Promise Of Systems Biology Research Articles

Systems biology for industrial biotechnology

In industrial biotechnology, microbial cell factories utilize renewable resources to produce energy, materials and chemicals. Industrial biotechnology plays an increasingly important role in solving the resource, energy and environmental problems. Systems biology has shed new light on industrial biotechnology, deepening our understanding of industrial microbial cell factories and their bioprocess from "Black-box" to "White-box". Systems-wide profiling of genome, transcriptome, proteome, metabolome, and fluxome has proven valuable to better unveil network operation and regulation on the genome scale. System biology has been successfully applied to create microbial cell factories for numerous products and derive attractive industrial processes, which has constantly expedited the development of industrial biotechnology. This review focused on the recent advance and applications of omics and trans-omics in industrial biotechnology, including genomics, transcriptomics, proteomics, metabolomics, fluxomics and genome scale modeling, and so on. Furthermore, this review also discussed the potential and promise of systems biology in industrial biotechnology.

Toward Prediction of Immune Mechanisms and Design of Immunotherapies in Melanoma

Malignant melanoma, the most lethal skin cancer, is considered as a representative model for cross talk between immune responses and malignancy. Efforts to elucidate the nature of these interactions have translated into immunotherapeutic strategies. Adjuvant therapeutics such as IL-2 and IFNα2b have reached clinical application, and emerging therapies targeting key immunomodulatory molecules such as CTLA-4 have renewed excitement in the field, highlighting the potential of manipulating immune responses in the clinical setting, but also the merits for further elucidating complex underlying immunological pathways. Screening technologies have yielded new insights leading to identification of biomarkers for disease prognosis and applied clinical immunotherapies. The promise of systems biology is to integrate diverse biomedical characterizations into detailed models of underlying mechanisms and therapies through suitable computational and mathematical formalisms. In this review, we discuss recent developments in dissecting the complex and diverse immune responses associated with melanoma through both computational and experimental means. We show the significance of devising new, improved approaches that can better serve as models of immune interactions and therapies. We propose that efforts in this direction may realize the potential of personalized medicine and facilitate development of the next generation of efficacious tools to treat patients.

Lung evolution as a cipher for physiology

In the postgenomic era, we need an algorithm to readily translate genes into physiologic principles. The failure to advance biomedicine is due to the false hope raised in the wake of the Human Genome Project (HGP) by the promise of systems biology as a ready means of reconstructing physiology from genes. like the atom in physics, the cell, not the gene, is the smallest completely functional unit of biology. Trying to reassemble gene regulatory networks without accounting for this fundamental feature of evolution will result in a genomic atlas, but not an algorithm for functional genomics. For example, the evolution of the lung can be "deconvoluted" by applying cell-cell communication mechanisms to all aspects of lung biology development, homeostasis, and regeneration/repair. Gene regulatory networks common to these processes predict ontogeny, phylogeny, and the disease-related consequences of failed signaling. This algorithm elucidates characteristics of vertebrate physiology as a cascade of emergent and contingent cellular adaptational responses. By reducing complex physiological traits to gene regulatory networks and arranging them hierarchically in a self-organizing map, like the periodic table of elements in physics, the first principles of physiology will emerge.

The Promise of Systems Biology in Clinical Applications

To summarize current excellent research in the field of bioinformatics. Synopsis of the articles selected for the IMIA Yearbook 2008. Current research in the field of Bioinformatics shows that the emergent field of systems biology is starting to offer innovative solutions to clinically-relevant problems. The approach used can be top-down, where models are created based on hypotheses to describe previously unexplained phenomena and then tested against experimental or clinical evidence. It can also be bottom-up, where mathematical models are built by harnessing existing information about the components (e.g. protein entities, interaction networks) of a system in order to discern critical system-level mechanisms that can be relevant for clinical applications. Progress in this area is aided by the ongoing development in data integration and management, whose current focus is on better semantics for facilitating translational research. Advances in other important areas, such as microarray technology, text mining and ontologies, are also noted. The best paper selection of articles on bioinformatics gives examples of original research that exploits mathematical modeling to tackle medical problems and of improved semantic solutions for data integration. As new directions are explored and the technologies mature, these approaches are expected to be increasingly integrated into clinical practice.

Metabolomics of temperature stress

Plants possess inducible tolerance mechanisms that extend the temperature range for survival during acute temperature stress. The inducible mechanisms of cold acclimation and acquired thermotolerance involve highly complex processes. These include perception and signal transduction of non-optimal temperatures or their physical consequences on cellular components that program extensive modification of the transcriptome, proteome, metabolome and composition and physical structure of the cytoplasm, membranes and cell walls. Therefore, a systems biology approach will be necessary to advance the understanding of plant stress responses and tolerance mechanisms. One promise of systems biology is that it will greatly enhance our understanding of individual and collective functions and thereby provide a more holistic view of plant stress responses. Past studies have found that several metabolites that could functionally contribute to induced stress tolerance have been associated with stress responses. Recent metabolite-profiling studies have refocused attention on these and other potentially important components found in the 'temperature-stress metabolome'. These metabolomic studies have demonstrated that active reconfiguration of the metabolome is regulated in part by changes in gene expression initiated by temperature-stress-activated signaling and stress-related transcription factors. One aspect of metabolism that is consistent across all of the temperature-stress metabolomic studies to date is the prominent role of central carbohydrate metabolism, which seems to be a major feature of the reprogramming of the metabolome during temperature stress. Future metabolomic studies of plant temperature-stress responses should reveal additional metabolic pathways that have important functions in temperature-stress tolerance mechanisms.