Metabolic Engineering
Methods and techniques used to genetically modify cells' biosynthetic product output and develop conditions for growing the cells as BIOREACTORS.
Genetic Engineering
Protein Engineering
Procedures by which protein structure and function are changed or created in vitro by altering existing or synthesizing new structural genes that direct the synthesis of proteins with sought-after properties. Such procedures may include the design of MOLECULAR MODELS of proteins using COMPUTER GRAPHICS or other molecular modeling techniques; site-specific mutagenesis (MUTAGENESIS, SITE-SPECIFIC) of existing genes; and DIRECTED MOLECULAR EVOLUTION techniques to create new genes.
Tissue Engineering
Metabolic Networks and Pathways
Biotechnology
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.
Bioengineering
Biofuels
Hydrocarbon-rich byproducts from the non-fossilized BIOMASS that are combusted to generate energy as opposed to fossilized hydrocarbon deposits (FOSSIL FUELS).
Genetic Enhancement
Industrial Microbiology
Xylose
Xylose is a monosaccharide, a type of sugar, that is commonly found in woody plants and fruits, and it is used in medical testing to assess the absorptive capacity of the small intestine.
Biosynthetic Pathways
Biomedical Engineering
Fermentation
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.
Synthetic Biology
Metabolic Phenomena
Succinic Acid
A water-soluble, colorless crystal with an acid taste that is used as a chemical intermediate, in medicine, the manufacture of lacquers, and to make perfume esters. It is also used in foods as a sequestrant, buffer, and a neutralizing agent. (Hawley's Condensed Chemical Dictionary, 12th ed, p1099; McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed, p1851)
Intramolecular Lyases
Corynebacterium glutamicum
A species of gram-positive, asporogenous, non-pathogenic, soil bacteria that produces GLUTAMIC ACID.
Escherichia coli
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.
Plants, Genetically Modified
PLANTS, or their progeny, whose GENOME has been altered by GENETIC ENGINEERING.
Bioreactors
Tools or devices for generating products using the synthetic or chemical conversion capacity of a biological system. They can be classical fermentors, cell culture perfusion systems, or enzyme bioreactors. For production of proteins or enzymes, recombinant microorganisms such as bacteria, mammalian cells, or insect or plant cells are usually chosen.
Butylene Glycols
4-carbon straight chain aliphatic hydrocarbons substituted with two hydroxyl groups. The hydroxyl groups cannot be on the same carbon atom.
Tissue Scaffolds
Cell growth support structures composed of BIOCOMPATIBLE MATERIALS. They are specially designed solid support matrices for cell attachment in TISSUE ENGINEERING and GUIDED TISSUE REGENERATION uses.
Catharanthus
A plant genus of the family Apocynaceae. It is the source of VINCA ALKALOIDS, used in leukemia chemotherapy.
Electronic Waste
Biomass
Geranylgeranyl-Diphosphate Geranylgeranyltransferase
An enzyme that catalyzes the condensation of two molecules of geranylgeranyl diphosphate to give prephytoene diphosphate. The prephytoene diphosphate molecule is a precursor for CAROTENOIDS and other tetraterpenes.
Zymomonas
A genus of gram-negative, facultatively anaerobic, rod-shaped bacteria that is not known to be pathogenic for man, animals, or plants. Its organisms are spoilers for beers and ciders and in sweet English ciders they are the causative agents of a secondary fermentation known as "cider sickness." The species Z. mobilis is used for experiments in molecular genetic studies.
Microalgae
A non-taxonomic term for unicellular microscopic algae which are found in both freshwater and marine environments. Some authors consider DIATOMS; CYANOBACTERIA; HAPTOPHYTA; and DINOFLAGELLATES as part of microalgae, even though they are not algae.
Polyesters
Thermoanaerobacterium
A genus of gram-positive, anaerobic bacteria in the family Thermoanaerobacteriaceae. They are thermophilic and saccharolytic.
Glucosinolates
Organisms, Genetically Modified
Organisms whose GENOME has been changed by a GENETIC ENGINEERING technique.
Saccharomyces cerevisiae
Methylomonas
Biocompatible Materials
Clostridium acetobutylicum
A species of gram-positive bacteria in the family Clostridiaceae, used for the industrial production of SOLVENTS.
