Metabolic networks and pathways. Medical search

Complex sets of enzymatic reactions connected to each other via their product and substrate metabolites.

The chemical reactions that occur within the cells, tissues, or an organism. These processes include both the biosynthesis (ANABOLISM) and the breakdown (CATABOLISM) of organic materials utilized by the living organism.

Comprehensive, methodical analysis of complex biological systems by monitoring responses to perturbations of biological processes. Large scale, computerized collection and analysis of the data are used to develop and test models of biological systems.

Theoretical representations that simulate the behavior or activity of biological processes or diseases. For disease models in living animals, DISEASE MODELS, ANIMAL is available. Biological models include the use of mathematical equations, computers, and other electronic equipment.

Computer-based representation of physical systems and phenomena such as chemical processes.

Interacting DNA-encoded regulatory subsystems in the GENOME that coordinate input from activator and repressor TRANSCRIPTION FACTORS during development, cell differentiation, or in response to environmental cues. The networks function to ultimately specify expression of particular sets of GENES for specific conditions, times, or locations.

A field of biology concerned with the development of techniques for the collection and manipulation of biological data, and the use of such data to make biological discoveries or predictions. This field encompasses all computational methods and theories for solving biological problems including manipulation of models and datasets.

The dynamic collection of metabolites which represent a cell's or organism's net metabolic response to current conditions.

A procedure consisting of a sequence of algebraic formulas and/or logical steps to calculate or determine a given task.

Biological molecules that possess catalytic activity. They may occur naturally or be synthetically created. Enzymes are usually proteins, however CATALYTIC RNA and CATALYTIC DNA molecules have also been identified.

Cellular processes, properties, and characteristics.

A computer architecture, implementable in either hardware or software, modeled after biological neural networks. Like the biological system in which the processing capability is a result of the interconnection strengths between arrays of nonlinear processing nodes, computerized neural networks, often called perceptrons or multilayer connectionist models, consist of neuron-like units. A homogeneous group of units makes up a layer. These networks are good at pattern recognition. They are adaptive, performing tasks by example, and thus are better for decision-making than are linear learning machines or cluster analysis. They do not require explicit programming.

Total mass of all the organisms of a given type and/or in a given area. (From Concise Dictionary of Biology, 1990) It includes the yield of vegetative mass produced from any given crop.

The systematic identification and quantitation of all the metabolic products of a cell, tissue, organ, or organism under varying conditions. The METABOLOME of a cell or organism is a dynamic collection of metabolites which represent its net response to current conditions.

The genetic complement of a BACTERIA as represented in its DNA.

Methods and techniques used to genetically modify cells' biosynthetic product output and develop conditions for growing the cells as BIOREACTORS.

Sequential operating programs and data which instruct the functioning of a digital computer.

The processes by which organisms use simple inorganic substances such as gaseous or dissolved carbon dioxide and inorganic nitrogen as nutrient sources. Contrasts with heterotrophic processes which make use of organic materials as the nutrient supply source. Autotrophs can be either chemoautotrophs (or chemolithotrophs), largely ARCHAEA and BACTERIA, which also use simple inorganic substances for their metabolic energy reguirements; or photoautotrophs (or photolithotrophs), such as PLANTS and CYANOBACTERIA, which derive their energy from light. Depending on environmental conditions some organisms can switch between different nutritional modes (autotrophy; HETEROTROPHY; chemotrophy; or PHOTOTROPHY) to utilize different sources to meet their nutrient and energy requirements.

A species of gram-negative, facultatively anaerobic, rod-shaped bacteria (GRAM-NEGATIVE FACULTATIVELY ANAEROBIC RODS) commonly found in the lower part of the intestine of warm-blooded animals. It is usually nonpathogenic, but some strains are known to produce DIARRHEA and pyogenic infections. Pathogenic strains (virotypes) are classified by their specific pathogenic mechanisms such as toxins (ENTEROTOXIGENIC ESCHERICHIA COLI), etc.

The protein complement of an organism coded for by its genome.

A series of oxidative reactions in the breakdown of acetyl units derived from GLUCOSE; FATTY ACIDS; or AMINO ACIDS by means of tricarboxylic acid intermediates. The end products are CARBON DIOXIDE, water, and energy in the form of phosphate bonds.

Methods for determining interaction between PROTEINS.

A nonmetallic element with atomic symbol C, atomic number 6, and atomic weight [12.0096; 12.0116]. It may occur as several different allotropes including DIAMOND; CHARCOAL; and GRAPHITE; and as SOOT from incompletely burned fuel.

The process of pictorial communication, between human and computers, in which the computer input and output have the form of charts, drawings, or other appropriate pictorial representation.

Theoretical representations that simulate the behavior or activity of genetic processes or phenomena. They include the use of mathematical equations, computers, and other electronic equipment.

A set of opposing, nonequilibrium reactions catalyzed by different enzymes which act simultaneously, with at least one of the reactions driven by ATP hydrolysis. The results of the cycle are that ATP energy is depleted, heat is produced and no net substrate-to-product conversion is achieved. Examples of substrate cycling are cycling of gluconeogenesis and glycolysis pathways and cycling of the triglycerides and fatty acid pathways. Rates of substrate cycling may be increased many-fold in association with hypermetabolic states resulting from severe burns, cold exposure, hyperthyroidism, or acute exercise.

Chemical reactions or functions, enzymatic activities, and metabolic pathways of living things.

A species of gram-negative, rod-shaped bacteria belonging to the K serogroup of ESCHERICHIA COLI. It lives as a harmless inhabitant of the human LARGE INTESTINE and is widely used in medical and GENETIC RESEARCH.

A metabolic process that converts GLUCOSE into two molecules of PYRUVIC ACID through a series of enzymatic reactions. Energy generated by this process is conserved in two molecules of ATP. Glycolysis is the universal catabolic pathway for glucose, free glucose, or glucose derived from complex CARBOHYDRATES, such as GLYCOGEN and STARCH.

The determination of the pattern of genes expressed at the level of GENETIC TRANSCRIPTION, under specific circumstances or in a specific cell.

The systematic study of the complete DNA sequences (GENOME) of organisms.

The portion of an interactive computer program that issues messages to and receives commands from a user.

A species of the genus SACCHAROMYCES, family Saccharomycetaceae, order Saccharomycetales, known as "baker's" or "brewer's" yeast. The dried form is used as a dietary supplement.

An oxidative decarboxylation process that converts GLUCOSE-6-PHOSPHATE to D-ribose-5-phosphate via 6-phosphogluconate. The pentose product is used in the biosynthesis of NUCLEIC ACIDS. The generated energy is stored in the form of NADPH. This pathway is prominent in tissues which are active in the synthesis of FATTY ACIDS and STEROIDS.

The processes by which organisms utilize organic substances as their nutrient sources. Contrasts with AUTOTROPHIC PROCESSES which make use of simple inorganic substances as the nutrient supply source. Heterotrophs can be either chemoheterotrophs (or chemoorganotrophs) which also require organic substances such as glucose for their primary metabolic energy requirements, or photoheterotrophs (or photoorganotrophs) which derive their primary energy requirements from light. Depending on environmental conditions some organisms can switch between different nutritional modes (AUTOTROPHY; heterotrophy; chemotrophy; or PHOTOTROPHY) to utilize different sources to meet their nutrients and energy requirements.

The intracellular transfer of information (biological activation/inhibition) through a signal pathway. In each signal transduction system, an activation/inhibition signal from a biologically active molecule (hormone, neurotransmitter) is mediated via the coupling of a receptor/enzyme to a second messenger system or to an ion channel. Signal transduction plays an important role in activating cellular functions, cell differentiation, and cell proliferation. Examples of signal transduction systems are the GAMMA-AMINOBUTYRIC ACID-postsynaptic receptor-calcium ion channel system, the receptor-mediated T-cell activation pathway, and the receptor-mediated activation of phospholipases. Those coupled to membrane depolarization or intracellular release of calcium include the receptor-mediated activation of cytotoxic functions in granulocytes and the synaptic potentiation of protein kinase activation. Some signal transduction pathways may be part of larger signal transduction pathways; for example, protein kinase activation is part of the platelet activation signal pathway.

Databases devoted to knowledge about specific genes and gene products.

Specifications and instructions applied to the software.

The chemical reactions involved in the production and utilization of various forms of energy in cells.

A set of statistical methods used to group variables or observations into strongly inter-related subgroups. In epidemiology, it may be used to analyze a closely grouped series of events or cases of disease or other health-related phenomenon with well-defined distribution patterns in relation to time or place or both.

Extensive collections, reputedly complete, of facts and data garnered from material of a specialized subject area and made available for analysis and application. The collection can be automated by various contemporary methods for retrieval. The concept should be differentiated from DATABASES, BIBLIOGRAPHIC which is restricted to collections of bibliographic references.

The genetic complement of an organism, including all of its GENES, as represented in its DNA, or in some cases, its RNA.

The process of cumulative change over successive generations through which organisms acquire their distinguishing morphological and physiological characteristics.

The process of cumulative change at the level of DNA; RNA; and PROTEINS, over successive generations.

Processes by which phototrophic organisms use sunlight as their primary energy source. Contrasts with chemotrophic processes which do not depend on light and function in deriving energy from exogenous chemical sources. Photoautotrophy (or photolithotrophy) is the ability to use sunlight as energy to fix inorganic nutrients to be used for other organic requirements. Photoautotrophs include all GREEN PLANTS; GREEN ALGAE; CYANOBACTERIA; and green and PURPLE SULFUR BACTERIA. Photoheterotrophs or photoorganotrophs require a supply of organic nutrients for their organic requirements but use sunlight as their primary energy source; examples include certain PURPLE NONSULFUR BACTERIA. Depending on environmental conditions some organisms can switch between different nutritional modes (AUTOTROPHY; HETEROTROPHY; chemotrophy; or phototrophy) to utilize different sources to meet their nutrients and energy requirements.

Amino acids containing an aromatic side chain.

The fundamental, structural, and functional units or subunits of living organisms. They are composed of CYTOPLASM containing various ORGANELLES and a CELL MEMBRANE boundary.

The complete gene complement contained in a set of chromosomes in a fungus.

Statistical formulations or analyses which, when applied to data and found to fit the data, are then used to verify the assumptions and parameters used in the analysis. Examples of statistical models are the linear model, binomial model, polynomial model, two-parameter model, etc.

One of the three domains of life (the others being Eukarya and ARCHAEA), also called Eubacteria. They are unicellular prokaryotic microorganisms which generally possess rigid cell walls, multiply by cell division, and exhibit three principal forms: round or coccal, rodlike or bacillary, and spiral or spirochetal. Bacteria can be classified by their response to OXYGEN: aerobic, anaerobic, or facultatively anaerobic; by the mode by which they obtain their energy: chemotrophy (via chemical reaction) or PHOTOTROPHY (via light reaction); for chemotrophs by their source of chemical energy: CHEMOLITHOTROPHY (from inorganic compounds) or chemoorganotrophy (from organic compounds); and by their source for CARBON; NITROGEN; etc.; HETEROTROPHY (from organic sources) or AUTOTROPHY (from CARBON DIOXIDE). They can also be classified by whether or not they stain (based on the structure of their CELL WALLS) with CRYSTAL VIOLET dye: gram-negative or gram-positive.

The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment.

One of the three domains of life (the others being BACTERIA and Eukarya), formerly called Archaebacteria under the taxon Bacteria, but now considered separate and distinct. They are characterized by: (1) the presence of characteristic tRNAs and ribosomal RNAs; (2) the absence of peptidoglycan cell walls; (3) the presence of ether-linked lipids built from branched-chain subunits; and (4) their occurrence in unusual habitats. While archaea resemble bacteria in morphology and genomic organization, they resemble eukarya in their method of genomic replication. The domain contains at least four kingdoms: CRENARCHAEOTA; EURYARCHAEOTA; NANOARCHAEOTA; and KORARCHAEOTA.

The study of the composition, chemical structures, and chemical reactions of living things.

A meshlike structure composed of interconnecting nerve cells that are separated at the synaptic junction or joined to one another by cytoplasmic processes. In invertebrates, for example, the nerve net allows nerve impulses to spread over a wide area of the net because synapses can pass information in any direction.

Any of the processes by which cytoplasmic or intercellular factors influence the differential control of gene action in bacteria.

A species of gram-positive bacteria in the family Clostridiaceae, used for the industrial production of SOLVENTS.

Theoretical representations that simulate the behavior or activity of systems, processes, or phenomena. They include the use of mathematical equations, computers, and other electronic equipment.

