From: Jeff Solka <[log in to unmask]>
Synergy or opportunism? Unraveling host-microbe interactions using systems biology
Amanda Payne Ph.D.(NSWCDD)
Trillions of microbes reside both in and on the human body, establishing the human body as the most biologically diverse ecosystem on the planet. Since 2008 several international initiatives such as the Human Microbiome Project (US-NIH), MetaHIT (Europe and China), Canadian Microbiome Initiative, MicroObes (France), Meta-GUT (China), Human Gastric Microbiome (Singapore) and the Australian Urogenital Consortium have been launched to both characterize species diversity and genetic capacities within distinct body sites. Despite the broad investigative nature of these initiatives, a disproportionate amount of research has been focused on microbes residing in the gut (termed gut microbiota) and related host-gut microbial interactions. The gut microbiota is comprised of thousands of species, assembled in highly organized niches with their metabolic functions affecting the immune system, nervous system, nutritive state and homeostasis. These processes are mediated in part by the close proximity in which commensal microorganisms reside to the intestinal epithelium, facilitating an intricate level of host-microbe cross-talk via complex signaling pathways. Human-based gut microbial studies, however, are scarce owing to ethics as well as the invasiveness of accessing the human gastrointestinal (GI) tract. As a result the current state of knowledge is derived primarily from in vitro, animal and ex vivo models coupled to exhaustive “-omics” analyses. This lecture will focus on advances in gut microbial ecology and immunology, driven by integrated systems biology. Particular emphasis will be made on the most significant breakthroughs as well as current technological gaps.
Integrative Bioinformatics for Knowledge Discovery in Systems Biology
Cathy Wu Ph.D. (University of Delaware)
Systems integration is becoming the driving force for the 21st century biology. Researchers are systematically tackling gene functions and complex regulatory processes by studying organisms at different levels of organization, from genomes and transcriptomes to proteomes, interactomes and metabolomes. To fully realize the value of such high-throughput data requires advanced bioinformatics for integration, mining, comparative analysis, and functional interpretation. The bioinformatics research infrastructure developed at the Protein Information Resource (PIR) and at the Delaware Center for Bioinformatics & Computational Biology provides an integrative approach for functional interpretation of high-throughput omics data in systems biology context. Linking data mining and text mining with ontologies for biological pathway and network analysis, the framework may allow researchers to gain better understanding of biological and disease processes, thereby facilitating knowledge and target discovery. One such bioinformatics resource being developed is the iPTMnet for exploring and discovering PTM networks for integrative understanding of protein post-translational modifications.