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)

Title:Metabolic Network Analysis: Current Status and Way Forward. VOLUME: 8 ISSUE: 3. Author(s):Shweta Kolhi and Ashok S. Kolaskar. Affiliation:Bioinformatics Center, University of Pune, Pune - 411007, India.. Keywords:Biological organization, metabolic categorization, metabolic networks analysis, metabolic pathways alignment, modular organization, network properties.. Abstract:One of the fundamental aims of life science is to gain insights into the functioning of an organism at systems level. Generation and systematic storage of enormous biological data in the post genomic era has made systems level studies a reality. For studies involving systems level investigation, metabolic pathways data inferred from intricate interactions amongst genes/enzymes/proteins are best suited and are being used extensively as they represent dynamic interactions in an organism. Consequently research in the field of comparative metabolomics as well as metabolic networks analysis is undergoing rapid improvement. ...
Most diseases are the consequence of the breakdown of cellular processes, but the relationships among genetic/epigenetic defects, the molecular interaction networks underlying them, and the disease phenotypes remain poorly understood. To gain insights into such relationships, here we constructed a bipartite human disease association network in which nodes are diseases and two diseases are linked if mutated enzymes associated with them catalyze adjacent metabolic reactions. We find that connected disease pairs display higher correlated reaction flux rate, corresponding enzyme-encoding gene coexpression, and higher comorbidity than those that have no metabolic link between them. Furthermore, the more connected a disease is to other diseases, the higher is its prevalence and associated mortality rate. The network topology-based approach also helps to uncover potential mechanisms that contribute to their shared pathophysiology. Thus, the structure and modeled function of the human metabolic network ...
Genome-scale metabolic network reconstructions are now routinely used in the study of metabolic pathways, their evolution and design. The development of such reconstructions involves the integration of information on reactions and metabolites from the scientific literature as well as public databases and existing genome-scale metabolic models. The reconciliation of discrepancies between data from these sources generally requires significant manual curation, which constitutes a major obstacle in efforts to develop and apply genome-scale metabolic network reconstructions. In this work, we discuss some of the major difficulties encountered in the mapping and reconciliation of metabolic resources and review three recent initiatives that aim to accelerate this process, namely BKM-react, MetRxn and MNXref (presented in this article). Each of these resources provides a pre-compiled reconciliation of many of the most commonly used metabolic resources. By reducing the time required for manual curation of ...
Recent development of high-throughput analytical techniques has made it possible to qualitatively identify a number of metabolites simultaneously. Correlation and multivariate analyses such as principal component analysis have been widely used to analyse those data and evaluate correlations among the metabolic profiles. However, these analyses cannot simultaneously carry out identification of metabolic reaction networks and prediction of dynamic behaviour of metabolites in the networks. The present study, therefore, proposes a new approach consisting of a combination of statistical technique and mathematical modelling approach to identify and predict a probable metabolic reaction network from time-series data of metabolite concentrations and simultaneously construct its mathematical model. Firstly, regression functions are fitted to experimental data by the locally estimated scatter plot smoothing method. Secondly, the fitted result is analysed by the bivariate Granger causality test to determine which
TY - JOUR. T1 - From genomes to in silico cells via metabolic networks. AU - Borodina, Irina. AU - Nielsen, Jens. PY - 2005. Y1 - 2005. N2 - Genome-scale metabolic models are the focal point of systems biology as they allow the collection of various data types in a form suitable for mathematical analysis. High-quality metabolic networks and metabolic networks with incorporated regulation have been successfully used for the analysis of phenotypes from phenotypic arrays and in gene-deletion studies. They have also been used for gene expression analysis guided by metabolic network structure, leading to the identification of commonly regulated genes. Thus, genome-scale metabolic modeling currently stands out as one of the most promising approaches to obtain an in silico prediction of cellular function based on the interaction of all of the cellular components. AB - Genome-scale metabolic models are the focal point of systems biology as they allow the collection of various data types in a form ...
Herein, autotrophic metabolism of Cupriavidus necator H16 growing on CO2, H2 and O2 gas mixture was analyzed by metabolic pathway analysis tools, specifically elementary mode analysis (EMA) and flux balance analysis (FBA). As case studies, recombinant strains of C. necator H16 for the production of short-chain (isobutanol) and long-chain (hexadecanol) alcohols were constructed and examined by a combined tools of EMA and FBA to comprehensively identify the cells metabolic flux profiles and its phenotypic spaces for the autotrophic production of recombinant products. The effect of genetic perturbations via gene deletion and overexpression on phenotypic space of the organism was simulated to improve strain performance for efficient bioconversion of CO2 to products at high yield and high productivity. EMA identified multiple gene deletion together with controlling gas input composition to limit phenotypic space and push metabolic fluxes towards high product yield, while FBA identified target gene
Powerful approach to design cells with optimized metabolic functionalities is to apply the metabolic pathway analysis tool to analyze cellular metabolism and elucidate interaction of cell genotype and phenotype as outlined in the recent review (4). A metabolic network describing a cellular metabolism typically contains hundreds to thousands of reactions catalyzed by functional enzymes to convert feed substrates into precursor metabolites used to synthesize cell components for growth or other metabolites secreted to extracellular environments. These functional enzymes are directly encoded by functional genes that determine cell phenotypes. By using elementary mode analysis as the metabolic pathway analysis tool, a metabolic network can be decomposed into unique pathways, each of which contains a minimal set of enzymatic reactions supporting cell functions (5). Each of these independent pathways can represent a physiological state of cell operation. The knowledge of these pathways allows the ...
Fingerprint Dive into the research topics of Non-linear reduction for kinetic models of metabolic reaction networks. Together they form a unique fingerprint. ...
Oxygen is thought to promote species and biomolecule diversity. Previous studies have suggested that oxygen expands metabolic networks by acquiring metabolites with different chemical properties (higher hydrophobicity, for example). However, such conclusions are typically based on biased evaluation, and are therefore non-conclusive. Thus, we re-investigated the effect of oxygen on metabolic evolution using a phylogenetic comparative method and metadata analysis to reduce the bias as much as possible. Notably, we found no difference in metabolic network expansion between aerobes and anaerobes when evaluating phylogenetic relationships. Furthermore, we showed that previous studies have overestimated or underestimated the degrees of differences in the chemical properties (e.g., hydrophobicity) between oxic and anoxic metabolites in metabolic networks of unicellular organisms; however, such overestimation was not observed when considering the metabolic networks of multicellular organisms. These findings
In this PhD, we present some algorithms and complexity results for two general problems that arise in the analysis of a metabolic network: the search for elementary modes of a network and the search for minimal precursors sets. Elementary modes is a common tool in the study of the cellular characteristic of a metabolic network. An elementary mode can be seen as a minimal set of reactions that can work in steady state independently of the rest of the network. It has therefore served as a mathematical model for the possible metabolic pathways of a cell. Their computation is not trivial and poses computational challenges. We show that some problems, like checking consistency of a network, finding one elementary mode or checking that a set of reactions constitutes a cut are easy problems, giving polynomial algorithms based on LP formulations. We also prove the hardness of central problems like finding a minimum size elementary mode, finding an elementary mode containing two given reactions, counting the
A minimal cut set is a minimal set of reactions whose inactivation would guarantee a failure in a certain network function or functions. Minimal cut sets (MCSs) were initially developed from the metabolic pathway analysis method (MPA) of elementary modes (EMs); they provide a way of identifying target genes for eliminating a certain objective function from a holistic perspective that takes into account the structure of the whole metabolic network. The concept of MCSs is fairly new and still being explored and developed; the initial concept has developed into a generalized form and its similarity to other network characterizations are discussed. MCSs can be used in conjunction with other constraints-based methods to get a better understanding of the capability of metabolic networks and the interrelationship between metabolites and enzymes/genes. The concept could play an important role in systems biology by contributing to fields such as metabolic and genetic engineering where it could assist in finding
Metabolic networks are extensively regulated to facilitate tissue-specific metabolic programs and robustly maintain homeostasis in response to dietary changes. Homeostatic metabolic regulation is achieved through metabolite sensing coupled to feedback regulation of metabolic enzyme activity or expression. With a wealth of transcriptomic, proteomic, and metabolomic data available for different cell types across various conditions, we are challenged with understanding global metabolic network regulation and the resulting metabolic outputs. Stoichiometric metabolic network modeling integrated with omics data has addressed this challenge by generating nonintuitive, testable hypotheses about metabolic flux rewiring. Model organism studies have also yielded novel insight into metabolic networks. This review covers three topics: the feedback loops inherent in metabolic regulatory networks, metabolic network modeling, and interspecies studies utilizing Caenorhabditis elegans and various bacterial ...
As most of the uses of plants are intimately linked to their metabolic output or activity, there is a renewed interest in understanding the behavior and regulation of plant metabolic networks. The only direct measure of metabolic activity, and the facet most closely related to biological function, is flux through the metabolic network (Libourel and Shachar-Hill, 2008). There has been a considerable research effort in the last few years to develop and refine methods that allow fluxes in large metabolic networks to be determined. The best established of these methods, steady-state metabolic flux analysis (MFA), involves measuring the redistribution of a supplied stable isotope, usually 13C, at metabolic and isotopic steady state (Ratcliffe and Shachar-Hill, 2006; Allen et al., 2009a). Flux maps of a range of heterotrophic plant cells and tissues have been produced, providing information on the operation of different flux modes (Sriram et al., 2004, 2007; Schwender et al., 2006; Allen et al., ...
In the post-genomic era, the biochemical information for individual compounds, enzymes, reactions to be found within named organisms has become readily available. The well-known KEGG and BioCyc databases provide a comprehensive catalogue for this information and have thereby substantially aided the scientific community. Using these databases, the complement of enzymes present in a given organism can be determined and, in principle, used to reconstruct the metabolic network. However, such reconstructed networks contain numerous properties contradicting biological expectation. The metabolic networks for a number of organisms are reconstructed from KEGG and BioCyc databases, and features of these networks are related to properties of their originating database.
p,Metabolic network rewiring is the rerouting of metabolism through the use of alternate enzymes to adjust pathway flux and accomplish specific anabolic or catabolic objectives. Here, we report the first characterization of two parallel pathways for the breakdown of the short chain fatty acid propionate in Caenorhabditis elegans. Using genetic interaction mapping, gene co-expression analysis, pathway intermediate quantification and carbon tracing, we uncover a vitamin B12-independent propionate breakdown shunt that is transcriptionally activated on vitamin B12 deficient diets, or under genetic conditions mimicking the human diseases propionic- and methylmalonic acidemia, in which the canonical B12-dependent propionate breakdown pathway is blocked. Our study presents the first example of transcriptional vitamin-directed metabolic network rewiring to promote survival under vitamin deficiency. The ability to reroute propionate breakdown according to B12 availability may provide C. elegans with ...
incollection{2087361, abstract = {Metabolism can be defined as the complete set of chemical reactions that occur in living organisms in order to maintain life. Enzymes are the main players in this process as they are responsible for catalyzing the chemical reactions. The enzyme--reaction relationships can be used for the reconstruction of a network of reactions, which leads to a metabolic model of metabolism. A genome-scale metabolic network of chemical reactions that take place inside a living organism is primarily reconstructed from the information that is present in its genome and the literature and involves steps such as functional annotation of the genome, identification of the associated reactions and determination of their stoichiometry, assignment of localization, determination of the biomass composition, estimation of energy requirements, and definition of model constraints. This information can be integrated into a stoichiometric model of metabolism that can be used for detailed ...
Pathway Tools is a comprehensive symbolic systems biology software system that supports several use cases in bioinformatics and systems biology: *Development of organism-specific databases called Pathway/Genome Databases (PGDBs) that integrate many bioinformatics datatypes, from genomes to pathways to regulatory networks. *Development of metabolic-flux models using flux-balance analysis *Scientific visualization, web publishing, and dissemination of those organism-specific databases, including: **Automatic display of metabolic pathways and full metabolic networks; generation of metabolic map diagram and of metabolic map poster ([http://bioinformatics.ai.sri.com/posters/ecoli-metab.pdf example]). **Genome browser; comparative genome browser; generation of genome poster ([http://bioinformatics.ai.sri.com/posters/ecoli-genome.pdf example]). **Display of operons, regulons, and full transcriptional regulatory networks *Analysis of omics datasets, including painting omics data on to diagrams of the ...
Metabolic reconstruction and subsequent mathematical computation has become a useful tool in the post‐genomic era by aiding both biological computation and experimentation. In this work, we present, characterize and utilize the iAF1260 metabolic reconstruction of E. coli K‐12 MG1655. The reconstruction serves as both a BiGG database containing the current knowledge of E. coli metabolism, as well as a framework for mathematical analysis. Accordingly, the major contributions from this work are: (1) an expansion in size, scope and detail of the metabolic network of E. coli, effectively exhausting the available literature, (2) an enumeration and description of the parameters and methods needed to utilize the reconstruction as a predictive model; examples of simulation results compared with high‐throughput experimental data are presented and (3) the inclusion of thermodynamic information and a novel thermodynamic consistency analysis for chemical transformations accounted for in the ...
A mass flux balance-based stoichiometric model of Bacillus licheniformis for the serine alkaline protease (SAP) fermentation process has been established. The model considers 147 reaction fluxes, and there are 105 metabolites that are assumed to be in pseudo-steady state. Metabolic flux distributions were obtained from the solution of the model based on the minimum SAP accumulation rate assumption in B. licheniformis in combination with the off-line extracellular analyses of the metabolites that were the sole carbon source citrate, dry cell, organic acids, amino acids, and SAP; variations in the intracellular fluxes were demonstrated for the three periods of the batch bioprocess. The flux distribution maps showed that the cells completed the TCA cycle and utilized the gluconeogenesis; pathway, pentose phosphate pathway, and anaplerotic reactions throughout the fermentation; however the glycolysis pathway was inactive in all the periods of the fermentation. The flux values toward SAP increased ...
Researchers are studying whether when animals eat affects what eventually happens to what they eat. Its a reasonable question since different metabolic pathways are most active at different times of the day.
Designing and executing a workflow having flow-based and constraint-based regions. A user selects one or more activities to be part of a constraint-based region. Each constraint-based region has a constraint associated therewith. The workflow is executed by executing the flow-based region and the constraint-based region. The flow-based region executes sequentially. The constraint is evaluated, and the constraint-based region executes responsive to the evaluated constraint.
ChEBI and genome-scale metabolic reconstructions Neil Swainston Manchester Centre for Integrative Systems Biology 2 nd ChEBI User Group Workshop, EMBL-EBI, Hi…
In biochemistry, metabolic pathways are series of chemical reactions occurring within a cell. In each pathway, a principal chemical is modified by a series of chemical reactions. Enzymes catalyze these reactions, and often require dietary minerals, vitamins, and other cofactors in order to function properly. Because of the many chemicals (a.k.a. metabolites) that may be involved, metabolic pathways can be quite elaborate. In addition, numerous distinct pathways co-exist within a cell. This collection of pathways is called the metabolic network. Pathways are important to the maintenance of homeostasis within an organism. Catabolic (break-down) and Anabolic (synthesis) pathways often work interdependently to create new biomolecules as the final end-products. [Metabolic pathway. Wikipedia] |br|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
SteatoNet metabolic network.The key metabolic pathways and their regulation by hormones, adipokines and transcriptional and post-translational regulatory factor
Biochemical network reconstructions have become popular tools in systems biology. Metabolicnetwork reconstructions are biochemically, genetically, and genomically (BiGG) structured databases of biochemical reactions and metabolites. They contain information such as exact reaction stoichiometry, reaction reversibility, and the relationships between genes, proteins, and reactions. Network reconstructions have been used extensively to study the phenotypic behavior of wild-type and mutant stains under a variety of conditions, linking genotypes with phenotypes. Such phenotypic simulations have allowed for the prediction of growth after genetic manipulations, prediction of growth phenotypes after adaptive evolution, and prediction of essential genes. Additionally, because network reconstructions are organism specific, they can be used to understand differences between organisms of species in a functional context.There are different types of reconstructions representing various types of biological networks
Metabolic network showing the number of O. carboxidovorans proteins identified in each COG category in the current study.Proteins (referred by locus tag number
The availability of annotated genome sequences has enabled the reconstruction of genome-scale metabolic networks for an increasing number of microorganisms. A popular and efficient method to study the characteristics and capabilities of such large-scale biochemical networks is flux balance analysis (FBA). In this tutorial we introduce the mathematical backgrounds of FBA and related methods, and present some of its recent biological applications ranging from biotechnology to evolutionary biology. ...
Metabolism is refer to all chemical reactions that occur in living organisms, including digestion and the transport of substances into and between different cells. Metabolism is usually divided into catabolism, that breaks down organic matter and harvests energy by way of cellular respiration, and anabolism that uses energy to construct components of cells such as proteins and nucleic acids. |br|The chemical reactions of metabolism are organized into metabolic pathways, in which one chemical is transformed through a series of steps into another chemical, by a sequence of enzymes. [Metabolism. Wikipedia] |br|The biochemical pathway map example Key metabolic processes 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. Metabolic Maps
Immune cell activation and differentiation occurs concurrently with metabolic reprogramming. This ensures that activated cells generate the energy and substrates necessary to perform their specified function. Likewise, the metabolic programs among different cells of the immune system vary. By targeting different metabolic pathways, these differences allow for selective regulation of immune responses. Further, the relative susceptibility of cells to a metabolic inhibitor is dictated by their metabolic demands; cellular selectivity is based on demand. Therefore, where differences exist in metabolic pathways between healthy and pathogenic cells, there is opportunity for selective regulation with agents lacking intrinsic specificity. There are now a host of studies demonstrating how inhibitors of metabolism (e.g., glycolysis, glutamine metabolism, and fatty acid oxidation) can regulate immune responses and treat immune-mediated pathogenesis. In this brief review we detail how inhibitors of ...