A loose confederation of computer communication networks around the world. The networks that make up the Internet are connected through several backbone networks. The Internet grew out of the US Government ARPAnet project and was designed to facilitate information exchange.

A species of METHYLOBACTERIUM which can utilize acetate, ethanol, or methylamine as a sole carbon source. (From Bergey's Manual of Determinative Bacteriology, 9th ed)

Principles, models, and laws that apply to complex interrelationships and interdependencies of sets of linked components which form a functioning whole, a system. Any system may be composed of components which are systems in their own right (sub-systems), such as several organs within an individual organism.

Techniques to alter a gene sequence that result in an inactivated gene, or one in which the expression can be inactivated at a chosen time during development to study the loss of function of a gene.

Devices for generating biological products that use light as the energy source. They are used for controlled BIOMASS production such as growing cyanobacteria, mosses, or algae.

Those genes found in an organism which are necessary for its viability and normal function.

Databases devoted to knowledge about specific chemicals.

A species of halophilic archaea whose organisms are nonmotile. Habitats include freshwater and marine mud, animal-waste lagoons, and the rumens of ungulates.

A genus of gram-negative bacteria which are obligately intracellular endosymbionts of APHIDS. The bacteria are found within specialized cells in the aphid body cavity.

The procedures involved in combining separately developed modules, components, or subsystems so that they work together as a complete system. (From McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)

The systematic study of the complete complement of proteins (PROTEOME) of organisms.

The relationships of groups of organisms as reflected by their genetic makeup.

The addition of descriptive information about the function or structure of a molecular sequence to its MOLECULAR SEQUENCE DATA record.

A plant genus of the family BRASSICACEAE that contains ARABIDOPSIS PROTEINS and MADS DOMAIN PROTEINS. The species A. thaliana is used for experiments in classical plant genetics as well as molecular genetic studies in plant physiology, biochemistry, and development.

Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in fungi.

Systems of enzymes which function sequentially by catalyzing consecutive reactions linked by common metabolic intermediates. They may involve simply a transfer of water molecules or hydrogen atoms and may be associated with large supramolecular structures such as MITOCHONDRIA or RIBOSOMES.

A genetic rearrangement through loss of segments of DNA or RNA, bringing sequences which are normally separated into close proximity. This deletion may be detected using cytogenetic techniques and can also be inferred from the phenotype, indicating a deletion at one specific locus.

A system containing any combination of computers, computer terminals, printers, audio or visual display devices, or telephones interconnected by telecommunications equipment or cables: used to transmit or receive information. (Random House Unabridged Dictionary, 2d ed)

Proteins obtained from ESCHERICHIA COLI.

A primary source of energy for living organisms. It is naturally occurring and is found in fruits and other parts of plants in its free state. It is used therapeutically in fluid and nutrient replacement.

The cycle by which the element carbon is exchanged between organic matter and the earth's physical environment.

A genus of gram-positive, anaerobic bacteria in the family Thermoanaerobacteriaceae. They are thermophilic and saccharolytic.

The external elements and conditions which surround, influence, and affect the life and development of an organism or population.

Stable carbon atoms that have the same atomic number as the element carbon, but differ in atomic weight. C-13 is a stable carbon isotope.

Multicellular, eukaryotic life forms of kingdom Plantae (sensu lato), comprising the VIRIDIPLANTAE; RHODOPHYTA; and GLAUCOPHYTA; all of which acquired chloroplasts by direct endosymbiosis of CYANOBACTERIA. They are characterized by a mainly photosynthetic mode of nutrition; essentially unlimited growth at localized regions of cell divisions (MERISTEMS); cellulose within cells providing rigidity; the absence of organs of locomotion; absence of nervous and sensory systems; and an alternation of haploid and diploid generations.

Anaerobic degradation of GLUCOSE or other organic nutrients to gain energy in the form of ATP. End products vary depending on organisms, substrates, and enzymatic pathways. Common fermentation products include ETHANOL and LACTIC ACID.

A rigorously mathematical analysis of energy relationships (heat, work, temperature, and equilibrium). It describes systems whose states are determined by thermal parameters, such as temperature, in addition to mechanical and electromagnetic parameters. (From Hawley's Condensed Chemical Dictionary, 12th ed)

A species of gram-positive, asporogenous, non-pathogenic, soil bacteria that produces GLUTAMIC ACID.

Organizations and individuals cooperating together toward a common goal at the local or grassroots level.

Changes in biological features that help an organism cope with its ENVIRONMENT. These changes include physiological (ADAPTATION, PHYSIOLOGICAL), phenotypic and genetic changes.

The statistical reproducibility of measurements (often in a clinical context), including the testing of instrumentation or techniques to obtain reproducible results. The concept includes reproducibility of physiological measurements, which may be used to develop rules to assess probability or prognosis, or response to a stimulus; reproducibility of occurrence of a condition; and reproducibility of experimental results.

Directed modification of the gene complement of a living organism by such techniques as altering the DNA, substituting genetic material by means of a virus, transplanting whole nuclei, transplanting cell hybrids, etc.

A microanalytical technique combining mass spectrometry and gas chromatography for the qualitative as well as quantitative determinations of compounds.

Physiological processes and properties of BACTERIA.

Information application based on a variety of coding methods to minimize the amount of data to be stored, retrieved, or transmitted. Data compression can be applied to various forms of data, such as images and signals. It is used to reduce costs and increase efficiency in the maintenance of large volumes of data.

The genetic complement of a plant (PLANTS) as represented in its DNA.

The functional hereditary units of FUNGI.

A synthetic naphthoquinone without the isoprenoid side chain and biological activity, but can be converted to active vitamin K2, menaquinone, after alkylation in vivo.

Theoretical representations that simulate the behavior or activity of chemical processes or phenomena; includes the use of mathematical equations, computers, and other electronic equipment.

Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control (induction or repression) of gene action at the level of transcription or translation.

Mathematical procedure that transforms a number of possibly correlated variables into a smaller number of uncorrelated variables called principal components.

Proteins obtained from the species SACCHAROMYCES CEREVISIAE. The function of specific proteins from this organism are the subject of intense scientific interest and have been used to derive basic understanding of the functioning similar proteins in higher eukaryotes.

Hybridization of a nucleic acid sample to a very large set of OLIGONUCLEOTIDE PROBES, which have been attached individually in columns and rows to a solid support, to determine a BASE SEQUENCE, or to detect variations in a gene sequence, GENE EXPRESSION, or for GENE MAPPING.

Nicotinamide adenine dinucleotide phosphate. A coenzyme composed of ribosylnicotinamide 5'-phosphate (NMN) coupled by pyrophosphate linkage to the 5'-phosphate adenosine 2',5'-bisphosphate. It serves as an electron carrier in a number of reactions, being alternately oxidized (NADP+) and reduced (NADPH). (Dorland, 27th ed)

The non-genetic biological changes of an organism in response to challenges in its ENVIRONMENT.

A network of membrane compartments, located at the cytoplasmic side of the GOLGI APPARATUS, where proteins and lipids are sorted for transport to various locations in the cell or cell membrane.

Organic compounds that generally contain an amino (-NH2) and a carboxyl (-COOH) group. Twenty alpha-amino acids are the subunits which are polymerized to form proteins.

The study of the structure, preparation, properties, and reactions of carbon compounds. (McGraw-Hill Dictionary of Scientific and Technical Terms, 6th ed)

Cells lacking a nuclear membrane so that the nuclear material is either scattered in the cytoplasm or collected in a nucleoid region.

Proteins found in any species of bacterium.

The synthesis by organisms of organic chemical compounds, especially carbohydrates, from carbon dioxide using energy obtained from light rather than from the oxidation of chemical compounds. Photosynthesis comprises two separate processes: the light reactions and the dark reactions. In higher plants; GREEN ALGAE; and CYANOBACTERIA; NADPH and ATP formed by the light reactions drive the dark reactions which result in the fixation of carbon dioxide. (from Oxford Dictionary of Biochemistry and Molecular Biology, 2001)

The rate dynamics in chemical or physical systems.

Databases containing information about PROTEINS such as AMINO ACID SEQUENCE; PROTEIN CONFORMATION; and other properties.

Theory and development of COMPUTER SYSTEMS which perform tasks that normally require human intelligence. Such tasks may include speech recognition, LEARNING; VISUAL PERCEPTION; MATHEMATICAL COMPUTING; reasoning, PROBLEM SOLVING, DECISION-MAKING, and translation of language.

Any detectable and heritable change in the genetic material that causes a change in the GENOTYPE and which is transmitted to daughter cells and to succeeding generations.

Approximate, quantitative reasoning that is concerned with the linguistic ambiguity which exists in natural or synthetic language. At its core are variables such as good, bad, and young as well as modifiers such as more, less, and very. These ordinary terms represent fuzzy sets in a particular problem. Fuzzy logic plays a key role in many medical expert systems.

The act of testing the software for compliance with a standard.

A species of rod-shaped, LACTIC ACID bacteria used in PROBIOTICS and SILAGE production.

Body of knowledge related to the use of organisms, cells or cell-derived constituents for the purpose of developing products which are technically, scientifically and clinically useful. Alteration of biologic function at the molecular level (i.e., GENETIC ENGINEERING) is a central focus; laboratory methods used include TRANSFECTION and CLONING technologies, sequence and structure analysis algorithms, computer databases, and gene and protein structure function analysis and prediction.

The biosynthesis of RNA carried out on a template of DNA. The biosynthesis of DNA from an RNA template is called REVERSE TRANSCRIPTION.

Organized activities related to the storage, location, search, and retrieval of information.

A theorem in probability theory named for Thomas Bayes (1702-1761). In epidemiology, it is used to obtain the probability of disease in a group of people with some characteristic on the basis of the overall rate of that disease and of the likelihood of that characteristic in healthy and diseased individuals. The most familiar application is in clinical decision analysis where it is used for estimating the probability of a particular diagnosis given the appearance of some symptoms or test result.

Graphs representing sets of measurable, non-covalent physical contacts with specific PROTEINS in living organisms or in cells.

The process of finding chemicals for potential therapeutic use.

The study, utilization, and manipulation of those microorganisms capable of economically producing desirable substances or changes in substances, and the control of undesirable microorganisms.

Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in plants.

The restriction of a characteristic behavior, anatomical structure or physical system, such as immune response; metabolic response, or gene or gene variant to the members of one species. It refers to that property which differentiates one species from another but it is also used for phylogenetic levels higher or lower than the species.

Any liquid or solid preparation made specifically for the growth, storage, or transport of microorganisms or other types of cells. The variety of media that exist allow for the culturing of specific microorganisms and cell types, such as differential media, selective media, test media, and defined media. Solid media consist of liquid media that have been solidified with an agent such as AGAR or GELATIN.

Linear POLYPEPTIDES that are synthesized on RIBOSOMES and may be further modified, crosslinked, cleaved, or assembled into complex proteins with several subunits. The specific sequence of AMINO ACIDS determines the shape the polypeptide will take, during PROTEIN FOLDING, and the function of the protein.

Endogenous substances, usually proteins, which are effective in the initiation, stimulation, or termination of the genetic transcription process.

