Metabolic network modellingMetabolic network modelling, also known as metabolic network reconstruction or metabolic pathway analysis, allows for an in-depth insight into the molecular mechanisms of a particular organism. In particular, these models correlate the genome with molecular physiology. A reconstruction breaks down metabolic pathways (such as glycolysis and the citric acid cycle) into their respective reactions and enzymes, and analyzes them within the perspective of the entire network.
Metabolic pathwayIn biochemistry, a metabolic pathway is a linked series of chemical reactions occurring within a cell. The reactants, products, and intermediates of an enzymatic reaction are known as metabolites, which are modified by a sequence of chemical reactions catalyzed by enzymes. In most cases of a metabolic pathway, the product of one enzyme acts as the substrate for the next. However, side products are considered waste and removed from the cell. These enzymes often require dietary minerals, vitamins, and other cofactors to function.
MetabolismMetabolism (məˈtæbəlɪzəm, from μεταβολή metabolē, "change") is the set of life-sustaining chemical reactions in organisms. The three main functions of metabolism are: the conversion of the energy in food to energy available to run cellular processes; the conversion of food to building blocks for proteins, lipids, nucleic acids, and some carbohydrates; and the elimination of metabolic wastes. These enzyme-catalyzed reactions allow organisms to grow and reproduce, maintain their structures, and respond to their environments.
Metabolic networkA metabolic network is the complete set of metabolic and physical processes that determine the physiological and biochemical properties of a cell. As such, these networks comprise the chemical reactions of metabolism, the metabolic pathways, as well as the regulatory interactions that guide these reactions. With the sequencing of complete genomes, it is now possible to reconstruct the network of biochemical reactions in many organisms, from bacteria to human.
Flux (metabolism)Flux, or metabolic flux is the rate of turnover of molecules through a metabolic pathway. Flux is regulated by the enzymes involved in a pathway. Within cells, regulation of flux is vital for all metabolic pathways to regulate the pathway's activity under different conditions. Flux is therefore of great interest in metabolic network modelling, where it is analysed via flux balance analysis and metabolic control analysis.
Cell biologyCell biology (also cellular biology or cytology) is a branch of biology that studies the structure, function, and behavior of cells. All living organisms are made of cells. A cell is the basic unit of life that is responsible for the living and functioning of organisms. Cell biology is the study of the structural and functional units of cells. Cell biology encompasses both prokaryotic and eukaryotic cells and has many subtopics which may include the study of cell metabolism, cell communication, cell cycle, biochemistry, and cell composition.
Cell signalingIn biology, cell signaling (cell signalling in British English) or cell communication is the ability of a cell to receive, process, and transmit signals with its environment and with itself. Cell signaling is a fundamental property of all cellular life in prokaryotes and eukaryotes. Signals that originate from outside a cell (or extracellular signals) can be physical agents like mechanical pressure, voltage, temperature, light, or chemical signals (e.g., small molecules, peptides, or gas).
Cell (biology)The cell is the basic structural and functional unit of all forms of life. Every cell consists of cytoplasm enclosed within a membrane, and contains many macromolecules such as proteins, DNA and RNA, as well as many small molecules of nutrients and metabolites. The term comes from the Latin word cellula meaning 'small room'. Cells can acquire specified function and carry out various tasks within the cell such as replication, DNA repair, protein synthesis, and motility. Cells are capable of specialization and mobility within the cell.
Dynamic rangeDynamic range (abbreviated DR, DNR, or DYR) is the ratio between the largest and smallest values that a certain quantity can assume. It is often used in the context of signals, like sound and light. It is measured either as a ratio or as a base-10 (decibel) or base-2 (doublings, bits or stops) logarithmic value of the difference between the smallest and largest signal values. Electronically reproduced audio and video is often processed to fit the original material with a wide dynamic range into a narrower recorded dynamic range that can more easily be stored and reproduced; this processing is called dynamic range compression.