Background: Constraint-based analysis of genome-scale metabolic models typically relies upon maximisation of a cellular objective function such as the rate or efficiency of biomass production. Whilst this assumption may be valid in the case of microorganisms growing under certain conditions, it is likely invalid in general, and especially for multicellular organisms, where cellular objectives differ greatly both between and within cell types. Moreover, for the purposes of biotechnological applications, it is normally the flux to a specific metabolite or product that is of interest rather than the rate of production of biomass per se. Results: An alternative objective function is presented, that is based upon maximising the correlation between experimentally measured absolute gene expression data and predicted internal reaction fluxes. Using quantitative transcriptomics data acquired from Saccharomyces cerevisiae cultures under two growth conditions, the method outperforms traditional approaches ...
Background: Constraint-based analysis of genome-scale metabolic models typically relies upon maximisation of a cellular objective function such as the rate or efficiency of biomass production. Whilst this assumption may be valid in the case of microorganisms growing under certain conditions, it is likely invalid in general, and especially for multicellular organisms, where cellular objectives differ greatly both between and within cell types. Moreover, for the purposes of biotechnological applications, it is normally the flux to a specific metabolite or product that is of interest rather than the rate of production of biomass per se. Results: An alternative objective function is presented, that is based upon maximising the correlation between experimentally measured absolute gene expression data and predicted internal reaction fluxes. Using quantitative transcriptomics data acquired from Saccharomyces cerevisiae cultures under two growth conditions, the method outperforms traditional approaches ...
De Martino, Daniele. Scales and Multimodal Flux Distributions in Stationary Metabolic Network Models via Thermodynamics. Physical Review E Statistical Nonlinear and Soft Matter Physics , vol. 95, no. 6, American Institute of Physics, 2017, p. 062419, doi:10.1103/PhysRevE.95.062419 ...
To address this challenge, the PIs propose IFPs that interface stress responsive feedback promoters with inducible timing control using RNA regulators. IFPs represent a new regulatory concept for metabolic pathway control and optimization: inducibility allows titration and timing of pathway expression to be rapidly explored, while stress responsive feedback allows autonomous expression optimization. The central objective of this proposal is to develop and validate IFPs in the context of two industrially important, yet different, metabolic pathways: terpenoid oxygenation (a critical technology for Manus Bio) and n-butanol production. This objective will be pursued in aims that validate the approach of IFP regulation, create a public resource of unique IFPs applicable to many different metabolic pathways, and fine-tune IFPs that are directly applicable for use by industry in large-scale bioprocesses ...
Metabolic networks are extensively regulated to facilitate tissue-specific metabolic programs and robustly maintain homeostasis in response to dietary changes. Homeostatic metabolic regulation is achieved through metabolite sensing coupled to feedback regulation of metabolic enzyme activity or expression. With a wealth … Continue reading →. ...
Schilling, C.H., Letscher, D., and Palsson, B.Ø (2000) Journal of Theoretical Biology, Vol. 203, 229-248, Theory for the Systemic Definition of Metabolic Pathways and their use in Interpreting Metabolic Function from a Pathway-Oriented Perspective. Papin, J.A., Price, N.D., and Palsson, B.Ø (2002) Genome Research, Vol. 12, 1889-1900, Extreme Pathway Lengths and Reaction Participation in Genome-Scale Metabolic Networks. Price, N.D., Reed, J.L., and Palsson B.Ø (2004) Nature Reviews Microbiology, Vol. 2, 886 - 897, Genome-scale models of microbial cells: evaluating the consequences of constraints. ...
Cells respond to fatty acid exposure by metabolic reorganization and proliferation of peroxisomes. Described here is the development and application of a genome-wide screen to identify nonessential yeast genes necessary for efficient metabolism of myristic and oleic acids. Comparison of the resultant fitness data set with an integrated data set of genes transcriptionally responsive to fatty acids revealed very little overlap between the data sets. Furthermore, the fitness data set enriched for genes involved in peroxisome biogenesis and other processes related to cell morphology, whereas the expression data set enriched for genes related to metabolism. These data suggest that in response to fatty acid exposure, transcriptional control is biased towards metabolic reorganization, and structural changes tend to be controlled post-transcriptionally. They also suggest that fatty acid responsive metabolic networks are more robust than those related to cell structure. Statistical analyses of these and ...
5-HTP is the intermediate metabolite between the amino acid L-tryptophan and the neurotransmitter serotonin.It is extracted from the seed of an African plant (Griffonia simplicifolia). It supports a positive mood.Capsules are gluten free, Non-GMO, nut free, soy free, and vegan. One capsule contains 100 mg 5-HTP. Product Features 5-HTP is the intermediate metabolite between the [More] ...
Vitamin B1 Thiamin is vital in many different metabolic pathways, and plays a large role in breaking down carbohydrates. It works to get the energy into a useable form as soon as possible to help you power yourself on.. Vitamin B6 is very similar. Its involved in over 100 metabolic pathways and is essential in breaking down your food into useable energy (particularly carbohydrates). Meaning its perfect to be taken on-the-go during your race.. Your Niacin level dictates how you feel, too much or too little can lead to unpleasant stuff such as diarrhoea and nausea.. Our blend of these 3 ingredients is largely responsible for how easy our stuff is on the stomach, and actually converting the fuel you take on board into real useable energy thats going to help delay fatigue and hopefully power you to a finish.. Performing At Your Best. As far as actually helping you perform, these are the ingredients that we use help you do that:. Vitamin A acts as an antioxidant during endurance training, making ...
Biological membranes constitute a chemical barrier to the environment and are thus the prerequisite for the establishment and maintenance of a controlled intracellular milieu, the cytoplasm. In eukaryotes, membranes are also responsible for the formation of chemically distinct intracellular compartments. The lipid bilayer membranes contain a great diversity of proteins that fulfill different functions and serve as an interface to the environment and between different compartments. Among these membrane proteins are receptors involved in signaling cascades and pathogen defense reactions, enzymes such as the apparatus for cell wall biosynthesis, and transporters responsible for the import and export of solutes and ions and the establishment of electrochemical gradients across membranes, thereby connecting the different metabolic pathways of the cellular compartments and organelles.
After adding core work to your daily routine, the next way you can take your fitness to the next level is to incorporate both types of cardio work: anaerobic and aerobic. Each one uses different metabolic pathways in our bodies, the first without oxygen and the second uses oxygen. I am going to explain why this is important and how to add each one to whatever kind of exercise you are currently doing.. Back in the 80s the emphasis was on aerobic exercise only. Now, research is supporting a mixture of both aerobic and anaerobic. It actually leads to more favorable effects on our hormones, including cortisol, insulin, glucagons and human growth hormone (HGH). This affects our energy levels, immune system, inflammation, as well as the way our body processes and stores sugar, protein and fat. Balancing aerobic and anaerobic training will allow your body to have more efficient metabolism.. Another reason to balance these two forms of working out is to better manage the end products of the pathways. ...
A wide range of research areas in bioinformatics, molecular biology and medicinal chemistry require precise chemical structure information about molecules and reactions, e.g. drug design, ligand docking, metabolic network reconstruction, and systems biology. Most available databases, however, treat chemical structures more as illustrations than as a datafield in its own right. Lack of chemical accuracy impedes progress in the areas mentioned above. We present a database of metabolites called BioMeta that augments the existing pathway databases by explicitly assessing the validity, correctness, and completeness of chemical structure and reaction information. The main bulk of the data in BioMeta were obtained from the KEGG Ligand database. We developed a tool for chemical structure validation which assesses the chemical validity and stereochemical completeness of a molecule description. The validation tool was used to examine the compounds in BioMeta, showing that a relatively small number of compounds
We developed a general approach for facilitating the reconstruction of plant metabolic networks from sequenced genomes or transcriptomes. Four components were created for the system: (1) PlantCyc, a pan-plant reference database of metabolic pathways and enzymes; (2) RESD, a reference enzyme sequence database containing protein sequences with literature-supported enzyme activities; (3) an enzyme sequence annotation pipeline that predicts enzyme functions from predicted protein sequences based on sequence similarity to RESD sequences; and (4) a modified pathway prediction procedure that uses both PlantCyc and MetaCyc as the reference for reconstructing single-species metabolic networks from the predicted enzymes. Using such a consensus approach will make it easier to interpret the results of cross-species metabolic comparisons. The individual components of the infrastructure can also be used on their own in a number of ways.. We applied the system to the sequenced genome of poplar (Poptr 1.1 ...
It is common to characterize metabolic models by the numbers of reactions and metabolites included, but these can be misleading measures without qualification. One reason is that there is a case during model building for adding more reactions than can be connected to the network. This will arise if a gene is annotated to an enzyme with a broad substrate range (e.g. alcohol dehydrogenase, EC 1.1.1.1), since it will not be clear while the model is incomplete as to which alcohols and aldehydes will be available by being produced or consumed by other enzymes in the network. A simple solution is to add more than is likely to be necessary and to remove at a later stage the ones that are not functional.. What criteria do we have for reactions that are non-functional? One test is where a metabolite is only involved in a single reaction in the network. In this case, the metabolite cannot reach a steady state because it is impossible to have its balanced production and consumption. Furthermore, the ...
ABSTRACT: BACKGROUND: Despite the availability of numerous complete genome sequences from E. coli strains, published genome-scale metabolic models exist only for two commensal E. coli strains. These models have proven useful for many applications, such as engineering strains for desired product formation, and we sought to explore how constructing and evaluating additional metabolic models for E. coli strains could enhance these efforts.$\backslash$n$\backslash$nRESULTS: We used the genomic information from 16 E. coli strains to generate an E. coli pangenome metabolic network by evaluating their collective 76,990 ORFs. Each of these ORFs was assigned to one of 17,647 ortholog groups including ORFs associated with reactions in the most recent metabolic model for E. coli K-12. For orthologous groups that contain an ORF already represented in the MG1655 model, the gene to protein to reaction associations represented in this model could then be easily propagated to other E. coli strain models. All ...
The PMN staff members work at the Carnegie Institution for Science in the Department of Plant Biology, located on the Stanford University campus. The PMN curators are involved in curating pathways from Arabidopsis into AraCyc, plus they also curate pathways from diverse species that can be entered into the appropriate species-specific metabolic databases, or directly into PlantCyc. In addition, all of the pathways supported by experimental evidence are entered into MetaCyc.. PMN staff members will also be involved in the generation of new species-specific metabolic pathway databases, such as PoplarCyc.. To send a general message to the PMN, please use our Feedback Form, but we also welcome messages to individual PMN staff members.. ...
The PMN staff members work at the Carnegie Institution for Science in the Department of Plant Biology, located on the Stanford University campus. The PMN curators are involved in curating pathways from Arabidopsis into AraCyc, plus they also curate pathways from diverse species that can be entered into the appropriate species-specific metabolic databases, or directly into PlantCyc. In addition, all of the pathways supported by experimental evidence are entered into MetaCyc.. PMN staff members will also be involved in the generation of new species-specific metabolic pathway databases, such as PoplarCyc.. To send a general message to the PMN, please use our Feedback Form, but we also welcome messages to individual PMN staff members.. ...
68. Reliance upon the morphologic wie sollte man kamagra einnehmen of lesions on arteri- ograms also carries known hazards. The genes for components in the RAS, b-AR systems, and lipoprotein metabolic pathways are better characterized; hence, more trans- genic animals have been produced for testing drugs targeted at these compo- nents. Med.
We built a topological map based on rCMRglc patterns measured with 18F-FDG PET. The map resampled a topology corresponding to clinical categorization and therefore can be used to rank and localize patients within this metabolic map (Figs. 2B and 2C). The Parkinson-related pattern and the dementia-related pattern are determined by metabolic changes, which are important predictors of the individual disease status and the extent of neurodegeneration (Fig. 4).. The construction of this topological map is solely based on the 2 contrast patterns derived from the AD , CON and PD , CON comparisons, with no statistical correction for clinical scores or severity of symptoms. However, the topological features PCcog and PCmot, representing each patients position on the metabolic map, were clearly influenced by the severity of cognitive and motor deficits as shown by our correlation analysis (Fig. 3).. The SPM group comparisons showed the typical and well-described metabolic characteristics (Fig. 1; ...
Cyclic dinucleotides (CDNs) of bacterial and host origin mediate cytosolic immune responses through the stimulator of interferon genes (STING) signaling pathway, though evidence suggests alternative receptors exist. We identified the oxidoreductase RECON as a high-affinity host receptor specific for bacterial CDNs. RECONs enzyme activity was inhibited by bacterial CDNs, which bound in the substrate and cosubstrate sites. During bacterial infection of macrophages, RECON antagonized STING activation by acting as a molecular sink for CDNs. In hepatocytes, RECON negatively regulated NF-kappaB activation via its enzymatic activity. Loss of RECON resulted in increased NF-kappaB activation and reduced bacterial survival. Therefore, CDN inhibition of RECON promotes a proinflammatory, antibacterial state. We investigated the molecular pathways by which RECON controls inflammation and found that several branches of the arachidonic acid inflammatory cascade were involved. At the top of the cascade, free ...
Bacillus megaterium is a microorganism widely used in industrial biotechnology for production of enzymes and recombinant proteins, as well as in bioleaching processes. Precise understanding of its metabolism is essential for designing engineering strategies to further optimize B. megaterium for biotechnology applications. Here, we present a genome-scale metabolic model for B. megaterium DSM319, iJA1121, which is a result of a metabolic network reconciliation process. The model includes 1709 reactions, 1349 metabolites, and 1121 genes. Based on multiple-genome alignments and available genome-scale metabolic models for other Bacillus species, we constructed a draft network using an automated approach followed by manual curation. The refinements were performed using a gap-filling process. Constraint-based modeling was used to scrutinize network features. Phenotyping assays were performed in order to validate the growth behavior of the model using different substrates. To verify the model accuracy,
NYU Abu Dhabi faculty member Kourosh Salehi-Ashtiani, has played a leading role in a noteworthy scientific achievement with the development of the first genome-scale metabolic model of an algal species. A four-year collaborative project supported by 11 experts from a range of international institutions has yielded an interpretive and predictive model that will act as a significant resource in the investigation of algaes potential as a source for biofuel and clean energy.. Most options for biofuel production utilize human or animal food resources, but algae are microorganisms that can be found abundantly in various environments, such as soil or water, and can be cultivated on non-agricultural lands. When nitrogen is removed from the media of these organisms they typically react by accumulating starch and generating lipids, the latter can then be processed into clean fuel.. Unlike conventional maps on the metabolic process, the genome-scale metabolic network of Clamydomonas reinhardtii was ...
BACKGROUND: Infections with Salmonella cause significant morbidity and mortality worldwide. Replication of Salmonella typhimurium inside its host cell is a model system for studying the pathogenesis of intracellular bacterial infections. Genome-scale modeling of bacterial metabolic networks provides a powerful tool to identify and analyze pathways required for successful intracellular replication during host-pathogen interaction.. RESULTS: We have developed and validated a genome-scale metabolic network of Salmonella typhimurium LT2 (iRR1083). This model accounts for 1,083 genes that encode proteins catalyzing 1,087 unique metabolic and transport reactions in the bacterium. We employed flux balance analysis and in silico gene essentiality analysis to investigate growth under a wide range of conditions that mimic in vitro and host cell environments. Gene expression profiling of S. typhimurium isolated from macrophage cell lines was used to constrain the model to predict metabolic pathways that ...
Steady-state (13)C metabolic flux analysis (MFA) is currently the experimental method of choice for generating flux maps of the compartmented network of primary metabolism in heterotrophic and mixotrophic plant tissues. While statistically robust protocols for the application of steady-state MFA to plant tissues have been developed by several research groups, the implementation of the method is still far from routine. The effort required to produce a flux map is more than justified by the information that it contains about the metabolic phenotype of the system, but it remains the case that steady-state MFA is both analytically and computationally demanding. This article provides an overview of principles that underpin the implementation of steady-state MFA, focusing on the definition of the metabolic network responsible for redistribution of the label, experimental considerations relating to data collection, the modelling process that allows a set of metabolic fluxes to be deduced from the labelling
Metabolic flux analysis (MFA) plays a central role in metabolic engineering and systems biology [1]. Metabolic fluxes most closely reflect the underlying metabolic phenotype, whereas other omics approaches only yield a sense of metabolic capacities (transcriptomics/proteomics) or thermodynamic driving forces (metabolomics). Metabolic flux analysis is particular important in rational strain engineering, where we specifically seek to manipulate the metabolic phenotype.. Due to the high complexity of the examined metabolic network, flux analysis typically involves the use of a stoichiometric model, in which the metabolic reactions available to the cell are parameterized before the fluxes are estimated from experimental data [2]. State-of-art flux analysis today includes the use of stable isotopes to overcome problems such as incomplete resolution of important cellular pathways or the need to rely on stoichiometric parameters with high uncertainty such as ATP yield (Yx/ATP) or P/O ratio which are ...
TY - JOUR. T1 - Computational Flux Balance Analysis Predicts that Stimulation of Energy Metabolism in Astrocytes and their Metabolic Interactions with Neurons Depend on Uptake of K+ Rather than Glutamate. AU - DiNuzzo, Mauro. AU - Giove, Federico. AU - Maraviglia, Bruno. AU - Mangia, Silvia. PY - 2017/1/1. Y1 - 2017/1/1. N2 - Brain activity involves essential functional and metabolic interactions between neurons and astrocytes. The importance of astrocytic functions to neuronal signaling is supported by many experiments reporting high rates of energy consumption and oxidative metabolism in these glial cells. In the brain, almost all energy is consumed by the Na+/K+ ATPase, which hydrolyzes 1 ATP to move 3 Na+ outside and 2 K+ inside the cells. Astrocytes are commonly thought to be primarily involved in transmitter glutamate cycling, a mechanism that however only accounts for few % of brain energy utilization. In order to examine the participation of astrocytic energy metabolism in brain ion ...