Where are we in genomics? (1/3529)

Genomic studies provide scientists with methods to quickly analyse genes and their products en masse. The first high-throughput techniques to be developed were sequencing methods. A great number of genomes from different organisms have thus been sequenced. Genomics is now shifting to the study of gene expression and function. In the past 5-10 years genomics, proteomics and high-throughput microarray technologies have fundamentally changed our ability to study the molecular basis of cells and tissues in health and diseases, giving a new comprehensive view. For example, in cancer research we have seen new diagnostic opportunities for tumour classification, and prognostication. A new exciting development is metabolomics and lab-on-a-chip techniques (which combine miniaturization and automation) for metabolic studies. However, to interpret the large amount of data, extensive computational development is required. In the coming years, we will see the study of biological networks dominating the scene in Physiology. The great accumulation of genomics information will be used in computer programs to simulate biologic processes. Originally developed for genome analysis, bioinformatics now encompasses a wide range of fields in biology from gene studies to integrated biology (i.e. combination of different data sets from genes to metabolites). This is systems biology which aims to study biological organisms as a whole. In medicine, scientific results and applied biotechnologies arising from genomics will be used for effective prediction of diseases and risk associated with drugs. Preventive medicine and medical therapy will be personalized. Widespread applications of genomics for personalized medicine will require associations of gene expression pattern with diagnoses, treatment and clinical data. This will help in the discovery and development of drugs. In agriculture and animal science, the outcomes of genomics will include improvement in food safety, in crop yield, in traceability and in quality of animal products (dairy products and meat) through increased efficiency in breeding and better knowledge of animal physiology. Genomics and integrated biology are huge tasks and no single lab can pursue this alone. We are probably at the end of the beginning rather than at the beginning of the end because Genomics will probably change Biology to a greater extent than previously forecasted. In addition, there is a great need for more information and better understanding of genomics before complete public acceptance. (+info)

Identification of metabolic system parameters using global optimization methods. (2/3529)

BACKGROUND: The problem of estimating the parameters of dynamic models of complex biological systems from time series data is becoming increasingly important. METHODS AND RESULTS: Particular consideration is given to metabolic systems that are formulated as Generalized Mass Action (GMA) models. The estimation problem is posed as a global optimization task, for which novel techniques can be applied to determine the best set of parameter values given the measured responses of the biological system. The challenge is that this task is nonconvex. Nonetheless, deterministic optimization techniques can be used to find a global solution that best reconciles the model parameters and measurements. Specifically, the paper employs branch-and-bound principles to identify the best set of model parameters from observed time course data and illustrates this method with an existing model of the fermentation pathway in Saccharomyces cerevisiae. This is a relatively simple yet representative system with five dependent states and a total of 19 unknown parameters of which the values are to be determined. CONCLUSION: The efficacy of the branch-and-reduce algorithm is illustrated by the S. cerevisiae example. The method described in this paper is likely to be widely applicable in the dynamic modeling of metabolic networks. (+info)

Metabolic complementarity and genomics of the dual bacterial symbiosis of sharpshooters. (3/3529)

Mutualistic intracellular symbiosis between bacteria and insects is a widespread phenomenon that has contributed to the global success of insects. The symbionts, by provisioning nutrients lacking from diets, allow various insects to occupy or dominate ecological niches that might otherwise be unavailable. One such insect is the glassy-winged sharpshooter (Homalodisca coagulata), which feeds on xylem fluid, a diet exceptionally poor in organic nutrients. Phylogenetic studies based on rRNA have shown two types of bacterial symbionts to be coevolving with sharpshooters: the gamma-proteobacterium Baumannia cicadellinicola and the Bacteroidetes species Sulcia muelleri. We report here the sequencing and analysis of the 686,192-base pair genome of B. cicadellinicola and approximately 150 kilobase pairs of the small genome of S. muelleri, both isolated from H. coagulata. Our study, which to our knowledge is the first genomic analysis of an obligate symbiosis involving multiple partners, suggests striking complementarity in the biosynthetic capabilities of the two symbionts: B. cicadellinicola devotes a substantial portion of its genome to the biosynthesis of vitamins and cofactors required by animals and lacks most amino acid biosynthetic pathways, whereas S. muelleri apparently produces most or all of the essential amino acids needed by its host. This finding, along with other results of our genome analysis, suggests the existence of metabolic codependency among the two unrelated endosymbionts and their insect host. This dual symbiosis provides a model case for studying correlated genome evolution and genome reduction involving multiple organisms in an intimate, obligate mutualistic relationship. In addition, our analysis provides insight for the first time into the differences in symbionts between insects (e.g., aphids) that feed on phloem versus those like H. coagulata that feed on xylem. Finally, the genomes of these two symbionts provide potential targets for controlling plant pathogens such as Xylella fastidiosa, a major agroeconomic problem, for which H. coagulata and other sharpshooters serve as vectors of transmission. (+info)

Potential compensatory responses through autophagic/lysosomal pathways in neurodegenerative diseases. (4/3529)

Intracellular protein degradation decreases with age, altering the important balance between protein synthesis and breakdown. Slowly, protein accumulation events increase causing axonopathy, synaptic deterioration, and subsequent cell death. As toxic species accumulate, autophagy-lysosomal protein degradation pathways are activated. Responses include autophagic vacuoles that degrade damaged cellular components and long-lived proteins, as well as enhanced levels of lysosomal hydrolases. Although such changes correlate with neuronal atrophy in age-related neurodegenerative disorders and in related models of protein accumulation, the autophagic/lysosomal responses appear to be compensatory reactions. Recent studies indicate that protein oligomerization/ aggregation induces autophagy and activates lysosomal protein degradation in an attempt to clear toxic accumulations. Such compensatory responses may delay cell death and account for the gradual nature of protein deposition pathology that can extend over months/years in model systems and years/decades in the human diseases. Correspondingly, enhancement of compensatory pathways shifts the balance from pathogenesis to protection. Positive modulation of protein degradation processes represents a strategy to promote clearance of toxic accumulations and to slow the synaptopathogenesis and associated cognitive decline in aging-related dementias. (+info)

Transcriptome kinetics of arsenic-induced adaptive response in zebrafish liver. (5/3529)

Arsenic is a prominent environmental toxicant and carcinogen; however, its molecular mechanism of toxicity and carcinogenicity remains poorly understood. In this study, we performed microarray-based expression profiling on liver of zebrafish exposed to 15 parts/million (ppm) arsenic [As(V)] for 8-96 h to identify global transcriptional changes and biological networks involved in arsenic-induced adaptive responses in vivo. We found that there was an increase of transcriptional activity associated with metabolism, especially for biosyntheses, membrane transporter activities, cytoplasm, and endoplasmic reticulum in the 96 h of arsenic treatment, while transcriptional programs for proteins in catabolism, energy derivation, and stress response remained active throughout the arsenic treatment. Many differentially expressed genes encoding proteins involved in heat shock proteins, DNA damage/repair, antioxidant activity, hypoxia induction, iron homeostasis, arsenic metabolism, and ubiquitin-dependent protein degradation were identified, suggesting strongly that DNA and protein damage as a result of arsenic metabolism and oxidative stress caused major cellular injury. These findings were comparable with those reported in mammalian systems, suggesting that the zebrafish liver coupled with the available microarray technology present an excellent in vivo toxicogenomic model for investigating arsenic toxicity. We proposed an in vivo, acute arsenic-induced adaptive response model of the zebrafish liver illustrating the relevance of many transcriptional activities that provide both global and specific information of a coordinated adaptive response to arsenic in the liver. (+info)

Dietary electrolyte-driven responses in the renal WNK kinase pathway in vivo. (6/3529)

WNK1 and WNK4 are unusual serine/threonine kinases with atypical positioning of the catalytic active-site lysine (WNK: With-No-K[lysine]). Mutations in these WNK kinase genes can cause familial hyperkalemic hypertension (FHHt), an autosomal dominant, hypertensive, hyperkalemic disorder, implicating this novel WNK pathway in normal regulation of BP and electrolyte balance. Full-length (WNK1-L) and short (WNK1-S) kinase-deficient WNK1 isoforms previously have been identified. Importantly, WNK1-S is overwhelmingly predominant in kidney. Recent Xenopus oocyte studies implicate WNK4 in inhibition of both thiazide-sensitive co-transporter-mediated Na+ reabsorption and K+ secretion via renal outer medullary K+ channel and now suggest that WNK4 is inhibited by WNK1-L, itself inhibited by WNK1-S. This study examined WNK pathway gene expression in mouse kidney and its regulation in vivo. Expression of WNK1-S and WNK4 is strongest in distal tubule, dropping sharply in collecting duct and with WNK4 also expressed in thick ascending limb and the macula densa. These nephron segments that express WNK1-S and WNK4 mRNA have major influence on long-term NaCl reabsorption, BP, K+, and acid-base balance, processes that all are disrupted in FHHt. In vivo, this novel WNK pathway responds with significant upregulation of WNK1-S and WNK4 with high K+ intake and reduction in WNK1-S on chronic lowering of K+ or Na+ intake. A two-compartment distal nephron model explains these in vivo findings and the pathophysiology of FHHt well, with WNK and classic aldosterone pathways responding to drivers from K+ balance, extracellular volume, and aldosterone and cross-talk through distal Na+ delivery regulating electrolyte balance and BP. (+info)

Reconstructing the regulatory kinase pathways of myogenesis from phosphopeptide data. (7/3529)

Multiple kinase activities are required for skeletal muscle differentiation. However, the mechanisms by which these kinase pathways converge to coordinate the myogenic process are unknown. Using multiple phosphoprotein and phosphopeptide enrichment techniques we obtained phosphopeptides from growing and differentiating C2C12 muscle cells and determined specific peptide sequences using LC-MS/MS. To place these phosphopeptides into a rational context, a bioinformatics approach was used. Phosphorylation sites were matched to known site-specific and to site non-specific kinase-substrate interactions, and then other substrates and upstream regulators of the implicated kinases were incorporated into a model network of protein-protein interactions. The model network implicated several kinases of known relevance to myogenesis including AKT, GSK3, CDK5, p38, DYRK, and MAPKAPK2 kinases. This combination of proteomics and bioinformatics technologies should offer great utility as the volume of protein-protein and kinase-substrate information continues to increase. (+info)

A network-based analysis of polyanion-binding proteins utilizing yeast protein arrays. (8/3529)

The high affinity of certain cellular polyanions for many proteins (polyanion-binding proteins (PABPs)) has been demonstrated previously. It has been hypothesized that such polyanions may be involved in protein structure stabilization, stimulation of folding through chaperone-like activity, and intra- and extracellular protein transport as well as intracellular organization. The purpose of the proteomics studies reported here was to seek evidence for the idea that the nonspecific but high affinity interactions of PABPs with polyanions have a functional role in intracellular processes. Utilizing yeast protein arrays and five biotinylated cellular polyanion probes (actin, tubulin, heparin, heparan sulfate, and DNA), we identified proteins that interact with these probes and analyzed their structural and amino acid sequence requirements as well as their predicted functions in the yeast proteome. We also provide evidence for the existence of a network-like system for PABPs and their potential roles as critical hubs in intracellular behavior. This investigation takes a first step toward achieving a better understanding of the nature of polyanion-protein interactions within cells and introduces an alternative way of thinking about intracellular organization. (+info)

"A Fortuitous Metabolic Pathway". Cambridge University Press. University of Sydney. "Resume Kristine Barlow-Stewart". University ... "Annual Report 2016" (PDF). Genetic Support Network of Victoria. HGSA. "Registration Brochure". Next Generation Coming of Age. ...

https://en.wikipedia.org/wiki/List_of_HGSA_Orations

Metabolite networks use nodes to represent chemical reactions and directed edges for the metabolic pathways and regulatory ... Many types of biological networks exist, including transcriptional, signalling and metabolic. Few such networks are known in ... Biological network inference is the process of making inferences and predictions about biological networks. By using networks ... "Text mining for metabolic pathways, signaling cascades, and protein networks". Science's STKE. 2005 (283): pe21. doi:10.1126/ ...

https://en.wikipedia.org/wiki/Biological_network_inference

... network List of omics topics in biology Mathematical biology Metabolic network Metabolic network modelling Metabolic pathway ... Even metabolic networks can be considered as molecular interaction networks: metabolites, i.e. chemical compounds in a cell, ... Similarly, gene regulatory networks overlap substantially with protein interaction networks and signaling networks. It has been ... "Text mining for metabolic pathways, signaling cascades, and protein networks". Science Signaling. 2005 (283): pe21. doi:10.1126 ...

https://en.wikipedia.org/wiki/Interactome

"Text mining for metabolic pathways, signaling cascades, and protein networks". Science's STKE. 2005 (283): pe21. doi:10.1126/ ... "The UMLS Semantic Network". semanticnetwork.nlm.nih.gov. Retrieved 2018-10-07. McCray AT, Srinivasan S, Browne AC (1994). " ... Jenssen TK, Laegreid A, Komorowski J, Hovig E (May 2001). "A literature network of human genes for high-throughput analysis of ... quality-controlled protein-protein association networks, made broadly accessible". Nucleic Acids Research. 45 (D1): D362-D368. ...

https://en.wikipedia.org/wiki/Biomedical_text_mining

178 Metabolic pathways can be targeted for clinically therapeutic uses. Within the mitochondrial metabolic network, for ... Metabolic pathways are often regulated by feedback inhibition. Some metabolic pathways flow in a 'cycle' wherein each component ... The end product of a pathway may be used immediately, initiate another metabolic pathway or be stored for later use. The ... In addition to the two distinct metabolic pathways is the amphibolic pathway, which can be either catabolic or anabolic based ...

