Kevin S. Myers
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View article: Orthogonal chemical genomics approaches reveal genomic targets for increasing anaerobic chemical tolerance in <i>Zymomonas mobilis</i>
Orthogonal chemical genomics approaches reveal genomic targets for increasing anaerobic chemical tolerance in <i>Zymomonas mobilis</i> Open
Genetically engineered microbes have the potential to increase efficiency in the bioeconomy by overcoming growth-limiting production stress. Screens of gene perturbation libraries against production stressors can identify high-value engine…
View article: <i>Novosphingobium aromaticivorans</i> LigR coordinates transcription of genes involved in metabolism of multiple types of aromatics
<i>Novosphingobium aromaticivorans</i> LigR coordinates transcription of genes involved in metabolism of multiple types of aromatics Open
Aromatic compounds are a ubiquitous and diverse family of chemicals with functions as biomolecules, natural products, industrial chemicals, and pollutants. Novosphingobium aromaticivorans DSM 12444 uses multiple inducible pathways to catab…
View article: Transcriptomic data sets for <i>Novosphingobium aromaticivorans</i> DSM12444 and a ΔSARO_RS14285 mutant grown in the presence of glucose and either protocatechuic, vanillic, syringic, or 4-coumaric acid
Transcriptomic data sets for <i>Novosphingobium aromaticivorans</i> DSM12444 and a ΔSARO_RS14285 mutant grown in the presence of glucose and either protocatechuic, vanillic, syringic, or 4-coumaric acid Open
The SARO_RS14285 gene, encoding a transcription factor, was deleted in Novosphingobium aromaticivorans DSM12444. The transcriptomes of the parent and ΔSARO_RS14285 strains were determined when grown in medium containing glucose with or wit…
View article: Using DNA affinity purification sequencing (DAP-seq) to identify <i>in vitro</i> binding sites of potential <i>Novosphingobium aromaticivorans</i> DSM12444 transcription factors
Using DNA affinity purification sequencing (DAP-seq) to identify <i>in vitro</i> binding sites of potential <i>Novosphingobium aromaticivorans</i> DSM12444 transcription factors Open
Genome-wide binding sites of 44 putative transcription factors (TFs) from Novosphingobium aromaticivorans DSM12444 were analyzed using DNA affinity purification sequencing. We report that 32 of these TFs have at least one area of enrichmen…
View article: Orthogonal chemical genomics approaches reveal genomic targets for increasing anaerobic chemical tolerance in <i>Zymomonas mobilis</i>
Orthogonal chemical genomics approaches reveal genomic targets for increasing anaerobic chemical tolerance in <i>Zymomonas mobilis</i> Open
Genetically-engineered microbes have the potential to increase efficiency in the bioeconomy by overcoming growth-limiting production stress. Screens of gene perturbation libraries against production stressors can identify high-value engine…
View article: Physiological roles of an <i>Acinetobacter</i> -specific σ factor
Physiological roles of an <i>Acinetobacter</i> -specific σ factor Open
The Gram-negative pathogen Acinetobacter baumannii is considered an “urgent threat” to human health due to its propensity to become antibiotic resistant. Understanding the distinct regulatory paradigms used by A. baumannii to mitigate cell…
View article: Metagenome-assembled genomes from microbial communities producing lactic acid from dairy residues
Metagenome-assembled genomes from microbial communities producing lactic acid from dairy residues Open
To advance the knowledge of microbial communities capable of fermenting agro-industrial residues into value-added products, we report metagenomes of microbial communities from four anaerobic bioreactors fed a mixture of ultra-filtered milk…
View article: Altering translation allows <i>E. coli</i> to overcome G-quadruplex stabilizers
Altering translation allows <i>E. coli</i> to overcome G-quadruplex stabilizers Open
G-quadruplex (G4) structures can form in guanine-rich DNA or RNA and have been found to modulate cellular processes, including replication, transcription, and translation. Many studies on the cellular roles of G4s have focused on eukaryoti…
View article: RB-TnSeq barcode abundance data sets for <i>Novosphingobium aromaticivorans</i> grown on the β-5-linked aromatic dimer dehydrodiconiferyl alcohol
RB-TnSeq barcode abundance data sets for <i>Novosphingobium aromaticivorans</i> grown on the β-5-linked aromatic dimer dehydrodiconiferyl alcohol Open
