Gene Expression Regulation: 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.Gene Expression Profiling: The determination of the pattern of genes expressed at the level of GENETIC TRANSCRIPTION, under specific circumstances or in a specific cell.Gene Expression Regulation, Plant: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in plants.Oligonucleotide Array Sequence Analysis: 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.Plants, Genetically Modified: PLANTS, or their progeny, whose GENOME has been altered by GENETIC ENGINEERING.MicroRNAs: Small double-stranded, non-protein coding RNAs, 21-25 nucleotides in length generated from single-stranded microRNA gene transcripts by the same RIBONUCLEASE III, Dicer, that produces small interfering RNAs (RNA, SMALL INTERFERING). They become part of the RNA-INDUCED SILENCING COMPLEX and repress the translation (TRANSLATION, GENETIC) of target RNA by binding to homologous 3'UTR region as an imperfect match. The small temporal RNAs (stRNAs), let-7 and lin-4, from C. elegans, are the first 2 miRNAs discovered, and are from a class of miRNAs involved in developmental timing.Gene Expression Regulation, Developmental: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action during the developmental stages of an organism.Gene Expression: The phenotypic manifestation of a gene or genes by the processes of GENETIC TRANSCRIPTION and GENETIC TRANSLATION.RNA, Messenger: RNA sequences that serve as templates for protein synthesis. Bacterial mRNAs are generally primary transcripts in that they do not require post-transcriptional processing. Eukaryotic mRNA is synthesized in the nucleus and must be exported to the cytoplasm for translation. Most eukaryotic mRNAs have a sequence of polyadenylic acid at the 3' end, referred to as the poly(A) tail. The function of this tail is not known for certain, but it may play a role in the export of mature mRNA from the nucleus as well as in helping stabilize some mRNA molecules by retarding their degradation in the cytoplasm.Transcription, Genetic: The biosynthesis of RNA carried out on a template of DNA. The biosynthesis of DNA from an RNA template is called REVERSE TRANSCRIPTION.Promoter Regions, Genetic: DNA sequences which are recognized (directly or indirectly) and bound by a DNA-dependent RNA polymerase during the initiation of transcription. Highly conserved sequences within the promoter include the Pribnow box in bacteria and the TATA BOX in eukaryotes.Base Sequence: The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.RNA, Untranslated: RNA which does not code for protein but has some enzymatic, structural or regulatory function. Although ribosomal RNA (RNA, RIBOSOMAL) and transfer RNA (RNA, TRANSFER) are also untranslated RNAs they are not included in this scope.Transcription Factors: Endogenous substances, usually proteins, which are effective in the initiation, stimulation, or termination of the genetic transcription process.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)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.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.Plant Roots: The usually underground portions of a plant that serve as support, store food, and through which water and mineral nutrients enter the plant. (From American Heritage Dictionary, 1982; Concise Dictionary of Biology, 1990)Genes, Plant: The functional hereditary units of PLANTS.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.Chromatin: The material of CHROMOSOMES. It is a complex of DNA; HISTONES; and nonhistone proteins (CHROMOSOMAL PROTEINS, NON-HISTONE) found within the nucleus of a cell.Genome: The genetic complement of an organism, including all of its GENES, as represented in its DNA, or in some cases, its RNA.Models, Genetic: 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.Gene Expression Regulation, Neoplastic: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in neoplastic tissue.Binding Sites: The parts of a macromolecule that directly participate in its specific combination with another molecule.Gene Expression Regulation, Archaeal: Any of the processes by which cytoplasmic or intercellular factors influence the differential control of gene action in archaea.Plant Extracts: Concentrated pharmaceutical preparations of plants obtained by removing active constituents with a suitable solvent, which is evaporated away, and adjusting the residue to a prescribed standard.Plant Shoots: New immature growth of a plant including stem, leaves, tips of branches, and SEEDLINGS.Gene Expression Regulation, Fungal: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in fungi.Algorithms: A procedure consisting of a sequence of algebraic formulas and/or logical steps to calculate or determine a given task.