https://en.wikipedia.org/wiki/Metabolic_pathway

Pyruvate is a key intersection in the network of metabolic pathways. Pyruvate can be converted into carbohydrates via ... Compound C00074 at KEGG Pathway Database. Enzyme 2.7.1.40 at KEGG Pathway Database. Compound C00022 at KEGG Pathway Database. ... Pyruvate, the conjugate base, CH3COCOO−, is an intermediate in several metabolic pathways throughout the cell. Pyruvic acid can ... Therefore, it unites several key metabolic processes. In glycolysis, phosphoenolpyruvate (PEP) is converted to pyruvate by ...

https://en.wikipedia.org/wiki/Pyruvic_acid

Similarly metabolic networks have multiple alternate pathways to produce many key metabolites. Protein mutation tolerance is ... Additionally the flux through a metabolic pathway is typically limited by only a few of the steps, meaning that changes in ... segment polarity network, neurogenic network and bone morphogenetic protein gradient, C. elegans fitness and vulval development ... 1997). "Neutral networks in protein space: A computational study based on knowledge-based potentials of mean force". Folding & ...

https://en.wikipedia.org/wiki/Robustness_(evolution)

"A Global Coexpression Network Approach for Connecting Genes to Specialized Metabolic Pathways in Plants". The Plant Cell. 29 (5 ... April 2017). "Genome-Wide Prediction of Metabolic Enzymes, Pathways, and Gene Clusters in Plants". Plant Physiology. 173 (4): ... discrete metabolic pathway. The genes are in physical vicinity to each other on the genome, and their expression is often ... Metabolic gene clusters are common features of bacterial and most fungal genomes, and are less often found in other organisms. ...

https://en.wikipedia.org/wiki/Metabolic_gene_cluster

... Research Network (2013). "Alterations in metabolic pathways and networks in mild cognitive impairment and ... Such metabolic profiles can provide a complete overview of individual metabolite or pathway alterations, providing a more ... This allows for the identification of the metabolic processes and pathways that are being altered by the treatment either ... This involves determining the metabolic profile of a patient prior to treatment, and correlating metabolic signatures with the ...

https://en.wikipedia.org/wiki/Pharmacometabolomics

"Cancer metabolic pathway identified as target for therapy: Researchers identify a". ScienceDaily. Retrieved 2021-01-07. " ... "Spotting Cancer at the Molecular Level". Cancer Research from Technology Networks. Retrieved 2021-01-07. ""Biopsy Without a ...

https://en.wikipedia.org/wiki/Irene_Georgakoudi

... to describe the control in metabolic pathways but was subsequently extended to describe signaling and genetic networks. MCA has ... Metabolic control analysis (MCA) is a mathematical framework for describing metabolic, signaling, and genetic pathways. MCA ... In a linear chain of reaction steps, flux control will tend to be biased towards the front of the pathway. From a metabolic ... The flux through the pathway is completely dependent on the first step. Under these conditions, no other step in the pathway ...

https://en.wikipedia.org/wiki/Metabolic_control_analysis

Metabolic disease networks (MDN), in which two diseases are connected by a shared metabolite or metabolic pathway, have also ... Graphical models Human disease network Interactome Metabolic network Network dynamics Network Science Network theory Network ... Others networks include cell signaling networks, gene regulatory networks, and RNA networks. Using interactome networks, one ... Three key networks for understanding human disease are the metabolic network, the disease network, and the social network. The ...

https://en.wikipedia.org/wiki/Network_medicine

2009). "Validation of candidate causal genes for obesity that affect shared metabolic pathways and networks". Nature Genetics. ... He is known for calling for a shift in molecular biology toward a network-oriented view of living systems to complement the ... They also published a paper in Cell reporting that a network of genes linked to inflammatory response plays a role in late- ... In 2013, Schadt and his team were awarded a grant from the National Institutes of Health to study biological networks in ...

https://en.wikipedia.org/wiki/Eric_Schadt

The complete set of all these biochemical reactions in all the pathways represents the metabolic network. Within the metabolic ... Signaling networks typically integrate protein-protein interaction networks, gene regulatory networks, and metabolic networks. ... It is possible to use network analyses to infer how selection acts on metabolic pathways. Signals are transduced within cells ... The use of network analysis can illuminate how pollination networks work and may, in turn, inform conservation efforts. Within ...

https://en.wikipedia.org/wiki/Biological_network

PMAP is to aid the protease researchers in reasoning about proteolytic networks and metabolic pathways. PMAP was originally ... Cytoscape Computational genomics Metabolic network modelling Protein-protein interaction prediction Igarashi, Y; Heureux, E; ... PathwayDB, just begun accumulation of metabolic pathways whose function can be dynamically modeled in a rule-based manner. ... Proteolytic pathways, or proteolysis, are the series of events controlled by proteases that occur in response to specific ...

https://en.wikipedia.org/wiki/The_Proteolysis_Map

... can represent metabolic and signaling pathways, molecular and genetic interactions and gene regulation networks. BioPAX ... BioPAX (Biological Pathway Exchange) is a RDF/OWL-based standard language to represent biological pathways at the molecular and ... Its major use is to facilitate the exchange of pathway data. Pathway data captures our understanding of biological processes, ... A database integrating human functional interaction networks PANTHER (List of Pathways) WikiPathways PharmGKB/PharmGKB* ...

https://en.wikipedia.org/wiki/BioPAX

"Operonic structure of key metabolic pathways in cyanobacteria - Pramod P. Wangikar". School of Informatics and Computing : ... Vinh, Nguyen Xuan; Chetty, Madhu; Coppel, Ross; Wangikar, Pramod P. (13 November 2011). Dynamic Bayesian Network Modeling of ... Wangikar is known to have done advanced research in the fields of structural bioinformatics and metabolic modeling. At IIT ... Modelling biological systems Biological network Please see Selected bibliography section "Pramod P Wangikar - Faculty profile ...

https://en.wikipedia.org/wiki/Pramod_P._Wangikar

Metabolic pathways consist of complex networks, which are responsible for processing of both energy and material. The metabolic ... The metabolic theory of ecology's main implication is that metabolic rate, and the influence of body size and temperature on ... The metabolic theory of ecology (MTE) is the ecological component of the more general Metabolic Scaling Theory and Kleiber's ... Extensions of metabolic theory to diversity that include eco-evolutionary theory show that an elaborated metabolic theory can ...

https://en.wikipedia.org/wiki/Metabolic_theory_of_ecology

Computational systems biology Metabolic control analysis Metabolic network Metabolic pathway Metagenomics Zanghellini, Jürgen; ... The Wikipedia page Metabolic pathway defines a pathway as "a metabolic pathway is a linked series of chemical reactions ... "A general definition of metabolic pathways useful for systematic organization and analysis of complex metabolic networks". ... This means that elementary modes cannot be decomposed further into simpler pathways. All possible flows through a network can ...

https://en.wikipedia.org/wiki/Elementary_modes

"A general definition of metabolic pathways useful for systematic organization and analysis of complex metabolic networks". ... These include, among others: Evolutionary game theory Metabolic control analysis Biochemical oscillations Metabolic pathway ... "Combining Metabolic Pathway Analysis with Evolutionary Game Theory. Explaining the occurrence of low-yield pathways by an ... Research on metabolic pathways includes flux balance analysis, which is used, for example, for explaining the Warburg effect. ...

https://en.wikipedia.org/wiki/Stefan_Schuster

The bacterium has a well-regulated metabolic network. Unlike many species in Azoarcus proper, it is incapable of fixing ... It has one chromosome and two plasmids, encoding for 10 anaerobic and 4 aerobic aromatic degradation pathways. The genome is ... "Functional proteomic view of metabolic regulation in "Aromatoleum aromaticum" strain EbN1". Proteomics. 7 (13): 2222-2239. doi: ...

https://en.wikipedia.org/wiki/Aromatoleum

The batteries can be used to power biosensors and sensor networks. Minteer looks to bioengineer natural metabolic pathways for ...

https://en.wikipedia.org/wiki/Shelley_D._Minteer

Targeted therapy inhibits the metabolic pathway that underlies that type of cancer's cell division. The classic example of ... In the two decades that followed the establishment of the NCCSC, a large network of cooperative clinical trial groups evolved ... In a particular cancer, such a network may be radically altered, due to a chance somatic mutation. ... Cancer (2015 PBS film) Weisse, Allen B. (1991). Medical Odysseys: The Different and Sometimes Unexpected Pathways to Twentieth- ...

https://en.wikipedia.org/wiki/History_of_cancer_chemotherapy

Metabolism Metabolic network Metabolic network modelling Johnson, E.S. Protein modification by SUMO. Annu. Rev. Biochem. 73, ... SUMO pathway is the most studied ubiquitin-like pathway that regulates a wide range of cellular events, evidenced by a large ... 16, 591-626 (2000) Boggio R et al., A mechanism for inhibiting the SUMO pathway. Mol Cell. 2004 Nov 19;16(4):549-61 Bernier- ... SUMO pathway modifies hundreds of proteins that participate in diverse cellular processes. ...

https://en.wikipedia.org/wiki/SUMO_enzymes

MEROPS UniProt Cytoscape Computational genomics Metabolic network modelling Protein-protein interaction prediction Lange, P. F ... In a later release analysis tools for the evaluation of proteolytic pathways in experimental data have been added. ... Also, a network view of all proteins showing their functional dependency as protease, substrate or protease inhibitor tied in ... "Network analyses reveal pervasive functional regulation between proteases in the human protease web". PLOS Biology. 12 (5): ...

https://en.wikipedia.org/wiki/TopFIND

Soybean metabolic pathway information (SoyCyc) was inferred by the Plant Metabolic Network project and was used to populate ... Metabolic data and biochemical pathway information is displayed using Pathway Tools. ... Plant Metabolic Network project Generic Model Organism Database project Legume Federation project Legume Information System ... 2010). "Genome-Wide Prediction of Metabolic Enzymes, and Gene Clusters in Plants". Plant Physiology. 173 (4): 2041-2059. doi: ...

https://en.wikipedia.org/wiki/SoyBase_Database

In FBA metabolic fluxes are estimated by first representing the metabolic reactions of a metabolic network in a numerical ... This allowed the construction of a model of the pathway and for FBA to analyze it. The results of this found multiple possible ... a number of relatively simple linear algebra methods use restricted metabolic networks or genome-scale metabolic network models ... Metabolic flux refers to the rate of metabolite conversion in a metabolic network. For a reaction this rate is a function of ...

https://en.wikipedia.org/wiki/Fluxomics

Find active subnetworks/pathway modules. The network is screened against gene expression data to identify connected sets of ... Computational genomics Graph drawing JavaScript framework JavaScript library Metabolic network modelling Protein-protein ... Zoom in/out and pan for browsing the network. Use the network manager to easily organize multiple networks. And this structure ... For instance, clusters in a protein-protein interaction network have been shown to be protein complexes and parts of pathways. ...

https://en.wikipedia.org/wiki/Cytoscape

Li J, Eriksson L; Humphreys K; Czene K (2010). "Genetic variation in the estrogen metabolic pathway and mammographic density as ... Build a network of all genes that are involved in the pathway Evaluate the consistency of the prior regulatory information ... SPIA (Signaling Pathway Impact analysis) is a method that uses the phenotype information to evaluate the pathway activity ... Denoising Algorithm based on Relevance network Topology improves molecular pathway activity inference". BMC Bioinformatics. 12 ...

https://en.wikipedia.org/wiki/Denoising_Algorithm_based_on_Relevance_network_Topology

... metabolic pathway analysis, modeling and simulation of biological networks. Genostar's software is platform independent and can ... Metabolic Pathway Builder is a bioinformatics environment dedicated to microbial research. This covers sequence assembly, ... values to the gene names and IDs Identify co-expressed genes and visually analyze the reactions and metabolic pathways in which ... gene prediction using a Hidden Markov model based method BlastX Automatic annotation transfer using BlastP Metabolic Pathway ...

https://en.wikipedia.org/wiki/Genostar

Masui, Kenta; Cavenee, Webster K.; Mischel, Paul S. (2014-07-25). "mTORC2 in the center of cancer metabolic reprogramming". ... "An LXR Agonist Promotes Glioblastoma Cell Death through Inhibition of an EGFR/AKT/SREBP-1/LDLR-Dependent Pathway". Cancer ... "Heterogeneity of epidermal growth factor receptor signalling networks in glioblastoma". Nature Reviews Cancer. 15 (5): 302-310 ... Bi, Junfeng; Wu, Sihan; Zhang, Wenjing; Mischel, Paul S. (2018-05-23). "Targeting cancer's metabolic co-dependencies: A ...

