 2015.

Bioessays 2015 Oct 10;37(10):1042-4. Epub 2015 Sep 10.

Stowers Institute for Medical Research, Kansas City, MO, USA.

St. Louis and its famous Gateway Arch were the setting of the Special Symposium: Evolution and Core Processes in Gene Regulation, sponsored by the American Society for Biochemistry and Molecular Biology. Biochemists and evolutionary biologists highlighted growing connections between studies of biochemical mechanism and natural selection on gene expression.
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http://dx.doi.org/10.1002/bies.201500106DOI Listing
October 2015

Evolution of ecological dominance of yeast species in high-sugar environments.

Evolution 2015 08 14;69(8):2079-93. Epub 2015 Jul 14.

Department of Genetics, Washington University, St. Louis, Missouri.

In budding yeasts, fermentation in the presence of oxygen evolved around the time of a whole genome duplication (WGD) and is thought to confer dominance in high-sugar environments because ethanol is toxic to many species. Although there are many fermentative yeast species, only Saccharomyces cerevisiae consistently dominates wine fermentations. In this study, we use coculture experiments and intrinsic growth rate assays to examine the relative fitness of non-WGD and WGD yeast species across environments to assess when S. cerevisiae's ability to dominate high-sugar environments arose. We show that S. cerevisiae dominates nearly all other non-WGD and WGD species except for its sibling species S. paradoxus in both grape juice and a high-sugar rich medium. Of the species we tested, S. cerevisiae and S. paradoxus have evolved the highest ethanol tolerance and intrinsic growth rate in grape juice. However, the ability of S. cerevisiae and S. paradoxus to dominate certain species depends on the temperature and the type of high-sugar environment. Our results indicate that dominance of high-sugar environments evolved much more recently than the WGD, most likely just prior to or during the differentiation of Saccharomyces species, and that evolution of multiple traits contributes to S. cerevisiae's ability to dominate wine fermentations.
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http://dx.doi.org/10.1111/evo.12707DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4751874PMC
August 2015

Using whole-genome sequences of the LG/J and SM/J inbred mouse strains to prioritize quantitative trait genes and nucleotides.

BMC Genomics 2015 May 28;16:415. Epub 2015 May 28.

Department of Genetics, Washington University School of Medicine, Campus Box 8108, 660 S Euclid Ave, St Louis, MO, 63110, USA.

Background: The laboratory mouse is the most commonly used model for studying variation in complex traits relevant to human disease. Here we present the whole-genome sequences of two inbred strains, LG/J and SM/J, which are frequently used to study variation in complex traits as diverse as aging, bone-growth, adiposity, maternal behavior, and methamphetamine sensitivity.

Results: We identified small nucleotide variants (SNVs) and structural variants (SVs) in the LG/J and SM/J strains relative to the reference genome and discovered novel variants in these two strains by comparing their sequences to other mouse genomes. We find that 39% of the LG/J and SM/J genomes are identical-by-descent (IBD). We characterized amino-acid changing mutations using three algorithms: LRT, PolyPhen-2 and SIFT. We also identified polymorphisms between LG/J and SM/J that fall in regulatory regions and highly informative transcription factor binding sites (TFBS). We intersected these functional predictions with quantitative trait loci (QTL) mapped in advanced intercrosses of these two strains. We find that QTL are both over-represented in non-IBD regions and highly enriched for variants predicted to have a functional impact. Variants in QTL associated with metabolic (231 QTL identified in an F16 generation) and developmental (41 QTL identified in an F34 generation) traits were interrogated and we highlight candidate quantitative trait genes (QTG) and nucleotides (QTN) in a QTL on chr13 associated with variation in basal glucose levels and in a QTL on chr6 associated with variation in tibia length.

Conclusions: We show how integrating genomic sequence with QTL reduces the QTL search space and helps researchers prioritize candidate genes and nucleotides for experimental follow-up. Additionally, given the LG/J and SM/J phylogenetic context among inbred strains, these data contribute important information to the genomic landscape of the laboratory mouse.
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http://dx.doi.org/10.1186/s12864-015-1592-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4445795PMC
May 2015

Heterochronic meiotic misexpression in an interspecific yeast hybrid.

Mol Biol Evol 2014 Jun 7;31(6):1333-42. Epub 2014 Mar 7.

Department of Genetics, Washington UniversityCenter for Genome Sciences and Systems Biology, Washington University.

