This chapter introduces different aspects of bioinformatics with a brief discussion in the systems biology context. Example applications in network pharmacology of traditional Chinese medicine, systems metabolic engineering, and plant genome-scale modelling are described. Lastly, this chapter concludes on how bioinformatics helps to integrate omics data derived from various studies described in previous chapters for a holistic understanding of secondary metabolite production in P. minus.
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http://dx.doi.org/10.1007/978-3-319-98758-3_5 | DOI Listing |
Sci Immunol
January 2025
Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
Human recombination-activating gene (RAG) deficiency can manifest with distinct clinical and immunological phenotypes. By applying a multiomics approach to a large group of -mutated patients, we aimed at characterizing the immunopathology associated with each phenotype. Although defective T and B cell development is common to all phenotypes, patients with hypomorphic variants can generate T and B cells with signatures of immune dysregulation and produce autoantibodies to a broad range of self-antigens, including type I interferons.
View Article and Find Full Text PDFMicrobiol Spectr
January 2025
Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado, Aurora, Colorado, USA.
Unlabelled: Studies have suggested that phytochemicals in green tea have systemic anti-inflammatory and neuroprotective effects. However, the mechanisms behind these effects are poorly understood, possibly due to the differential metabolism of phytochemicals resulting from variations in gut microbiome composition. To unravel this complex relationship, our team utilized a novel combined microbiome analysis and metabolomics approach applied to low complexity microbiome (LCM) and human colonized (HU) gnotobiotic mice treated with an acute dose of powdered matcha green tea.
View Article and Find Full Text PDFYi Chuan
January 2025
Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.
Being the most magnificent plateau in elevation and size on Earth, the Qinghai-Tibet Plateau has a profound impact on biodiversity due to the unique geographic and climatic conditions. Here we review the speciation patterns and genetic diversity of the birds from the Qinghai-Tibet Plateau in relation to the geological history and climatic changes. First, the uplift of the Qinghai-Tibet Plateau forms a geographic barrier and promotes interspecific and intraspecific genetic differentiation.
View Article and Find Full Text PDFProteomics
January 2025
School of Public Health, University of Haifa, Haifa, Israel.
Chronic kidney disease (CKD) poses a significant and growing global health challenge, making early detection and slowing disease progression essential for improving patient outcomes. Traditional diagnostic methods such as glomerular filtration rate and proteinuria are insufficient to capture the complexity of CKD. In contrast, omics technologies have shed light on the molecular mechanisms of CKD, helping to identify biomarkers for disease assessment and management.
View Article and Find Full Text PDFAnim Microbiome
January 2025
Department of Large Animal Clinical Sciences, University of Florida, Gainesville, FL, 32610, USA.
Background: Cows that develop metritis experience dysbiosis of their uterine microbiome, where opportunistic pathogens overtake uterine commensals. An effective immune response is critical for maintaining uterine health. Nonetheless, periparturient cows experience immune dysregulation, which seems to be intensified by prepartum over-condition.
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