https://en.wikipedia.org/wiki/Paul_Mischel

These two sites catalyze the last two steps of the de novo uridine monophosphate (UMP) biosynthetic pathway. After addition of ... A UMP synthase deficiency can result in a metabolic disorder called orotic aciduria. Deficiency of this enzyme is an inherited ... "A human protein-protein interaction network: a resource for annotating the proteome". Cell. 122 (6): 957-68. doi:10.1016/j.cell ... P. falciparum OPRTase follows a random pathway in OMP synthesis and degradation. Transition state analyses have used isotopic ...

https://en.wikipedia.org/wiki/Uridine_monophosphate_synthase

... more so than energy flow pathways. Functional webs have compartments, which are sub-groups in the larger network where there ... Different consumers are going to have different metabolic assimilation efficiencies in their diets. Each trophic level ... "Ecological networks, especially mutualistic networks, are generally very heterogeneous, consisting of areas with sparse links ... Food webs are complex networks. As networks, they exhibit similar structural properties and mathematical laws that have been ...

https://en.wikipedia.org/wiki/Food_web

May 2016). "Deep biomarkers of human aging: Application of deep neural networks to biomarker development". Aging. 8 (5): 1021- ... metabolic rate is a poor predictor of lifespan for birds, bats and other species that, it is presumed, have reduced mortality ... Study of these organisms has revealed the presence of at least two conserved aging pathways. Gene expression is imperfectly ... metabolic rate does not correlate with longevity in mammals or birds. With respect to specific types of chemical damage caused ...

https://en.wikipedia.org/wiki/Senescence

Garcia AJ, 3rd; Zanella, S; Koch, H; Doi, A; Ramirez, JM (2011). Chapter 3--networks within networks: the neuronal control of ... The frequency and amplitude change according to the behavioral and metabolic demands of the organism it controls. Breathing is ... or inhibit the NALCN channels depending on the neurotransmitter that binds the receptor and the specific signaling pathway that ... The pre-Bötzinger complex is a rhythm generating network, which is composed of micro networks that function within larger ...

https://en.wikipedia.org/wiki/Pre-Bötzinger_complex

ISBN 0-7923-3681-X. Imam S, Noguera D, Donohue T. "Global insights into energetic and metabolic networks in Rhodobacter ... the Entner-Doudoroff pathway (ED) and the Pentose phosphate pathway (PP). The ED pathway is the predominant glycolytic pathway ... Several pathways for glucose catabolism are present in its genome, such as the Embden-Meyerhof-Parnas pathway (EMP), ... A genome-scale reconstruction of the Rhodobacter sphaeroides metabolic network". BMC Systems Biology. 5: 116. doi:10.1186/1752- ...

https://en.wikipedia.org/wiki/Rhodobacter_sphaeroides

Appropriate radioisotopes of elements within chemical compounds of the metabolic pathway being examined are used to make the ... Recent development in deep learning and convolutional neural network techniques have made it possible to analyze and quantify ... PET enables visual image analysis of multiple different metabolic chemical processes and is thus one of the most flexible ...

https://en.wikipedia.org/wiki/Cardiac_imaging

... metabolic and signaling pathways and thus play an inevitable role in causing disease. Much is still to be known about these ... This, in addition to SINEs' direct role in regulatory networks (as discussed in SINEs as long non-coding RNAs) is crucial to ... metabolic and regulatory pathways and SINEs have become a great source of genetic variability. They seem to play a particularly ... The genes that had high hybridization E-values were genes particularly involved in metabolic and signaling pathways. Almost all ...

https://en.wikipedia.org/wiki/Short_interspersed_nuclear_element

The access networks of a city enable and constrain pedestrian flows; it is the capacity or possibility to walk. Like density ... Winter 2006). "Many Pathways from Land Use to Health" (PDF). Journal of the American Planning Association. p. 77. Frank; et al ... Thus for instance, an increase in neighborhood Walk Score has linked with both better Cardio metabolic risk profiles and a ... Access networks are also multi-modal and need to be understood from the perspective of those who choose between modes of ...

https://en.wikipedia.org/wiki/Walkability

Enzyme inhibition is a common feature of metabolic pathway control in cells. Metabolic flux through a pathway is often ... Linking Cellular Networks and Bioprocesses. Berlin: Springer Science & Business Media. pp. 77-78. ISBN 978-3-642-13865-2. Okar ... The metabolic processes targeted by natural poisons encompass more than enzymes in metabolic pathways and can also include the ... For example, enzymes in a metabolic pathway may be inhibited by molecules produced later in the pathway, thus curtailing the ...

https://en.wikipedia.org/wiki/Enzyme_inhibitor

Through this pathway, Hsc70 also contributes to the degradation of the proapoptotic BBC3/PUMA under normal conditions, thus ... Henstridge DC, Whitham M, Febbraio MA (2014). "Chaperoning to the metabolic party: The emerging therapeutic role of heat-shock ... "A human protein-protein interaction network: a resource for annotating the proteome". Cell. 122 (6): 957-68. doi:10.1016/j.cell ... Hsp70 member proteins, including Hsp72, inhibit apoptosis by acting on the caspase-dependent pathway and against apoptosis- ...

https://en.wikipedia.org/wiki/HSPA8

... metabolic pathway - metabolism - metabotropic glutamate receptor - metalloprotein - metaphase - metazoa - methionine - micelle ... gene regulatory network - genetic carrier - genetic code - genetic drift - genetic engineering - genetic fingerprint - genetic ...

https://en.wikipedia.org/wiki/Index_of_biochemistry_articles

... querying and visualization of gene regulation and protein interaction networks, metabolic and signaling pathways. WZL Gear ... LRE Analyzer Neuroph is a lightweight Java neural network framework for developing common neural network architectures. It ... It utilizes local and global optimization for bio-network inference, text mining techniques for network validation and ... INTViewer, by Interactive Network Technologies, Inc., is a visualization application for analysis and quality control of ...

https://en.wikipedia.org/wiki/List_of_NetBeans-based_software

Some of these receptors such as FXR, LXR, and PPAR bind a number of metabolic intermediates such as fatty acids, bile acids and ... with members of the same subfamily having very similar NR dimerization partners and the underlying dimerization network has ... much sense as closely related receptors of subfamilies bound ligands originating from entirely different biosynthetic pathways ... These receptors hence may function as metabolic sensors. Other nuclear receptors, such as CAR and PXR appear to function as ...

https://en.wikipedia.org/wiki/Nuclear_receptor

... of KEGG metabolic pathways. The fold is extremely versatile in that it can accommodate a wide range of ligands. They can ... a structure network approach". PLOS ONE. 7 (12): e51676. Bibcode:2012PLoSO...751676B. doi:10.1371/journal.pone.0051676. PMC ... Metabolic enzymes normally have one specific function, and in the case of UDP-glucose 6-dehydrogenase, the primary function is ... "Functional analysis of Rossmann-like domains reveals convergent evolution of topology and reaction pathways". PLOS ...

https://en.wikipedia.org/wiki/Rossmann_fold

For example, proteins involved in the same metabolic pathway are likely to be present in a genome together or are absent ... Granger BR, Chang YC, Wang Y, DeLisi C, Segrè D, Hu Z (April 2016). "Visualization of Metabolic Interaction Networks in ... Several networks based on different data sources can be combined into a composite network, which can then be used by a ... These networks serve as a representation of the evidence for shared/similar function within a group of genes, where nodes ...

https://en.wikipedia.org/wiki/Protein_function_prediction

In parallel to the work on botulinum toxin, he worked on the enzymes involved in the catecholamine biosynthetic pathway, ... The company currently has two drugs in clinical trials for pulmonary and metabolic diseases. Named to the PharmaVoice 100 (2022 ... and the GPCR Network, all funded by the National Institutes of Health with direct guidance from NIGMS. In 2012, Stevens co- ...

https://en.wikipedia.org/wiki/Raymond_C._Stevens

It is important to note that control coefficients are not fixed values but will change depending on the state of the pathway or ... doi:10.1111/j.1432-1033.1974.tb03318.x. Hearon, John Z. (1 October 1952). "Rate Behavior of Metabolic Systems". Physiological ... coefficients are useful because they tell us how much influence each enzyme or protein has in a biochemical reaction network. ... If an organism shifts to a new nutritional source, then the control coefficients in the pathway will change. One criticism of ...

https://en.wikipedia.org/wiki/Control_coefficient_(biochemistry)

... have supported the hypothesis that schizophrenia is associated with alterations of the tryptophane-kynurenine metabolic pathway ... found in some individuals with schizophrenia could be due to aberrant neural networks established as a compensation for left ... Compounds found in cannabis, such as THC, have been shown to increase the activity of dopamine pathways in the brain, ... Larkin, W; Larkin, J (2008). "Childhood trauma and psychosis: evidence, pathways, and implications". Journal of Postgraduate ...

https://en.wikipedia.org/wiki/Risk_factors_of_schizophrenia

"The C word: how we react to cancer today". NHS Networks. Retrieved 13 April 2020. Chochinov HM, Breitbart W (2009). Handbook of ... Yadav UP, Singh T, Kumar P, Mehta K (2020). "Metabolic Adaptations in Cancer Stem Cells". Frontiers in Oncology. 10: 1010. doi: ... A further mutation may cause loss of a tumor suppressor gene, disrupting the apoptosis signaling pathway and immortalizing the ... Al-Azzam N (2020). "Sirtuin 6 and metabolic genes interplay in Warburg effect in cancers". Journal of Clinical Biochemistry and ...

https://en.wikipedia.org/wiki/Cancer

The specific metabolic pathways that occur exclusively in mammalian peroxisomes are: α-oxidation of phytanic acid β-oxidation ... Innovative Training Network PERICO Schrader M, Costello J, Godinho LF, Islinger M (2015). "Peroxisome-mitochondria interplay ... Peroxisomes interact with mitochondria in several metabolic pathways, including β-oxidation of fatty acids and the metabolism ... Antonenkov, Vasily D. (Jul 1989). "Dehydrogenases of the pentose phosphate pathway in rat liver peroxisomes". European Journal ...

https://en.wikipedia.org/wiki/Peroxisome

If the UPR pathway is activated in an abnormal fashion, such as when obesity triggers chronic ER stress and the pathway is ... Successful protein folding requires a tightly controlled environment of substrates that include glucose to meet the metabolic ... a specialized ER network in skeletal muscles. This calcium then interacts with calcineurin and calcium/calmodulin-dependent ... Therefore, this UPR pathway mediates changes in muscles that have undergone endurance training by making them more resistant to ...

https://en.wikipedia.org/wiki/Unfolded_protein_response

... synthesized through the metabolic pathway of benzylisoquinoline. First, the amino acid phenylalanine, through the enzyme ... Opium became a major colonial commodity, moving legally and illegally through trade networks on the Indian subcontinent, ... which carries the benzylisoquinoline skeleton that gives its name to this pathway. The conversion of (S) -norcoclaurin to (S) - ...

https://en.wikipedia.org/wiki/Papaver_somniferum

Furthermore, antiquitin functions as an aldehyde dehydrogenase for α-AASA in the pipecolic acid pathway of lysine catabolism. ... Journal of Inherited Metabolic Disease. 33 (5): 571-81. doi:10.1007/s10545-010-9187-2. PMC 3112356. PMID 20814824. Giacalone NJ ... "A human protein-protein interaction network: a resource for annotating the proteome". Cell. 122 (6): 957-68. doi:10.1016/j.cell ...

https://en.wikipedia.org/wiki/ALDH7A1

Some metabolic actions of metformin do appear to occur by AMPK-independent mechanisms. Metformin has indirect antiandrogenic ... March 2022). "Low-dose metformin targets the lysosomal AMPK pathway through PEN2". Nature. 603 (7899): 159-165. Bibcode: ... A network meta-analysis of randomized controlled trials". Obesity Reviews. 20 (1): 1-12. doi:10.1111/obr.12753. PMID 30230172. ... Rosilio C, Ben-Sahra I, Bost F, Peyron JF (May 2014). "Metformin: a metabolic disruptor and anti-diabetic drug to target human ...

https://en.wikipedia.org/wiki/Metformin

... by photosynthesis have potential to help regulate the circadian rhythm and certain photosynthetic and metabolic pathways. As ... Armenian Medical Network. Retrieved 2007-09-19. "The Rhythms of Life: The Biological Clocks That Control the Daily Lives of ... This appears to be consistent with the proposed phenomenon known as metabolic dawn. According to the metabolic dawn hypothesis ... Shift work also leads to increased metabolic risks for cardio-metabolic syndrome, hypertension, and inflammation. Due to the ...

