transcriptome
Commentary | Novel Systems Biology TechniquesPathovar TranscriptomesArchetypal pathogenic bacterial strains are often used to elucidate regulatory networks of an entire pathovar, which encompasses multiple lineages and phylogroups. With enteropathogenic Escherichia coli (EPEC) as a model system, Hazen and colleagues (mSystems 6:e00024-17, 2017, https://doi.org/10.1128/mSystems.00024-...
Editor's Pick Research Article | Novel Systems Biology TechniquesTranscriptional Variation of Diverse Enteropathogenic Escherichia coli Isolates under Virulence-Inducing ConditionsRecent studies have demonstrated that there is considerable genomic diversity among EPEC isolates; however, it is unknown if this genomic diversity leads to differences in their global transcription. This study used RNA-Seq to compare the global transcriptomes of EPEC isolates from diverse phylogenomic lineages. We demonstrate that there are lineage- and isolate-specific differences in the transcriptomes of genomically diverse EPEC...
Research Article | Ecological and Evolutionary ScienceIndirect Interspecies Regulation: Transcriptional and Physiological Responses of a Cyanobacterium to Heterotrophic PartnershipThis study elucidates how a cyanobacterial primary producer acclimates to heterotrophic partnership by modulating the expression levels of key metabolic genes. Heterotrophic bacteria can indirectly regulate the physiology of the photoautotrophic primary producers, resulting in physiological changes identified here, such as increased intracellular ROS. Some of the interactions inferred from this model system represent putative principles...
Research Article | Molecular Biology and PhysiologyTranscriptional Profiling of the Oral Pathogen Streptococcus mutans in Response to Competence Signaling Peptide XIPGenetic competence provides bacteria with an opportunity to increase genetic diversity or acquire novel traits conferring a survival advantage. In the cariogenic pathogen Streptococcus mutans, DNA transformation is regulated by the competence stimulating peptide XIP (ComX-inducing p...
Research Article | Molecular Biology and PhysiologyProteome Remodeling in Response to Sulfur Limitation in “Candidatus Pelagibacter ubique”
Methods and Protocols | Novel Systems Biology Techniquescual-id: Globally Unique, Correctable, and Human-Friendly Sample Identifiers for Comparative Omics StudiesThe adoption of identifiers that are globally unique, correctable, and easily handwritten or manually entered into a computer will be a major step forward for sample tracking in comparative omics studies. As the fields transition to more-centralized sample management, for example, across labs within an institution, across projects funded under a common program, or in systems designed to facilitate meta- and/or integrated analysis,...