Daniel M. Stoebel
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View article: Human body temperature cues widespread changes in virulence gene expression in uropathogenic <i>Escherichia coli</i>
Human body temperature cues widespread changes in virulence gene expression in uropathogenic <i>Escherichia coli</i> Open
As a bacterial pathogen enters a human host, it immediately encounters a temperature upshift to 37°C. Mimicking the early hours of infection, we analyzed the transcriptome and proteome of uropathogenic Escherichia coli CFT073 initially gro…
View article: The transcriptional response to low temperature is weakly conserved across the <i>Enterobacteriaceae</i>
The transcriptional response to low temperature is weakly conserved across the <i>Enterobacteriaceae</i> Open
Bacteria respond to changes in their external environment, such as temperature, by changing the transcription of their genes. We know little about how these regulatory patterns evolve. We used RNA-seq to study the transcriptional response …
View article: The transcriptional response to low temperature is weakly conserved across the<i>Enterobacteriaceae</i>
The transcriptional response to low temperature is weakly conserved across the<i>Enterobacteriaceae</i> Open
Bacteria respond to changes in their external environment like temperature by changing the transcription of their genes, but we know little about how these regulatory patterns evolve. We used RNA-seq to study the transcriptional response o…
View article: The timing of transcription of RpoS-dependent genes varies across multiple stresses in <i>Escherichia coli</i> K-12
The timing of transcription of RpoS-dependent genes varies across multiple stresses in <i>Escherichia coli</i> K-12 Open
The alternative sigma factor RpoS regulates transcription of over 1,000 genes in Escherichia coli in response to many different stresses. RpoS levels rise continuously after exposure to stress, and the consequences of changing levels of Rp…
View article: The timing of transcription of RpoS-dependent genes varies across multiple stresses in<i>Escherichia coli</i>K-12
The timing of transcription of RpoS-dependent genes varies across multiple stresses in<i>Escherichia coli</i>K-12 Open
The alternative sigma factor RpoS regulates transcription of over 1000 genes in Escherichia coli in response to many different stresses. RpoS levels rise continuously after exposure to stress, and the consequences of changing levels of Rpo…
View article: Erratum for Beck et al., “Cra and cAMP Receptor Protein Have Opposing Roles in the Regulation of <i>fruB</i> in Vibrio cholerae”
Erratum for Beck et al., “Cra and cAMP Receptor Protein Have Opposing Roles in the Regulation of <i>fruB</i> in Vibrio cholerae” Open
Volume 203, no. 10, e00044-21, 2021, https://doi.org/10.1128/JB.00044-21. Supplemental material: In Table S2, the labels for qRT-PCR primers were swapped. Revised supplemental material was posted online 20 July 2021.
View article: Cra and cAMP Receptor Protein Have Opposing Roles in the Regulation of <i>fruB</i> in Vibrio cholerae
Cra and cAMP Receptor Protein Have Opposing Roles in the Regulation of <i>fruB</i> in Vibrio cholerae Open
Vibrio cholerae is the causative agent of cholera disease. While current treatments of care are accessible, we still lack an understanding of the molecular mechanisms that allow V. cholerae to survive in both aquatic reservoirs and the hum…
View article: History in the Education of Scientists: Encouraging Judgment and Social Action
History in the Education of Scientists: Encouraging Judgment and Social Action Open
The authors of this essay reflect on the experience of co-teaching a course on the history of genetics and race. The collaboration has pushed them both—a historian of science and a biologist—to consider how to make space for moral and scie…
View article: Redefining the H-NS protein family: a diversity of specialized core and accessory forms exhibit hierarchical transcriptional network integration
Redefining the H-NS protein family: a diversity of specialized core and accessory forms exhibit hierarchical transcriptional network integration Open
H-NS is a nucleoid structuring protein and global repressor of virulence and horizontally-acquired genes in bacteria. H-NS can interact with itself or with homologous proteins, but protein family diversity and regulatory network overlap re…
View article: The transcriptional response of genes to RpoS concentration in <i>Escherichia coli</i> is not determined by core promoter sequences
The transcriptional response of genes to RpoS concentration in <i>Escherichia coli</i> is not determined by core promoter sequences Open
The alternative sigma factor RpoS is an important regulatory protein in Escherichia coli , responsible for mediating the general stress response. RpoS levels vary continuously in response to different stresses. Previous work has shown that…
View article: Additional file 1 of xenoGI: reconstructing the history of genomic island insertions in clades of closely related bacteria
Additional file 1 of xenoGI: reconstructing the history of genomic island insertions in clades of closely related bacteria Open
A more detailed description of the correspondence between xenoGI islands and validation islands. A tab-delimited text file containing each validation range used in the five species we looked at. Includes the assemblies used to compare with…
View article: Additional file 2 of xenoGI: reconstructing the history of genomic island insertions in clades of closely related bacteria
Additional file 2 of xenoGI: reconstructing the history of genomic island insertions in clades of closely related bacteria Open
Comparisons with commonly used GI finding software. A tab-delimited text file containing comparisons between xenoGI and four other commonly used GI finding programs: SIGI-HMM, IslandPick, IslandPath-DIMOB, and Islander. These were done usi…
View article: xenoGI: reconstructing the history of genomic island insertions in clades of closely related bacteria
xenoGI: reconstructing the history of genomic island insertions in clades of closely related bacteria Open
Background Genomic islands play an important role in microbial genome evolution, providing a mechanism for strains to adapt to new ecological conditions. A variety of computational methods, both genome-composition based and comparative hav…
View article: Selecting between-sample RNA-Seq normalization methods from the perspective of their assumptions
Selecting between-sample RNA-Seq normalization methods from the perspective of their assumptions Open
RNA-Seq is a widely-used method for studying the behavior of genes under different biological conditions. An essential step in an RNA-Seq study is normalization, in which raw data are adjusted to account for factors that prevent direct com…
View article: Genome-Wide Transcriptional Response to Varying RpoS Levels in Escherichia coli K-12
Genome-Wide Transcriptional Response to Varying RpoS Levels in Escherichia coli K-12 Open
The alternative sigma factor RpoS is a central regulator of many stress responses in Escherichia coli . The level of functional RpoS differs depending on the stress. The effect of these differing concentrations of RpoS on global transcript…
View article: The genome-wide transcriptional response to varying RpoS levels in<i>Escherichia coli</i>K-12
The genome-wide transcriptional response to varying RpoS levels in<i>Escherichia coli</i>K-12 Open
The alternative sigma factor RpoS is a central regulator of a many stress responses in Escherichia coli. The level of functional RpoS differs depending on the stress. The effect of these differing concentrations of RpoS on global transcrip…
View article: Selecting between-sample RNA-Seq normalization methods from the\n perspective of their assumptions
Selecting between-sample RNA-Seq normalization methods from the\n perspective of their assumptions Open
RNA-Seq is a widely-used method for studying the behavior of genes under\ndifferent biological conditions. An essential step in an RNA-Seq study is\nnormalization, in which raw data are adjusted to account for factors that\nprevent direct …
View article: Benefit of transferred mutations is better predicted by the fitness of recipients than by their ecological or genetic relatedness
Benefit of transferred mutations is better predicted by the fitness of recipients than by their ecological or genetic relatedness Open
Significance The fitness effect of many mutations depends on the genotype of the individual in which they occur. Are these dependencies predictable? Do dependencies build on existing variation between individuals to promote divergence, or …