systems biology
Research Article | Molecular Biology and PhysiologySulfur Metabolites Play Key System-Level Roles in Modulating DenitrificationNitrate-reducing bacteria (NRB) and sulfate-reducing bacteria (SRB) colonize diverse anoxic environments, including soil subsurface, groundwater, and wastewater. NRB and SRB compete for resources, and their interplay has major implications on the global cycling of nitrogen and sulfur species, with undesirable outcomes in some contexts.
Research Article | Novel Systems Biology TechniquesExtreme Antibiotic Persistence via Heterogeneity-Generating Mutations Targeting TranslationBacterial persistence is a fascinating phenomenon in which a small subpopulation of bacteria becomes phenotypically tolerant to lethal antibiotic exposure. There is growing evidence that populations of bacteria in chronic clinical infections develop a hyperpersistent phenotype, enabling a substantially larger subpopulation to survive repeated antibiotic treatment. The mechanisms of persistence and modes of increasing persistence rates...
Research Article | Novel Systems Biology TechniquesMICOM: Metagenome-Scale Modeling To Infer Metabolic Interactions in the Gut MicrobiotaThe bacterial communities that live within the human gut have been linked to health and disease. However, we are still just beginning to understand how those bacteria interact and what potential interventions to our gut microbiome can make us healthier. Here, we present a mathematical modeling framework (named MICOM) that can recapitulate the growth rates of diverse bacterial species in the gut and can simulate metabolic interactions...
Research Article | Molecular Biology and PhysiologyConserved Central Intraviral Protein Interactome of the Herpesviridae FamilyHerpesviruses are an important socioeconomic burden for both humans and livestock. Throughout their long evolutionary history, individual herpesvirus species have developed remarkable host specificity, while collectively the Herpesviridae family has evolved to infect a large variety of eukaryotic hosts. The development of approaches to fight herpesvirus infections has been hampered by the complexity of herpesviruses’ genomes,...
Research Article | Molecular Biology and PhysiologyA Novel Cys2His2 Zinc Finger Homolog of AZF1 Modulates Holocellulase Expression in Trichoderma reeseiIn this work, we used a systems biology approach to map new regulatory interactions in Trichoderma reesei controlling the expression of genes encoding cellulase and hemicellulase. By integrating transcriptomics related to complex biomass degradation, we were able to identify a novel transcriptional regulator which is able to activate the expression of these genes in...
Special Issue Perspective | Ecological and Evolutionary ScienceThe Power of Metabolism for Predicting Microbial Community DynamicsQuantitative understanding and prediction of microbial community dynamics are an outstanding challenge. We test the hypothesis that metabolic mechanisms provide a foundation for accurate prediction of dynamics in microbial systems. In our research, metabolic models have been able to accurately predict species interactions, evolutionary trajectories, and response to perturbation in simple synthetic consortia.
Special Issue Perspective | Ecological and Evolutionary ScienceRole of Multiple Infections on Immunological Variation in Wild PopulationsA central challenge in the fields of evolutionary immunology and disease ecology is to understand the causes and consequences of natural variation in host susceptibility to infectious diseases. As hosts progress from birth to death in the wild, they are exposed to a wide variety of microorganisms that influence their physical condition, immune system maturation, and susceptibility to concurrent and future infection.
Research Article | Molecular Biology and PhysiologyMinor Isozymes Tailor Yeast Metabolism to Carbon AvailabilityGene duplication is one of the main evolutionary paths to new protein function. Typically, duplicated genes either accumulate mutations and degrade into pseudogenes or are retained and diverge in function. Some duplicated genes, however, show long-term persistence without apparently acquiring new function. An important class of isozymes consists of those that catalyze the same reaction in the same compartment, where knockout of one...
Research Article | Ecological and Evolutionary ScienceMachine Learning Reveals Missing Edges and Putative Interaction Mechanisms in Microbial Ecosystem NetworksDifferent organisms in a microbial community may drastically affect each other’s growth phenotypes, significantly affecting the community dynamics, with important implications for human and environmental health. Novel culturing methods and the decreasing costs of sequencing will gradually enable high-throughput measurements of pairwise interactions in systematic coculturing studies. However, a thorough characterization of all...
EditorialAnnouncement of the 2019 BLAST Conference: “BLAST XV: 15th International Conference on Bacterial Locomotion and Signal Transduction”An exciting conference showcasing cutting edge research in bacterial signal transduction, chemotaxis, and motility will be held in January 2019. This conference, called Bacterial Locomotion and Signal Transduction (BLAST), will be held in New Orleans, LA, USA, under the auspices of chair Birgit Scharf.