Systems Biology and the Reconstruction of the Cell: From Molecular Components to Integral Function

Multi -omics and metabolic modelling pipelines: challenges and tools for systems microbiology

10.1101/013532 ◽

2015 ◽

Author(s):

Marco Fondi ◽

Pietro Liò

Keyword(s):

Systems Biology ◽

Large Scale ◽

Biological Information ◽

Special Focus ◽

Metabolic Modelling ◽

Microbial Life ◽

Multi Scale ◽

Integrated Omics ◽

Molecular Components ◽

Omics Data Integration

Integrated -omics approaches are quickly spreading across microbiology research labs, leading to i) the possibility of detecting previously hidden features of microbial cells like multi-scale spatial organisation and ii) tracing molecular components across multiple cellular functional states. This promises to reduce the knowledge gap between genotype and phenotype and poses new challenges for computational microbiologists. We underline how the capability to unravel the complexity of microbial life will strongly depend on the integration of the huge and diverse amount of information that can be derived today from -omics experiments. In this work, we present opportunities and challenges of multi –omics data integration in current systems biology pipelines. We here discuss which layers of biological information are important for biotechnological and clinical purposes, with a special focus on bacterial metabolism and modelling procedures. A general review of the most recent computational tools for performing large-scale datasets integration is also presented, together with a possible framework to guide the design of systems biology experiments by microbiologists.

Download Full-text

Constraints in Clinical Cardiology and Personalized Medicine: Interrelated Concepts in Clinical Cardiology

Cardiogenetics ◽

10.3390/cardiogenetics11020007 ◽

2021 ◽

Vol 11 (2) ◽

pp. 50-67

Author(s):

Katerina G. Lourida ◽

George E. Louridas

Keyword(s):

Systems Biology ◽

Personalized Medicine ◽

Legal Status ◽

Clinical Cardiology ◽

Natural Progression ◽

Interacting Networks ◽

Status Data ◽

Molecular Components ◽

And Personalized Medicine ◽

Scientific Fields

Systems biology is established as an integrative computational analysis methodology with practical and theoretical applications in clinical cardiology. The integration of genetic and molecular components of a disease produces interacting networks, modules and phenotypes with clinical applications in complex cardiovascular entities. With the holistic principle of systems biology, some of the features of complexity and natural progression of cardiac diseases are approached and explained. Two important interrelated holistic concepts of systems biology are described; the emerging field of personalized medicine and the constraint-based thinking with downward causation. Constraints in cardiovascular diseases embrace three scientific fields related to clinical cardiology: biological and medical constraints; constraints due to limitations of current technology; and constraints of general resources for better medical coverage. Systems healthcare and personalized medicine are connected to the related scientific fields of: ethics and legal status; data integration; taxonomic revisions; policy decisions; and organization of human genomic data.

Download Full-text

Systems biology primer: the basic methods and approaches

Essays in Biochemistry ◽

10.1042/ebc20180003 ◽

2018 ◽

Vol 62 (4) ◽

pp. 487-500 ◽

Cited By ~ 26

Author(s):

Iman Tavassoly ◽

Joseph Goldfarb ◽

Ravi Iyengar

Keyword(s):

Systems Biology ◽

Computational Methods ◽

Information Flow ◽

Computational Models ◽

Control Cell ◽

Systems Pharmacology ◽

Cell Tissue ◽

Organ Systems ◽

Wide Range ◽

Molecular Components

Systems biology is an integrative discipline connecting the molecular components within a single biological scale and also among different scales (e.g. cells, tissues and organ systems) to physiological functions and organismal phenotypes through quantitative reasoning, computational models and high-throughput experimental technologies. Systems biology uses a wide range of quantitative experimental and computational methodologies to decode information flow from genes, proteins and other subcellular components of signaling, regulatory and functional pathways to control cell, tissue, organ and organismal level functions. The computational methods used in systems biology provide systems-level insights to understand interactions and dynamics at various scales, within cells, tissues, organs and organisms. In recent years, the systems biology framework has enabled research in quantitative and systems pharmacology and precision medicine for complex diseases. Here, we present a brief overview of current experimental and computational methods used in systems biology.

Download Full-text

A systems-biology analysis of isogenic megakaryocytic and granulocytic cultures identifies new molecular components of megakaryocytic apoptosis

BMC Genomics ◽

10.1186/1471-2164-8-384 ◽

2007 ◽

Vol 8 (1) ◽

pp. 384 ◽

Cited By ~ 15

Author(s):

Chi Chen ◽

Peter G Fuhrken ◽

Li Huang ◽

Pani Apostolidis ◽

Min Wang ◽

...

Keyword(s):

Systems Biology ◽

Molecular Components

Download Full-text

Combining integrated systems-biology approaches with intervention-based experimental design provides a higher-resolution path forward for microbiome research

Behavioral and Brain Sciences ◽

10.1017/s0140525x18002911 ◽

2019 ◽

Vol 42 ◽

Author(s):

J. Alfredo Blakeley-Ruiz ◽

Carlee S. McClintock ◽

Ralph Lydic ◽

Helen A. Baghdoyan ◽

James J. Choo ◽

...

Keyword(s):

Systems Biology ◽

High Resolution ◽

Experimental Design ◽

Integrated Systems ◽

Microbiome Research ◽

Constructive Criticism

Abstract The Hooks et al. review of microbiota-gut-brain (MGB) literature provides a constructive criticism of the general approaches encompassing MGB research. This commentary extends their review by: (a) highlighting capabilities of advanced systems-biology “-omics” techniques for microbiome research and (b) recommending that combining these high-resolution techniques with intervention-based experimental design may be the path forward for future MGB research.

Download Full-text

Microscopic investigations of novel intracellular bodies of a Nocardia SP

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100169511 ◽

1994 ◽

Vol 52 ◽

pp. 356-357

Author(s):

J. L. Stites

Keyword(s):

Uranyl Acetate ◽

Electron Microscopic ◽

En Bloc ◽

Ribonucleic Acids ◽

Transmission Electron ◽

Nocardia Sp ◽

Internal Constitution ◽

Membrane Bound ◽

Molecular Components ◽

Protein Rich

A Nocardia sp.was found during an initial transmission electron microscopic (TEM) examination to have unusual intracellular bodies (ICB's) which do not appear to have been described previously in the literature. Most intracellular structures within bacteria have been classified as storage granules, a product of membrane invagination (i.e. mesosomes), or vacuoles. In bacteria there are no known intracellular membrane-bound organelles, and all internal membranes are invaginations of the unit membrane. Several microscopic-level examinations of the Nocardia sp. ICB's were initiated in order to determine their overall structure, classification, and internal constitution.Different TEM staining procedures were performed to determine possible molecular components of the ICB. In all of the staining protocols the ICB's showed a lack of electron density similar to the cell wall. Because the ICB's showed no affinity to any stain, it appeared they do not have strong positive charge (phosphotungstic acid), are not protein rich (en bloc uranyl acetate), lack glycogen and are not phosphate or sulphur rich (lead citrate), nor do they contain lipids or ribonucleic acids (osmium tetroxide).

Download Full-text