Genome-scale metabolic models (GEMs) allow predicting metabolic phenotypes from limited data on uptake and secretion fluxes by defining the space of all the feasible solutions and excluding physio-chemically and biologically unfeasible behaviors. The integration of additional biological information in genome-scale models, e.g., transcriptomic or proteomic profiles, has the potential to improve phenotype prediction accuracy. This is particularly important for metabolic engineering applications where more accurate model predictions can translate to more reliable model-based strain design. Here we present a GEM with Enzymatic Constraints using Kinetic and Omics data (GECKO) model of Bacillus subtilis, which uses publicly available proteomic data and enzyme kinetic parameters for central carbon (CC) metabolic reactions to constrain the flux solution space. This model allows more accurate prediction of the flux distribution and growth rate of wild-type and single-gene/operon deletion strains compared to a
Implementing light‐regulated constraints and basic environmental exchange constraints (Supplementary Table S6) yielded photoautotrophic, heterotrophic, and mixotrophic models from iRC1080. We simulated various growth conditions (Supplementary Table S7) and all gene knockouts for which phenotypes have been published and are assessable in our network (Supplementary Table S8) to validate the predictive ability of the models. All 30 validations involving environmental parameters displayed very close agreement with experimental results (Supplementary Table S7). Of particular note is the ability of our photosynthetic model in sunlight to accurately recapitulate O2‐PAR (photosynthetically active radiation) energy conversion efficiency, predicting an efficiency of 2% compared with the experimental result (Greenbaum, 1988) of 1.3-4.5%. Of the 14 gene knockouts simulated, 7 were partially or completely validated relative to experimental results (Supplementary Table S8). The unconfirmed gene knockout ...
Genome-Scale reconstruction of the transcriptional and translational machinery in Escherichia coli: A knowledge-database and its mathematical formulation, 1st Bioinfo Expo, San Diego, February 2009, Ines Thiele, Neema Jamshidi, Ronan M.T. Fleming, and Bernhard Ø. Palsson. Genome-Scale reconstruction of the transcriptional and tr anslational machinery in Escherichia coli: A knowledge-database and its mathematical formulation, 16th Annual International Conference on Microbial Genomes, Lake Arrowhead, September 2008, Ines Thiele, Neema Jamshidi, Ronan M.T. Fleming, and Bernhard Ø. Palsson. From Network to Function: Systematic annotation of gene function using metabolic network reconstructions., Workshop on the Biological Annotation of Novel Proteins, San Diego, March 2008, Ines Thiele and Bernhard Ø. Palsson.. Genome-Scale reconstruction of the transcriptional and translational machinery in Escherichia coli: A knowledge-database and its mathematical formulation, ICSB 2007, Long Beach, ...
The metabolic fluxes through the central carbon pathways were calculated for the genus Bacillus separately for the enzymes serine alkaline protease (SAP), neutral protease (NP) and alpha -amylase (AMY) on five carbon sources that have different reduction degrees (gamma), to determine the theoretical ultimate limits of the production capacities of Bacillus species and to predict the selective substrate for the media design. Glucose (gamma = 4.0), acetate (gamma = 4.0), and the TCA cycle organic-acids succinate (gamma = 3.5), malate (gamma = 3.0), and citrate (gamma = 3.0) were selected for the theoretical analyses and comparisons. A detailed mass flux balance-based general stoichiometric model based on the proposed metabolic reaction network starting with the alternative five carbon sources for the synthesis of each enzyme in Bacillus licheniformis that simulates the behaviour of the metabolic pathways with 107 metabolites and 150 reaction fluxes is developed. Highest and lowest specific cell ...
Drug side effects cause a significant clinical and economic burden. However, mechanisms of drug action underlying side effect pathogenesis remain largely unknown. Here, we integrate pharmacogenomic and clinical data with a human metabolic network and find that non-pharmacokinetic metabolic pathways dysregulated by drugs are linked to the development of side effects. We show such dysregulated metabolic pathways contain genes with sequence variants affecting side effect incidence, play established roles in pathophysiology, have significantly altered activity in corresponding diseases, are susceptible to metabolic inhibitors and are effective targets for therapeutic nutrient supplementation. Our results indicate that metabolic dysregulation represents a common mechanism underlying side effect pathogenesis that is distinct from the role of metabolism in drug clearance. We suggest that elucidating the relationships between the cellular response to drugs, genetic variation of patients and cell ...
Yeasts degrade glucose through different metabolic pathways, where the choice of the pathway is dependent on the nature of the limitation in the various substrates. When oxygen is limiting in addn. to glucose, yeasts often grow according to a mixt. of oxidative and reductive metab. Oxygen may be limiting either by supply or by inherent biol. restrictions such as the respiratory bottleneck in Saccharomyces cerevisiae or by both. A unified model incorporating both supply and biol. limitations is proposed for the quant. prediction of growth rates, consumption and prodn. rates, as well as key metabolite concns. during mixed oxidoreductive metab. occurring as a result of such oxygen limitations. This simple unstructured model can be applied to different yeast strains while at the same time requiring a min. no. of measured parameters. Estimators are utilized in order to predict the presence of supply-side or biol. limitations. The values of these estimators also characterize the relative importance of ...
QT: looked at the entire human metabolic network and found that concentrations of about 10 percent of the bodys 2,763 metabolites could be used to determine the levels of all the rest.. http://www.scientificamerican.com/article.cfm?id=influential-few-predict-behavior. ...
In this article, we combine multi-level profiling methods with bioinformatic and theoretical modeling approaches to characterize the molecular repertoire of C. reinhardtii under reference conditions. We analyzed and integrated (i) a combination of database resources, such as existing genome annotations from JGI v3.1, EST collections, six-frame translation of the genomic sequence, protein domain scanning, and pathway annotation information; (ii) systematic high-resolution shotgun proteomics for high-throughput protein identification; (iii) systematic metabolite profiling and projection of identified metabolites to the reconstructed metabolic draft network in Chlamydomonas on the basis of existing gene annotation; and (iv) structural modeling of the reconstructed metabolic network to identify minimum extension pathways on the basis of the presence of identified metabolites.. MapMan classification of the predicted Chlamydomonas protein set and comparison with other organisms yielded information for ...
TY - JOUR. T1 - Whole-body metabolic map with positron emission tomography of a man after running [3]. AU - Fujimoto, T.. AU - Itoh, M.. AU - Kumano, H.. AU - Tashiro, M.. AU - Ido, T.. N1 - Copyright: Copyright 2021 Elsevier B.V., All rights reserved.. PY - 1996. Y1 - 1996. UR - http://www.scopus.com/inward/record.url?scp=0030055711&partnerID=8YFLogxK. UR - http://www.scopus.com/inward/citedby.url?scp=0030055711&partnerID=8YFLogxK. U2 - 10.1016/S0140-6736(05)65572-9. DO - 10.1016/S0140-6736(05)65572-9. M3 - Letter. C2 - 8684213. AN - SCOPUS:0030055711. VL - 348. SP - 266. JO - The Lancet. JF - The Lancet. SN - 0140-6736. IS - 9022. ER - ...
We analyzed the carbon fluxes in the central metabolism ofGeobacter metallireducens strain GS-15 using 13C isotopomer modeling.Acetate labeled in the 1st or 2nd position was the sole carbon source,and Fe-NTA was the sole terminal electron acceptor. The measured labeledacetate uptake rate was 21 mmol/gdw/h in the exponential growth phase.The resulting isotope labeling pattern of amino acids allowed an accuratedetermination of the in vivo global metabolic reaction rates (fluxes)through the central metabolic pathways using a computational isotopomermodel. The tracer experiments showed that G. metallireducens containedcomplete biosynthesis pathways for essential metabolism, and this strainmight also have an unusual isoleucine biosynthesis route (usingacetyl-CoA and pyruvate as the precursors). The model indicated that over90 percent of the acetate was completely oxidized to CO2 via a completetricarboxylic acid (TCA) cycle while reducing iron. Pyruvate carboxylaseand phosphoenolpyruvate carboxykinase were
Read Integrated bioinformatics to decipher the ascorbic acid metabolic network in tomato, Plant Molecular Biology on DeepDyve, the largest online rental service for scholarly research with thousands of academic publications available at your fingertips.
Division of Cardiovascular Medicine Professor of Clinical Medicine State University of New York Downstate Medical Center Brooklyn, NY, ...
The utility of flux balance models depends on the extent to which realistic flux distributions can be predicted from them. While the biomass constraint has proved effective in predicting fluxes in microbes (Feist and Palsson, 2010), it is less clear whether this constraint provides sufficient bounds for flux prediction in more complex organisms such as plants. Even though it has been previously shown that there is significant agreement in the flux predictions for heterotrophic plant metabolism and those estimated by 13C-MFA (Williams et al., 2010; Hay and Schwender, 2011), certain fluxes, such as those in the central pathways of glycolysis, the TCA cycle, and particularly the OPPP, were not well matched.. The main issue is that these central pathways, in addition to providing carbon skeletons for the synthesis of biomass components, are also the main routes for energy transformation. Although synthesis of biomass consumes energy, there are other substantial energy drains in the cell, including ...
Introduction to methods for modeling and analyzing biological networks such as genetic regulatory networks, metabolic networks, and signal transduction networks. A particular emphasis will be given to methods inspired by models used by engineers for circuit analysis. Other topics include: stochastic analysis using Monte Carlo methods, differential equation models, Bayesian network models, flux balance analysis, learning methods, pathway databases, and synthesized gene ...
Within bioprocesses, organic compounds are converted by either isolated enzymes or whole-cell biocatalysts. Biotransformations can be differentiated into enzymatic and metabolic bioconversions. A bioprocess is based on a biological catalyst that is used to conduct a chemical reaction leading to a defined product. In the early times of bioprocess engineering, water was used principally for the reaction medium, because it was assumed that a higher stability and activity can be reached in the natural medium of enzymes. Metabolic bioconversions need the metabolic system of living and growing microorganisms, e.g., bacteria, yeasts, or fungi. A goal of systems biology is predictive metabolic engineering, where genes within metabolic pathways are purposefully amplified or deleted based on the consideration of the metabolic network as an entirety. Microreaction technology is an interdisciplinary field combining natural science and engineering. Bioprocess engineering must focus on downstream processing in
The Csr system was recently demonstrated to be a major controller of upper glycolysis fluxes (16), but its involvement in metabolic adaptation is less clear in the literature. CsrA is known to positively regulate glycolytic genes and negatively regulate gluconeogenic genes (15, 16). A study of the BarA/UvrY two-component system during the metabolic switch suggested that the Csr system is crucial for efficient adaptation between different metabolic pathways (2). Here, we showed that gene expression in the CCM (glycolysis, gluconeogenesis, the pentose phosphate pathway, and the tricarboxylic acid cycle) did not present strong discrepancies between the Csr system mutants during the acetate consumption phase, in deep contrast to the situation during glucose consumption. It will be awkward to totally rule out any control of these genes by CsrA, since regulation could be at the posttranscriptional level. The control by CsrA could also be counterbalanced by its higher sequestration by CsrB, since the ...
Therapeutic proteins development becomes more challenging due to the complexity of the diverse molecule formats. In-depth characterization of high producer cell lines and bioprocesses is essential to ensure robust and consistent production of recombinant therapeutic proteins in high quantity and quality for clinical applications. Controlling the environmental stress present during the cultivation of cells is a key for the successful production of an intended bio-therapeutic protein. The captured data is applied in a metabolic network model for the analysis of intracellular metabolic fluxes of Roches working horse of therapeutic protein production - the Chinese Hamster Ovary cell. The generated metabolic information has the potential to set a new standard for efficient and innovative process development bridging from research to market. Innovative approach of analyzing the stored data is key towards process development of therapeutic proteins 2.0. In conclusion, the combination of quantitative
Kotte, Oliver; Volkmer, Benjamin; Radzikowski, Jakub L; Heinemann, Matthias (2014). Phenotypic bistability in Escherichia colis central carbon metabolism. Molecular Systems Biology, 10:736.. Zampar, Guillermo G; Kümmel, Anne; Ewald, Jennifer; Jol, Stefan; Niebel, Bastian; Picotti, Paola; Aebersold, Ruedi; Sauer, Uwe; Zamboni, Nicola; Heinemann, Matthias (2013). Temporal system-level organization of the switch from glycolytic to gluconeogenic operation in yeast. Molecular Systems Biology, 9:online.. Jol, Stefan J; Kümmel, Anne; Terzer, Marco; Stelling, Jörg; Heinemann, Matthias (2012). System-Level Insights into Yeast Metabolism by Thermodynamic Analysis of Elementary Flux Modes. PLoS Computational Biology, 8(3):e1002415.. Huberts, Daphne H E W; Niebel, Bastian; Heinemann, Matthias (2011). A flux-sensing mechanism could regulate the switch between respiration and fermentation. FEMS Yeast Research, 12(2):118-128.. Costenoble, Roeland; Picotti, Paola; Reiter, Lukas; Stallmach, Robert; ...
The effect can be explained; as the yeast being facultative anaerobes can produce energy using two different metabolic pathways. While the oxygen concentration is low, the product of glycolysis, pyruvate, is turned into ethanol and carbon dioxide, and the energy production efficiency is low (2 moles of ATP per mole of glucose). If the oxygen concentration grows, pyruvate is converted to acetyl CoA that can be used in the citric acid cycle, which increases the efficiency to 32 moles of ATP per mole of glucose. Therefore, about 16 times as much glucose must be consumed anaerobically as aerobically to yield the same amount of ATP.[2]. Under anaerobic conditions, the rate of glucose metabolism is faster, but the amount of ATP produced (as already mentioned) is smaller. When exposed to aerobic conditions, the ATP and Citrate production increases and the rate of glycolysis slows, because the ATP and citrate produced act as allosteric inhibitors for phosphofructokinase 1, the third enzyme in the ...
Tuberculosis is a notorious disease responsible for the deaths of 1.4 million people worldwide. A third of the worlds population is infected with Mycobacterium tuberculosis, the bacterium causing the disease. The increase of multi drug-resistant strains worsens the situation, and the World Health Organization has declared tuberculosis to be a global emergency. The bacterium envelopes itself with a unique set of very long-chain lipids that play an important role in virulence and drug resistance. Therefore enzymes involved in lipid metabolism are putative drug targets. To allow entry into different metabolic pathways and transmembrane transport, fatty acids have to be activated. This is done primarily by fatty acyl-CoA synthetases (ACSs). We identified an ACS possibly involved in the bacteriums virulence and solved its structure. Structural interpretation combined with previously reported data gives us insights into the details of its function. This enzyme is known to harbor lipid substrates ...
L-arginine and L-citrulline are chemically related amino acids, and they are frequently converted back and forth in your cells. However, the conversion from L-arginine to L-citrulline requires a different metabolic pathway than the conversion from L-citrulline to L-arginine. The conversion of citrulline to arginine utilizes a pathway that first produces ornithine. The arginine-to-citrulline conversion is more direct and produces a molecule of nitric oxide. One of nitric oxides many effects is to dilate your arteries, which improves blood flow to exercising muscles. It is believed that supplementation with L-citrulline increases arginine synthesis, which in turn enhances nitric oxide production.. Considerations. Supplementation with L-citrulline malate could improve exercise performance through two mechanisms. By facilitating removal of ammonia from exercising muscles, citrulline enhances cellular metabolism, improves energy production and extends exercise times. By increasing nitric oxide ...
Montana State University. My work here is part of a broader ongoing careful study of Escherichia coli metabolism intended to improve predictive interpretation of biological networks. In this position I worked with a doctoral student providing my expertise in microbiology and proteomics. This project includes characterization of overflow metabolism, protein expression and biomass composition of cells grown in chemostats under iron, carbon and nitrogen limitation. In addition, I worked with another graduate student on efforts to improve the labs computational capability for the calculation of the elementary flux mode set for biological networks. Several papers from this work are in preparation. I also managed lab inventory by ordering supplies. Dr. Philip Stewart, Center for Biofilm Engineering June 2007 - June 2009 ...
The structure of N-linked glycosylation is a very important quality attribute for therapeutic monoclonal antibodies. Different carbon sources in cell culture media, such as mannose and galactose, have been reported to have different influences on the glycosylation patterns. Accurate prediction and control of the glycosylation profile are important for the process development of mammalian cell cultures. In this study, a mathematical model, that we named Glycan Residues Balance Analysis (GReBA), was developed based on the concept of Elementary Flux Mode (EFM), and used to predict the glycosylation profile for steady state cell cultures. Experiments were carried out in pseudo-perfusion cultivation of antibody producing Chinese Hamster Ovary (CHO) cells with various concentrations and combinations of glucose, mannose and galactose. Cultivation of CHO cells with mannose or the combinations of mannose and galactose resulted in decreased lactate and ammonium production, and more matured glycosylation ...
Deluxe Revised RECON® RPG - RECON is set in a fictional world that parallels that of 20th Century Earth and focuses on the realistic military combat
Author SummaryCellular systems comprise many diverse components and component interactions spanning signal transduction, transcriptional regulation, and metabolism. Although signaling, metabolic, and regulatory activities are often investigated independently of one another, there is growing evidence that considerable interplay occurs among them, and that the malfunctioning of this interplay is associated with disease. The computational analysis of integrated networks has been challenging because of the varying time scales involved as well as the sheer magnitude of such systems (e.g., the numbers of rate constants involved). To this end, we developed a novel computational framework called integrated dynamic flux balance analysis (idFBA) that generates quantitative, dynamic predictions of species concentrations spanning signaling, regulatory, and metabolic processes. idFBA extends an existing approach called flux balance analysis (FBA) in that it couples
MetaCyc has been designed for multiple types of uses. It is often used as an extensive online encyclopedia of metabolism. In addition, MetaCyc is used as a reference data set for computationally predicting the metabolic network of organisms from their sequenced genomes; it has been used to perform pathway predictions for thousands of organisms, including those in the BioCyc Database Collection. MetaCyc is also used in metabolic engineering and metabolomics research. MetaCyc includes mini reviews for pathways and enzymes that provide background information as well as relevant literature references. It also provides extensive data on individual enzymes, describing their subunit structure, cofactors, activators and inhibitors, substrate specificity, and, when available, kinetic constants. MetaCyc data on metabolites includes chemical structures, predicted Standard energy of formation, and links to external databases. Reactions in MetaCyc are presented in a visual display that includes the ...
Scientists from Pacific Northwest National Laboratory (PNNL) and the University of California-San Diego (UCSD) have completed the most advanced genome-scale metabolic model for a microbe in the domain Archaea, one of the three domains of life on Earth.