A randomly barcoded transposon insertion sequencing (RB-TnSeq) library of Novosphingobium aromaticivorans DSM12444 was grown in media containing either glucose or the β-5-linked aromatic dimer dehydrodiconiferyl alcohol (DC-A) as the sole …
View article: Transcriptomic data sets for <i>Novosphingobium aromaticivorans</i> grown with the β-5-linked aromatic dimer dehydrodiconiferyl alcohol and the related G-aromatic monomers vanillin and ferulic acid
Transcriptomic data sets for <i>Novosphingobium aromaticivorans</i> grown with the β-5-linked aromatic dimer dehydrodiconiferyl alcohol and the related G-aromatic monomers vanillin and ferulic acid Open
The transcriptomes of a 2-pyrone-4,6-dicarboxylic acid-producing strain of Novosphingobium aromaticivorans DSM12444 were determined when grown in minimal medium containing glucose alone or glucose plus vanillin, ferulic acid, or the β-5-li…
View article: Effect of Temperature and pH on Microbial Communities Fermenting a Dairy Coproduct Mixture
Effect of Temperature and pH on Microbial Communities Fermenting a Dairy Coproduct Mixture Open
Organic-rich industrial residues can serve as renewable feedstocks for the generation of useful products by microbial fermentation. We investigated fermenting communities enriched in a mixture of ultra-filtered milk permeate (UFMP) and aci…
View article: Altering translation allows<i>E. coli</i>to overcome chemically stabilized G-quadruplexes
Altering translation allows<i>E. coli</i>to overcome chemically stabilized G-quadruplexes Open
G-quadruplex (G4) structures can form in guanine-rich DNA or RNA and have been found to modulate cellular processes including replication, transcription, and translation. Many studies on the cellular roles of G4s have focused on eukaryotic…
View article: Auto-MuRCiS: a streamlined software package for analysis of multiplex, randomized CRISPR interference sequencing data
Auto-MuRCiS: a streamlined software package for analysis of multiplex, randomized CRISPR interference sequencing data Open
Multiplex, randomized CRISPR interference sequencing (MuRCiS) allows for the simultaneous identification of multiple gene knockouts that together influence microbial processes. Here, we report on an updated analysis tool called Auto-MuRCiS…
View article: Catabolism of β-5 linked aromatics by <i>Novosphingobium aromaticivorans</i>
Catabolism of β-5 linked aromatics by <i>Novosphingobium aromaticivorans</i> Open
Aromatic compounds are an important source of commodity chemicals traditionally produced from fossil fuels. Aromatics derived from plant lignin can potentially be converted into commodity chemicals through depolymerization followed by micr…
View article: Physiological Roles of an<i>Acinetobacter</i>-specific σ Factor
Physiological Roles of an<i>Acinetobacter</i>-specific σ Factor Open
The Gram-negative pathogen Acinetobacter baumannii is considered an “urgent threat” to human health due to its propensity to become antibiotic resistant. Understanding the distinct regulatory paradigms used by A. baumannii to mitigate cell…
View article: Metagenome-assembled genomes from microbiomes fermenting dairy coproducts
Metagenome-assembled genomes from microbiomes fermenting dairy coproducts Open
To advance knowledge of microbial communities capable of fermenting agro-industrial residues into value-added products, we report metagenomes of microbial communities from six anaerobic bioreactors that were fed a mixture of ultra-filtered…
View article: Targeted, Genome-scale Overexpression in Proteobacteria
Targeted, Genome-scale Overexpression in Proteobacteria Open
Targeted, genome-scale gene perturbation screens using Clustered Regularly Interspaced Short Palindromic Repeats interference (CRISPRi) and activation (CRISPRa) have revolutionized eukaryotic genetics, advancing medical, industrial, and ba…
View article: Refinement of the “ <i>Candidatus</i> Accumulibacter” genus based on metagenomic analysis of biological nutrient removal (BNR) pilot-scale plants operated with reduced aeration
Refinement of the “ <i>Candidatus</i> Accumulibacter” genus based on metagenomic analysis of biological nutrient removal (BNR) pilot-scale plants operated with reduced aeration Open
Members of the “ Candidatus Accumulibacter” genus are widely studied as key polyphosphate-accumulating organisms (PAOs) in biological nutrient removal (BNR) facilities performing enhanced biological phosphorus removal (EBPR). This diverse …
View article: A randomized multiplex CRISPRi-Seq approach for the identification of critical combinations of genes
A randomized multiplex CRISPRi-Seq approach for the identification of critical combinations of genes Open
