Samuel Miller - Academia.edu (original) (raw)

Papers by Samuel Miller

Molecular biology and evolution, Jan 6, 2015

Despite the general assumption that site-specific mutation rates are independent of the local seq... more Despite the general assumption that site-specific mutation rates are independent of the local sequence context, a growing body of evidence suggests otherwise. To further examine contextdependent patterns of mutation, we amassed 5645 spontaneous mutations in wild-type and mismatch-repair deficient mutation accumulation lines of the gram-positive model organism Bacillus subtilis. We then analyzed > 7500 spontaneous base-substitution mutations across Bacillus subtilis, Escherichia coli, and Mesoplasma florum wild-type and mismatch-repair deficient mutation-accumulation lines, finding a context-dependent mutation pattern that is asymmetric around the origin of replication. Different neighbouring nucleotides can alter sitespecific mutation rates by as much as 75-fold, with sites neighbouring G:C base pairs or dimers involving alternating pyrimidine-purine and purine-pyrimidine nucleotides having significantly elevated mutation rates. The influence of context-dependent mutation on genome architecture is strongest in M. florum, consistent with the reduced efficiency of selection in organisms with low effective population size. If not properly accounted for, the disparities arising from patterns of context-dependent mutation can significantly influence interpretations of positive and purifying selection. 2 by guest on June 15, 2016

Genome biology and evolution, 2014

High levels of genetic diversity exist among natural isolates of the bacterium Pseudomonas fluore... more High levels of genetic diversity exist among natural isolates of the bacterium Pseudomonas fluorescens, and are especially elevated around the replication terminus of the genome, where strain-specific genes are found. In an effort to understand the role of genetic variation in the evolution of Pseudomonas, we analyzed 31,106 base substitutions from 45 mutation accumulation lines of P. fluorescens ATCC948, naturally deficient for mismatch repair, yielding a base-substitution mutation rate of 2.34 Â 10 À8 per site per generation (SE: 0.01 Â 10 À8 ) and a small-insertion-deletion mutation rate of 1.65 Â 10 À9 per site per generation (SE: 0.03 Â 10 À9 ). We find that the spectrum of mutations in prophage regions, which often contain virulence factors and antibiotic resistance, is highly similar to that in the intergenic regions of the host genome. Our results show that the mutation rate varies around the chromosome, with the lowest mutation rate found near the origin of replication. Consistent with observations from other studies, we find that site-specific mutation rates are heavily influenced by the immediately flanking nucleotides, indicating that mutations are context dependent.

Nature Reviews Microbiology, 2015

Salmonellae invasion and intracellular replication within host cells result in a range of disease... more Salmonellae invasion and intracellular replication within host cells result in a range of diseases, including gastroenteritis, bacteraemia, enteric fever and focal infections. In recent years, considerable progress has been made in our understanding of the molecular mechanisms that salmonellae use to alter host cell physiology; through the delivery of effector proteins with specific activities and through the modulation of defence and stress response pathways. In this Review, we summarize our current knowledge of the complex interplay between bacterial and host factors that leads to inflammation, disease and, in most cases, control of the infection by its animal hosts, with a particular focus on Salmonella enterica subsp. enterica serovar Typhimurium. We also highlight gaps in our knowledge of the contributions of salmonellae and the host to disease pathogenesis, and we suggest future avenues for further study.

Genome announcements, 2014

Pseudomonas aeruginosa can cause large and prolonged outbreaks in hospitals. We have sequenced an... more Pseudomonas aeruginosa can cause large and prolonged outbreaks in hospitals. We have sequenced and annotated the genomes of two multidrug-resistant P. aeruginosa isolates from the same strain obtained 12 years apart from different patients. Genomic analysis provided insight on the genes acquired and lost by P. aeruginosa during its spread.

Environmental management, 2005

An optical plankton counter (OPC) potentially provides an assessment tool for zooplankton conditi... more An optical plankton counter (OPC) potentially provides an assessment tool for zooplankton condition in ecosystems that is rapid, economical, and spatially extensive. We collected zooplankton data with an OPC in 20 nearshore regions of 4 of the Laurentian Great Lakes. The zoo-plankton size information was used to compute mean size, biomass density, and size-spectra parameters for each location. The resulting metrics were analyzed for their ability to discriminate among the Great Lakes. Biomass density provided discrimination among lakes, as did several parameters describing spectra shape and distribution. A proposed zooplankton indicator, mean size (determined with OPC measurements in this study), was found to provide discrimination among lakes. Size-spectra-related parameters added increased ability to discriminate in conjunction with the biomass density (or mean size) metric. A discriminant function analysis of the multiple metrics (mean size, biomass density, and distribution parameters) suggests that a multi metric size-based approach might be used to classify communities among lakes improving a mean-size metric. The feasibility OPCs and size-based metrics for zooplankton assessment was found to have potential for further development as assessment tools for the biological condition of zooplankton communities in the Great Lakes.