https://en.wikipedia.org/wiki/Circadian_rhythm

... the definition of a pathway in terms of elementary modes, three reviews on metabolic control analysis including a republication ... he was ideally positioned to consider a more quantitative approach to studying the properties of cellular networks. It was ... Poolman, M. G.; Miguet, L.; Sweetlove, L. J.; Fell, D. A. (2009). "A Genome-Scale Metabolic Model of Arabidopsis and Some of ... Fell, D A; Sauro, H M (1986). "Metabolic control and its analysis: additional relationships between elasticities and control ...

https://en.wikipedia.org/wiki/David_Fell_(biochemist)

"Efficacy and metabolic effects of lurasidone versus brexpiprazole in schizophrenia: a network meta-analysis". Journal of ... In the nigrostratial pathway, it reduces EPS. In the tuberoinfundibular pathway, it reduces or eliminates prolactin elevation. ... predictors of metabolic dysregulation, and association with psychopathology: a systematic review and network meta-analysis". ... Dopamine release in the mesolimbic pathway from 5-HT2A antagonism does not appear to be as robust as in the other pathways of ...

https://en.wikipedia.org/wiki/Atypical_antipsychotic

These typically involve metabolic networks or cell signaling networks. Systems biology can be considered from a number of ... the enzymes and metabolites in a metabolic pathway or the heart beats). As a paradigm, systems biology is usually defined in ... systems Metabolic network modelling Modelling biological systems Molecular pathological epidemiology Network biology Network ... by which one can study the biochemical networks and analyze the flow of metabolites through a particular metabolic network, by ...

https://en.wikipedia.org/wiki/Systems_biology

Phosphorus is involved in all major metabolic processes including photosynthesis, energy transfer, signal transduction, ... Holmgren, David (2007). "Essence of Permaculture" (PDF). Permaculture: Principles & Pathways Beyond Sustainability: 7. This ... Food Revolution Network. Retrieved 8 June 2020. Netting, Robert McC. (1993) Smallholders, Householders: Farm Families and the ... "Implications of current net zero targets for long-term emissions pathways and warming levels". EGU General Assembly Conference ...

https://en.wikipedia.org/wiki/Sustainable_agriculture

Dysregulation of multiple metabolic networks related to brain transmethylation and polyamine pathways in Alzheimer disease: A ... Dysregulation of multiple metabolic networks related to brain transmethylation and polyamine pathways in Alzheimer disease: A ... Correction: Dysregulation of multiple metabolic networks related to brain transmethylation and polyamine pathways in Alzheimer ... Integrated summary of alterations in metabolite concentrations and gene expression within metabolic pathways linked to ...

https://pubmed.ncbi.nlm.nih.gov/31978055/

Improvements of Algorithms for Detecting Stoichiometrically Feasible Pathways in Metabolic ...

https://www.mi.fu-berlin.de/en/math/groups/mathlife/BSc/brosch/index.html

... This section is dedicated to discussions related to the use of metabolic networks in ... In fact, these networks can be used to put metabolic profiles in a biochemical context, predict metabolic fluxes and help in ... Genome scale network analysis 4 Posts. 1 Topics Re: Avoiding connecti... by Fabien JourdanLast post: October 31, 2016, 02:39:39 ...

http://www.metabolomics-forum.com/index.php?board=79.0

As accumulating evidence for roles of an intricate and elaborate network of metabolic processes, including lipid, amino acid ... Metabolic reprogramming of immune cells is essential for both inflammatory as well as anti-inflammatory responses. Four anti- ... Evidence is emerging for the targeting of specific metabolic events as a strategy to limit inflammation in different contexts. ... we here turn our attention to glycolysis and the TCA cycle to provide examples of how metabolic intermediates and enzymes can ...

https://www.nature.com/articles/s41422-020-0291-z?error=cookies_not_supported

... exploring the plant metabolic network describes current developments in the genomic reconstruction of metabolic networks, the ... It also requires a focus on metabolic flux as the key to understanding the regulation of metabolic activity and the ... Further progress in this direction requires tools to facilitate the structural description of the network on the basis of fully ... The papers also highlight insights that can be obtained from pathway analysis, particularly in relation to the thermodynamic ...

https://www.neuroscience.ox.ac.uk/publications/316314?229abaf4-fd47-11ed-a697-061ab7f93640

Metabolic Networks and Pathways / genetics * Milk, Human / microbiology * Multigene Family * Polysaccharides / chemistry ... Exploring metabolic pathway reconstruction and genome-wide expression profiling in Lactobacillus reuteri to define functional ... and compared using a pan-metabolic model representing all known metabolic reactions present in these strains. Both strains ... The production of bioactive metabolites by human-derived probiotics may be predicted using metabolic modeling and ...

https://pubmed.ncbi.nlm.nih.gov/21559529/

By building an extensive computer network of molecular relationships, researchers have been able to uncover links to diseases ... The metabolic disease network uncovered a total of 193 pairs of diseases that are metabolically linked and tend to occur ... The network can expand as researchers identify more disease-gene associations and help uncover the metabolic origins of other ... On average, a disease is connected in the metabolic disease network to about 5 other diseases. Most diseases have links to only ...

https://www.nih.gov/news-events/nih-research-matters/metabolic-network-finds-disease-links

Using Metabolomics to Investigate Biological Pathways and Networks (R01) RFA-RM-06-010. Roadmap ... Examples of network relationships could be between intercellular coordination of catabolic and anabolic metabolic pathways or ... and activating or inhibiting feedback effects on pathway or network regulation. These aspects of pathways and networks can be ... expansion of biological pathway and network model paradigms to both fully define pathway components and explore unknown network ...

http://grants.nih.gov/grants/guide/rfa-files/RFA-RM-06-010.html

Differential metabolic network analysis of tumor progression. FROMMER, WOLF B. CARNEGIE INSTITUTION OF WASHINGTON, D.C.. Sugar ... National Technology Centers for Networks and Pathways. The Building Blocks, Biological Pathways and Networks program has ... Pathways. Metabolomics Technology Development. Using Metabolomics to Investigate Biological Pathways and Networks (R01). RFA-RM ... Networks, Pathways and Dynamics of Lysine Modification. ROUT, MICHAEL P. ROCKEFELLER UNIVERSITY. New Tools for Exploring the ...

http://commonfund.nih.gov/bbpn/fundedresearch

Technology Description: This invention is a process that reconstructs the metabolic pathways of a modified E. coli strain to ... Though researchers have previously managed to produce succinate using metabolic pathways none of these methods have approached ... Modified Metabolic Pathways in E. coli for Improved Succinate Production Similar National Plans. Crop growing under plastic ... Technology Description: This invention is a process that reconstructs the metabolic pathways of a modified E. coli strain to ...

https://www.ctc-n.org/products/modified-metabolic-pathways-e-coli-improved-succinate-production

Metabolic Networks and Pathways in Alzheimers Disease (R01AG046171). Principal Investigator:. Rima F. Kaddurah-Daouk, Duke ... Metabolic Network Analysis of Biochemical Trajectories in Alzheimers Disease (RF1AG057452). Contact Principal Investigator:. ... Gain a systems-level understanding of the gene, protein, and metabolic networks within which these novel targets operate ... Dominantly Inherited Alzheimers Network Trials Unit (DIAN-TU) (R01AG046179). Principal Investigator:. Randall Bateman, ...

https://www.nia.nih.gov/research/dn/amp-ad-target-discovery-and-preclinical-validation-project

Metabolic Networks and Pathways* Actions. * Search in PubMed * Search in MeSH * Add to Search ... Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas Joshua D Campbell 1 , Christina Yau 2 , ... Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas Joshua D Campbell et al. Cell Rep. 2018. ... Cancer Genome Atlas Research Network; Joshua M Stuart 31 , Peter W Laird 6 , Katherine A Hoadley 32 , John N Weinstein 4 , ...

https://www.ncbi.nlm.nih.gov/pubmed/29617660

Metabolic Networks and Pathways. Peptide Hydrolases--metabolism. Publication Types: Lecture. Webcast Rights: This is a work of ... CIT): This presentation will describe the mission and the activities of the Center on Proteolytic Pathways (CPP), a technology ... This presentation will describe the mission and the activities of the Center on Proteolytic Pathways (CPP), a technology ... purpose of the CPP is to develop technological advances relevant to the interrogation of proteases and proteolytic pathways. A ...

https://videocast.nih.gov/watch=6278

Metabolic Pathways. Molecular Libraries Screening Center Network. Natural Products. NIH Substance Repository. Physical ...

http://www.chemspider.com/Chemical-Structure.3336660.html?rid=15b0d4c5-34ea-4958-b44f-4a78eef66398&page_num=0

Metabolic Networks and Pathways; Polychlorinated Biphenyls/chemistry; Polychlorinated Biphenyls/metabolism*; Populus/chemistry ... The results suggest that the hydroxylated metabolic pathway of CB77 is via an epoxide intermediate in poplar. ... Title: Identification of hydroxylated metabolites of 3,3,4,4-tetrachlorobiphenyl and metabolic pathway in whole poplar plants ...

https://tools.niehs.nih.gov/portfolio/index.cfm?do=portfolio.publicationDetail&id=1682868

3. KEGG Metabolic Reaction Network (Undirected): KEGG Metabolic pathways modeled as un-directed reaction network. Variety of ... 2. KEGG Metabolic Relation Network (Directed): KEGG Metabolic pathways modeled as directed relation network. Variety of ... This data can be used to study machine learning methods as well as do some social network research. ...

https://archive.ics.uci.edu/ml/datasets.php?format=&task=cla&att=&area=&numAtt=10to100&numIns=greater1000&type=uvar&sort=typeUp&view=list

One-carbon metabolism is a crucial network of pathways involved in cellular methylation reactions and nucleotide biosynthesis. ... Workshop on Metabolic Interactions between Folic Acid Excess and Vitamin B12 Deficiency. July 31. - Aug. 1, 2019. Contacts ... The network is regulated by and dependent on several micronutrients. Of these, folate (Vitamin B9) and vitamin B12 play central ... Workshop on Metabolic Interactions between Folic Acid Excess and Vitamin B12 Deficiency ...

https://www.niddk.nih.gov/news/meetings-workshops/2019/metabolic-interaction-folates-folic-acid-vitamin-b12-deficiency

Text mining for metabolic pathways, signaling cascades, and protein networks.. Hoffmann R; Krallinger M; Andres E; Tamames J; ... Integrative mining of traditional Chinese medicine literature and MEDLINE for functional gene networks.. Zhou X; Liu B; Wu Z; ...

https://pubmedhh.nlm.nih.gov/biomarkers/search.php?id=19060303&mod=related&page=1&outid=&proj=

... metabolic pathways, signaling networks ... The PSI:Biology Network Director. The PSI:Biology Network ... External Input to the Network. The PSI Advisory Committee will provide external input to the PSI:Biology Network Steering ... The PSI:Biology Network Director will serve as a Scientific Liaison to the overall PSI:Biology Network and all of its ... The PSI Network Director will not also serve as the NIH program official for any component of the PSI:Biology network. ...

http://grants1.nih.gov/grants/guide/rfa-files/RFA-GM-10-005.html

Metabolic Pathway 20% * Glucose Homeostasis 20% * Protein Interaction 20% * Anabolism 20% * Amino Acids 20% ... Dive into the research topics of A proteome-integrated, carbon source dependent genetic regulatory network in Saccharomyces ... A proteome-integrated, carbon source dependent genetic regulatory network in Saccharomyces cerevisiae. ...

https://research.vu.nl/en/publications/a-proteome-integrated-carbon-source-dependent-genetic-regulatory-/fingerprints/

Metabolic Pathways Molecular Libraries Screening Center Network NIH Substance Repository Physical Properties ...

http://pubchem.ncbi.nlm.nih.gov/search/search.cgi

Text mining for metabolic pathways, signaling cascades, and protein networks. R Hoffmann, M Krallinger, E Andres, J Tamames, C ...

https://scholar.google.es/citations?user=cSRnhsUAAAAJ&hl=es&oe=ASCII

Pathways and Damage: Determine how the peripheral and central auditory and vestibular pathways are reorganized following injury ... Simonyan K, Fuertinger S. Speech networks at rest and in action: interactions between functional brain networks controlling ... Glucose transporters and ATP-gated K+ (KATP) metabolic sensors are present in type 1 taste receptor 3 (T1r3)-expressing taste ... Hedgehog pathway blockade with the cancer drug LDE225 disrupts taste organs and taste sensation. J Neurophysiol. 2015;113(3): ...