Carotenoids
Ethanol
A clear, colorless liquid rapidly absorbed from the gastrointestinal tract and distributed throughout the body. It has bactericidal activity and is used often as a topical disinfectant. It is widely used as a solvent and preservative in pharmaceutical preparations as well as serving as the primary ingredient in ALCOHOLIC BEVERAGES.
Psychotria
A plant genus of the family RUBIACEAE. Members contain psychotridine and brachycerine (indole alkaloids).
Clostridium beijerinckii
A species of gram-positive bacteria in the family Clostridiaceae, capable of solventogenesis, and isolated from SOIL, infected WOUNDS, fermenting OLIVES, and spoiled CANDY.
Clostridium cellulolyticum
A species of gram-positive bacteria in the family Clostridiaceae. It is a cellulolytic, mesophilic species isolated from decayed GRASS.
Pyruvate Decarboxylase
Enzymes
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.
Polyhydroxyalkanoates
Fatty acid biopolymers that are biosynthesized by microbial polyhydroxyalkanoate synthase enzymes. They are being investigated for use as biodegradable polyesters.
Molecular Sequence Data
Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.
Systems Biology
Models, Biological
Phosphate Acetyltransferase
Monoterpenes
Compounds with a core of 10 carbons generally formed via the mevalonate pathway from the combination of 3,3-dimethylallyl pyrophosphate and isopentenyl pyrophosphate. They are cyclized and oxidized in a variety of ways. Due to the low molecular weight many of them exist in the form of essential oils (OILS, VOLATILE).
Cell Engineering
Methods and techniques used to modify or select cells and develop conditions for growing cells for biosynthetic production of molecules (METABOLIC ENGINEERING), for generation of tissue structures and organs in vitro (TISSUE ENGINEERING), or for other BIOENGINEERING research objectives.
Metabolism
Directed Molecular Evolution
The techniques used to produce molecules exhibiting properties that conform to the demands of the experimenter. These techniques combine methods of generating structural changes with methods of selection. They are also used to examine proposed mechanisms of evolution under in vitro selection conditions.
Sugar Alcohol Dehydrogenases
Indole Alkaloids
Group of alkaloids containing a benzylpyrrole group (derived from TRYPTOPHAN)
Pentoses
A class of carbohydrates that contains five carbon atoms.
Batch Cell Culture Techniques
Cupriavidus necator
Saussurea
Xanthophylls
Gene Deletion
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.
Chemical Engineering
"Chemical Engineering is a branch of engineering that deals with the design, construction, and operation of plants and machinery for large-scale chemical processing of raw materials into finished or partially finished products and for the disposal or recycling of byproducts."
Transformation, Genetic
UTP-Glucose-1-Phosphate Uridylyltransferase
An enzyme that catalyzes the formation of UDPglucose from UTP plus glucose 1-phosphate. EC 2.7.7.9.
Castor Oil
Oil obtained from seeds of Ricinus communis that is used as a cathartic and as a plasticizer.
Gene Knockout Techniques
Pentose Phosphate Pathway
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.
Genome, Bacterial
The genetic complement of a BACTERIA as represented in its DNA.
D-Xylulose Reductase
An enzyme that plays a role in the PENTOSES and GLUCURONATES interconversion pathway by catalyzing the oxidation of XYLITOL to D-xylulose. This enzyme has been found to be specific for NAD+.
Lactococcus lactis
A non-pathogenic species of LACTOCOCCUS found in DAIRY PRODUCTS and responsible for the souring of MILK and the production of LACTIC ACID.
Plasmids
Extrachromosomal, usually CIRCULAR DNA molecules that are self-replicating and transferable from one organism to another. They are found in a variety of bacterial, archaeal, fungal, algal, and plant species. They are used in GENETIC ENGINEERING as CLONING VECTORS.
Phosphoglucomutase
Transketolase
An enzyme of the transferase class that catalyzes the conversion of sedoheptulose 7-phosphate and D-glyceraldehyde 3-phosphate to D-ribose 5-phosphate and D-xylulose 5-phosphate in the PENTOSE PHOSPHATE PATHWAY. (Dorland, 27th ed) EC 2.2.1.1.
Escherichia coli Proteins
Proteins obtained from ESCHERICHIA COLI.
Glucose
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.
Carbon
Computational Biology
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.
Plant Proteins
Proteins found in plants (flowers, herbs, shrubs, trees, etc.). The concept does not include proteins found in vegetables for which VEGETABLE PROTEINS is available.