Identifying virulence-critical genes from pathogens is often limited by functional redundancy. To rapidly interrogate the contributions of combinations of genes to a biological outcome, we have developed a mu ltiplex, r andomized C RISPR i…
View article: Identification of <i>recG</i> genetic interactions in <i>Escherichia coli</i> by transposon sequencing
Identification of <i>recG</i> genetic interactions in <i>Escherichia coli</i> by transposon sequencing Open
Maintaining the integrity of the genome is of utmost importance for cell division and propagation. In Escherichia coli , the RecG protein has been implicated in processing branched recombination intermediates during DNA repair processes, b…
View article: Refinement of the “<i>Candidatus</i>Accumulibacter” Genus Based on a Metagenomic Analysis of Biological Nutrient Removal (BNR) Pilot-Scale Plants Operated with Reduced Aeration
Refinement of the “<i>Candidatus</i>Accumulibacter” Genus Based on a Metagenomic Analysis of Biological Nutrient Removal (BNR) Pilot-Scale Plants Operated with Reduced Aeration Open
Members of the “ Candidatus Accumulibacter” genus are widely studied as key polyphosphate-accumulating organisms (PAOs) in biological nutrient removal (BNR) facilities performing enhanced biological phosphorus removal (EBPR). This diverse …
View article: Author Response: A randomized multiplex CRISPRi-Seq approach for the identification of critical combinations of genes
Author Response: A randomized multiplex CRISPRi-Seq approach for the identification of critical combinations of genes Open
Identifying virulence-critical genes from pathogens is often limited by functional redundancy. To rapidly interrogate the contributions of combinations of genes to a biological outcome, we have developed a multiplex, randomized CRISPR inte…
View article: A randomized multiplex CRISPRi-Seq approach for the identification of critical combinations of genes
A randomized multiplex CRISPRi-Seq approach for the identification of critical combinations of genes Open
Identifying virulence-critical genes from pathogens is often limited by functional redundancy. To rapidly interrogate the contributions of combinations of genes to a biological outcome, we have developed a multiplex, randomized CRISPR inte…
View article: Regulatory response to a hybrid ancestral nitrogenase in <i>Azotobacter vinelandii</i>
Regulatory response to a hybrid ancestral nitrogenase in <i>Azotobacter vinelandii</i> Open
Biological nitrogen fixation, the microbial reduction of atmospheric nitrogen to bioavailable ammonia, represents both a major limitation on biological productivity and a highly desirable engineering target for synthetic biology. However, …
View article: Developmental Programming of Mitochondrial Function Limits Lifespan in Short-Lived Animals
Developmental Programming of Mitochondrial Function Limits Lifespan in Short-Lived Animals Open
The contribution of mitochondria to lifespan determination remains controversial, as impaired mitochondrial function can paradoxically both shorten and extend longevity. During ageing, mitochondria accumulate defects that disrupt electron …
View article: A hybrid nitrogenase with regulatory elasticity in<i>Azotobacter vinelandii</i>
A hybrid nitrogenase with regulatory elasticity in<i>Azotobacter vinelandii</i> Open
Biological nitrogen fixation, the microbial reduction of atmospheric nitrogen to bioavailable ammonia, represents both a major limitation on biological productivity and a highly desirable engineering target for synthetic biology. However, …
View article: Reviewer #1 (Public Review): A randomized multiplex CRISPRi-Seq approach for the identification of critical combinations of genes
Reviewer #1 (Public Review): A randomized multiplex CRISPRi-Seq approach for the identification of critical combinations of genes Open
Identifying virulence-critical genes from pathogens is often limited by functional redundancy. To rapidly interrogate the contributions of combinations of genes to a biological outcome, we have developed a multiplex, randomized CRISPR inte…
View article: A randomized multiplex CRISPRi-Seq approach for the identification of critical combinations of genes
A randomized multiplex CRISPRi-Seq approach for the identification of critical combinations of genes Open
Identifying virulence-critical genes from pathogens is often limited by functional redundancy. To rapidly interrogate the contributions of combinations of genes to a biological outcome, we have developed a mu ltiplex, r andomized C RISPR i…