Emerging infectious diseases (EIDs) pose a major threat to public health and security. Given the dynamic nature and significant impact of EIDs, the most effective way to prevent and protect against them is to develop vaccines in advance. Systems biology approaches provide an integrative way to understand the complex immune response to pathogens. They can lead to a greater understanding of EID pathogenesis and facilitate the evaluation of newly developed vaccine-induced immunity in a timely manner. In recent years, advances in high throughput technologies have enabled researchers to successfully apply systems biology methods to analyze immune responses to a variety of pathogens and vaccines. Despite recent advances, computational and biological challenges impede wider application of systems biology approaches. This review highlights recent advances in the fields of systems immunology and vaccinology, and presents ways that systems biology-based platforms can be applied to accelerate a deeper understanding of the molecular mechanisms of immunity against EIDs.
*Communicable Diseases, Emerging ; Humans ; *Immunity ; Research ; Systems Biology/*methods ; Vaccines/*immunology

Heterotopic ossification (HO) refers to the abnormal formation of bone in soft tissue. Although some of the underlying processes of HO have been described, there are currently no clinical tests using validated biomarkers for predicting HO formation. As such, the diagnosis is made radiographically after HO has formed. To identify potential and novel biomarkers for HO, we used isobaric tags for relative and absolute quantitation (iTRAQ) and high-throughput antibody arrays to produce a semi-quantitative proteomics survey of serum and tissue from subjects with (HO) and without (HO) heterotopic ossification. The resulting data were then analyzed using a systems biology approach. We found that serum samples from subjects experiencing traumatic injuries with resulting HO have a different proteomic expression profile compared to those from the matched controls. Subsequent quantitative ELISA identified five blood serum proteins that were differentially regulated between the HO and HO groups. Compared to HO samples, the amount of insulin-like growth factor I (IGF1) was up-regulated in HO samples, whereas a lower amount of osteopontin (OPN), myeloperoxidase (MPO), runt-related transcription factor 2 (RUNX2), and growth differentiation factor 2 or bone morphogenetic protein 9 (BMP-9) was found in HO samples (Welch two sample t-test; P < 0.05). These proteins, in combination with potential serum biomarkers previously reported, are key candidates for a serum diagnostic panel that may enable early detection of HO prior to radiographic and clinical manifestations.
Adult ; Aged ; Aged, 80 and over ; Biomarkers ; metabolism ; Case-Control Studies ; Female ; Humans ; Male ; Middle Aged ; Ossification, Heterotopic ; blood ; diagnosis ; metabolism ; Proteome ; analysis ; Proteomics ; methods ; Systems Biology ; methods ; Young Adult

The complex interaction of molecules within a biological system constitutes a functional module. These modules are then acted upon by both internal and external factors, such as genetic and environmental stresses, which under certain conditions can manifest as complex disease phenotypes. Recent advances in high-throughput biological analyses, in combination with improved computational methods for data enrichment, functional annotation, and network visualization, have enabled a much deeper understanding of the mechanisms underlying important biological processes by identifying functional modules that are temporally and spatially perturbed in the context of disease development. Systems biology approaches such as these have produced compelling observations that would be impossible to replicate using classical methodologies, with greater insights expected as both the technology and methods improve in the coming years. Here, we examine the use of systems biology and network analysis in the study of a wide range of rheumatic diseases to better understand the underlying molecular and clinical features.
Animals ; Antirheumatic Agents/therapeutic use ; Biomedical Research/*methods ; Cytokines/genetics/metabolism ; Genetic Markers ; Genetic Predisposition to Disease ; Humans ; Inflammation Mediators/metabolism ; Molecular Targeted Therapy ; Phenotype ; Prognosis ; *Rheumatic Diseases/drug therapy/genetics/metabolism/physiopathology ; Rheumatology/*methods ; Risk Factors ; Signal Transduction ; *Systems Biology ; Systems Integration

The prevalence of coronary heart disease (CHD) is increasing, and has been a severe burden on society and family worldwide. New ideas need to be achieved for developing more efficacious and safe therapies to treat CHD. Chinese medicine (CM) uses multicomponent drugs to prevent disease and ameliorate symptoms based on patients' different syndromes. The benefit of CM in CHD has recently been proven by increasing clinical evidence. More importantly, linking CM syndrome differentiation and biomedical diagnosis might provide innovative thinking for treating CHD. According to epidemiological investigations, blood stasis syndrome (BSS) is the major type of syndrome in CHD. Investigating the biomedical mechanisms of BSS of CHD is a topic of CM research. Because the holistic perspective of systems biology is well matched with CM, the application of omics techniques and other integrative approaches appears inherently appropriate. A wide range of omics techniques, including transcriptomics and proteomics, have been used in studies of BSS of CHD to search for a common ground of understanding. These approaches could be useful for understanding BSS of CHD from clinical and biological viewpoints. Nevertheless, current studies mainly contain results from a single approach, and they have not achieved the holistic, systematic and integrative concept of system biology. Therefore, we discuss the progress and challenges in exploring the biomedical mechanisms of BSS of CHD by systems biology approaches. With further development of systems biology, a better platform to study BSS of CHD may be provided, and biomarkers for BSS of CHD and therapeutic targets may be found. The study of BSS of CHD by systems biology approaches will also be beneficial for developing personalized treatment for BSS of CHD patients.
Coronary Disease ; diagnosis ; metabolism ; Humans ; Syndrome ; Systems Biology ; methods