Herrgard, M. J., Swainston, N., Dobson, P., Dunn, W. B., Arga, K. Y., Arvas, M., Bluthgen, N., Borger, S., Costenoble, R., Heinemann, M., Hucka, M., Le Novere, N., Li, P., Liebermeister, W., Mo, M. L., Oliveira, A. P., Petranovic, D., Pettifer, S., Simeonidis, E., Smallbone, K., Spasic, I., Weichart, D., Brent, R., Broomhead, D. S., Westerhoff, H. V., Kirdar, B., Penttila, M., Klipp, E., Palsson, B. O., Sauer, U., Oliver, S. G., Mendes, P., Nielsen, J., Kell, D. B. (2008). A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology. Nat Biotechnol 26:1155-1160.18846089 ...
Herrgard, M. J., Swainston, N., Dobson, P., Dunn, W. B., Arga, K. Y., Arvas, M., Bluthgen, N., Borger, S., Costenoble, R., Heinemann, M., Hucka, M., Le Novere, N., Li, P., Liebermeister, W., Mo, M. L., Oliveira, A. P., Petranovic, D., Pettifer, S., Simeonidis, E., Smallbone, K., Spasic, I., Weichart, D., Brent, R., Broomhead, D. S., Westerhoff, H. V., Kirdar, B., Penttila, M., Klipp, E., Palsson, B. O., Sauer, U., Oliver, S. G., Mendes, P., Nielsen, J., Kell, D. B. (2008). A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology. Nat Biotechnol 26:1155-1160.18846089 ...
Estimation of fluxes through metabolic networks from redistribution patterns of (13)C has become a well developed technique in recent years. However, the approach is currently limited to systems at metabolic steady-state; dynamic changes in metabolic fluxes cannot be assessed. This is a major impediment to understanding the behaviour of metabolic networks, because steady-state is not always experimentally achievable and a great deal of information about the control hierarchy of the network can be derived from the analysis of flux dynamics. To address this issue, we have developed a method for estimating non-steady-state fluxes based on the mass-balance of mass isotopomers. This approach allows multiple mass-balance equations to be written for the change in labelling of a given metabolite pool and thereby permits over-determination of fluxes. We demonstrate how linear regression methods can be used to estimate non-steady-state fluxes from these mass balance equations. The approach can be used to
TY - CHAP. T1 - Control of Metabolism by Dynamic Macromolecular Interactions. AU - Keleti, T.. AU - OvÁdi, J.. PY - 1988/1/1. Y1 - 1988/1/1. N2 - This chapter discusses the control of metabolism by dynamic macromolecular interactions. Metabolic pathways are controlled and directed by pacemaker, bottleneck, and key enzymes. In general, no single enzyme is responsible for the control of a whole metabolic pathway. In pursuing the pacemaker theory, attempts are made to quantify metabolic regulation, and one studies each enzyme in a sequence separately in situ, determines its kinetic properties in the greatest possible detail and accuracy, and then seeks to determine how it works when it is in the intact cell. In prokaryotes and in eukaryotes the largest macrocompartment is the cytoplasm, containing quantities of soluble enzymes and is full of membranes associated with a great variety of organelles. A theoretical analysis of glycolysis in human erythrocytes has been provided, implicitly assuming ...
The explosive growth of microbiome research has yielded great quantities of data. These data provide us with many answers, but raise just as many questions. 16S rDNA-the backbone of microbiome analyses-allows us to assess α-diversity, β-diversity, and microbe-microbe associations, which characterize the overall properties of an ecosystem. However, we are still unable to use 16S rDNA data to directly assess the microbe-microbe and microbe-environment interactions that determine the broader ecology of that system. Thus, properties such as competition, cooperation, and nutrient conditions remain insufficiently analyzed. Here, we apply predictive community metabolic models of microbes identified with 16S rDNA data to probe the ecology of microbial communities. We developed a methodology for the large-scale assessment of microbial metabolic interactions (MMinte) from 16S rDNA data. MMinte assesses the relative growth rates of interacting pairs of organisms within a community metabolic network and whether
We studied the steady-state responses to changes in growth rate of yeast when ethanol is the sole source of carbon and energy. Analysis of these data, together with data from studies where glucose was the carbon source, allowed us to distinguish a universal growth rate response (GRR) common to all media studied from a GRR specific to the carbon source. Genes with positive universal GRR include ribosomal, translation, and mitochondrial genes, and those with negative GRR include autophagy, vacuolar, and stress response genes. The carbon source-specific GRR genes control mitochondrial function, peroxisomes, and synthesis of vitamins and cofactors, suggesting this response may reflect the intensity of oxidative metabolism. All genes with universal GRR, which comprise 25% of the genome, are expressed periodically in the yeast metabolic cycle (YMC). We propose that the universal GRR may be accounted for by changes in the relative durations of the YMC phases. This idea is supported by oxygen ...
Table 18a. Drug Interactions Between Protease Inhibitors and Other Drugs. This table provides known or predicted information regarding PK interactions between PIs and non-ARV drugs. When information is available, interactions for specific PK-boosted (with either RTV or COBI) and unboosted ATV are listed separately. The term All PIs refers to both unboosted ATV and PIs boosted with either RTV or COBI, except the PIs noted below. For interactions between ARV agents and for dosing recommendations, refer to Tables 18c, 19a, and 19b. Recommendations for managing a particular drug interaction may differ depending on whether a new ARV drug is being initiated in a patient on a stable concomitant medication or if a new concomitant medication is being initiated in a patient on a stable ARV regimen. The magnitude and significance of drug interactions are difficult to predict when several drugs with competing metabolic pathways are prescribed concomitantly. Note: Fosamprenavir (FPV), indinavir (IDV), ...
TY - JOUR. T1 - Regulation of bacterial metabolism by small RNAs using diverse mechanisms. AU - Bobrovskyy, Maksym. AU - Vanderpool, Carin K.. PY - 2013/11. Y1 - 2013/11. N2 - Bacteria live in many dynamic environments with alternating cycles of feast or famine that have resulted in the evolution of mechanisms to quickly alter their metabolic capabilities. Such alterations often involve complex regulatory networks that modulate expression of genes involved in nutrient uptake and metabolism. A great number of protein regulators of metabolism have been characterized in depth. However, our ever-increasing understanding of the roles played by RNA regulators has revealed far greater complexity to regulation of metabolism in bacteria. Here, we review the mechanisms and functions of selected bacterial RNA regulators and discuss their importance in modulating nutrient uptake as well as primary and secondary metabolic pathways.. AB - Bacteria live in many dynamic environments with alternating cycles of ...
Metabolic alterations relevant to postprandial dyslipidemia were previously identified in the intestine of obese insulin-resistant subjects. The aim of the study was to identify the genes deregulated by systemic insulin resistance in the intestine of severely obese subjects. Transcripts from duodenal samples of insulin-sensitive (HOMA-IR | 3, n = 9) and insulin-resistant (HOMA-IR | 7, n = 9) obese subjects were assayed by microarray (Illumina HumanHT-12). A total of 195 annotated genes were identified as differentially expressed between these two groups (Fold change | 1.2). Of these genes, 36 were found to be directly involved in known intestinal functions, including digestion, extracellular matrix, endocrine system, immunity and cholesterol metabolism. Interestingly, all differentially expressed genes (n = 8) implicated in inflammation and oxidative stress were found to be upregulated in the intestine of insulin-resistant compared to insulin-sensitive subjects. Metabolic pathway analysis revealed that
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"Text mining for metabolic pathways, signaling cascades, and protein networks". Science Signaling. 2005 (283): pe21. doi:10.1126 ... Even metabolic networks can be considered as molecular interaction networks: metabolites, i.e. chemical compounds in a cell, ... Network structure and topology[edit]. Interaction networks can be analyzed using the tools of graph theory. Network properties ... Network properties[edit]. Protein interaction networks can be analyzed with the same tool as other networks. In fact, they ...
Biological pathways, metabolic pathways, and gene interaction networks are available. The tool was initially released in 2007. ... "Software aids pathway analysis and life sciences research". news.thomasnet.com. "MTB Europe -". mtbeurope.info. "Sigma-Aldrich ... The tool allows users to search for genes, protein, function, disease, species, tissue, or pathway and match them with 150,000 ... a repository of biological and chemical networks that is the largest database of its kind. ...
"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. ...
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 a key intermediate in several metabolic pathways throughout the cell. Pyruvic acid ... Therefore, it unites several key metabolic processes. In glycolysis, phosphoenolpyruvate (PEP) is converted to pyruvate by ...
Bioinformatics including phylogenetic trees, protein-protein interaction networks, and metabolic pathways. In addition, the ... Cytoscape, open-source software for visualizing molecular interaction networks Gephi, open-source network analysis and ... A drawing of a graph or network diagram is a pictorial representation of the vertices and edges of a graph. This drawing should ... Graphs and graph drawings arising in other areas of application include Sociograms, drawings of a social network, as often ...
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 & ...
... 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 ...
More complex reactions are involved in metabolic pathways and metabolic networks in biological systems. The transition to order ... 3.0.CO;2-F. Askadskii, A. A. (1990). "Influence of crosslinking density on the properties of polymer networks". Polymer Science ... It is known that an important metabolic cycle, glycolysis, displays temporal order. Glycolysis consists of the degradation of ... In 1995 Stuart Kauffman proposed that life initially arose as autocatalytic chemical networks. British ethologist Richard ...
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 syste 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 ...
Metabolic pathway Cytoscape Computational genomics Metabolic network modelling Protein-protein interaction prediction MEROPS ... PMAP is to aid the protease researchers in reasoning about proteolytic networks and metabolic pathways. PMAP was originally ... 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 ...
"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. ...
... enables visualization of metabolic pathways and molecular interaction networks captured in the transcriptome. In addition to ... "KEGG PATHWAY Database". Transrate: understand your transcriptome assembly. http://hibberdlab.com/transrate Li B; et al. (2014 ...
... including metabolic networks, cell signaling pathways, regulatory networks, infectious diseases, and many others. It has been ... Examples of phenomena that have been modeled in this way include gene regulatory networks and signaling pathways, basing the ... bionet.metabolic-reg. "ANNOUNCEMENT: Portable Metabolic Binary Standard". Retrieved 13 December 2010. Kell, D. B.; Mendes, P. ( ... some members of these groups also had discussed the creation of a portable file format for metabolic network models in the ...
... 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* ...
... 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 ...
... such as metabolic pathways and gene regulatory networks. Evolutionary trees, ecological networks, and hierarchical clustering ... Grandjean, Martin (2015). "Social network analysis and visualization: Moreno's Sociograms revisited". Redesigned network ... and the subject that expresses and understands the real-world systems as a network is called network science. In computer ... notably through the use of social network analysis software. Under the umbrella of social networks are many different types of ...
... several important enzymatic cascades and signal transduction cascades participate in metabolic pathways or signaling networks, ... wiring diagrams of interaction networks and reaction networks (KEGG PATHWAY), and ontologies for pathway reconstruction (BRITE ... Pathway building has been performed by individual groups studying a network of interest (e.g., immune signaling pathway) as ... For example, 'pathway' can denote a metabolic pathway involving a sequence of enzyme-catalyzed reactions of small molecules, or ...
Metabolic flux refers to the rate of flow of metabolites through a biochemical network, along a linear metabolic pathway, or ... Metabolic control analysis and flux balance analysis provide frameworks for understanding metabolic fluxes and their ... and the presence of metabolic activators or repressors. Metabolic flux in biologic systems can refer to biosynthesis rates of ... as well as the flow of intermediary metabolites through pathways. ...
... where the genes encode components of a metabolic pathway or network, developmental pathway, signalling pathway or transcription ... This occurs when genes do not interact with each other, for example by acting through different metabolic pathways. Simply, ... "Prevalent positive epistasis in Escherichia coli and Saccharomyces cerevisiae metabolic networks". Nature Genetics. 42 (3): 272 ... penicillin is of no use to a fungus without the enzymes that synthesize the necessary precursors in the metabolic pathway. Just ...
... signal transduction networks, and metabolic pathways. Probabilistic graphical models, a machine learning technique for ... The most commonly used methods are radial basis function networks, deep learning, Bayesian classification, decision trees, and ... and genetic network induction. This technology is especially useful for monitoring the expression of genes within a genome, ... which relies on the machine learning model of artificial neural networks to achieve an accuracy of approximately 84% when ...
... exchange and reuse of information about signaling pathways, metabolic networks, and gene regulatory networks amongst ... It can be used to show all the molecular interactions taking place in a network of biochemical entities, with the same entity ... The SBGN Activity Flow (AF) language depicts the flow of information between biochemical entities in a network. It omits ... Using these three notations, a life scientist can represent in an unambiguous way networks of interactions (for example ...
... cell-signaling pathways, regulatory networks, infectious diseases, and many others. COPASI is based on the Gepasi simulation ... software application for creating and solving mathematical models of biological processes such as metabolic networks, ... COPASI (COmplex PAthway SImulator) is an open-source ... metabolic control analysis, computation of Lyapunov exponent, ... a COmplex PAthway SImulator". Bioinformatics. 22 (24): 3067-3074. doi:10.1093/bioinformatics/btl485. PMID 17032683. Mendes, P ...
... identification of involved gene regulatory networks and metabolic pathways, and by informing models of how tumors grow and ...
Metabolic networks can vary in scope from those describing a single pathway, up to the cell, tissue or organism. The main ... Extending this idea to metabolic networks, it is possible to represent a metabolic network as a stoichiometry balanced set of ... The related method of Metabolic pathway analysis seeks to find and list all possible pathways between metabolites. FBA finds ... In addition to constraints applied at the edges of a metabolic network, constraints can be applied to reactions deep within the ...
... a metabolic pathway database for representation and analysis of correlation networks of gene co-expression and metabolite co- ... KaPPA-View4' is a metabolic pathway database containing data about metabolic regulation from 'omics' data. Metabolic pathway ...
... 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, ... biochemical and metabolic data approximately 1100 bacterial and archaeal organisms. ChemAxon Pathway Solutions KoriLog INRIA ( ... values to the gene names and IDs Identify co-expressed genes and visually analyze the reactions and metabolic pathways in which ...
Metabolic Pathway Databases (KEGG, BioCyc), Interaction Analysis Databases, Functional Networks Used in design of synthetic ... Network analysis seeks to understand the relationships within biological networks such as metabolic or protein-protein ... At a more integrative level, it helps analyze and catalogue the biological pathways and networks that are an important part of ... Although biological networks can be constructed from a single type of molecule or entity (such as genes), network biology often ...
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 ...
It is possible to use network analyses to infer how selection acts on metabolic pathways. Signals are transduced within cells ... Signaling networks typically integrate protein-protein interaction networks, gene regulatory networks, and metabolic networks. ... Thus, all compounds in a cell are parts of an intricate biochemical network of reactions called a metabolic network. ... A biological network is any network that applies to biological systems. A network is any system with sub-units that are linked ...
... more so than energy flow pathways. Functional webs have compartments, which are sub-groups in the larger network where there ... The energy ingested is utilized for metabolic processes and transformed into biomass. The energy flow continues on its path if ... Food webs are complex networks. As networks, they exhibit similar structural properties and mathematical laws that have been ... "Ecological networks, especially mutualistic networks, are generally very heterogeneous, consisting of areas with sparse links ...
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 ...
Multiple additional regulatory pathways integral to cell cycle regulation and involving both phospho signaling pathways and ... The genetic network logic responds to signals received from the environment and from internal cell status sensors to adapt the ... The "housekeeping" metabolic and catabolic subsystems provide the energy and the molecular raw materials for protein synthesis ... The phosphosignaling network monitors the state of progression of the cell cycle and plays an essential role in accomplishing ...
... neurotransmitter pathway, metabolic pathway, blood flow, or other), and a radionuclide (usually either a gamma-emitter or a ... The Church also established a network of cathedral schools and universities where medicine was studied. The Schola Medica ...
The foundation provides a support network and source of hope for the families of patients with Coffin-Lowry Syndrome.[citation ... RSK2 is involved at the distal end of the Ras/MAPK signaling pathway. Mutations in the RPS6KA3 disturb the function of the ... Metabolic. *Amino acid: Ornithine transcarbamylase deficiency. *Oculocerebrorenal syndrome. *Dyslipidemia: Adrenoleukodystrophy ... The protein is involved in cell signaling pathways that are required for learning, the formation of long-term memories, and the ...
The first pathway is through an internal medicine pathway leading to an Internal Medicine/Nephrology specialty, and sometimes ... The Renal Support Network (RSN) is a nonprofit, patient-focused, patient-run organization that provides non-medical services to ... and metabolic diseases (diabetes, cystinosis). ... The training pathway is overseen and accredited by the Royal ... known as "adult nephrology". The second pathway is through Pediatrics leading to a speciality in Pediatric Nephrology. In the ...
Metabolic network. *Metabolic supermice. *Polygene. References[edit]. *^ a b Paaby, Annalise B.; Rockman, Matthew V. (2016-11- ... "Transcriptome Profiling of Peripheral Blood in 22q11.2 Deletion Syndrome Reveals Functional Pathways Related to Psychosis and ...
amyloid precursor protein metabolic process. • neutrophil degranulation. • regulation of canonical Wnt signaling pathway. • ... "Functional gamma-secretase complex assembly in Golgi/trans-Golgi network: interactions among presenilin, nicastrin, Aph1, Pen-2 ... Wnt signaling pathway[edit]. Wnt signaling pathway has been shown to be involved in several critical steps in embryogenesis and ... canonical Wnt signaling pathway. • dorsal/ventral neural tube patterning. • neural retina development. • positive regulation of ...
Most of the metabolic pathways, which are the object of the majority of an organism's genes, are common between Archaea and ... Yonkers, NY: Mindspark Interactive Network. Associated Press. Retrieved 2015-10-20.. *^ Bell, Elizabeth A.; Boehnike, Patrick; ... Romano A; Conway T (1996). "Evolution of carbohydrate metabolic pathways". Res Microbiol. 147 (6-7): 448-55. doi:10.1016/0923- ... Many basic metabolic pathways are shared between all forms of life; for example, archaea use a modified form of glycolysis (the ...
Multiple pathways for the conversion of different biofuel feedstocks are being used. In the next few years, the cost data of ... Metabolic Engineering. 49: 153-163. doi:10.1016/j.ymben.2018.08.004. PMID 30107263.. ... Quantum network. *Quantum neural network. *Quantum optics. *Quantum programming. *Quantum sensing. *Quantum simulator ...