Proceedings of the National Academy of Sciences, 2015

We previously reported that lagging-strand genes accumulate mutations faster than those encoded o... more We previously reported that lagging-strand genes accumulate mutations faster than those encoded on the leading strand in Bacillus subtilis. Although we proposed that orientation-specific encounters between replication and transcription underlie this phenomenon, the mechanism leading to the increased mutagenesis of lagging-strand genes remained unknown. Here, we report that the transcription-dependent and orientation-specific differences in mutation rates of genes require the B. subtilis Y-family polymerase, PolY1 (yqjH). We find that without PolY1, association of the replicative helicase, DnaC, and the recombination protein, RecA, with lagging-strand genes increases in a transcription-dependent manner. These data suggest that PolY1 promotes efficient replisome progression through lagging-strand genes, thereby reducing potentially detrimental breaks and single-stranded DNA at these loci. Y-family polymerases can alleviate potential obstacles to replisome progression by facilitating DNA lesion bypass, extension of D-loops, or excision repair. We find that the nucleotide excision repair (NER) proteins UvrA, UvrB, and UvrC, but not RecA, are required for transcription-dependent asymmetry in mutation rates of genes in the two orientations. Furthermore, we find that the transcription-coupling repair factor Mfd functions in the same pathway as PolY1 and is also required for increased mutagenesis of lagging-strand genes. Experimental and SNP analyses of B. subtilis genomes show mutational footprints consistent with these findings. We propose that the interplay between replication and transcription increases lesion susceptibility of, specifically, lagging-strand genes, activating an Mfd-dependent error-prone NER mechanism. We propose that this process, at least partially, underlies the accelerated evolution of lagging-strand genes.

Principles of Bacterial Pathogenesis, 2001

CHAPTER 7 Molecular Pathogenesis of Salmonellae CHRISTINA A. SCHERER SAMUEL I. MILLER 1. Introduc... more CHAPTER 7 Molecular Pathogenesis of Salmonellae CHRISTINA A. SCHERER SAMUEL I. MILLER 1. Introduction II. ... 270 CHRISTINA A. SCHERER AND SAMUEL I. MILLER although the contamination of fresh produce with animal waste is also a significant problem [18]. ...

Trends in Microbiology, 1996

Current Opinion in Microbiology, 2014

…, 2010

Genome-wide association studies are beginning to elucidate how our genetic differences contribute... more Genome-wide association studies are beginning to elucidate how our genetic differences contribute to susceptibility and severity of disease. While computational tools have previously been developed to support various aspects of genome-wide association studies, there is currently a need for informatics solutions that facilitate the integration of data from multiple sources. Results: Here we present GWAS Analyzer, a database driven webbased tool that integrates genotype and phenotype data, association analysis results and genomic annotations from multiple public resources. GWAS Analyzer contains features for browsing these interrelated data, exploring phenotypic values by family or genotype, and filtering association results based on multiple criteria. The utility of the tool has been demonstrated by a genome-wide association study of human in vitro susceptibility to bacterial infection. GWAS Analyzer facilitated management of large sets of phenotype and genotype data, analysis of phenotypic variation and heritability, and most importantly, generation of a refined set of candidate single nucleotide polymorphisms (SNPs). The tool revealed a SNP that was experimentally validated to be associated with increased cell death among Salmonella infected HapMap cell lines. Availability: http://www.nwrce.org/gwas-analyzer

The American Journal of Pathology, 2014

nature immunology, 2002

Lipopolysaccharide (LPS) is the principal proinflammatory component of the Gram-negative bacteria... more Lipopolysaccharide (LPS) is the principal proinflammatory component of the Gram-negative bacterial envelope and is recognized by the Toll-like receptor 4 (TLR4)-MD-2 receptor complex. Bacteria can alter the acylation state of their LPS in response to environmental changes. One opportunistic bacterium, Pseudomonas aeruginosa, synthesizes more highly acylated (hexa-acylated) LPS structures during adaptation to the cystic fibrosis airway. Here we show that human, but not murine, TLR4-MD-2 recognizes this adaptation and transmits robust proinflammatory signals in response to hexa-acylated but not penta-acylated LPS from P. aeruginosa. Whereas responses to lipid IVA and taxol are dependent on murine MD-2, discrimination of P. aeruginosa LPS structures is mediated by an 82-amino-acid region of human TLR4 that is hypervariable across species. Thus, in contrast to mice, humans use TLR4 to recognize a molecular signature of bacterial-host adaptation to modulate the innate immune response.