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.Nucleic Acid Conformation: The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape.DNA, Plant: Deoxyribonucleic acid that makes up the genetic material of plants.Plants, Medicinal: Plants whose roots, leaves, seeds, bark, or other constituent parts possess therapeutic, tonic, purgative, curative or other pharmacologic attributes, when administered to man or animals.Reverse Transcriptase Polymerase Chain Reaction: A variation of the PCR technique in which cDNA is made from RNA via reverse transcription. The resultant cDNA is then amplified using standard PCR protocols.Plant Development: Processes orchestrated or driven by a plethora of genes, plant hormones, and inherent biological timing mechanisms facilitated by secondary molecules, which result in the systematic transformation of plants and plant parts, from one stage of maturity to another.Plants, Toxic: Plants or plant parts which are harmful to man or other animals.Transcriptome: The pattern of GENE EXPRESSION at the level of genetic transcription in a specific organism or under specific circumstances in specific cells.Plant Cells: Basic functional unit of plants.Signal Transduction: 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.Plant Stems: Parts of plants that usually grow vertically upwards towards the light and support the leaves, buds, and reproductive structures. (From Concise Dictionary of Biology, 1990)Gene Expression Regulation, Enzymologic: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in enzyme synthesis.Genome, Plant: The genetic complement of a plant (PLANTS) as represented in its DNA.RNA Stability: The extent to which an RNA molecule retains its structural integrity and resists degradation by RNASE, and base-catalyzed HYDROLYSIS, under changing in vivo or in vitro conditions.Cell Line: Established cell cultures that have the potential to propagate indefinitely.Gene Regulatory Networks: 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.DNA-Binding Proteins: Proteins which bind to DNA. The family includes proteins which bind to both double- and single-stranded DNA and also includes specific DNA binding proteins in serum which can be used as markers for malignant diseases.Evolution, Molecular: The process of cumulative change at the level of DNA; RNA; and PROTEINS, over successive generations.Down-Regulation: A negative regulatory effect on physiological processes at the molecular, cellular, or systemic level. At the molecular level, the major regulatory sites include membrane receptors, genes (GENE EXPRESSION REGULATION), mRNAs (RNA, MESSENGER), and proteins.Amino Acid Sequence: The order of amino acids as they occur in a polypeptide chain. This is referred to as the primary structure of proteins. It is of fundamental importance in determining PROTEIN CONFORMATION.Gene Expression Regulation, Bacterial: Any of the processes by which cytoplasmic or intercellular factors influence the differential control of gene action in bacteria.Sequence Analysis, RNA: A multistage process that includes cloning, physical mapping, subcloning, sequencing, and information analysis of an RNA SEQUENCE.Up-Regulation: A positive regulatory effect on physiological processes at the molecular, cellular, or systemic level. At the molecular level, the major regulatory sites include membrane receptors, genes (GENE EXPRESSION REGULATION), mRNAs (RNA, MESSENGER), and proteins.Gene Expression Regulation, Viral: Any of the processes by which cytoplasmic factors influence the differential control of gene action in viruses.3' Untranslated Regions: The sequence at the 3' end of messenger RNA that does not code for product. This region contains transcription and translation regulating sequences.Plant Structures: The parts of plants, including SEEDS.Plant Growth Regulators: Any of the hormones produced naturally in plants and active in controlling growth and other functions. There are three primary classes: auxins, cytokinins, and gibberellins.Plants, Edible: An organism of the vegetable kingdom suitable by nature for use as a food, especially by human beings. Not all parts of any given plant are edible but all