This step is only one of the central metabolic pathway carried out by eukaryotes, in which glucose is oxidized to form carbon ... 2006). "Global, in vivo, and site-specific phosphorylation dynamics in signaling networks". Cell. 127 (3): 635-48. doi:10.1016/ ... glucose metabolic process. • pyruvate metabolic process. • regulation of acetyl-CoA biosynthetic process from pyruvate. • ... Interactive pathway mapEdit. Click on genes, proteins and metabolites below to link to respective articles. [§ 1] ...
Romano A, Conway T (1996). "Evolution of carbohydrate metabolic pathways". Res Microbiol 147 (6-7): 448-55. PMID 9084754. doi: ... "The net of life: reconstructing the microbial phylogenetic network". Genome Res. 15 (7): 954-9. PMC 1172039. PMID 15965028 ... A fifth pathway of carbon fixation". Science 318 (5857): 1732-3. PMID 18079388. doi:10.1126/science.1152209.. ... "A 3-hydroxypropionate/4-hydroxybutyrate autotrophic carbon dioxide assimilation pathway in Archaea". Science 318 (5857): 1782-6 ...
... have been implanted for a decade or two will usually have attachments to the patient's body at various places in the pathway ... that detect changes in the patient's physical activity and automatically adjust the pacing rate to fulfill the body's metabolic ... the patient transmitting their pacemaker data using an at-home transmitter connected to their geographical cellular network. ...
White HB (Mar 1976). "Coenzymes as fossils of an earlier metabolic state". Journal of Molecular Evolution. 7 (2): 101-4. ... One of the challenges posed by the RNA world hypothesis is to discover the pathway by which an RNA-based system transitioned to ... A research project completed in March 2015 by the Sutherland group found that a network of reactions beginning with hydrogen ... The hypothesized existence of an RNA world does not exclude a "Pre-RNA world", where a metabolic system based on a different ...
... particularly through the metabolic pathways of protein catabolism. In a 2012 study conducted by the University of Texas ... R. Kang, H. J. Zeh, M. T. Lotze, and D. Tang, 'The Beclin 1 Network Regulates Autophagy and Apoptosis', Cell Death Differ, 18 ( ... Process and pathways[edit]. There are four pathways of autophagy and these are mediated by the autophagy-related genes and ... The increase in metabolic energy is offset by autophagy functions. These metabolic stresses include hypoxia, nutrient ...
... particularly through the metabolic pathways of protein catabolism. In a 2012 study conducted by the University of Texas ... "The Beclin 1 network regulates autophagy and apoptosis". Cell Death and Differentiation. 18 (4): 571-80. doi:10.1038/cdd. ... The increase in metabolic energy is offset by autophagy functions. These metabolic stresses include hypoxia, nutrient ... Liu Y, Bassham DC (2012). "Autophagy: pathways for self-eating in plant cells". Annual Review of Plant Biology. 63: 215-37. doi ...
Typically, biologics do not target metabolic pathways like anti-viral drugs, but stimulate immune cells such as lymphocytes, ... "The generation of influenza outbreaks by a network of host immune responses against a limited set of antigenic types" ...
Metabolic pathway. *Metabolic network. *Primary nutritional groups. Energy. metabolism. Aerobic respiration. *Glycolysis → ... disorders of lipid glycosylation and disorders of other glycosylation pathways and of multiple glycosylation pathways. No ... NetNGlyc: The NetNglyc server predicts N-glycosylation sites in human proteins using artificial neural networks that examine ...
Major metabolic pathways in metro-style map. Click any text (name of pathway or metabolites) to link to the corresponding ... Glycolysis is a metabolic pathway that takes place in the cytosol of cells in all living organisms. Glycolysis can be literally ... Single lines: pathways common to most lifeforms. Double lines: pathways not in humans (occurs in e.g. plants, fungi, ... Metabolic network. *Primary nutritional groups. Energy. metabolism. Aerobic respiration. *Glycolysis → Pyruvate decarboxylation ...
displaystyle \mathrm {Metabolic\ Rate} =70M^{0.75}}. where M. {\displaystyle M}. is body mass, and metabolic rate is measured ... The morphology for heat exchange occurs via cerebral arteries and the ophthalmic rete, a network of arteries originating from ... continuing through the conducting pathway of the heart the bundle of his shows the highest amount of these purkinje fibers.[71] ... the metabolic rate in a resting, unfed bird, that is producing heat is known as the standard metabolic rate (SMR) or resting ...
Robergs, R; Ghiasvand, F; Parker, D (2004). "Biochemistry of exercise-induced metabolic acidosis". Am J Physiol Regul Integr ... In another take on the argument, Andrikou and Arnone use the newly available data on gene regulatory networks to look at how ... Besides surrounding each fascicle, the perimysium is a pathway for nerves and the flow of blood within the muscle. The ... Through their analysis, Andrikou and Arnone found that there were conserved orthologues of the gene regulatory network in both ...
metabolic pathway. PRIAM. profile. PDB structures. RCSB PDB PDBe PDBsum. Gene Ontology. AmiGO / QuickGO. ... "Chromatin Network". Retrieved 1 March 2012.. *^ a b Kouzarides T (February 2007). "Chromatin modifications and their function ... The methylation of histone lysine has an important role in choosing the pathway for repairing DNA double-strand breaks.[21] As ... while dimethylated H4K20 can recruit the 53BP1 protein for repair by the pathway of non-homologous end joining. ...
... s perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, ... "Characterization and prediction of protein interfaces to infer protein-protein interaction networks". Current Pharmaceutical ... can conserve energy by taking up the amino acids from their surroundings and downregulating their biosynthetic pathways. ... and digestive/metabolic enzymes obtained from slaughterhouses. In the 1950s, the Armour Hot Dog Co. purified 1 kg of pure ...
hyaluronan metabolic process. • positive regulation of natural killer cell differentiation. • regulation of T cell ... In rodent lymphocytes, IL-15 prevents apoptosis by inducing BCL2L1/BCL-x(L), an inhibitor of the apoptosis pathway.[10] In ... Maślińska D (2001). "The cytokine network and interleukin-15 (IL-15) in brain development". Folia Neuropathologica. 39 (2): 43- ... Signaling pathway of IL-15 begins with binding to IL-15Rα receptor, with subsequent presentation to surrounding cells bearing ...
The glucose that enters the fat cells in this manner is converted into triglycerides (via the same metabolic pathways as are ... Inhibitory neurons using GABA, make compensating changes in the neuronal networks preventing runaway levels of excitation.[61] ... The metabolic rate is increased, initially by non-shivering thermogenesis,[32] followed by shivering thermogenesis if the ... The metabolic processes of all organisms can only take place in very specific physical and chemical environments. The ...
intrinsic apoptotic signaling pathway. • cellular senescence. • positive regulation of reactive oxygen species metabolic ... "Towards a proteome-scale map of the human protein-protein interaction network". Nature. 437 (7062): 1173-8. doi:10.1038/ ... intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator. • mitotic cell cycle arrest. • cellular ... cytokine-mediated signaling pathway. • negative regulation of vascular smooth muscle cell proliferation. ...
... the choroidal network, which supplies the choroid and the outer retina, and the retinal network, which supplies the retina's ... In the transfer of visual signals to the brain, the visual pathway, the retina is vertically divided in two, a temporal (nearer ... This is considered to enhance metabolic rate of the pecten, thereby exporting more nutritive molecules to meet the stringent ... The bifurcations and other physical characteristics of the inner retinal vascular network are known to vary among individuals,[ ...
Drugs that increase GABA activity alleviate muscle stiffness caused by a lack of GABAergic tone.[2] They increase pathways that ... The excessive firing of motor neurons may be caused by malfunctions in spinal and supra-segmental inhibitory networks that ... These deaths are usually caused by metabolic acidosis or an autonomic crisis.[37] ...
Idiotype Network theory, proposed by Jerne, wherein a network of antibodies capable of neutralizing self-reactive antibodies ... the attack on cells may be the consequence of cycling metabolic processes necessary to keep the blood chemistry in homeostasis. ... Autoreactive B cells in spontaneous autoimmunity are seen as surviving because of subversion both of the T cell help pathway ... Jerne N (1974). "Towards a network theory of the immune system". Ann Immunol. Paris. 125C (1-2): 373-89. PMID 4142565.. ...
The metabolic network is described as a weighted graph in which all the compounds are included, but each compound is assigned a ... An approach is presented for computing meaningful pathways in the network of small molecule metabolism comprising the chemical ... Inferring meaningful pathways in weighted metabolic networks J Mol Biol. 2006 Feb 10;356(1):222-36. doi: 10.1016/j.jmb.2005.09. ... The metabolic network is described as a weighted graph in which all the compounds are included, but each compound is assigned a ...
Rational suggestion of specific metabolic pathways as candidates for real pathway wil.. ... Development of metabolomics has made completion of metabolic map an important issue. ... Concept of chemical reaction as atom network leads us to concept of metabolic network as atom network. In the atom network ... Strategy for Exploring Metabolic Pathways: Generation of Hypothetical Metabolic Network Jun Ohta* Graduate School of Medicine, ...
A Global Coexpression Network Approach for Connecting Genes to Specialized Metabolic Pathways in Plants. Jennifer H. Wisecaver ... A Global Coexpression Network Approach for Connecting Genes to Specialized Metabolic Pathways in Plants ... A Global Coexpression Network Approach for Connecting Genes to Specialized Metabolic Pathways in Plants ... A Global Coexpression Network Approach for Connecting Genes to Specialized Metabolic Pathways in Plants ...
Nuclear magnetic resonance-based metabolomics and metabolic pathway networks from patient-matched esophageal carcinoma, ... Our study revealed a significant number of altered metabolites and metabolic pathway networks in EC patient urine and tumor ... Nuclear magnetic resonance-based metabolomics and metabolic pathway networks from patient-matched esophageal carcinoma, ... Nuclear magnetic resonance-based metabolomics and metabolic pathway networks from patient-matched esophageal carcinoma, ...
Barley Grain Maturation and Germination: Metabolic Pathway and Regulatory Network Commonalities and Differences Highlighted by ... Barley Grain Maturation and Germination: Metabolic Pathway and Regulatory Network Commonalities and Differences Highlighted by ... Barley Grain Maturation and Germination: Metabolic Pathway and Regulatory Network Commonalities and Differences Highlighted by ... Barley Grain Maturation and Germination: Metabolic Pathway and Regulatory Network Commonalities and Differences Highlighted by ...
2007). Linking metabolic QTL with network and cis-eQTL controlling biosynthetic pathways. PLoS Genet. 3: e162. ... Network Quantitative Trait Loci Mapping of Circadian Clock Outputs Identifies Metabolic Pathway-to-Clock Linkages in ... Network Quantitative Trait Loci Mapping of Circadian Clock Outputs Identifies Metabolic Pathway-to-Clock Linkages in ... Network Quantitative Trait Loci Mapping of Circadian Clock Outputs Identifies Metabolic Pathway-to-Clock Linkages in ...
Poly-pathway model, a novel approach to simulate multiple metabolic states by reaction network-based model-Application to amino ...
Technology Networks is an internationally recognised publisher that provides access to the latest scientific news, products, ... 3.4 Metabolic Pathway Builder software.. Genostars IOGMA(R) 3.4 Metabolic Pathway Builder is a new package that integrates ... "With IOGMA 3.4 Metabolic Pathway Builder in our labs, our research teams now have access to improved tools and data that allow ... Merial Selects Genostars IOGMA Metabolic Pathway Builder Bioinformatics Software News Apr 21, 2008 ...
Technology Networks is an internationally recognised publisher that provides access to the latest scientific news, products, ... we didnt have enough information about how to tap into the reverse metabolic pathway without disrupting the pathways that were ... Researchers Identify Key Mechanism in Metabolic Pathway that Fuels Cancers News May 23, 2014 ... has taken a significant step in cracking the code of an atypical metabolic pathway that allows certain cancerous tumors to ...
According to the high conservation of primary metabolic reactions in Streptomyces species, the metabolic network model of ... As the lower production in bio-fermentation, global metabolic analysis is required to further explore its biosynthetic network ... To achieve this goal, an engineering approach guided by a metabolic network model was implemented to better understand ... ascomyceticus showed that the general metabolic network model of Streptomyces species could be used to analyze the ...
National Plant Diagnostic Network by University of Florida: an excellent example of on-line training, monitoring organisation ... A web site designed to provide links to information on metabolic pathways in potato (Solanum tuberosum) including disease ... To provide molecular and biochemical information on metabolic pathways in potato (Solanum tuberosum), Arabidopsis signaling ... National Plant Diagnostic Network by University of Florida: an excellent example of on-line training, monitoring organisation ...
... potential targets and pathways involved in these effects have not been systematically investigated. Here, we proposed a novel ... Metabolic pathway analysis. The potential metabolic pathway was analysed by using MetPA. Potential biological roles were ... a metabolic network related to anti-HCC through MetScape based on the metabolites belonging to six metabolic pathways that were ... System-wide assembly of pathways and modules hierarchically reveal metabolic mechanism of cerebral ischemia. Sci rep 5, 17068 ( ...
To achieve this, the biophysical, evolutionary and physiological constraints that act on those networks need to be identified ... One of the challenging tasks in systems biology is to understand how molecular networks give rise to emergent functionality and ... whether universal design principles apply to molecular networks. ... Optimal Gene Expression in Un-branched Metabolic Pathways. The ... Together these networks form, what we will call, the metabolic regulatory network (MRN, Figure 1). This complex network ...
Minimal cut sets (MCSs) were initially developed from the metabolic pathway analysis method (MPA) of elementary modes (EMs); ... a certain objective function from a holistic perspective that takes into account the structure of the whole metabolic network. ... used in conjunction with other constraints-based methods to get a better understanding of the capability of metabolic networks ... The concept could play an important role in systems biology by contributing to fields such as metabolic and genetic engineering ...
Pathway Analyses. Pathway analyses identified multiple pathways related to amino acid, triglyceride, and sugar and carbohydrate ... Metabolic Networks and Metabolites Underlie Associations Between Maternal Glucose During Pregnancy and Newborn Size at Birth. ... Metabolic Networks and Metabolites Underlie Associations Between Maternal Glucose During Pregnancy and Newborn Size at Birth ... Metabolic Networks and Metabolites Underlie Associations Between Maternal Glucose During Pregnancy and Newborn Size at Birth ...
It serves as a high-quality reference on known metabolic pathways, enzymes, and reactions. ... Metacyc allows scientists to search and analyze metabolic pathways. ... or metabolic network of an organism, instead consult the organism-specific pathway/genome database (PGDB). ... MetaCyc Metabolic Pathway Database. MetaCyc is a curated database of experimentally elucidated metabolic pathways from all ...
Pathway Analysis and Network Visualization. Sixteen miRTarBase identifiers served as input to the Pathway Finder bioinformatics ... Pathway analysis revealed metabolic regulatory roles for miR-122, including regulation of IR pathways (AMPK, target of ... A gene list from the "insulin signaling" pathway was used to perform a selection within the complete miRNA gene target network ... In addition, in pathway analyses, miR-122 appeared to target PRKAB1, a member of the AMPK pathway, a regulator of IR in muscle ...
SteatoNet metabolic network.The key metabolic pathways and their regulation by hormones, adipokines and transcriptional and ... pcbi-1003993-g002: SteatoNet metabolic network.The key metabolic pathways and their regulation by hormones, adipokines and ... pcbi-1003993-g002: SteatoNet metabolic network.The key metabolic pathways and their regulation by hormones, adipokines and ... Steatosis Network) in a systematic workflow (Fig. 1) to form a closed multi-pathway metabolic network (Fig. 2). The dynamics of ...
The metabolic network model of Chlamydomonas was updated based on the genome annotation data and sensitivity analysis revealed ... The metabolic network model of Chlamydomonas was updated based on the genome annotation data and sensitivity analysis revealed ... Our updated metabolic network was compared to previous model and it showed more consistent results once considering the ... In this present study, flux balance analysis (FBA) was performed to identify sensitive metabolic pathways of Chlamydomonas ...
Pathway discovery in metabolic networks by subgraph extraction.. par Faust, Karoline ;Dupont, Pierre;Callut, Jérôme;van Helden ... Predicting metabolic pathways by sub-network extraction. par Faust, Karoline , van Helden, Jacques Publication 2012 ... Metabolic pathfinding using RPAIR annotation. par Faust, Karoline , Croes, Didier , van Helden, Jacques Publication 2009-05 ... In response to Can sugars be produced from fatty acids? A test case for pathway analysis tools. par Faust, Karoline , Croes, ...
Metabolic pathways (2). * Biochemical networks (1). Date ​ Choose a date option to show results from those dates only. * Today ... A new ESI-LC/MS approach for comprehensive metabolic profiling of phytocannabinoids in Cannabis *Paula Berman ... Rights & permissionsfor article Network-based prediction of human tissue-specific metabolism . Opens in a new window. ... Rights & permissionsfor article A new ESI-LC/MS approach for comprehensive metabolic profiling of phytocannabinoids in ,i, ...
Conference Paper: DMPFinder - Finding differentiating pathways with gaps from two groups of metabolic networks. *Show simple ... DMPFinder - Finding differentiating pathways with gaps from two groups of metabolic networks. en_US. ... DMPFinder - Finding differentiating pathways with gaps from two groups of metabolic networks. ... In this paper, we formulate the DMP (Differentiating Metabolic Pathway) problem for finding conserved pathways exist in first ...
... an automatic genome annotation and pathway reconstruction server. ... Metabolic Network Model of a Human Oral Pathogen � ‡ by Varun ... Biological pathways contain complex pathway structure information. For example, a metabolic pathway in KEGG can be natural... ... ched pathways. Many groups have developed pathway analysis tools relative to annotation and identification. These tools include ... KAAS: an automatic genome annotation and pathway reconstruction server. (2007) by Y Moriya, M Itoh, S Okuda, Yoshizawa AC, M ...