Glycoconjugates
Carbohydrates covalently linked to a nonsugar moiety (lipids or proteins). The major glycoconjugates are glycoproteins, glycopeptides, peptidoglycans, glycolipids, and lipopolysaccharides. (From Biochemical Nomenclature and Related Documents, 2d ed; From Principles of Biochemistry, 2d ed)
Transformation, Bacterial
The heritable modification of the properties of a competent bacterium by naked DNA from another source. The uptake of naked DNA is a naturally occuring phenomenon in some bacteria. It is often used as a GENE TRANSFER TECHNIQUE.
Anaerobiosis
Plants
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.
Biological Products
Gene Expression Regulation, Bacterial
Any of the processes by which cytoplasmic or intercellular factors influence the differential control of gene action in bacteria.
Bioartificial Organs
Lactic Acid
A normal intermediate in the fermentation (oxidation, metabolism) of sugar. The concentrated form is used internally to prevent gastrointestinal fermentation. (From Stedman, 26th ed)
Ergosterol
A steroid of interest both because its biosynthesis in FUNGI is a target of ANTIFUNGAL AGENTS, notably AZOLES, and because when it is present in SKIN of animals, ULTRAVIOLET RAYS break a bond to result in ERGOCALCIFEROL.
Alkyl and Aryl Transferases
A somewhat heterogeneous class of enzymes that catalyze the transfer of alkyl or related groups (excluding methyl groups). EC 2.5.
Computer Simulation
Arabidopsis
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.
Sequence Analysis, DNA
Genetic Vectors
DNA molecules capable of autonomous replication within a host cell and into which other DNA sequences can be inserted and thus amplified. Many are derived from PLASMIDS; BACTERIOPHAGES; or VIRUSES. They are used for transporting foreign genes into recipient cells. Genetic vectors possess a functional replicator site and contain GENETIC MARKERS to facilitate their selective recognition.
Bacteria
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.
Escherichia coli K12
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.
Hydrogels
Culture Media
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.
beta Carotene
A carotenoid that is a precursor of VITAMIN A. It is administered to reduce the severity of photosensitivity reactions in patients with erythropoietic protoporphyria (PORPHYRIA, ERYTHROPOIETIC). (From Reynolds JEF(Ed): Martindale: The Extra Pharmacopoeia (electronic version). Micromedex, Inc, Engewood, CO, 1995.)
Alcohol Oxidoreductases
A subclass of enzymes which includes all dehydrogenases acting on primary and secondary alcohols as well as hemiacetals. They are further classified according to the acceptor which can be NAD+ or NADP+ (subclass 1.1.1), cytochrome (1.1.2), oxygen (1.1.3), quinone (1.1.5), or another acceptor (1.1.99).
Anthocyanins
A group of FLAVONOIDS derived from FLAVONOLS, which lack the ketone oxygen at the 4-position. They are glycosylated versions of cyanidin, pelargonidin or delphinidin. The conjugated bonds result in blue, red, and purple colors in flowers of plants.
Base Sequence
Gene Expression
Lignin
The most abundant natural aromatic organic polymer found in all vascular plants. Lignin together with cellulose and hemicellulose are the major cell wall components of the fibers of all wood and grass species. Lignin is composed of coniferyl, p-coumaryl, and sinapyl alcohols in varying ratios in different plant species. (From Merck Index, 11th ed)
Algorithms
Porosity
Amino Acid Sequence
Phenotype
Synechocystis
Genes, Plant
The functional hereditary units of PLANTS.
Tobacco
Recombination, Genetic
Gene Expression Regulation, Plant
Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in plants.
Molecular Structure
Regenerative Medicine
A field of medicine concerned with developing and using strategies aimed at repair or replacement of damaged, diseased, or metabolically deficient organs, tissues, and cells via TISSUE ENGINEERING; CELL TRANSPLANTATION; and ARTIFICIAL ORGANS and BIOARTIFICIAL ORGANS and tissues.
Materials Testing
Cloning, Molecular
Glycerol
A trihydroxy sugar alcohol that is an intermediate in carbohydrate and lipid metabolism. It is used as a solvent, emollient, pharmaceutical agent, and sweetening agent.