parts of edible plants have been known to figure as raw or cooked food: leaves, roots, tubers, stems, seeds, buds, fruits, and flowers. The most commonly edible parts of plants are FRUIT, usually sweet, fleshy, and succulent. Most edible plants are commonly cultivated for their nutritional value and are referred to as VEGETABLES.Epigenesis, Genetic: A genetic process by which the adult organism is realized via mechanisms that lead to the restriction in the possible fates of cells, eventually leading to their differentiated state. Mechanisms involved cause heritable changes to cells without changes to DNA sequence such as DNA METHYLATION; HISTONE modification; DNA REPLICATION TIMING; NUCLEOSOME positioning; and heterochromatization which result in selective gene expression or repression.Cells, Cultured: Cells propagated in vitro in special media conducive to their growth. Cultured cells are used to study developmental, morphologic, metabolic, physiologic, and genetic processes, among others.5' Untranslated Regions: The sequence at the 5' end of the messenger RNA that does not code for product. This sequence contains the ribosome binding site and other transcription and translation regulating sequences.Models, Biological: 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.Arabidopsis Proteins: Proteins that originate from plants species belonging to the genus ARABIDOPSIS. The most intensely studied species of Arabidopsis, Arabidopsis thaliana, is commonly used in laboratory experiments.Alternative Splicing: A process whereby multiple RNA transcripts are generated from a single gene. Alternative splicing involves the splicing together of other possible sets of EXONS during the processing of some, but not all, transcripts of the gene. Thus a particular exon may be connected to any one of several alternative exons to form a mature RNA. The alternative forms of mature MESSENGER RNA produce PROTEIN ISOFORMS in which one part of the isoforms is common while the other parts are different.Cell Line, Tumor: A cell line derived from cultured tumor cells.Conserved Sequence: A sequence of amino acids in a polypeptide or of nucleotides in DNA or RNA that is similar across multiple species. A known set of conserved sequences is represented by a CONSENSUS SEQUENCE. AMINO ACID MOTIFS are often composed of conserved sequences.Histones: Small chromosomal proteins (approx 12-20 kD) possessing an open, unfolded structure and attached to the DNA in cell nuclei by ionic linkages. Classification into the various types (designated histone I, histone II, etc.) is based on the relative amounts of arginine and lysine in each.DNA Methylation: Addition of methyl groups to DNA. DNA methyltransferases (DNA methylases) perform this reaction using S-ADENOSYLMETHIONINE as the methyl group donor.Tobacco: A plant genus of the family SOLANACEAE. Members contain NICOTINE and other biologically active chemicals; its dried leaves are used for SMOKING.Gene Expression Regulation, Leukemic: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in leukemia.Plant Immunity: The inherent or induced capacity of plants to withstand or ward off biological attack by pathogens.Sequence Analysis, DNA: A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.Software: Sequential operating programs and data which instruct the functioning of a digital computer.Mutation: 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.Cluster Analysis: 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.Plant Epidermis: A thin layer of cells forming the outer integument of seed plants and ferns. (Random House Unabridged Dictionary, 2d ed)Phenotype: The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment.Genes, Reporter: Genes whose expression is easily detectable and therefore used to study promoter activity at many positions in a target genome. In recombinant DNA technology, these genes may be attached to a promoter region of interest.DNA Primers: Short sequences (generally about 10 base pairs) of DNA that are complementary to sequences of messenger RNA and allow reverse transcriptases to start copying the adjacent sequences of mRNA. Primers are used extensively in genetic and molecular biology techniques.Phylogeny: The relationships of groups of organisms as reflected by their genetic makeup.Angiosperms: Members of the group of vascular plants which bear flowers. They are differentiated from GYMNOSPERMS by their production of seeds within a closed chamber (OVARY, PLANT). The Angiosperms division is composed of two classes, the monocotyledons (Liliopsida) and dicotyledons (Magnoliopsida). Angiosperms represent approximately 80% of all known living plants.Plant Stomata: Closable openings in the epidermis of plants on the underside of leaves. They allow the exchange of gases between the internal tissues of the plant and the outside atmosphere.