Regulatory changes rapidly accumulate between species, and interspecific hybrids often misexpress genes. Hybrid misexpression, expression levels outside the range of both parental species, can result from cis- and trans-acting regulatory changes that interact abnormally in hybrids. Thus, misexpressed genes may contribute to hybrid sterility. However, in the context of a whole organism, misexpression may not result directly from cis-trans interactions but rather indirectly from differences between hybrid and parental abundance of cell types. Here we eliminate the confounding effects of cell types by examining gene expression in a sterile interspecific yeast hybrid during meiosis. We investigated gene expression of the yeasts Saccharomyces cerevisiae, S. paradoxus, and their hybrid at multiple meiotic stages. Although the hybrid and parents exhibit similar changes in expression levels across meiosis, the hybrid meiotic program occurs earlier than either parent. The timing change produces a heterochronic pattern of misexpression during midmeiosis. Coincident with the timing of misexpression, we find a transition from predominantly trans-acting to cis-acting expression divergence and an increase in the number of opposing cis-trans changes. However, we find no direct relationship between opposing cis-trans changes and misexpression. Contrary to the notion that cis-trans interactions cause misexpression, a heterochronic shift in the normal meiotic gene expression program produces patterns of misexpression in an yeast hybrid. Our results imply that temporal dynamics of single cell types is important to understanding hybrid misexpression and its relationship to cis-trans interactions.
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http://dx.doi.org/10.1093/molbev/msu098DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4032130PMC
June 2014

The molecular basis of phenotypic variation in yeast.

Authors:
Justin C Fay

Curr Opin Genet Dev 2013 Dec 21;23(6):672-7. Epub 2013 Nov 21.

Department of Genetics and Center for Genome Sciences and Systems Biology, Washington University, St. Louis, MO, United States. Electronic address:

The power of yeast genetics has now been extensively applied to phenotypic variation among strains of Saccharomyces cerevisiae. As a result, over 100 genes and numerous sequence variants have been identified, providing us with a general characterization of mutations underlying quantitative trait variation. Most quantitative trait alleles exert considerable phenotypic effects and alter conserved amino acid positions within protein coding sequences. When examined, quantitative trait alleles influence the expression of numerous genes, most of which are unrelated to an allele's phenotypic effect. The profile of quantitative trait alleles has proven useful to reverse quantitative genetics approaches and supports the use of systems genetics approaches to synthesize the molecular basis of trait variation across multiple strains.
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http://dx.doi.org/10.1016/j.gde.2013.10.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3899683PMC
December 2013

Fine-mapping an association of FSHR with preterm birth in a Finnish population.

PLoS One 2013 29;8(10):e78032. Epub 2013 Oct 29.

Computational and Systems Biology Program, Washington University, St. Louis, Missouri, United States of America.

Preterm birth is a complex disorder defined by gestations of less than 37 weeks. While preterm birth is estimated to have a significant genetic component, relative few genes have been associated with preterm birth. Polymorphism in one such gene, follicle-stimulating hormone receptor (FSHR), has been associated with preterm birth in Finnish and African American mothers but not other populations. To refine the genetic association of FSHR with preterm birth we conducted a fine-mapping study at the FSHR locus in a Finnish cohort. We sequenced a total of 44 kb, including protein-coding and conserved non-coding regions, in 127 preterm and 135 term mothers. Overall, we identified 288 single nucleotide variants and 65 insertion/deletions of 1-2 bp across all subjects. While no common SNPs in protein-coding regions were associated with preterm birth, including one previously associated with timing of fertilization, multiple SNPs spanning the first and second intron showed the strongest associations. Analysis of the associated SNPs revealed that they form both a protective (OR = 0.50, 95% CI = 0.25-0.93) as well as a risk (OR = 1.89, 95% CI = 1.08-3.39) haplotype with independent effects. In these haplotypes, two SNPs, rs12052281 and rs72822025, were predicted to disrupt ZEB1 and ELF3 transcription factor binding sites, respectively. Our results show that multiple haplotypes at FSHR are associated with preterm birth and we discuss the frequency and structure of these haplotypes outside of the Finnish population as a potential explanation for the absence of FSHR associations in some populations.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0078032PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3812121PMC
September 2014

Genomic sequence diversity and population structure of Saccharomyces cerevisiae assessed by RAD-seq.

G3 (Bethesda) 2013 Dec 9;3(12):2163-71. Epub 2013 Dec 9.

Institute for Systems Biology, Seattle, Washington 98109.

The budding yeast Saccharomyces cerevisiae is important for human food production and as a model organism for biological research. The genetic diversity contained in the global population of yeast strains represents a valuable resource for a number of fields, including genetics, bioengineering, and studies of evolution and population structure. Here, we apply a multiplexed, reduced genome sequencing strategy (restriction site-associated sequencing or RAD-seq) to genotype a large collection of S. cerevisiae strains isolated from a wide range of geographical locations and environmental niches. The method permits the sequencing of the same 1% of all genomes, producing a multiple sequence alignment of 116,880 bases across 262 strains. We find diversity among these strains is principally organized by geography, with European, North American, Asian, and African/S. E. Asian populations defining the major axes of genetic variation. At a finer scale, small groups of strains from cacao, olives, and sake are defined by unique variants not present in other strains. One population, containing strains from a variety of fermentations, exhibits high levels of heterozygosity and a mixture of alleles from European and Asian populations, indicating an admixed origin for this group. We propose a model of geographic differentiation followed by human-associated admixture, primarily between European and Asian populations and more recently between European and North American populations. The large collection of genotyped yeast strains characterized here will provide a useful resource for the broad community of yeast researchers.
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http://dx.doi.org/10.1534/g3.113.007492DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3852379PMC
December 2013