A Unified Resource of Plant Metabolic Pathway Databases: The Plant Metabolic Network. We applied this computational pipeline to ... Ubiquitous Plant Pathways. CVP. Common Viridiplantae Pathways. NPP. Non-PMN Pathways. AIPP. Accept-If-Predicted Pathways. CAPP ... Partial Clustering of Metabolic Pathways. To determine how many of the metabolic pathways in our databases contained clustered ... Metabolic pathways partially encoded by clustered genes. The percentage of metabolic pathways with at least two reactions ...
... we extract the union of all metabolic pathways from KEGG, and then find all-to-all pairwise network alignments between species ... Note that all of the metabolic networks that we align are derived from a mix of experimentally obtained data and network ... The most common methods for such network comparisons are network alignments.. Network alignment is the problem of finding ... topological similarity of metabolic pathways combining global network properties, such as the diameter and clustering ...
... gene expression and gene regulatory networks; deduction of metabolic pathways; micro-array design and analysis; proteomics; ...
Metabolic Networks and Pathways Substances * Archaeal Proteins * Bacterial Proteins * Acetyltransferases * Lysine Grant support ... pathways associated with central metabolism and stress responses. Intriguingly, specific acetylated lysine residues map to ...
Natural and synthetic metabolic pathways need to retain stability when faced against random changes in gene expression levels ... From the themed collection: Integrative Approaches for Signalling and Metabolic Networks Integr. Biol., 2015,7, 837-837. http ... From the themed collection: Integrative Approaches for Signalling and Metabolic Networks Integr. Biol., 2015,7, 838-838. http ... From the themed collection: Integrative Approaches for Signalling and Metabolic Networks The article was first published on 22 ...
Metabolic pathway analyses further revealed relationships between complex networks of metabolites. Seventeen CRC patients ... and showed networks for metabolic pathway aberrations. In addition, we found differences between the CRC and stool metabolomes ... Metabolic pathway analysis revealed significant perturbations of short-chain fatty acid metabolism, fructose, mannose, and ... Stool metabolite profiles were limited for direct associations with CRC and adjacent mucosa, yet metabolic pathways were ...
Expression of individual metabolic pathways in tumors. The biochemical pathways defined in the KEGG database (see for pathway ... Metabolic pathways without significant expression changes are primarily clustered on the left of the figure. Pathways that are ... Heterogeneity of tumor-induced gene expression changes in the human metabolic network.. Hu J1, Locasale JW, Bielas JH, ... Although expression changes of some metabolic pathways (e.g., upregulation of nucleotide biosynthesis and glycolysis) are ...
  • For the sake of comparison, paths are computed also in the un-weighted raw (all compounds and reactions) and filtered (highly connected pool metabolites removed) metabolic graphs, respectively. (nih.gov)
  • We then show that the average distance between pairs of metabolites is significantly larger in the weighted graph than in the raw unfiltered graph, suggesting that the small-world properties previously reported for metabolic networks probably result from irrelevant shortcuts through pool metabolites. (nih.gov)
  • Metabolite dependent network is generated from a given set of metabolites based on stoichiometry. (omicsonline.org)
  • Hypothetical metabolites and BRPs are considered to appear in BRP-dependent and metabolite-dependent networks, respectively. (omicsonline.org)
  • In most of those studies, metabolic network is defined as network of metabolites connected via enzyme reactions [ 1 - 3 ], where each reaction is decomposed and reduced to set of binary relationships between a pair of substrate and product, for example, substrate-product relationships. (omicsonline.org)
  • RPAIR in KEGG describes pattern of chemical transformation between a pair of substrate and product in enzyme reactions [ 6 ], which may be used for prediction of pathways including hypothetical metabolites. (omicsonline.org)
  • ascomyceticus showed that the general metabolic network model of Streptomyces species could be used to analyze the intracellular metabolism and predict the potential key limiting steps for target metabolites overproduction. (biomedcentral.com)
  • MCSs can be used in conjunction with other constraints-based methods to get a better understanding of the capability of metabolic networks and the interrelationship between metabolites and enzymes/genes. (mdpi.com)
  • Maternal metabolites and metabolic networks underlying associations between maternal glucose during pregnancy and newborn birth weight and adiposity demand fuller characterization. (diabetesjournals.org)
  • We performed metabolomics analysis using mass spectrometry validating the modulation of carbon dioxide responsive pathways and metabolites. (frontiersin.org)
  • Rahnuma represents metabolic networks as hypergraphs and computes all possible pathways between two or more metabolites. (ox.ac.uk)
  • Cytoscape Pathway Classification Network view of CRC versus adjacent mucosa metabolites. (biomedcentral.com)
  • Metabolites and metabolic pathways are represented by nodes with a numeric pathway impact score for ( a ) lipid ( b ) carbohydrate ( c ) amino acid and ( d ) cofactors and vitamin metabolism. (biomedcentral.com)
  • Red nodes represent metabolites and pathways with higher expression in CRC (p ≤ 0.05). (biomedcentral.com)
  • Even metabolic networks can be considered as molecular interaction networks: metabolites, i.e. chemical compounds in a cell, are converted into each other by enzymes , which have to bind their substrates physically. (wikipedia.org)
  • There are 12 key metabolites and they are all in the glycolytic pathway and the TCA cycle. (igem.org)
  • These results predict that artemisinin sensitive and resistant parasites differentially utilize scavenging and biosynthetic pathways for multiple essential metabolites, including folate and polyamines. (biomedcentral.com)
  • In fact, in addition to the Warburg effect, other alterations in the synthesis of nucleotides, amino acids, and lipids ( 5 ), mutations in metabolic genes, and accumulations of key metabolites ( 6 ) have been reported. (aacrjournals.org)
  • Pathways are required for the maintenance of homeostasis within an organism and the flux of metabolites through a pathway is regulated depending on the needs of the cell and the availability of the substrate. (wikipedia.org)
  • Given that genes comprising SM pathways exhibit environmentally dependent coregulation, we hypothesized that genes within a SM pathway would form tight associations (modules) with each other in coexpression networks, facilitating their identification. (plantcell.org)
  • Network biology offers a promising alternative for identifying SM pathways and their constituent genes. (plantcell.org)
  • And it was found that metabolic reactions are more highly conserved than the enzymes themselves because of its lower diversity of metabolic functions than that of genes. (biomedcentral.com)
  • they provide a way of identifying target genes for eliminating a certain objective function from a holistic perspective that takes into account the structure of the whole metabolic network. (mdpi.com)
  • However, it is not known how the expression of metabolic genes in tumors differs from that in normal tissues, or whether different tumor types exhibit similar metabolic changes. (nih.gov)
  • Here we compare expression patterns of metabolic genes across 22 diverse types of human tumors. (nih.gov)
  • Our analysis also suggests that the expression changes of some metabolic genes (e.g., isocitrate dehydrogenase and fumarate hydratase) may enhance or mimic the effects of recurrent mutations in tumors. (nih.gov)
  • Therefore, a suitable strategy to enhance these pathways is to introduce genes encoding key enzymes free from feedback control ( 5 - 7 ). (pnas.org)
  • Notably, reduced copy number in key metabolic genes located adjacent to VHL (a tumor suppressor gene frequently deleted in this cancer) recapitulates these defects. (pnas.org)
  • A significant yet limited set of metabolic genes that explained the partial divergence of ccRCC metabolism correlated with loss of von Hippel-Lindau tumor suppressor ( VHL ) and a potential activation of signal transducer and activator of transcription 1. (pnas.org)
  • Notably, this behavior is recapitulated by recurrent loss of heterozygosity in multiple metabolic genes adjacent to VHL . (pnas.org)
  • Introduction of new genes and modification of existing genes have complex effects on the behavior of biological reaction networks. (mathworks.com)
  • Another extensively studied type of interactome is the protein-DNA interactome, also called a gene-regulatory network , a network formed by transcription factors, chromatin regulatory proteins, and their target genes. (wikipedia.org)
  • Genes that are connected in such a way form genetic interaction networks . (wikipedia.org)
  • Some of the goals of these networks are: develop a functional map of a cell's processes, drug target identification, and to predict the function of uncharacterized genes. (wikipedia.org)
  • Using WGCNA, we identified 3 network modules that were significantly correlated with psoriasis and 6 network modules significantly correlated with biologic treatment, with only 16 % of the psoriasis-associated and 5 % of the treatment-associated coexpressed genes being identified by differential expression analysis. (biomedcentral.com)
  • This study has identified several networks of coding and non-coding genes associated with psoriasis and biologic drug treatment, including networks enriched for short-chain fatty acid metabolism and olfactory receptor activity, pathways that were not previously identified through differential expression analysis and may be dysregulated in psoriatic skin. (biomedcentral.com)
  • As these networks are comprised mostly of non-coding genes, it is likely that non-coding genes play critical roles in the regulation of pathways involved in the pathogenesis of psoriasis. (biomedcentral.com)
  • However, while differential expression analyses have successfully revealed transcriptomic signatures comprised of many individual DEGs, differential expression analysis may fail to detect important biological pathways or gene-gene interactions associated with disease due to a focus on the effect of individual genes rather than on the effect of networks of genes. (biomedcentral.com)
  • Gene coexpression network analysis methods were developed to understand the relationship between pairs of genes and ultimately, gene networks or modules that are associated with a distinct biological function. (biomedcentral.com)
  • Weighted gene coexpression network analysis (WGCNA) [ 9 ] builds upon these previous unweighted methods by implementing a correlation-based soft-thresholding weight that prioritizes the strongest pairwise correlations and penalizes weaker ones and complements differential expression analysis by testing for association between a disease and networks of correlated genes. (biomedcentral.com)
  • Furthermore, WGCNA offers a way to prioritize the most important genes in a given network by calculating a measure of connectivity for each gene which is based on the number of correlations between each gene and all other genes in the network. (biomedcentral.com)
  • In practice this involves understanding how genetic and developmental networks operate when there is allelic variation in their genes. (duke.edu)
  • However, we have yet to make the transition from a linear one-dimensional sequence of genes to an integrated multidimensional model of metabolic and regulatory networks. (genetics.org)
  • This study aimed to elucidate potential candidate hub genes and key pathways related to BD in a pre-frontal cortex sample. (frontiersin.org)
  • After data pre-processing, 10,094 genes were selected for weighted gene co-expression network analysis (WGCNA). (frontiersin.org)
  • Hub genes with a high degree of connectivity in the PPI network are significantly enriched in positive regulation of transcription. (frontiersin.org)
  • Taken together, the identification of these 30 hub genes and enrichment pathways might have important clinical implications for BD treatment and diagnosis. (frontiersin.org)
  • Discovering how genes participate in the aromatic amino acid pathway of S.cerevisiae . (salford.ac.uk)
  • The activity of many metabolic modules was significantly associated with prognosis at a stronger magnitude than any of their constituent genes. (aacrjournals.org)
  • Recent studies show that genes involved in metabolic pathways shows a remarkable heterogeneity across various cancer types ( 8 ), which suggests that personalized therapies are likely to be successful if the context of the intervention is accurately depicted. (aacrjournals.org)
  • An approach is presented for computing meaningful pathways in the network of small molecule metabolism comprising the chemical reactions characterized in all organisms. (nih.gov)
  • Viewing the entire metabolism as a network has been popular since the report by Barabasi's group [ 1 ]. (omicsonline.org)
  • These results suggest that most predicted plant BGCs are not genuine SM pathways and argue that BGCs are not a hallmark of plant specialized metabolism. (plantcell.org)
  • One network that is known to be naturally variable while also having global ramifications for organisms across metabolism and development is the circadian clock. (plantcell.org)
  • The main source of the observed metabolic differences was from the diversity of secondary metabolism. (biomedcentral.com)
  • Our results indicated that CKI exerted anti-HCC effects via the key targets MMP2, MYC, CASP3, and REG1A and the key pathways of glycometabolism and amino acid metabolism. (nature.com)
  • Metabolic engineers use MetaCyc as an encyclopedia of metabolic pathways and enzymes that may be genetically engineered into an organism to alter its metabolism. (sri.com)
  • Validation and identification of flux disturbances that have been proven experimentally in liver patients and animal models highlights the ability of SteatoNet to effectively describe biological behaviour.Cholesterol metabolism and its transcription regulators are highlighted as novel steatosis factors.SteatoNet thus serves as an intuitive in silico platform to identify systemic changes associated with complex hepatic metabolic disorders. (nih.gov)
  • We generated the SteatoNet, a multi-pathway, multi-tissue model and in silico platform to investigate hepatic metabolism and its associated deregulations. (nih.gov)
  • The sensitive analysis revealed mitochondrial compartment as the major affected by changes on the CO 2 concentrations and glycolysis/gluconeogenesis, glyoxylate, and dicarboxylate metabolism among the affected metabolic pathways. (frontiersin.org)
  • The changes on CO 2 levels mostly affected the metabolism of amino acids found in the photorespiration pathway. (frontiersin.org)
  • Possible roles of the sensitive pathways in the biomass metabolism are discussed. (frontiersin.org)
  • Studying the metabolism of the two groups of strains may discover the corresponding pathways that are conserved in the first group but not in the second group. (hku.hk)
  • To engineer and improve metabolic traits, we need comprehensive and accurate knowledge of the organization and regulation of plant metabolism at the genome scale. (plantphysiol.org)
  • We particularly focus on lysine acetylation, which recent studies show can occur in proteins involved in transcription, translation, pathways associated with central metabolism and stress responses. (nih.gov)
  • It is suggested that regulation of metabolism is a point of convergence of many different cancer-associated pathways. (pnas.org)
  • Here we challenged the validity of this assertion and verified that a transversal metabolic signature in cancer emerges chiefly in the regulation of nucleotide metabolism. (pnas.org)
  • We observed a metabolic shift that associates differential regulation of enzymes in one-carbon metabolism with high tumor stage and poor clinical outcome. (pnas.org)
  • Further network-dependent analyses revealed unique defects in nucleotide, one-carbon, and glycerophospholipid metabolism at the transcript and protein level, which contrasts findings in other tumors. (pnas.org)
  • Biochemical topics include structure/function relationships, enzyme mechanisms, bioenergetics, metabolism and valuable metabolic products. (bangor.ac.uk)
  • Enrichment analysis of these correlated modules revealed that short-chain fatty acid metabolism and olfactory signaling are amongst the top pathways enriched for in modules associated with psoriasis, while regulation of leukocyte mediated cytotoxicity and regulation of cell killing are amongst the top pathways enriched for in modules associated with biologic treatment. (biomedcentral.com)
  • Currently metabolic networks (e.g. folate metabolism) are being used to develop a deeper understanding of the functional relationships between genetic variation and trait variation, and of the mechanisms by which genetic and environmental variables interact to produce phenotypes. (duke.edu)
  • Studies on the pathways that are involved in intermediary metabolism as they impact endocrine and metabolic diseases. (nih.gov)
  • Studies address whole-body fluxes in carbohydrate and lipid metabolism as well as the role of single key molecules or set of molecules in the regulation of these metabolic pathways. (nih.gov)
  • To understand the potential contribution of metabolism to strain-specific infectivity differences, we present a constraint-based metabolic model of the opportunistic parasite, Toxoplasma gondii. (biomedsearch.com)
  • The increasing interest in systems biology has resulted in extensive experimental data describing networks of interactions (or associations) between molecules in metabolism, protein-protein interactions and gene regulation. (imperial.ac.uk)
  • The most similar metabolic subgraphs were generally found to occur in processes central to life, such as purine, pyrimidine and amino acid metabolism. (imperial.ac.uk)
  • Despite its inherent complexity, cellular metabolism can be decomposed into functional modules that represent fundamental metabolic processes. (aacrjournals.org)
  • Actually, it has long been known that key signaling pathways that are altered in cancer are important regulators of metabolism ( 4 ). (aacrjournals.org)
  • This observation, along with the discovery of the therapeutic potential of metabolic targets in cancer ( 9 ), has sparked a growing interest in cancer metabolism ( 3, 4 ). (aacrjournals.org)
  • The metabolism of a cell consists of an elaborate network of interconnected pathways that enable the synthesis and breakdown of molecules (anabolism and catabolism). (wikipedia.org)
  • Arita constructed a database for atomic tracing based on substrate-product relationship extracted from known enzyme reactions [ 4 , 5 ], where possible pathways can be found as combinations of established substrate-product relationships. (omicsonline.org)
  • Specifically, genetic manipulation of a secondary metabolic enzyme led to altered free-running rhythms. (plantcell.org)
  • We now believe there is a specific enzyme critical to the reverse pathway that can be deleted without impairing normal function. (technologynetworks.com)
  • The novelty in the approach utilized to generate SteatoNet is the definition of model parameters as a mathematical formalism based on reaction reversibility r, the distribution of the metabolic influx f into alternative pathways, the total influx φI and the ratio between bound and free enzyme, w. (nih.gov)
  • As part of this process, each metabolic enzyme is associated with an Enzyme Commission (EC) number that characterizes its function. (psu.edu)
  • It is widely recognized that complexity of metabolic networks arises from duplication, recruitment and recombination of enzyme protein domains. (sciweavers.org)
  • In most cases of a metabolic pathway, the product of one enzyme acts as the substrate for the next. (wikipedia.org)
  • An example of a coupled reaction is the phosphorylation of fructose-6-phosphate to form the intermediate fructose-1,6-bisphosphate by the enzyme phosphofructokinase accompanied by the hydrolysis of ATP in the pathway of glycolysis. (wikipedia.org)
  • Three different hypothetical metabolic networks abbreviated as BRP-dependent network, metabolite-dependent network and CFB network are considered. (omicsonline.org)
  • Binary relationships between substrate and product can be used for calculating metabolic pathway as metabolite sequence to connect 2 compounds. (omicsonline.org)
  • Network analyses modeling metabolite correlations provided context for individual metabolite associations and elucidated collective associations of multiple classes of metabolic fuels with newborn size and adiposity, including acylcarnitines, fatty acids, carbohydrates, and organic acids. (diabetesjournals.org)
  • The prevalence of metabolic gene clusters offers an intriguing possibility of an untapped source for uncovering new metabolite biosynthesis pathways. (plantphysiol.org)