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.DNA, Complementary: Single-stranded complementary DNA synthesized from an RNA template by the action of RNA-dependent DNA polymerase. cDNA (i.e., complementary DNA, not circular DNA, not C-DNA) is used in a variety of molecular cloning experiments as well as serving as a specific hybridization probe.Flowers: The reproductive organs of plants.Blotting, Northern: Detection of RNA that has been electrophoretically separated and immobilized by blotting on nitrocellulose or other type of paper or nylon membrane followed by hybridization with labeled NUCLEIC ACID PROBES.Microarray Analysis: The simultaneous analysis, on a microchip, of multiple samples or targets arranged in an array format.Polymerase Chain Reaction: In vitro method for producing large amounts of specific DNA or RNA fragments of defined length and sequence from small amounts of short oligonucleotide flanking sequences (primers). The essential steps include thermal denaturation of the double-stranded target molecules, annealing of the primers to their complementary sequences, and extension of the annealed primers by enzymatic synthesis with DNA polymerase. The reaction is efficient, specific, and extremely sensitive. Uses for the reaction include disease diagnosis, detection of difficult-to-isolate pathogens, mutation analysis, genetic testing, DNA sequencing, and analyzing evolutionary relationships.Lycopersicon esculentum: A plant species of the family SOLANACEAE, native of South America, widely cultivated for their edible, fleshy, usually red fruit.RNA: A polynucleotide consisting essentially of chains with a repeating backbone of phosphate and ribose units to which nitrogenous bases are attached. RNA is unique among biological macromolecules in that it can encode genetic information, serve as an abundant structural component of cells, and also possesses catalytic activity. (Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed)Time Factors: Elements of limited time intervals, contributing to particular results or situations.Transfection: The uptake of naked or purified DNA by CELLS, usually meaning the process as it occurs in eukaryotic cells. It is analogous to bacterial transformation (TRANSFORMATION, BACTERIAL) and both are routinely employed in GENE TRANSFER TECHNIQUES.Cell Differentiation: Progressive restriction of the developmental potential and increasing specialization of function that leads to the formation of specialized cells, tissues, and organs.Transcriptional Activation: Processes that stimulate the GENETIC TRANSCRIPTION of a gene or set of genes.In Situ Hybridization: A technique that localizes specific nucleic acid sequences within intact chromosomes, eukaryotic cells, or bacterial cells through the use of specific nucleic acid-labeled probes.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)Trans-Activators: Diffusible gene products that act on homologous or heterologous molecules of viral or cellular DNA to regulate the expression of proteins.Zea mays: A plant species of the family POACEAE. It is a tall grass grown for its EDIBLE GRAIN, corn, used as food and animal FODDER.Repressor Proteins: Proteins which maintain the transcriptional quiescence of specific GENES or OPERONS. Classical repressor proteins are DNA-binding proteins that are normally bound to the OPERATOR REGION of an operon, or the ENHANCER SEQUENCES of a gene until a signal occurs that causes their release.Plant Poisoning: Poisoning by the ingestion of plants or its leaves, berries, roots or stalks. The manifestations in both humans and animals vary in severity from mild to life threatening. In animals, especially domestic animals, it is usually the result of ingesting moldy or fermented forage.Plant Transpiration: The loss of water vapor by plants to the atmosphere. It occurs mainly from the leaves through pores (stomata) whose primary function is gas exchange. The water is replaced by a continuous column of water moving upwards from the roots within the xylem vessels. (Concise Dictionary of Biology, 1990)Seedling: Very young