transcriptomics
Editor's Pick Research Article | Host-Microbe BiologyPersistent Interactions with Bacterial Symbionts Direct Mature-Host Cell Morphology and Gene Expression in the Squid-Vibrio SymbiosisA long-term relationship between symbiotic partners is often characterized by development and maturation of host structures that harbor the symbiont cells over the host’s lifetime. To understand the mechanisms involved in symbiosis maintenance more fully, we studied the mature bobtail squid, whose light-emitting organ, under experimental conditions, can be transiently or persistently colonized by...
Research Article | Novel Systems Biology TechniquesModeling the Pseudomonas Sulfur Regulome by Quantifying the Storage and Communication of InformationBacteria sense and respond to their environments using a sophisticated array of sensors and regulatory networks to optimize their fitness and survival in a constantly changing environment. Understanding how these regulatory and sensory networks work will provide the capacity to predict bacterial behaviors and, potentially, to manipulate their interactions with an environment or host. Leveraging the information theory provides useful...
Special Issue Perspective | Host-Microbe BiologyInsect Transmission of Plant Pathogens: a Systems Biology PerspectiveInsect-vectored pathogens pose one of the greatest threats to plant and animal, including human, health on a global scale. Few effective control strategies have been developed to thwart the transmission of any insect-transmitted pathogen.
Editor's Pick Research Article | Host-Microbe BiologyMulti-omics Comparative Analysis Reveals Multiple Layers of Host Signaling Pathway Regulation by the Gut MicrobiotaMultiple host pathways were affected by its adaptation to the microbiota. We have found significant transcriptome-proteome discordance caused by the microbiota. This discovery leads to the definite conclusion that transcript-level analysis is not sufficient to predict protein levels and their influence on the function of many specific cellular pathways, so only analysis of combinations of the quantitative data determined at different...
Editor's Pick Research Article | Host-Microbe BiologyClostridium difficile Colonizes Alternative Nutrient Niches during Infection across Distinct Murine Gut MicrobiomesInfection by the bacterium Clostridium difficile causes an inflammatory diarrheal disease which can become life threatening and has grown to be the most prevalent nosocomial infection. Susceptibility to C. difficile infection is strongly associated with previous antibiotic treatment, which disrupts the gut microbiota and reduces its ability to prevent colonization. In this study, we demonstrated that C. difficile...
Resource Report | Host-Microbe BiologyListeriomics: an Interactive Web Platform for Systems Biology of ListeriaIn the last decades, Listeria has become a key model organism for the study of host-pathogen interactions, noncoding RNA regulation, and bacterial adaptation to stress. To study these mechanisms, several genomics, transcriptomics, and proteomics data sets have been produced. We have developed Listeriomics, an interactive web platform to browse and correlate these heterogeneous sources of information. Our website will allow...
Research Article | Molecular Biology and PhysiologyGlobal Analysis and Comparison of the Transcriptomes and Proteomes of Group A Streptococcus BiofilmsProkaryotes are thought to regulate their proteomes largely at the level of transcription. However, the results from this first set of global transcriptomic and proteomic analyses of paired microbial samples presented here show that this assumption is false for the majority of genes and their products in S. pyogenes. In addition, the tenuousness of the link between...
Research Article | Ecological and Evolutionary ScienceClades of Photosynthetic Bacteria Belonging to the Genus Rhodopseudomonas Show Marked Diversity in Light-Harvesting Antenna Complex Gene Composition and ExpressionRhodopseudomonas palustris is a phototrophic purple nonsulfur bacterium that adapts its photosystem to allow growth at a range of light intensities. It does this by adjusting the amount and composition of peripheral light-harvesting (LH) antenna complexes that it synthesizes. Rhodopseudomonas strains are notable for containing numerous sets of light-...