Cellular respirationCellular respiration is the process by which biological fuels are oxidised in the presence of an inorganic electron acceptor, such as oxygen, to drive the bulk production of adenosine triphosphate (ATP), which contains energy. Cellular respiration may be described as a set of metabolic reactions and processes that take place in the cells of organisms to convert chemical energy from nutrients into ATP, and then release waste products.
Signal transductionSignal transduction is the process by which a chemical or physical signal is transmitted through a cell as a series of molecular events. Most commonly, protein phosphorylation is catalyzed by protein kinases, ultimately resulting in a cellular response. Proteins responsible for detecting stimuli are generally termed receptors, although in some cases the term sensor is used. The changes elicited by ligand binding (or signal sensing) in a receptor give rise to a biochemical cascade, which is a chain of biochemical events known as a signaling pathway.
OmicsThe branches of science known informally as omics are various disciplines in biology whose names end in the suffix -omics, such as genomics, proteomics, metabolomics, metagenomics, phenomics and transcriptomics. Omics aims at the collective characterization and quantification of pools of biological molecules that translate into the structure, function, and dynamics of an organism or organisms. The related suffix -ome is used to address the objects of study of such fields, such as the genome, proteome or metabolome respectively.
High dynamic rangeHigh dynamic range (HDR) is a dynamic range higher than usual, synonyms are wide dynamic range, extended dynamic range, expanded dynamic range. The term is often used in discussing the dynamic range of various signals such as s, videos, audio or radio. It may apply to the means of recording, processing, and reproducing such signals including analog and digitized signals. The term is also the name of some of the technologies or techniques allowing to achieve high dynamic range images, videos, or audio.
Biological systemA biological system is a complex network which connects several biologically relevant entities. Biological organization spans several scales and are determined based different structures depending on what the system is. Examples of biological systems at the macro scale are populations of organisms. On the organ and tissue scale in mammals and other animals, examples include the circulatory system, the respiratory system, and the nervous system.
Modelling biological systemsModelling biological systems is a significant task of systems biology and mathematical biology. Computational systems biology aims to develop and use efficient algorithms, data structures, visualization and communication tools with the goal of computer modelling of biological systems. It involves the use of computer simulations of biological systems, including cellular subsystems (such as the networks of metabolites and enzymes which comprise metabolism, signal transduction pathways and gene regulatory networks), to both analyze and visualize the complex connections of these cellular processes.
Cell migrationCell migration is a central process in the development and maintenance of multicellular organisms. Tissue formation during embryonic development, wound healing and immune responses all require the orchestrated movement of cells in particular directions to specific locations. Cells often migrate in response to specific external signals, including chemical signals and mechanical signals. Errors during this process have serious consequences, including intellectual disability, vascular disease, tumor formation and metastasis.
Signaling (telecommunications)In telecommunication, signaling is the use of signals for controlling communications. This may constitute an information exchange concerning the establishment and control of a telecommunication circuit and the management of the network. Signaling systems may be classified based on several principal characteristics. In the public switched telephone network (PSTN), in-band signaling is the exchange of call control information within the same physical channel, or within the same frequency band, that the telephone call itself is using.
Notch signaling pathwayThe Notch signaling pathway is a highly conserved cell signaling system present in most animals. Mammals possess four different notch receptors, referred to as NOTCH1, NOTCH2, NOTCH3, and NOTCH4. The notch receptor is a single-pass transmembrane receptor protein. It is a hetero-oligomer composed of a large extracellular portion, which associates in a calcium-dependent, non-covalent interaction with a smaller piece of the notch protein composed of a short extracellular region, a single transmembrane-pass, and a small intracellular region.
Channel access methodIn telecommunications and computer networks, a channel access method or multiple access method allows more than two terminals connected to the same transmission medium to transmit over it and to share its capacity. Examples of shared physical media are wireless networks, bus networks, ring networks and point-to-point links operating in half-duplex mode. A channel access method is based on multiplexing, that allows several data streams or signals to share the same communication channel or transmission medium.