  • The pathway that was used to process this metabolite, was a part of the 2-methylcitrate cycle. (igem.org)
  • Metabolite Profiling with GC-MS and LC-MS.- The Application of Electrochemistry to Metabolic Profiling. (ebooks.com)
  • With this finding, we have learned there are particular enzymes that work together to enable the reverse pathway to function, much like the tiny gears that turn in opposite directions to power a mechanical clock," said Dr. DeBerardinis, director of CRI's Genetic and Metabolic Disease Program and associate professor in the Department of Pediatrics and the Eugene McDermott Center for Human Growth and Development at UT Southwestern Medical Center. (technologynetworks.com)
  • The concept could play an important role in systems biology by contributing to fields such as metabolic and genetic engineering where it could assist in finding ways of producing industrially relevant compounds from renewable resources, not only for economical, but also for sustainability, reasons. (mdpi.com)
  • 2010) is used to generate a genetic interaction network for the apoptosis phenotype. (rsc.org)
  • Mathematical modeling, simulation and optimization of these networks aid in the understanding and guiding of genetic modifications and support the rational design for maximal product yield. (mathworks.com)
  • In the current study, an artificial neural network (ANN)-based breast cancer prediction model was developed from the data of folate and xenobiotic pathway genetic polymorphisms along with the nutritional and demographic variables to investigate how micronutrients modulate susceptibility to breast cancer. (cdc.gov)
  • Here, we aim to look beyond genetic mechanisms of resistance to identify resistance-associated metabolic adaptation. (biomedcentral.com)
  • Metabolic or phenotypic 'background' could be as important as genetic background in the development of resistance. (biomedcentral.com)
  • Rahnuma: hypergraph-based tool for metabolic pathway prediction and network comparison. (ox.ac.uk)
  • SUMMARY: We present a tool called Rahnuma for prediction and analysis of metabolic pathways and comparison of metabolic networks. (ox.ac.uk)
  • Such integrative and network-dependent analysis enables prediction of how systems-level perturbations are translated into alterations in distinct and biologically meaningful modules and, at the same time, elucidation of genotype-phenotype relationships ( 12 ). (pnas.org)
  • We also use Markov chain Monte Carlo simulation for the prediction of networks with maximum probability under our model. (genetics.org)
  • Modern systems biology permits the study of complex networks, such as circadian clocks, and the use of complex methodologies, such as quantitative genetics. (plantcell.org)
  • One of the challenging tasks in systems biology is to understand how molecular networks give rise to emergent functionality and whether universal design principles apply to molecular networks. (mdpi.com)
  • A systems biology library of objects corresponding to biological entities was utilised to compile the SteatoNet (Steatosis Network) in a systematic workflow (Fig. 1) to form a closed multi-pathway metabolic network (Fig. 2). (nih.gov)
  • As more biological network data are becoming available, comparative analyses of these networks across species are proving to be valuable, since such systems biology types of comparisons may lead to transfer of knowledge between species as well as to exciting discoveries in evolutionary biology. (royalsocietypublishing.org)
  • In this context, systems biology approaches have been demonstrated to lead to the identification of altered metabolic processes in disease development with regard to those disorders that are driven or accompanied by metabolic reprogramming, including cancer ( 8 ⇓ ⇓ - 11 ). (pnas.org)
  • Using this systems biology approach, we identify metabolic shifts that arise with or in support of the resistant phenotype. (biomedcentral.com)
  • Development of metabolomics has made completion of metabolic map an important issue. (omicsonline.org)
  • The potential targets and pathways involved in the anti-HCC effects of CKI were predicted by a network pharmacology approach, and some of the crucial proteins and pathways were further validated by western blotting and metabolomics approaches. (nature.com)
  • To address possible metabolic linkages between maternal hyperglycemia and offspring phenotypes, we performed targeted and nontargeted metabolomics together with pathway, network, and random forest analyses in 400 European ancestry HAPO mothers. (diabetesjournals.org)
  • Metabolomics combines strategies to identify and quantify endogenous small molecules that are products of biochemical reactions, and thereby to reveal connections between different pathways that operate within a living cell. (intechopen.com)
  • The metabolic network is described as a weighted graph in which all the compounds are included, but each compound is assigned a weight equal to the number of reactions in which it participates. (nih.gov)
  • Performance is evaluated systematically by computing paths between the first and last reactions in annotated metabolic pathways, and comparing the intermediate reactions in the computed pathways to those in the annotated ones. (nih.gov)
  • We suggest that the success of our simplistic approach is rooted in the high degree of specificity of the reactions in metabolic pathways, presumably reflecting thermodynamic constraints operating in these pathways. (nih.gov)
  • In this circumstance, informatics technique to explore metabolic pathways including new reactions will be useful. (omicsonline.org)
  • According to the high conservation of primary metabolic reactions in Streptomyces species, the metabolic network model of Streptomyces hygroscopicus var. (biomedcentral.com)
  • A minimal cut set is a minimal set of reactions whose inactivation would guarantee a failure in a certain network function or functions. (mdpi.com)
  • Instead, MetaCyc serves as a high-quality reference on known metabolic pathways, enzymes, and reactions. (sri.com)
  • The metabolic network model of Chlamydomonas was updated based on the genome annotation data and sensitivity analysis revealed CO 2 sensitive reactions. (frontiersin.org)
  • Biomass backtracking supports the integration of dynamic metabolic models into a genome scale metabolic model and provides exact drain reactions. (rsc.org)
  • On the level of individual biochemical reactions, many hundreds of metabolic isoenzymes show significant and tumor-specific expression changes. (nih.gov)
  • However, only a fraction of the metabolic reactions potentially occurring in a generic human cell are typically involved in such processes. (pnas.org)
  • So the following reactions and pathways were also implemented in CNA. (igem.org)
  • The reactions for this pathway are shown in figure 8. (igem.org)
  • For all even numbered alkanes the above reactions completely link them to the main network in CNA. (igem.org)
  • The reactions for this pathway are shown in figure 9. (igem.org)
  • In metabolic networks, a metabolic pathway means a set of chemical reactions occurring within a cell in which a principal chemical is. (springer.com)
  • Understanding how metabolic reactions translate the genome of an organism into its phenotype is a grand challenge in biology. (degruyter.com)
  • Energy is obtained from breaking down nutrients through a process of metabolic reactions known as respiration. (scientificamerican.com)
  • they then break down the ATP to fuel their metabolic reactions. (scientificamerican.com)
  • In biochemistry, a metabolic pathway is a linked series of chemical reactions occurring within a cell. (wikipedia.org)
  • Each metabolic pathway consists of a series of biochemical reactions that are connected by their intermediates: the products of one reaction are the substrates for subsequent reactions, and so on. (wikipedia.org)
  • Glycolysis results in the breakdown of glucose, but several reactions in the glycolysis pathway are reversible and participate in the re-synthesis of glucose (gluconeogenesis). (wikipedia.org)
  • In times of excess lipid or protein energy sources, certain reactions in the glycolysis pathway may run in reverse to produce glucose 6-phosphate, which is then used for storage as glycogen or starch. (wikipedia.org)
  • A catabolic pathway is a series of reactions that bring about a net release of energy in the form of a high energy phosphate bond formed with the energy carriers adenosine diphosphate (ADP) and guanosine diphosphate (GDP) to produce adenosine triphosphate (ATP) and guanosine triphosphate (GTP), respectively. (wikipedia.org)
  • The respective regulatory webs are linked to auxin and ethylene controlled networks. (plantphysiol.org)
  • Here, we outline the use of several optimisation principles applied to biological networks, with an emphasis on metabolic regulatory networks. (mdpi.com)
  • Pathway analysis revealed metabolic regulatory roles for miR-122, including regulation of IR pathways (AMPK, target of rapamycin signaling, and mitogen-activated protein kinase). (diabetesjournals.org)
  • SteatoNet metabolic network.The key metabolic pathways and their regulation by hormones, adipokines and transcriptional and post-translational regulatory factors are represented in the hepatic, adipose, macrophage, peripheral tissue and pancreatic compartments with inter-tissue connectivity via the blood. (nih.gov)
  • Similarly, gene regulatory networks overlap substantially with protein interaction networks and signaling networks. (wikipedia.org)
  • Regulatory networks provide control over complex cell behavior in all kingdoms of life. (genetics.org)
  • Note that, rather than trying to reproduce the actual genesis of regulatory networks in evolution, our model has the more modest purpose of providing each network with a probability value in such a way that networks having more features typical of real networks have higher probabilities. (genetics.org)
  • Biological network analysis further identified c-MYC as a common prominent regulatory protein in pancreatic cancer and chronic pancreatitis. (mcponline.org)
  • In gene regulatory networks, it often means the mechanism under which expression quantitative trait loci regulate the expression of their target transcripts. (springer.com)
  • These four characteristics apply to all types of pathways, including metabolic pathways, signaling pathways, and gene regulatory pathways. (springer.com)
  • Genome-wide association studies (GWAS) statistically connect genotypes to phenotypes, without any recourse to known molecular interactions, whereas a molecular mechanistic description ties gene function to phenotype through gene regulatory networks (GRNs), protein-protein interactions (PPIs) and molecular pathways. (degruyter.com)
  • Here, we have merged GRNs, PPIs and genome-scale metabolic networks (GSMNs) approaches into a single framework for rice via omics' regulatory information reconstruction and integration. (degruyter.com)
  • This provides a reference for understanding genotype-phenotype relationship of rice, and for analysis of its molecular regulatory network. (degruyter.com)
  • Mathematical modeling of signaling and gene regulatory networks has provided unique insights about systems behaviors for many cell biological problems of medical importance. (mdpi.com)
  • or "what cofactor biosynthesis pathways are known in bacteria? (sri.com)
  • They found that CKI exerted anti-cancer effects likely through the regulation of the cell cycle, cell apoptosis, lncRNAs and other pathways 10 . (nature.com)
  • Indeed, animal models suggest exquisite regulation of circulating ex-RNAs in the development and resolution of obesity and in metabolic cross talk between various organs involved in adipocyte dysfunction ( 2 ), suggesting their importance as clinical and functional biomarkers. (diabetesjournals.org)
  • SteatoNet: the first integrated human metabolic model with multi-layered regulation to investigate liver-associated pathologies. (nih.gov)
  • Overall, our findings reveal that the transcriptional activation of p75 NTR is under circadian regulation in the nervous system and peripheral tissues, and plays an important role in the maintenance of clock and metabolic gene oscillation. (jneurosci.org)
  • Here we show that even in the heterogeneity of metabolic regulation a distinct signature encompassed most cancers. (pnas.org)
  • On the other hand, clear cell renal cell carcinoma (ccRCC) strongly deviated in terms of metabolic gene expression changes, showing widespread down-regulation. (pnas.org)
  • Only recently a systemic study using transcriptional regulation has attempted to rule out the possibility that other metabolic processes in the network may achieve equal importance in cancer cells ( 6 ), and the idea that all cancer cells display a unique metabolic phenotype has spurred disputes that mainly highlighted a lack of comprehensive evidence ( 7 ). (pnas.org)
  • Metabolic reconstruction identifies strain-specific regulation of virulence in Toxoplasma gondii. (biomedsearch.com)
  • One of the most remarkable significant pathways is the Hippo signaling pathway and its positive transcriptional regulation. (frontiersin.org)
  • To do so, a model must provide reliable descriptions of key system properties-in particular, the network of metabolic pathways and their dynamic regulation. (pnnl.gov)
  • The researches found that modeling cellular regulation with cybernetic control laws provides an efficient route to describing the complex dynamic behavior of S. oneidensis MR-1 particularly when considering large-scale metabolic networks. (pnnl.gov)
  • Growth regulation and the insulin signaling pathway. (aimsciences.org)
  • Innovative approaches to the study of metabolic regulation in microbial, plant and animal systems are increasingly facilitating the emergence of systems approaches in biology. (ebooks.com)
  • By coupling with flux balance analysis and using minimization of metabolic adjustment algorithm, potential targets for ascomycin overproduction were predicted. (biomedcentral.com)
  • SteatoNet identifies crucial pathway branches (transport of glucose, lipids and ketone bodies) where changes in flux distribution drive the healthy liver towards hepatic steatosis, the primary stage of non-alcoholic fatty liver disease. (nih.gov)
  • In this present study, flux balance analysis (FBA) was performed to identify sensitive metabolic pathways of Chlamydomonas reinhardtii under varied CO 2 inputs. (frontiersin.org)
  • For example, 4 polymorphisms at the lcye locus in corn were recently shown to alter the flux between the α-carotene and β-carotene branches of the carotenoid pathway, potentially allowing breeding for enhanced β-carotene levels ( 4 ). (pnas.org)
  • To further the quest to harness microbes for beneficial uses, scientists from Pacific Northwest National Laboratory and Purdue University developed a promising computational tool for analyzing microbial flux distribution and metabolic engineering. (pnnl.gov)
  • Flux distributions in S. oneidensis MR-1 predicted by the L-HCM compare very favorably with 13 C-metabolic flux analysis results reported in the literature. (pnnl.gov)
  • 13C-metabolic flux ratio and carbon path analyses confirmed that Trichoderma reesei uses primarily the respirative pathway also on the preferred carbon source glucose. (helsinki.fi)
  • Targeted Drug Design and Metabolic Pathway Flux. (ebooks.com)
  • In conclusion it is feasible and effective means using GC-MS, isotope experiment and MATLAB software to integrate research the metabolic flux distribution of lactic acid bacteria, and the results provide the theoretical foundation for similar metabolic flux distribution. (wiley.com)
  • In fact, many of the molecular pathways that are altered with CR are also known to be altered in cancer. (isharonline.org)
  • In this review, we summarize recent advances in applying human iPSC reprogramming to generate patient-specific neural subtypes in order to reveal molecular pathways affected in various neurodegenerative diseases. (intechopen.com)
  • For example, a metabolic pathway in KEGG can be natural. (psu.edu)
  • they were first introduced in 2004 by S. Klamt and Gilles [ 12 ], motivated by their desire to gain deeper insight into the functionality and capability of an organism by further analyzing the structure of its metabolic network. (mdpi.com)
  • For questions that require information about the complete genome, proteome, or metabolic network of an organism, instead consult the organism-specific pathway/genome database (PGDB). (sri.com)
  • One of MetaCyc's primary applications is to serve as a reference database for computationally predicting the metabolic network of an organism from its annotated genome, such as by the PathoLogic algorithm, part of Pathway Tools . (sri.com)
  • It provides an intuitive way to answer biological ques- tions focusing on differences between organisms or the evolution of different species by allowing pathway-based metabolic network comparisons at an organism as well as at a phylogenetic level. (ox.ac.uk)
  • Furthermore, we assume that once a given pair has proven effective, nature will tend to reuse it in other networks within the same organism, as well as in other organisms. (genetics.org)
  • Citation Query KAAS: an automatic genome annotation and pathway reconstruction server. (psu.edu)
  • To this end, the reconstruction of genome-scale metabolic models (GEMs) is instrumental to knit high-throughput data into the metabolic network topology. (pnas.org)
  • An Integrative Bioinformatics Framework for Genome-scale Multiple Level Network Reconstruction of Rice" Journal of Integrative Bioinformatics , vol. 10, no. 2, 2013, pp. 94-102. (degruyter.com)
  • As a result, tools for rapid automated reconstruction of metabolic models are becoming critically important for supporting the analysis of new genome sequences. (osti.gov)
  • article{osti_1493924, title = {Methods for automated genome-scale metabolic model reconstruction}, author = {Faria, José P. and Rocha, Miguel and Rocha, Isabel and Henry, Christopher S.}, abstractNote = {In the era of next-generation sequencing and ubiquitous assembly and binning of metagenomes, new putative genome sequences are being produced from isolate and microbiome samples at ever-increasing rates. (osti.gov)
  • However, the lack of curated metabolic model of rice is blocking the exploration of genome-scale multi-level network reconstruction. (degruyter.com)
  • To achieve this, the biophysical, evolutionary and physiological constraints that act on those networks need to be identified in addition to the characterisation of the molecular components and interactions. (mdpi.com)
  • One reason for being so is the emergent behaviour that arises from the interactions within these networks. (mdpi.com)
  • To achieve understanding of the function of a molecular network and how this results from molecular interactions requires the identification of the molecular make-up as an obvious first (and important) step. (mdpi.com)
  • including physical systems such as electrical power grids and communication networks, social systems such as networks of friendships or corporate and political hierarchies, physical relationships such as residue interactions in a folded protein, or software systems such as call graphs or expression and syntax trees. (royalsocietypublishing.org)
  • Whenever such molecules are connected by physical interactions, they form molecular interaction networks that are generally classified by the nature of the compounds involved. (wikipedia.org)
  • For instance, the Sirt-1 protein interactome and Sirt family second order interactome [5] [6] is the network involving Sirt-1 and its directly interacting proteins where as second order interactome illustrates interactions up to second order of neighbors (Neighbors of neighbors). (wikipedia.org)
  • Artificial neural network-based exploration of gene-nutrient interactions in folate and xenobiotic metabolic pathways that modulate susceptibility to breast cancer. (cdc.gov)
  • Here we describe a statistical model, based on representing proteins as collections of domains or motifs, which predicts unknown molecular interactions within these biological networks. (genetics.org)
  • Using known protein-protein interactions of Saccharomyces cerevisiae as training data, we were able to predict the links within this network with only 7% false-negative and 10% false-positive error rates. (genetics.org)
  • Furthermore, 90,358 pairs of protein-protein interactions, 662,936 pairs of gene regulations and 1,763 microRNA-target interactions were integrated into the metabolic model. (degruyter.com)
  • The objective is to determine the set of boolean rules that describe the interactions of the nodes within this plant signaling network. (uci.edu)
  • Theoretical concepts derived from mathematical modeling of this metabolic nexus provide insights into the properties of this system, some of which seem to be paradoxical at first glance. (isharonline.org)
  • This webinar will provide metabolic engineers and synthetic biologists with an introduction to cellular modeling and optimization with MATLAB and SimBiology using a real life example of engineering yeast cells for the overproduction of succinate. (mathworks.com)
  • In this use, L-HCM predicted experimentally determined dynamic metabolic shifts, a capability well beyond the scope of constraint-based modeling approaches. (pnnl.gov)