L-Lactate Dehydrogenase
Seeds
The encapsulated embryos of flowering plants. They are used as is or for animal feed because of the high content of concentrated nutrients like starches, proteins, and fats. Rapeseed, cottonseed, and sunflower seed are also produced for the oils (fats) they yield.
Acetates
Gene Expression Regulation, Fungal
Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in fungi.
Plant Leaves
Expanded structures, usually green, of vascular plants, characteristically consisting of a bladelike expansion attached to a stem, and functioning as the principal organ of photosynthesis and transpiration. (American Heritage Dictionary, 2d ed)
Metabolomics
Fungi
A kingdom of eukaryotic, heterotrophic organisms that live parasitically as saprobes, including MUSHROOMS; YEASTS; smuts, molds, etc. They reproduce either sexually or asexually, and have life cycles that range from simple to complex. Filamentous fungi, commonly known as molds, refer to those that grow as multicellular colonies.
Biomimetic Materials
Sesquiterpenes
Sesquiterpenes are a class of terpenes consisting of three isoprene units, forming a 15-carbon skeleton, which can be found in various plant essential oils and are known for their diverse chemical structures and biological activities, including anti-inflammatory, antimicrobial, and cytotoxic properties.
NAD
A coenzyme composed of ribosylnicotinamide 5'-diphosphate coupled to adenosine 5'-phosphate by pyrophosphate linkage. It is found widely in nature and is involved in numerous enzymatic reactions in which it serves as an electron carrier by being alternately oxidized (NAD+) and reduced (NADH). (Dorland, 27th ed)
Mutation
Pyruvic Acid
An intermediate compound in the metabolism of carbohydrates, proteins, and fats. In thiamine deficiency, its oxidation is retarded and it accumulates in the tissues, especially in nervous structures. (From Stedman, 26th ed)
Mixed Function Oxygenases
Widely distributed enzymes that carry out oxidation-reduction reactions in which one atom of the oxygen molecule is incorporated into the organic substrate; the other oxygen atom is reduced and combined with hydrogen ions to form water. They are also known as monooxygenases or hydroxylases. These reactions require two substrates as reductants for each of the two oxygen atoms. There are different classes of monooxygenases depending on the type of hydrogen-providing cosubstrate (COENZYMES) required in the mixed-function oxidation.
Nanofibers
Software
Acyltransferases
Models, Genetic
Gene Expression Profiling
Alkaloids
Organic nitrogenous bases. Many alkaloids of medical importance occur in the animal and vegetable kingdoms, and some have been synthesized. (Grant & Hackh's Chemical Dictionary, 5th ed)
Guided Tissue Regeneration
Procedures for enhancing and directing tissue repair and renewal processes, such as BONE REGENERATION; NERVE REGENERATION; etc. They involve surgically implanting growth conducive tracks or conduits (TISSUE SCAFFOLDING) at the damaged site to stimulate and control the location of cell repopulation. The tracks or conduits are made from synthetic and/or natural materials and may include support cells and induction factors for CELL GROWTH PROCESSES; or CELL MIGRATION.
Gas Chromatography-Mass Spectrometry
A microanalytical technique combining mass spectrometry and gas chromatography for the qualitative as well as quantitative determinations of compounds.
Hydrogen
The first chemical element in the periodic table. It has the atomic symbol H, atomic number 1, and atomic weight [1.00784; 1.00811]. It exists, under normal conditions, as a colorless, odorless, tasteless, diatomic gas. Hydrogen ions are PROTONS. Besides the common H1 isotope, hydrogen exists as the stable isotope DEUTERIUM and the unstable, radioactive isotope TRITIUM.
DNA Primers
Saccharomyces cerevisiae Proteins
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.
Mass Spectrometry
Bone Regeneration
Polymers
Substrate Specificity
Multigene Family
A set of genes descended by duplication and variation from some ancestral gene. Such genes may be clustered together on the same chromosome or dispersed on different chromosomes. Examples of multigene families include those that encode the hemoglobins, immunoglobulins, histocompatibility antigens, actins, tubulins, keratins, collagens, heat shock proteins, salivary glue proteins, chorion proteins, cuticle proteins, yolk proteins, and phaseolins, as well as histones, ribosomal RNA, and transfer RNA genes. The latter three are examples of reiterated genes, where hundreds of identical genes are present in a tandem array. (King & Stanfield, A Dictionary of Genetics, 4th ed)
Genes, Bacterial
The functional hereditary units of BACTERIA.