plant after GERMINATION of SEEDS.Species Specificity: 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.Sequence Alignment: The arrangement of two or more amino acid or base sequences from an organism or organisms in such a way as to align areas of the sequences sharing common properties. The degree of relatedness or homology between the sequences is predicted computationally or statistically based on weights assigned to the elements aligned between the sequences. This in turn can serve as a potential indicator of the genetic relatedness between the organisms.Chromosomes, Plant: Complex nucleoprotein structures which contain the genomic DNA and are part of the CELL NUCLEUS of PLANTS.Real-Time Polymerase Chain Reaction: Methods used for detecting the amplified DNA products from the polymerase chain reaction as they accumulate instead of at the end of the reaction.Nuclear Proteins: Proteins found in the nucleus of a cell. Do not confuse with NUCLEOPROTEINS which are proteins conjugated with nucleic acids, that are not necessarily present in the nucleus.Plant Tumors: A localized proliferation of plant tissue forming a swelling or outgrowth, commonly with a characteristic shape and unlike any organ of the normal plant. Plant tumors or galls usually form in response to the action of a pathogen or a pest. (Holliday, P., A Dictionary of Plant Pathology, 1989, p330)Cell Nucleus: Within a eukaryotic cell, a membrane-limited body which contains chromosomes and one or more nucleoli (CELL NUCLEOLUS). The nuclear membrane consists of a double unit-type membrane which is perforated by a number of pores; the outermost membrane is continuous with the ENDOPLASMIC RETICULUM. A cell may contain more than one nucleus. (From Singleton & Sainsbury, Dictionary of Microbiology and Molecular Biology, 2d ed)Gene Silencing: Interruption or suppression of the expression of a gene at transcriptional or translational levels.Protein Binding: The process in which substances, either endogenous or exogenous, bind to proteins, peptides, enzymes, protein precursors, or allied compounds. Specific protein-binding measures are often used as assays in diagnostic assessments.Plant Components, Aerial: The above-ground plant without the roots.Expressed Sequence Tags: Partial cDNA (DNA, COMPLEMENTARY) sequences that are unique to the cDNAs from which they were derived.Mice, Inbred C57BLDNA: A deoxyribonucleotide polymer that is the primary genetic material of all cells. Eukaryotic and prokaryotic organisms normally contain DNA in a double-stranded state, yet several important biological processes transiently involve single-stranded regions. DNA, which consists of a polysugar-phosphate backbone possessing projections of purines (adenine and guanine) and pyrimidines (thymine and cytosine), forms a double helix that is held together by hydrogen bonds between these purines and pyrimidines (adenine to thymine and guanine to cytosine).Oxylipins: Eighteen-carbon cyclopentyl polyunsaturated fatty acids derived from ALPHA-LINOLENIC ACID via an oxidative pathway analogous to the EICOSANOIDS in animals. Biosynthesis is inhibited by SALICYLATES. A key member, jasmonic acid of PLANTS, plays a similar role to ARACHIDONIC ACID in animals.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.Bacterial Proteins: Proteins found in any species of bacterium.Homeodomain Proteins: Proteins encoded by homeobox genes (GENES, HOMEOBOX) that exhibit structural similarity to certain prokaryotic and eukaryotic DNA-binding proteins. Homeodomain proteins are involved in the control of gene expression during morphogenesis and development (GENE EXPRESSION REGULATION, DEVELOPMENTAL).Stress, Physiological: The unfavorable effect of environmental factors (stressors) on the physiological functions of an organism. Prolonged unresolved physiological stress can affect HOMEOSTASIS of the organism, and may lead to damaging or pathological conditions.Cyclopentanes: A group of alicyclic hydrocarbons with the general formula R-C5H9.Liver: A large lobed glandular organ in the abdomen of vertebrates that is responsible for detoxification, metabolism, synthesis and storage of various substances.Databases, Genetic: Databases devoted to knowledge about specific genes and gene products.Plant Preparations: Material prepared from plants.Photosynthesis: 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)Organ Specificity: Characteristic restricted to a particular organ of the body, such as a