systems biology
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.
Special Issue Perspective | Novel Systems Biology TechniquesToward Personalized Control of Human Gut Bacterial CommunitiesA key challenge in microbiology will be developing tools for manipulating human gut bacterial communities. Our ability to predict and control the dynamics of these communities is now in its infancy.
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 | Novel Systems Biology TechniquesMetabolic Network Analysis and Metatranscriptomics Reveal Auxotrophies and Nutrient Sources of the Cosmopolitan Freshwater Microbial Lineage acIThe metabolic activity of uncultivated microorganisms contributes to numerous ecosystem processes, ranging from nutrient cycling in the environment to influencing human health and disease. Advances in sequencing technology have enabled the assembly of genomes for these microorganisms, but our ability to generate reference genomes far outstrips our ability to analyze them. Common approaches to analyzing microbial metabolism require...