Medicine, Chinese Traditional ; methods ; Systems Biology

Along with progress of modern science and technology, human is utilizing natural resources and their inherent law more effectively and more efficiently according to their own purposes. Chinese medicine pair (CMP) is relatively fixed combination of two TCMs which was proven to be effective in clinical application. CMP has its inner specification, and it is an intermediate point between single herb and many TCM formulae. With the aid of modern science and technology, and by means of choosing appropriate strategies and approaches, the compatibility rules of CMP might be revealed, which will be significant to develop the compatibility theory of TCM formulae and create modern TCM new drugs.
Animals ; Clinical Trials as Topic ; Drug Interactions ; Humans ; Medicine, Chinese Traditional ; methods ; Research Design ; Systems Biology

Natural products (NPs) are important drug pools for human disease prevention and treatment. The great advances in synthetic biology have greatly revolutionized the strategies of NPs development and production. This review entitled with design and construction of artificial biological systems for complex NPs biosynthesis, mainly introduced the progresses in artificial design of synthetic biological parts, naturally mining novel synthetic parts of NPs, the assembly & adaption of the artificial biological modules & systems.
Biological Products ; chemistry ; metabolism ; Escherichia coli ; genetics ; metabolism ; Neural Networks (Computer) ; Recombinant Proteins ; biosynthesis ; genetics ; Synthetic Biology ; methods ; Systems Biology ; methods

Chronic kidney disease (CKD) is a major public health problem that affects about 10% of the general population. Current approaches to characterize the category and progression of CKD are normally based on renal histopathological results and clinical parameters. However, this information is not sufficient to predict CKD progression risk reliably or to guide preventive interventions. Nowadays, the appearance of systems biology has brought forward the concepts of "-omics" technologies, including genomics, transcriptomics, proteomics, and metabolomics. Systems biology, together with molecular analysis approaches such as microarray analysis, genome-wide association studies (GWAS), and serial analysis of gene expression (SAGE), has provided the framework for a comprehensive analysis of renal disease and serves as a starting point for generating novel molecular diagnostic tools for use in nephrology. In particular, analysis of urinary mRNA and protein levels is rapidly evolving as a non-invasive approach for CKD monitoring. All these systems biological molecular approaches are required for application of the concept of "personalized medicine" to progressive CKD, which will result in tailoring therapy for each patient, in contrast to the "one-size-fits-all" therapies currently in use.
Computational Biology ; Gene Expression Profiling ; Genome-Wide Association Study ; Humans ; Renal Insufficiency, Chronic ; genetics ; metabolism ; Systems Biology ; methods

Taxus is the source plant of anti-cancer drug paclitaxel and its biosynthetic precursor, analogs and derivatives, which has been studying for decades. There are many endemic Taxus species in China, which have been studied in the field of multiple disciplines. Based on the recent studies of the researchers, this review comments on the study of Taxus biology and chemistry. The bibliometric method is used to quantify the global scientific production of Taxus-related research, and identify patterns and tendencies of Taxus-related articles. Gaps are present in knowledge about the genomics, epigenomics, transcriptomics, proteomics, metabolomics and bioinformatics of Taxus and their endophytic fungi. Systems biology and various omics technologies will play an increasingly important role in the coming decades.
Computational Biology ; Endophytes ; chemistry ; isolation & purification ; Epigenomics ; methods ; Fungi ; chemistry ; isolation & purification ; Gene Expression Profiling ; Genomics ; methods ; Metabolomics ; Molecular Biology ; Paclitaxel ; biosynthesis ; chemistry ; isolation & purification ; Phylogeny ; Plants, Medicinal ; chemistry ; classification ; genetics ; microbiology ; Proteomics ; Systems Biology ; Taxus ; chemistry ; classification ; genetics ; microbiology

The era of targeted cancer therapies has arrived. However, due to the complexity of biological systems, the current progress is far from enough. From biological network modeling to structural/dynamic network analysis, network systems biology provides unique insight into the potential mechanisms underlying the growth and progression of cancer cells. It has also introduced great changes into the research paradigm of cancer-associated drug discovery and drug resistance.
Antineoplastic Agents ; therapeutic use ; Drug Discovery ; methods ; Drug Resistance, Neoplasm ; Humans ; Models, Biological ; Molecular Targeted Therapy ; Neoplasms ; drug therapy ; Systems Biology ; methods