cell type, metabolic response or expression of a particular protein or antigen.Symbiosis: The relationship between two different species of organisms that are interdependent; each gains benefits from the other or a relationship between different species where both of the organisms in question benefit from the presence of the other.Blotting, Western: Identification of proteins or peptides that have been electrophoretically separated by blot transferring from the electrophoresis gel to strips of nitrocellulose paper, followed by labeling with antibody probes.Luciferases: Enzymes that oxidize certain LUMINESCENT AGENTS to emit light (PHYSICAL LUMINESCENCE). The luciferases from different organisms have evolved differently so have different structures and substrates.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.RNA Interference: A gene silencing phenomenon whereby specific dsRNAs (RNA, DOUBLE-STRANDED) trigger the degradation of homologous mRNA (RNA, MESSENGER). The specific dsRNAs are processed into SMALL INTERFERING RNA (siRNA) which serves as a guide for cleavage of the homologous mRNA in the RNA-INDUCED SILENCING COMPLEX. DNA METHYLATION may also be triggered during this process.Fabaceae: The large family of plants characterized by pods. Some are edible and some cause LATHYRISM or FAVISM and other forms of poisoning. Other species yield useful materials like gums from ACACIA and various LECTINS like PHYTOHEMAGGLUTININS from PHASEOLUS. Many of them harbor NITROGEN FIXATION bacteria on their roots. Many but not all species of "beans" belong to this family.Indoleacetic Acids: Acetic acid derivatives of the heterocyclic compound indole. (Merck Index, 11th ed)Recombinant Fusion Proteins: Recombinant proteins produced by the GENETIC TRANSLATION of fused genes formed by the combination of NUCLEIC ACID REGULATORY SEQUENCES of one or more genes with the protein coding sequences of one or more genes.Gene Library: A large collection of DNA fragments cloned (CLONING, MOLECULAR) from a given organism, tissue, organ, or cell type. It may contain complete genomic sequences (GENOMIC LIBRARY) or complementary DNA sequences, the latter being formed from messenger RNA and lacking intron sequences.Herbivory: The act of feeding on plants by animals.Tumor Cells, Cultured: Cells grown in vitro from neoplastic tissue. If they can be established as a TUMOR CELL LINE, they can be propagated in cell culture indefinitely.Biomass: 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.Salicylic Acid: A compound obtained from the bark of the white willow and wintergreen leaves. It has bacteriostatic, fungicidal, and keratolytic actions.Green Fluorescent Proteins: Protein analogs and derivatives of the Aequorea victoria green fluorescent protein that emit light (FLUORESCENCE) when excited with ULTRAVIOLET RAYS. They are used in REPORTER GENES in doing GENETIC TECHNIQUES. Numerous mutants have been made to emit other colors or be sensitive to pH.Reproducibility of Results: 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.Power Plants: Units that convert some other form of energy into electrical energy.Genomics: The systematic study of the complete DNA sequences (GENOME) of organisms.Light: That portion of the electromagnetic spectrum in the visible, ultraviolet, and infrared range.Solanum tuberosum: A plant species of the genus SOLANUM, family SOLANACEAE. The starchy roots are used as food. SOLANINE is found in green parts.Regulatory Sequences, Nucleic Acid: Nucleic acid sequences involved in regulating the expression of genes.Transgenes: Genes that are introduced into an organism using GENE TRANSFER TECHNIQUES.Immunohistochemistry: Histochemical localization of immunoreactive substances using labeled antibodies as reagents.Abscisic Acid: Abscission-accelerating plant growth substance isolated from young cotton fruit, leaves of sycamore, birch, and other plants, and from potatoes, lemons, avocados, and other fruits.Plant Nectar: Sugar-rich liquid produced in plant glands called nectaries. It is either produced in flowers or other plant structures, providing a source of attraction for pollinating insects and animals, as well as being a nutrient source to animal mutualists which provide protection of plants against herbivores.RNA, Small Interfering: Small double-stranded, non-protein coding RNAs (21-31 nucleotides) involved in GENE SILENCING functions, especially RNA INTERFERENCE (RNAi). Endogenously, siRNAs are generated from