  • The ability to exploit the biotechnological potential of S. oneidensis MR-1 will benefit greatly from metabolic modeling and simulations that not only promote fundamental understanding, but also point to new strategies for performance improvements. (pnnl.gov)
  • Quantitative single cell monitoring has a crucial role in advancing systems modeling of molecular networks. (mdpi.com)
  • In this essay, I focus on some technical aspects that are often under-appreciated, yet critical in harnessing live cell imaging methods to achieve single-cell-level understanding and quantitative modeling of molecular networks. (mdpi.com)
  • The metabolic conservation of Streptomyces species was first investigated by comparing the metabolic enzymes of Streptomyces coelicolor A3(2) with those of 31 Streptomyces strains, the results showed that more than 72% of the examined proteins had high sequence similarity with counterparts in every surveyed strain. (biomedcentral.com)
  • Molecular-interaction networks feature proteins, nucleic acids, and small molecules as primary players. (genetics.org)
  • In this work, we assume that the existence of a network connection between proteins, which may or may not involve a physical interaction between them, is a function of the domain composition of each. (genetics.org)
  • For convenience of description, we treat nonprotein network nodes as single-domain proteins. (genetics.org)
  • The inclusion of network context information in the comparison of protein interaction networks increased the number of similar subgraphs found consisting of proteins involved in the same functional process. (imperial.ac.uk)
  • A catabolic pathway is an exergonic system that produces chemical energy in the form of ATP, GTP, NADH, NADPH, FADH2, etc. from energy containing sources such as carbohydrates, fats, and proteins. (wikipedia.org)
  • This increases importance of metabolic map as the basis of analysis of metabolome data and opportunity to validate the present knowledge of metabolic pathways . (omicsonline.org)
  • As the lower production in bio-fermentation, global metabolic analysis is required to further explore its biosynthetic network and determine the key limiting steps for rationally engineering. (biomedcentral.com)
  • These results provide insights into the mechanism of CKI by combining quantitative analysis of components, network pharmacology and experimental validation. (nature.com)
  • In the current study, network pharmacology analysis was performed focusing on the main active compounds of CKI. (nature.com)
  • MetaCyc is used as a readily accessible source of up-to-date, literature-curated information on metabolic pathways and enzymes by researchers for basic research and genome analysis, and by students and teachers for educational purposes. (sri.com)
  • Many groups have developed pathway analysis tools relative to annotation and identification. (psu.edu)
  • However, differential expression analysis may fail to detect perturbations in gene coexpression networks. (biomedcentral.com)
  • In this study, we applied weighted gene coexpression network analysis (WGCNA) on RNA-seq data from psoriasis patients and healthy controls. (biomedcentral.com)
  • Machine learning has yielded new insights into health risks and the spread of disease via analysis of social networks, Web-search queries, and hospital data. (acm.org)
  • Functional annotation and pathway enrichment analysis for modules, which indicated some key pathways, were conducted based on the Enrichr database. (frontiersin.org)
  • Genome-scale metabolic models have enormous utility for supporting the analysis and predictive characterization of these genomes based on sequence data. (osti.gov)
  • For this analysis, a mathematical model for the pathways is first established using a system of differential equations. (aimsciences.org)
  • Equilibria and stability analysis of a branched metabolic network with feedback inhibition. (aimsciences.org)
  • Comparative analysis of these networks is central to understanding biological systems. (imperial.ac.uk)
  • Finally, the polygenic score approach was used to identify an alternative genome-wide significance threshold before pathway analysis and those results were compared with those based on the classical genome-wide significance threshold. (edu.au)
  • Pathway analysis utilizing the best polygenic score for TC uncovered extra information compared with using only genome-wide significant loci. (edu.au)
  • In other words, a mechanistic understanding of biological networks that are used to generate these datasets is lacking behind. (mdpi.com)
  • Comparison and alignment of biological networks will probably have a similar impact. (royalsocietypublishing.org)
  • We apply it to biological networks to produce by far the most complete topological alignments of biological networks to date. (royalsocietypublishing.org)
  • Given a group of such biological networks, the matrix of pairwise global network similarities can be used to infer phylogenetic relationships. (royalsocietypublishing.org)
  • Adapting Community Detection Algorithms for Disease Module Identification in Heterogeneous Biological Networks. (nih.gov)
  • Though interactomes may be described as biological networks , they should not be confused with other networks such as neural networks or food webs . (wikipedia.org)
  • Below, we describe our model and how its parameters are estimated, verify its validity with cross-validation, and show sample applications to real biological networks. (genetics.org)
  • Pathway refers to a functional path in the biological networks. (springer.com)
  • Discovering refinements to biological networks, such as metabolic pathways. (salford.ac.uk)
  • Offspring of mothers with preexisting or gestational diabetes mellitus (GDM) are at risk for higher birth weight (BW) and adiposity as well as childhood metabolic disorders, including obesity, impaired glucose tolerance, and dyslipidemia ( 1 - 3 ). (diabetesjournals.org)
  • In synthetic medium, 60.6% of the glucose entered the Embden-Meyerhof-Parnas (EMP) to produce lactic acid, whereas 36.4% of the glucose entered the pentose phosphate metabolic pathway (HMP). (wiley.com)
  • Why do cancer cells choose this inefficient metabolic pathway when they could obtain 16 times as much ATP per molecule of glucose by opting for normal respiration? (scientificamerican.com)
  • Once inside the cell, the glucose is broken down by aerobic glycolysis into lactic acid, in order to speedily produce ATP and metabolic precursors through various metabolic pathways. (scientificamerican.com)
  • Glycolysis was the first metabolic pathway discovered: As glucose enters a cell, it is immediately phosphorylated by ATP to glucose 6-phosphate in the irreversible first step. (wikipedia.org)
  • In a discovery at the Children's Medical Center Research Institute at UT Southwestern (CRI), a research team led by Ralph DeBerardinis, M.D., Ph.D., has taken a significant step in cracking the code of an atypical metabolic pathway that allows certain cancerous tumors to thrive, providing a possible roadmap for defeating such cancers. (technologynetworks.com)
  • The identification of the mechanism could provide a future target for drugs that would attack tumors relying upon the reverse pathway for sustenance and growth. (technologynetworks.com)
  • Tumors of this type, often found in the brain, lungs and kidneys, tend to be difficult for oncologists to treat because cells using the atypical pathway seem to resist existing treatments like chemotherapy. (technologynetworks.com)
  • Overall, the metabolic gene expression program in tumors is similar to that in the corresponding normal tissues. (nih.gov)
  • Although expression changes of some metabolic pathways (e.g., upregulation of nucleotide biosynthesis and glycolysis) are frequently observed across tumors, expression changes of other pathways (e.g., oxidative phosphorylation) are very heterogeneous. (nih.gov)
  • Global differences in metabolic gene expression between tumors and normal tissues. (nih.gov)
  • Expression of individual metabolic pathways in tumors. (nih.gov)
  • However, the most common form of renal cancer deviates from this behavior and presents some defects in its metabolic network not present in the normal kidney and unseen in other tumors. (pnas.org)
  • Genostar, a developer of bioinformatics software that enables biologists and bioinformaticians to expertly mine and analyze diverse biological data, today announced that Merial, a world leader in animal health, has purchased its IOGMA(R) 3.4 Metabolic Pathway Builder software. (technologynetworks.com)
  • Genostar's IOGMA(R) 3.4 Metabolic Pathway Builder is a new package that integrates three modules of the company's successful bioinformatics products - GenoAnnot, ProteoAnnot, and PathwayExplorer. (technologynetworks.com)
  • This book highlights analytical and bioinformatics strategies now available for investigating metabolic networks in microbial, plant and animal systems. (ebooks.com)
  • 6 Bioinformatics in Rare Diseases (BiER), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), FPS, Hospital Virgen del Rocio, Sevilla, Spain. (aacrjournals.org)
  • Plants produce numerous compounds to cope with their environments but the biosynthetic pathways for most of these compounds have not yet been elucidated. (plantphysiol.org)
  • As such, studies in small groups of patients with obesity and IR have identified candidate ex-RNAs associated with metabolic dysfunction ( 3 - 6 ), though there is absence of validation in large at-risk populations and against metabolic phenotypes (e.g., visceral and hepatic adiposity) known to impact cardiometabolic risk. (diabetesjournals.org)
  • SteatoNet thus serves as an intuitive in silico platform to identify systemic changes associated with complex hepatic metabolic disorders. (nih.gov)
  • However, it is difficult to combine these approaches due to factorial expansion in experiments when networks are examined using complex methods. (plantcell.org)
  • it adds to the increasing importance of MPA methods [ 5 , 6 , 7 ], and the capacity to employ metabolic engineering and biological systems to produce industrially relevant compounds from renewable resources, by providing a means of finding suitable targets for repressing undesirable metabolic functions. (mdpi.com)
  • Advances in high throughput experimental methods have yielded large amounts of biological network data, such as protein-protein interaction (PPI) networks. (royalsocietypublishing.org)
  • The most common methods for such network comparisons are network alignments. (royalsocietypublishing.org)
  • Anabolic and catabolic pathways in eukaryotes often occur independently of each other, separated either physically by compartmentalization within organelles or separated biochemically by the requirement of different enzymes and co-factors. (wikipedia.org)
  • One goal of the MetaCyc project is for MetaCyc to contain a representative example of every experimentally determined metabolic pathway. (sri.com)
  • In contrast, glycolysis, pentose phosphate pathway, and fatty acid biosynthesis all occur in the cytosol of a cell. (wikipedia.org)
  • We hypothesize that metabolic changes must occur to support the resistance phenotype and resistance-conferring mutations. (biomedcentral.com)
  • For example, one pathway may be responsible for the synthesis of a particular amino acid, but the breakdown of that amino acid may occur via a separate and distinct pathway. (wikipedia.org)
  • Such approaches have led to the determination of the topology of metabolic networks for a great number of organisms [ 4 , 5 ]. (mdpi.com)
  • Guest editors Vassily Hatzimanikatis and Julio Saez-Rodriguez introduce the Integrative Approaches for Signalling and Metabolic Networks themed issue of Integrative Biology . (rsc.org)
  • Metabolic pathways are often regulated by feedback inhibition. (wikipedia.org)
  • Our alignment of the protein-protein interaction networks of two very different species-yeast and human-indicate that even distant species share a surprising amount of network topology, suggesting broad similarities in internal cellular wiring across all life on Earth. (royalsocietypublishing.org)
  • In protein-protein interaction networks, it is often the same as the signaling pathways. (springer.com)
  • We report similar subgraphs in metabolic pathways and in protein-protein interaction networks. (imperial.ac.uk)
  • The similar pairs of subgraphs found in the protein-protein interaction networks of Drosophila melanogaster and Saccharomyces cerevisiae also include central processes such as cell division but, interestly, also include protein sub-networks involved in pre-mRNA processing. (imperial.ac.uk)
  • Here, we present a computational pipeline to identify metabolic enzymes, pathways, and gene clusters from a sequenced genome. (plantphysiol.org)
  • ReTrace is a computational method for inferring branching pathways in genome-scale metabolic networks. (helsinki.fi)
  • Increasing the default number of shortest paths computed with -k results in more pathways being found and a higher computational cost at every search level. (helsinki.fi)
  • Rational strain development of E. coli achieved by metabolic engineering strategies has provided new processes for efficiently biotechnological production of various high-value chemical building blocks. (mendeley.com)
  • and oncology to advance the understanding of biological pathways that link behavioral processes and cancer. (cancer.gov)
  • Furthermore, different metabolic processes are driven by distinct evolution mechanisms. (sciweavers.org)
  • In addition, we provide evidence that the length of the shortest path in the weighted graph represents a valid measure of the "metabolic distance" between enzymes. (nih.gov)
  • There are two types of metabolic pathways that are characterized by their ability to either synthesize molecules with the utilization of energy (anabolic pathway), or break down complex molecules and release energy in the process (catabolic pathway). (wikipedia.org)
  • We sought to characterize the relationship between ex-RNAs and metabolic phenotypes in a large community-based human cohort. (diabetesjournals.org)
  • Combining gene expression with metabolic modules identifies molecular mechanisms of cancer undetected on an individual gene level and allows discovery of new potential therapeutic targets. (aacrjournals.org)
  • Rational suggestion of specific metabolic pathways as candidates for real pathway will promote study to complete metabolic map. (omicsonline.org)
  • Indeed, many common oncogenic signaling pathways have been implicated in the emergence of specific metabolic features in cancer cells that have been associated with both survival and sustained abnormal proliferation rate ( 2 ⇓ ⇓ - 5 ). (pnas.org)
  • We develop microbial systems and metabolic pathways. (ncl.ac.uk)
  • Cells use a signal transduction mechanism to regulate certain metabolic pathways. (aimsciences.org)
  • These fascinating new techniques provide a powerful tool for setting scientific hypotheses and linking cellular pathways to biological mechanism. (intechopen.com)
  • Cellular needs supported by this network are met by use of parallel metabolic tracks that are differentially controlled by intermediates in the pathway. (isharonline.org)
  • Supported are studies that investigate these pathways from a whole-body perspective as well as within specific tissues (e.g., liver, fat, muscle) and at the cellular and molecular level. (nih.gov)
  • Integration of gene expression levels into metabolic modules suggests that the activity of specific modules differs between cancers and the corresponding tissues of origin. (aacrjournals.org)
  • Modulating (patho)physiological biochemistry networks on a cellular level and, more importantly, on a tissue or organ level, or systemic level, will eventually determine the treatment outcome for a patient. (springer.com)
  • This is within metabolic compartments and underlying biochemistry. (ncl.ac.uk)
  • These 3 vitamins represent 3 entirely different metabolic pathways, and the only way to achieve such a radical change in the nutritional properties of an elite breeding variety of corn so rapidly is to take advantage of multigene engineering via direct DNA transfer ( 9 ). (pnas.org)
  • Different metabolic pathways function based on the position within a eukaryotic cell and the significance of the pathway in the given compartment of the cell. (wikipedia.org)
  • A network (or graph) is a collection of nodes (or vertices), and connections between them called edges. (royalsocietypublishing.org)
  • I'd like to create the fully-connected pathway, with captions on all the nodes. (stackoverflow.com)
  • Predicting metabolic pathways by sub-network extraction. (ac.be)
  • It considers both structural and functional components of metabolic systems and is capable of predicting complex organismal response without over-parameterizing the model. (pnnl.gov)
  • ascomyceticus was constructed based on the latest reported metabolic model of S. coelicolor A3(2) and validated experimentally. (biomedcentral.com)
  • We expect our approach to find useful applications in inferring metabolic pathways in newly sequenced genomes. (nih.gov)
  • Inferring branching pathways in genome-scale metabolic networks. (helsinki.fi)
  • In biology, due to the strong forces of selective pressure and natural selection, network functions can often be understood as the outcome of fitness optimisation. (mdpi.com)
  • From bulk chemicals and complex natural products to biologicals - the fields of Synthetic Biology, Metabolic Engineering and Bioprocess Development are increasingly combined for the engineering of biological systems. (mathworks.com)
  • NBBPC is a consortium designed to support knowledge of the molecular and signaling pathways that link psychological, behavioral, and social factors to cancer biology and apply that knowledge toward the development of efficacious interventions to reduce cancer risk and improve clinical outcomes. (cancer.gov)
  • Five years ago, a handful of cancer researchers with training in cell biology, psychology, public health, and related fields, set out to study the pathways that link psychological, behavioral, and social factors to cancer. (cancer.gov)
  • The National Cancer Institute (NCI) Basic Biobehavioral and Psychological Sciences Branch led the effort to explore how psychological phenomena might be affecting the biology of cancer and disease outcomes via the Network on Biobehavioral Pathways in Cancer. (cancer.gov)
  • Metabolic network model guided engineering ethylmalonyl-CoA pathway to improve ascomycin production in Streptomyces hygroscopicus var. (biomedcentral.com)
  • To achieve this goal, an engineering approach guided by a metabolic network model was implemented to better understand ascomycin biosynthesis and improve its production. (biomedcentral.com)
  • The successful constructing and experimental validation of the metabolic model of S. hygroscopicus var. (biomedcentral.com)
  • In the presented model, 1046 or 25% of the total model parameters that describe the network must be manually set, the rest are calculated from the steady-state relations. (nih.gov)
  • Our updated metabolic network was compared to previous model and it showed more consistent results once considering the experimental data. (frontiersin.org)
  • Compared to previous reviews, this review focuses on recent advances in metabolic engineering of the industrial model bacteria E. coli that lead to efficient recombinant biocatalysts for the production of high-value organic acids like succinic acid, lactic acid, 3-hydroxypropanoic acid and glucaric acid as well as alcohols like 1,3-propanediol, xylitol, mannitol, and glycerol with the discussion of the future research in this area. (mendeley.com)
  • Thus the model we describe here is based on quantifying, from data taken from known networks, the frequency with which a domain in one protein is observed immediately upstream or downstream of domains in another protein. (genetics.org)
  • The model we now describe assigns probabilities to all possible networks formed from a fixed number of vertices. (genetics.org)
  • They used the Lumped Hybrid Cybernetic Model (L-HCM), developed by Purdue researchers Dr. Hyun-Seob Song and Dr. Doraiswami Ramkrishna, to predict and simulate the metabolic dynamics of Shewanella oneidensis MR-1 during aerobic growth in a bioreactor. (pnnl.gov)
  • This approach is unique in that it is able to model metabolic dynamics. (pnnl.gov)
  • The L-HCM provides an appropriate framework for a detailed network-based dynamic model,' said Dr. Alex Beliaev, PNNL scientist and principal investigator on PNNL's Biofuels Science Scientific Focus Area (BSFA). (pnnl.gov)
  • A mathematical model of BCR-ABL autophosphorylation, signaling through the CRKL pathway, and Gleevec dynamics in chronic myeloid leukemia. (aimsciences.org)
  • Using a multi-cellular, pathway model approach, we investigate the Drosophila sp. (nsti.org)
  • Design of a Neural Network Model as a Decision Making Aid in Renal Transplant. (barnesandnoble.com)
  • In addition to the two distinct metabolic pathways is the amphibolic pathway, which can be either catabolic or anabolic based on the need for or the availability of energy. (wikipedia.org)