https://www.nidcd.nih.gov/about/strategic-plan/2017-2021-nidcd-strategic-plan

The JAK-STAT pathway at 30: Much learned, much more to do. Philips RL, Wang Y, Cheon H, Kanno Y, Gadina M, Sartorelli V, ... Metabolic Regulation of Epigenetics. As satellite cells exit from quiescence during muscle regeneration, they are accompanied ... We develop general operating principles and conduct gene network modeling based on genome-wide experimental data. ... Metabolic Reprogramming of Stem Cell Epigenetics. Ryall JG, Cliff T, Dalton S, Sartorelli V ...

http://www.niams.nih.gov/Research/Ongoing_Research/Branch_Lab/Muscle_Stem_Cells_and_Gene_Regulation/default.asp

For plant generic pathways, ATP- and NADPH-demands per CO2 assimilated are higher by 1.3- and 1.5-fold, respectively. If the ... For plant generic pathways, ATP- and NADPH-demands per CO2 assimilated are higher by 1.3- and 1.5-fold, respectively. If the ... Independent of specific pathways and per unit carbon assimilated, energy content and biosynthetic demands in reducing ... Independent of specific pathways and per unit carbon assimilated, energy content and biosynthetic demands in reducing ...

https://www.frontiersin.org/articles/10.3389/fpls.2022.787265/full

... the redesigning of an organisms metabolic pathways to produce a specific compound. Metabolic engineering is more complex than ... "The product is a property of the overall network of reactions, not the outcome of a single reaction or a single gene," he says ... Using a combination of synthetic biology and metabolic engineering, the researchers have overhauled the biochemical pathways in ... One of the most crucial modifications was blocking a pathway for making a cholesterol-like substance. This pathway uses the ...

https://www.technologyreview.com/2006/04/13/229332/cheaper-malaria-drugs/

Linkage of organic anion transporter-1 to metabolic pathways through integrated "omics"-driven network and functional analysis ... Network reconstruction of platelet metabolism identifies metabolic signature for aspirin resistance. Nature Scientific Reports ... Insight into human alveolar macrophage and M. tuberculosis interactions via metabolic reconstructions. Molecular Systems ... Flux-concentration duality in dynamic nonequilibrium biological networks. Biophysical Journal. 2009; 97(5):L11-3. PMID 19720010 ...

https://www.uclahealth.org/providers/neema-jamshidi

Metabolic engineering applications - Cell simulation and modeling - Metabolic, regulatory and signaling models/ networks: ... Identification of metabolic pathways - Functional genomics - Biomarker identification - Molecular docking and drug design - ... Complex Networks 2023 12 th International Conference on Complex Networks and their Applications ... Metabolomics/ metabolic fingerprints - Health-care applications - Bio imaging Computacional areas of interest include, but are ...

In fact, these networks can be used to put metabolic profiles in a biochemical context, predict metabolic fluxes and help in metabolite annotation. (metabolomics-forum.com)
The task was daunting: The cell's metabolism involves thousands of molecules in a complicated network of biochemical reactions. (nih.gov)
The vector stencils library " Biochemistry of metabolism" contains 46 metabolite symbols for drawing metabolic pathways maps, biochemical diagrams and metabolism process flow charts using the ConceptDraw PRO diagramming and vector drawing software. (conceptdraw.com)
The biochemical diagram example "Metabolic pathway map" was created using the ConceptDraw PRO diagramming and vector drawing software extended with the Biology solution from the Science and Education area of ConceptDraw Solution Park. (conceptdraw.com)
Use these shapes for drawing carbohydrate metabolism schematics, biochemical diagrams and metabolic pathways maps. (conceptdraw.com)
Using a combination of synthetic biology and metabolic engineering, the researchers have overhauled the biochemical pathways in yeast to generate large quantities of artemisinic acid, a precursor of the drug artemisinin. (technologyreview.com)

The metabolomic analysis showed that key metabolic pathways including citrate cycle, biosynthesis of aminoacyl- tRNA , and metabolism of amino acids , sphingolipids , carbohydrates , nucleotides , and glutathione were activated in rice plants exposed to DnBP and its primary metabolite mono-n- butyl phthalate (MnBP). (bvsalud.org)
As accumulating evidence for roles of an intricate and elaborate network of metabolic processes, including lipid, amino acid and nucleotide metabolism provides key focal points for developing new therapies, we here turn our attention to glycolysis and the TCA cycle to provide examples of how metabolic intermediates and enzymes can provide potential novel therapeutic targets. (nature.com)
A concept is emerging whereby the repolarizing of immune cells towards a less inflamed phenotype by manipulating metabolism using small molecules and metabolic intermediates might be possible. (nature.com)
The transition from a pathway-centred view of plant metabolism to a network-wide perspective is still incomplete. (ox.ac.uk)
Progress is being made on several fronts and this Special Issue on 'Pathways and fluxes: exploring the plant metabolic network' describes current developments in the genomic reconstruction of metabolic networks, the application of flux-balance analysis to such networks, kinetic modelling, and both steady-state-and non-steady state isotope-based measurements of multiple fluxes in the network of central carbon metabolism. (ox.ac.uk)
They chose metabolic diseases because high-quality molecular interaction maps already exist for human cell metabolism, and earlier attempts at linking these diseases based on shared genes proved disappointing. (nih.gov)
One-carbon metabolism is a crucial network of pathways involved in cellular methylation reactions and nucleotide biosynthesis. (nih.gov)
Thomas A, Rahmanian S, Bordbar A, Palsson BØ, * Jamshidi N . Network reconstruction of platelet metabolism identifies metabolic signature for aspirin resistance. (uclahealth.org)

Reconstruction of functional networks of regulatory proteins and metabolic enzyme pathways from genome sequence. (nih.gov)
This, along with de novo proteins' propensity to interact, increases the chance that some will use their novel structures (and possibly novel functionalities) to integrate into existing genetic networks and survive for a long evolutionary time. (iscb.org)
Given the complexity of the mitochondrial proteome, it is clear that the focus must be on regulatory networks and manipulations of functional pathways, not on a few lone proteins. (nih.gov)
He and his colleagues study post-translational modifications of mitochondrial proteins to understand how proteins and enzymes rapidly adjust to maintain metabolic homeostasis under acute changes in energy demand. (nih.gov)
From this reductionist approach we have gained valuable information on how the metabolites, proteins, RNA and genes interact and the interaction networks. (futurelearn.com)
His work at the NIH has focused on stimulus-secretion-synthesis coupling, characterization of the vesicular and secretory proteins mediating chemically coded neurotransmission, including chromogranin A, VMAT1, VMAT2, and VAChT and signaling pathways underlying neuropeptide-mediated stress responses. (nih.gov)
They had to upregulate the production of precursors, drop in new chemical pathways, and adapt proteins from other organisms. (technologyreview.com)

The production of bioactive metabolites by human-derived probiotics may be predicted using metabolic modeling and transcriptomics. (nih.gov)
Identification of hydroxylated metabolites of 3,3',4,4'-tetrachlorobiphenyl and metabolic pathway in whole poplar plants. (nih.gov)
Because of the many chemicals (a.k.a. "metabolites") that may be involved, metabolic pathways can be quite elaborate. (conceptdraw.com)
For example, the complete metabolic network composed of thousands of metabolites has been broken down over more than 100 years of biochemistry in to metabolic pathways including the glycolysis pathway and the Kreb's cycle. (futurelearn.com)

The growing field of immunometabolism has taught us how metabolic cellular reactions and processes not only provide a means to generate ATP and biosynthetic precursors, but are also a way of controlling immunity and inflammation. (nature.com)
Through the differential metabolic requirements of effector and regulatory immune cell populations we have a therapeutic opportunity that allows for cellular selectivity when regulating immune responses. (nature.com)
These aspects of pathways and networks can be studied at a subcellular, cellular, tissue, organ system or whole organism level of integration. (nih.gov)
Methods and approaches developed to utilize these technologies should provide a basis for future studies of critical pathway and networks involved in the maintenance of cellular and system functions and should foster collaboration between technology experts and biological subject area specialists. (nih.gov)
We are already using recent advances in science and technology to discover how changes to the molecular, cellular, and systemic pathways can cause communication disorders. (nih.gov)
Dr. Balaban bases his research on the hypothesis that mitochondria are modulated to support cellular metabolic homeostasis chronically by altering mitochondrial content, composition, and cellular location. (nih.gov)
The cellular protein components of this 'non-canonical' cAMP transcriptional activation pathway are not known, although its importance in mediating cellular plasticity in the synaptic response to stress in both brain and peripheral neuroendocrine networks is quickly becoming clear. (nih.gov)
More recently, the laboratory has been involved in microarray- and bioinformatics-aided gene discovery within neuropeptide-dependent stress-activated cellular signaling pathways in the central nervous system, and has characterized a novel cAMP sensor for neuroendocrine cell-specific GPCR-initiated signaling to the MAP kinase ERK. (nih.gov)
As a consequence, feedback processes, dominant metabolic pathways, and other aspects of cellular function were altered in the host or microbe. (creation.com)
Therefore, the exposure of E. coli DH5α to Wi-Fi radiofrequency radiation for 5 hours influenced several bacterial cellular and metabolic processes. (hpathy.com)

Comparative genome analysis and pathway reconstruction. (ncl.edu.tw)

Additionally, a complete pathway for thiamine biosynthesis was predicted in strain 55730 for the first time in this species. (nih.gov)
For instance, the annotation of CC1617 (a Caulobacter cresentus gene) as guaB (E.C.# 1.1.1.205) is supported by the fact that CC1617 is part of a predicted operon with guaA (E.C.# 6.3.5.2) and the pathway for de novo biosynthesis of purine nucleotides (I) includes both of these reactions. (biomedcentral.com)

It also requires a focus on metabolic flux as the key to understanding the regulation of metabolic activity and the relationship between the inputs and outputs of the network. (ox.ac.uk)
The goal of the current funding opportunity is to apply metabolomics technology to the study of pathway and network regulation in normal and disease states that are not easily approached by other technologies. (nih.gov)
Ideally, applications will study more complete views of pathways and networks defined by changes in metabolite concentrations including their sources, destinations, and activating or inhibiting feedback effects on pathway or network regulation. (nih.gov)
Metabolic pathway analysis confirmed the presence, and photoperiodic regulation of the MEP/DOXP Terpenoid Backbone synthesis pathway. (bl.uk)

10. Integrative mining of traditional Chinese medicine literature and MEDLINE for functional gene networks. (nih.gov)
Linkage of organic anion transporter-1 to metabolic pathways through integrated "omics"-driven network and functional analysis. (uclahealth.org)

The researchers, funded by several NIH Institutes, pulled together information from 2 databases of known metabolic reactions and the molecules involved in them. (nih.gov)
Two diseases were considered connected if the products of their associated genes were involved in metabolic reactions with a common molecule. (nih.gov)
The scientists found that 31% of the diseases whose reactions are coupled in the network showed a statistically significant tendency to occur together-3 times more than the average for all diseases. (nih.gov)
Transcriptomes of L. reuteri strains in different growth phases were monitored using strain-specific microarrays, and compared using a pan-metabolic model representing all known metabolic reactions present in these strains. (nih.gov)
The metabolome forms a large network of metabolic reactions, where outputs from one enzymatic chemical reaction are inputs to other chemical reactions. (conceptdraw.com)
In biochemistry, metabolic pathways are series of chemical reactions occurring within a cell. (conceptdraw.com)
In each pathway, a principal chemical is modified by a series of chemical reactions. (conceptdraw.com)
PathoLogic determines the set of reactions composing those pathways from the enzymes annotated in the organism's genome. (biomedcentral.com)
Pathway holes occur when a genome appears to lack the enzymes needed to catalyze reactions in a pathway. (biomedcentral.com)
We achieved 71% precision at a probability threshold of 0.9 during cross-validation using known reactions in computationally-predicted pathway databases. (biomedcentral.com)
For each pathway in a set of reference pathways, if one or more reactions is present in the organism, PathoLogic adds that pathway to the set of pathways present in that organism. (biomedcentral.com)
Figure 1 shows an example reference pathway and the reactions that PathoLogic has identified in the organism's genome. (biomedcentral.com)
Metabolic engineering is more complex than traditional genetic engineering, because it requires the coordination of many different reactions, says Gregory Stephanopoulos , a chemical engineer at MIT. (technologyreview.com)
The product is a property of the overall network of reactions, not the outcome of a single reaction or a single gene," he says. (technologyreview.com)