dsRNAs (RNA, DOUBLE-STRANDED) by the same ribonuclease, Dicer, that generates miRNAs (MICRORNAS). The perfect match of the siRNAs' antisense strand to their target RNAs mediates RNAi by siRNA-guided RNA cleavage. siRNAs fall into different classes including trans-acting siRNA (tasiRNA), repeat-associated RNA (rasiRNA), small-scan RNA (scnRNA), and Piwi protein-interacting RNA (piRNA) and have different specific gene silencing functions.Adaptation, Physiological: The non-genetic biological changes of an organism in response to challenges in its ENVIRONMENT.Rats, Sprague-Dawley: A strain of albino rat used widely for experimental purposes because of its calmness and ease of handling. It was developed by the Sprague-Dawley Animal Company.Enhancer Elements, Genetic: Cis-acting DNA sequences which can increase transcription of genes. Enhancers can usually function in either orientation and at various distances from a promoter.Chromatin Immunoprecipitation: A technique for identifying specific DNA sequences that are bound, in vivo, to proteins of interest. It involves formaldehyde fixation of CHROMATIN to crosslink the DNA-BINDING PROTEINS to the DNA. After shearing the DNA into small fragments, specific DNA-protein complexes are isolated by immunoprecipitation with protein-specific ANTIBODIES. Then, the DNA isolated from the complex can be identified by PCR amplification and sequencing.Mice, Transgenic: Laboratory mice that have been produced from a genetically manipulated EGG or EMBRYO, MAMMALIAN.Response Elements: Nucleotide sequences, usually upstream, which are recognized by specific regulatory transcription factors, thereby causing gene response to various regulatory agents. These elements may be found in both promoter and enhancer regions.Plant Bark: The outer layer of the woody parts of plants.Germination: The initial stages of the growth of SEEDS into a SEEDLINGS. The embryonic shoot (plumule) and embryonic PLANT ROOTS (radicle) emerge and grow upwards and downwards respectively. Food reserves for germination come from endosperm tissue within the seed and/or from the seed leaves (COTYLEDON). (Concise Dictionary of Biology, 1990)Cloning, Molecular: The insertion of recombinant DNA molecules from prokaryotic and/or eukaryotic sources into a replicating vehicle, such as a plasmid or virus vector, and the introduction of the resultant hybrid molecules into recipient cells without altering the viability of those cells.Mycorrhizae: Symbiotic combination (dual organism) of the MYCELIUM of FUNGI with the roots of plants (PLANT ROOTS). The roots of almost all higher plants exhibit this mutually beneficial relationship, whereby the fungus supplies water and mineral salts to the plant, and the plant supplies CARBOHYDRATES to the fungus. There are two major types of mycorrhizae: ectomycorrhizae and endomycorrhizae.Soil: The unconsolidated mineral or organic matter on the surface of the earth that serves as a natural medium for the growth of land plants.Root Nodules, Plant: Knobbed structures formed from and attached to plant roots, especially of LEGUMES, which result from symbiotic infection by nitrogen fixing bacteria such as RHIZOBIUM or FRANKIA. Root nodules are structures related to MYCORRHIZAE formed by symbiotic associations with fungi.Recombinant Proteins: Proteins prepared by recombinant DNA technology.Chloroplasts: Plant cell inclusion bodies that contain the photosynthetic pigment CHLOROPHYLL, which is associated with the membrane of THYLAKOIDS. Chloroplasts occur in cells of leaves and young stems of plants. They are also found in some forms of PHYTOPLANKTON such as HAPTOPHYTA; DINOFLAGELLATES; DIATOMS; and CRYPTOPHYTA.Chromosome Mapping: Any method used for determining the location of and relative distances between genes on a chromosome.Host-Pathogen Interactions: The interactions between a host and a pathogen, usually resulting in disease.Nitrogen: An element with the atomic symbol N, atomic number 7, and atomic weight [14.00643; 14.00728]. Nitrogen exists as a diatomic gas and makes up about 78% of the earth's atmosphere by volume. It is a constituent of proteins and nucleic acids and found in all living cells.Germ Cells, Plant: The reproductive cells of plants.Droughts: Prolonged dry periods in natural climate cycle. They are slow-onset phenomena caused by rainfall deficit combined with other predisposing factors.Plant Physiological Processes: Physiological functions characteristic of plants.Cell