This section is dedicated to discussions related to the use of metabolic networks in metabolomics. (metabolomics-forum.com)
Metabolomics has the capability of expanding our understanding of normal homeostatic and disease mechanisms by investigating pathway and network systems having many known or unknown components, relationships, or interactions through the use of high throughput methodologies. (nih.gov)
These Research Project applications need to assess the feasibility of applying metabolomics techniques to a particular biological problem that may lead to a breakthrough in the ability to further study of targeted pathways and networks. (nih.gov)

Targeting metabolic processes therapeutically will, unlike the approach of global immunosuppression, specifically and selectively target cells with high metabolic demands whilst not affecting other immune cells hence potentially reducing unwanted side effects. (nature.com)
In higher plants molecular clocks have been well defined and transcript profiling has revealed a sophisticated network of circadian scheduling of metabolic processes. (bl.uk)

If a protein has not been assigned a specific function during the annotation process, any reaction catalyzed by that protein will appear as a missing enzyme or pathway hole in a Pathway/Genome database. (biomedcentral.com)

The Building Blocks, Biological Pathways and Networks program has transitioned from Common Fund support. (nih.gov)
Please note that since the Building Blocks, Biological Pathways and Networks program is no longer supported by the Common Fund, the program website is being maintained as an archive and will not be updated on a regular basis. (nih.gov)
This model is constructed first with one or multiple networks to qualitatively define the components and interactions, then additional quantitative biological data is added as the next layer on to the networks. (futurelearn.com)
Flux-concentration duality in dynamic nonequilibrium biological networks. (uclahealth.org)

Pathways are important to the maintenance of homeostasis within an organism. (conceptdraw.com)
Since his discovery some years ago that mitochondria in the heart can supply energy at a rate that perfectly matches a range of physiological demands, Dr. Balaban has sought to understand how mitochondria are regulated to ensure this metabolic homeostasis. (nih.gov)
These models will feed back into experimental design in a positive spiral of research to form an increasingly sophisticated view of metabolic homeostasis. (nih.gov)

KEGG Metabolic pathways modeled as un-directed reaction network. (uci.edu)
We present a systematic method for comparing the metabolic pathways (pathways for short) of different organisms based on KEGG reference pathway data. (ncl.edu.tw)
Kyoto encyclopedia of genes and genomes (KEGG) pathways analysis showed that the pathways for flagellar assembly, chemotaxis and two-component system were affected. (hpathy.com)

By utilizing both the traditional anaerobic pathway and the glyoxylate cycle this method maximizes the carbon converted to succinic acid by recapturing maximum quantities of NADH for diversion to succinate synthesis. (ctc-n.org)
Catabolic (break-down) and Anabolic (synthesis) pathways often work interdependently to create new biomolecules as the final end-products. (conceptdraw.com)
In previous research, Keasling and his colleagues engineered bacteria to boost their production of terpenoids and convert the compounds into a molecule found later in the pathway for artemisinin synthesis (see TR10 2005 . (technologyreview.com)

We develop general operating principles and conduct gene network modeling based on genome-wide experimental data. (nih.gov)

The citrate cleavage pathway and lipogenesis in rat adipose tissue: replenishment of oxaloacetate. (ncl.edu.tw)

However, subtle shifts in the complex network of molecular interactions in the body can also cause disease. (nih.gov)
Choice of cooperative agreement is based on the need for NIH staff involvement in interactions between the many components of the PSI:Biology network to be established. (nih.gov)
The reductionist approach simplifies the complex networks down in to individual components and interactions. (futurelearn.com)
These simpler and reduced metabolic pathways normally contain 20 or fewer components and interactions. (futurelearn.com)
Bordbar A, Lewis NE, Schellenberger J, Palsson BØ, * Jamshidi N . Insight into human alveolar macrophage and M. tuberculosis interactions via metabolic reconstructions. (uclahealth.org)

First, elements of the gene regulatory network, particularly the non-coding region of the chromosome, may have been altered. (creation.com)

By building an extensive computer network of molecular relationships, researchers have been able to uncover links to diseases they never before suspected. (nih.gov)
To see whether the links in the metabolic disease network could predict which diseases occur together, the researchers analyzed the Medicare records of over 13 million elderly patients in the United States. (nih.gov)
The network can expand as researchers identify more disease-gene associations and help uncover the metabolic origins of other diseases. (nih.gov)
Though researchers have previously managed to produce succinate using metabolic pathways none of these methods have approached the product yield of nonrenewable sources. (ctc-n.org)
Our pathway hole filler can be used not only to increase the utility of Pathway/Genome databases to both experimental and computational researchers, but also to improve predictions of protein function. (biomedcentral.com)
Our comparison of over 100 pathways simultaneously can help researchers to unravel what have happened during the course of evolution and adaptation in each well-defined pathway. (ncl.edu.tw)

Vitis OneGenE is a transcriptomic data mining tool that finds direct correlations between genes, thus producing association networks. (mdpi.com)
Such knowledge is essential for the industrial applications of B. braunii, either directly or through the engineering of selected B. braunii genes or molecular pathways into alternative chassis. (bl.uk)

20. Text mining for metabolic pathways, signaling cascades, and protein networks. (nih.gov)
Operon- and pathway-based information can provide additional clues about protein function, and can clarify incomplete or nonspecific annotations. (biomedcentral.com)

We also found two carbohydrate related pathways that are quite different among these Vibrios. (ncl.edu.tw)

Low-CNA SCCs tended to be HPV(+) and display hypermethylation with repression of TET1 demethylase and FANCF, previously linked to predisposition to SCC, or harbor mutations affecting CASP8, RAS-MAPK pathways, chromatin modifiers, and immunoregulatory molecules. (nih.gov)
We study the integration of signaling pathways and the logics of transcription factors and chromatin regulators. (nih.gov)

The PathoLogic program constructs Pathway/Genome databases by using a genome's annotation to predict the set of metabolic pathways present in an organism. (biomedcentral.com)
We have developed a method that efficiently combines homology and pathway-based evidence to identify candidates for filling pathway holes in Pathway/Genome databases. (biomedcentral.com)

Pathways and fluxes: exploring the plant metabolic network. (ox.ac.uk)

The central goal of the AMP AD Target Discovery and Preclinical Validation Project was to shorten the time between the discovery of potential drug targets and the development of new drugs for Alzheimer's disease treatment and prevention, by integrating the analyses of large-scale molecular data from human brain samples with network modeling approaches and experimental validation. (nih.gov)

The papers also highlight insights that can be obtained from pathway analysis, particularly in relation to the thermodynamic and kinetic efficiency of the predicted and observed flux distributions. (ox.ac.uk)
In this context, constraint-based analysis has the promise to improve metabolic engineering strategies. (frontiersin.org)
The CAMP (Comparative Analysis of Metabolic Pathways) system will be freely available for academic or nonprofit use at http://gel.ym.edu.tw/camp. (ncl.edu.tw)
Pathway alignment: application to the comparative analysis of glycolytic enzymes. (ncl.edu.tw)
Phylogenetic analysis of metabolic pathways. (ncl.edu.tw)
Go enrichment analysis indicated that the up-regulated DEGs are involved in metabolic pathways, transposition, response to stimuli, motility, chemotaxis and cell adhesion. (hpathy.com)

Independent of specific pathways and per unit carbon assimilated, energy content and biosynthetic demands in reducing equivalents are about 1.3 to 1.4 times higher for TAG than for sucrose. (frontiersin.org)

This FOA solicits applications to establish Centers for High-Throughput Structure Determination that will become the backbone of the NIGMS PSI:Biology network for high-throughput-enabled structural biology. (nih.gov)

Our program not only identifies potential candidate sequences for pathway holes, but combines data from multiple, heterogeneous sources to assess the likelihood that a candidate has the required function. (biomedcentral.com)

We turned down that pathway so the yeast made just enough of the [cholesterol-like molecule] to live," says Keasling. (technologyreview.com)

The abundance of transcriptomic data and the development of causal inference methods have paved the way for gene network analyses in grapevine. (mdpi.com)

In the July 22, 2008, issue of Proceedings of the National Academy of Sciences , the scientists reported that over 300 of the 1,437 disorders from the gene-disease database are related to at least one metabolic reaction. (nih.gov)

Further progress in this direction requires tools to facilitate the structural description of the network on the basis of fully annotated genomes, techniques for modelling the properties of the network, and experimental methods for constraining the models and verifying their outputs. (ox.ac.uk)

One of the most crucial modifications was blocking a pathway for making a cholesterol-like substance. (technologyreview.com)

For plant generic pathways, ATP- and NADPH-demands per CO 2 assimilated are higher by 1.3- and 1.5-fold, respectively. (frontiersin.org)

In addition, numerous distinct pathways co-exist within a cell. (conceptdraw.com)

This data can be used to study machine learning methods as well as do some social network research. (uci.edu)

The down-regulated DEGs are associated with metabolic pathways and localization of ions and organic molecules. (hpathy.com)

Without the full delineation of molecular pathways involved in cAMP-mediated neuronal response to metabolic, ischemic and psychogenic stress, development of innovative pharmacological therapeutic strategies to treat stress-associated disorders will be severely limited. (nih.gov)

The metabolic disease network uncovered a total of 193 pairs of diseases that are metabolically linked and tend to occur together. (nih.gov)

Metabolic reprogramming of immune cells is essential for both inflammatory as well as anti-inflammatory responses. (nature.com)
Immunologists have recently turned their attention to metabolic changes occurring in immune cells that have a determining role in their effector responses. (nature.com)

Evidence is emerging for the targeting of specific metabolic events as a strategy to limit inflammation in different contexts. (nature.com)
The finding is among the first pharmaceutical successes for metabolic engineering - the redesigning of an organism's metabolic pathways to produce a specific compound. (technologyreview.com)

In this study, our method was applied to compare the Vibrio species (V. cholerae, V. vulnificus CMCP6 and V. parahaemolyticus) against Vibrio vulnificus YJ016 among 112 metabolic pathways. (ncl.edu.tw)

Anatomy4

Organisms14

Chemicals and Drugs17

Analytical, Diagnostic and Therapeutic Techniques and Equipment21

Phenomena and Processes46

Disciplines and Occupations12

Anthropology, Education, Sociology and Social Phenomena1

Technology, Industry, Agriculture4

Humanities1

Information Science22

Health Care7

Where are we in genomics? (1/3529)

Identification of metabolic system parameters using global optimization methods. (2/3529)

Metabolic complementarity and genomics of the dual bacterial symbiosis of sharpshooters. (3/3529)

Potential compensatory responses through autophagic/lysosomal pathways in neurodegenerative diseases. (4/3529)

Transcriptome kinetics of arsenic-induced adaptive response in zebrafish liver. (5/3529)

Dietary electrolyte-driven responses in the renal WNK kinase pathway in vivo. (6/3529)

Reconstructing the regulatory kinase pathways of myogenesis from phosphopeptide data. (7/3529)

A network-based analysis of polyanion-binding proteins utilizing yeast protein arrays. (8/3529)

Metabolic Networks and Pathways

Metabolism

Systems Biology

Models, Biological

Computer Simulation

Gene Regulatory Networks

Computational Biology

Metabolome

Algorithms

Enzymes

Cell Physiological Phenomena

Neural Networks (Computer)

Biomass

Metabolomics

Genome, Bacterial

Metabolic Engineering

Software

Autotrophic Processes

Escherichia coli

Proteome

Citric Acid Cycle

Protein Interaction Mapping

Carbon

Computer Graphics

Models, Genetic

Substrate Cycling

Biochemical Processes

Escherichia coli K12

Glycolysis

Gene Expression Profiling

Genomics

User-Computer Interface

Saccharomyces cerevisiae

Pentose Phosphate Pathway

Heterotrophic Processes

Signal Transduction

Databases, Genetic

Software Design

Energy Metabolism

Cluster Analysis

Databases, Factual

Genome

Biological Evolution

Evolution, Molecular

Phototrophic Processes

Amino Acids, Aromatic

Cells

Genome, Fungal

Models, Statistical

Bacteria

Phenotype

Archaea

Biochemistry

Nerve Net

Gene Expression Regulation, Bacterial

Clostridium acetobutylicum

Models, Theoretical

Internet

Glyoxylates

Methylobacterium extorquens

Systems Theory

Gene Knockout Techniques

Photobioreactors

Genes, Essential

Databases, Chemical

Methanosarcina barkeri

Buchnera

Systems Integration

Proteomics

Phylogeny

Molecular Sequence Annotation

Arabidopsis

Gene Expression Regulation, Fungal

Multienzyme Complexes

Gene Deletion

Computer Communication Networks

Escherichia coli Proteins

Glucose

Carbon Cycle

Thermoanaerobacterium