Proliferation: All of the processes involved in increasing CELL NUMBER including CELL DIVISION.Protein Biosynthesis: The biosynthesis of PEPTIDES and PROTEINS on RIBOSOMES, directed by MESSENGER RNA, via TRANSFER RNA that is charged with standard proteinogenic AMINO ACIDS.Ecosystem: A functional system which includes the organisms of a natural community together with their environment. (McGraw Hill Dictionary of Scientific and Technical Terms, 4th ed)Brassica: A plant genus of the family Cruciferae. It contains many species and cultivars used as food including cabbage, cauliflower, broccoli, Brussel sprouts, kale, collard greens, MUSTARD PLANT; (B. alba, B. junica, and B. nigra), turnips (BRASSICA NAPUS) and rapeseed (BRASSICA RAPA).Carrier Proteins: Transport proteins that carry specific substances in the blood or across cell membranes.Transformation, Genetic: Change brought about to an organisms genetic composition by unidirectional transfer (TRANSFECTION; TRANSDUCTION, GENETIC; CONJUGATION, GENETIC, etc.) and incorporation of foreign DNA into prokaryotic or eukaryotic cells by recombination of part or all of that DNA into the cell's genome.Saccharomyces cerevisiae: 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.Pollen: The fertilizing element of plants that contains the male GAMETOPHYTES.Genetic Variation: Genotypic differences observed among individuals in a population.Hordeum: A plant genus of the family POACEAE. The EDIBLE GRAIN, barley, is widely used as food.NF-kappa B: Ubiquitous, inducible, nuclear transcriptional activator that binds to enhancer elements in many different cell types and is activated by pathogenic stimuli. The NF-kappa B complex is a heterodimer composed of two DNA-binding subunits: NF-kappa B1 and relA.Nucleic Acid Hybridization: Widely used technique which exploits the ability of complementary sequences in single-stranded DNAs or RNAs to pair with each other to form a double helix. Hybridization can take place between two complimentary DNA sequences, between a single-stranded DNA and a complementary RNA, or between two RNA sequences. The technique is used to detect and isolate specific sequences, measure homology, or define other characteristics of one or both strands. (Kendrew, Encyclopedia of Molecular Biology, 1994, p503)Apoptosis: One of the mechanisms by which CELL DEATH occurs (compare with NECROSIS and AUTOPHAGOCYTOSIS). Apoptosis is the mechanism responsible for the physiological deletion of cells and appears to be intrinsically programmed. It is characterized by distinctive morphologic changes in the nucleus and cytoplasm, chromatin cleavage at regularly spaced sites, and the endonucleolytic cleavage of genomic DNA; (DNA FRAGMENTATION); at internucleosomal sites. This mode of cell death serves as a balance to mitosis in regulating the size of animal tissues and in mediating pathologic processes associated with tumor growth.Membrane Proteins: Proteins which are found in membranes including cellular and intracellular membranes. They consist of two types, peripheral and integral proteins. They include most membrane-associated enzymes, antigenic proteins, transport proteins, and drug, hormone, and lectin receptors.Triticum: A plant genus of the family POACEAE that is the source of EDIBLE GRAIN. A hybrid with rye (SECALE CEREALE) is called TRITICALE. The seed is ground into FLOUR and used to make BREAD, and is the source of WHEAT GERM AGGLUTININS.Plant Lectins: Protein or glycoprotein substances of plant origin that bind to sugar moieties in cell walls or membranes. Some carbohydrate-metabolizing proteins (ENZYMES) from PLANTS also bind to carbohydrates, however they are not considered lectins. Many plant lectins change the physiology of the membrane of BLOOD CELLS to cause agglutination, mitosis, or other biochemical changes. They may play a role in plant defense mechanisms.Medicine, Traditional: Systems of medicine based on cultural beliefs and practices handed down from generation to generation. The concept includes mystical and magical rituals (SPIRITUAL THERAPIES); PHYTOTHERAPY; and other treatments which may not be explained by modern medicine.HeLa Cells: The first continuously cultured human malignant CELL LINE, derived from the cervical carcinoma of Henrietta Lacks. These cells are used for VIRUS CULTIVATION and antitumor drug screening assays.Phytotherapy: Use of plants or herbs to treat diseases or to alleviate pain.Plant Exudates: Substances released by PLANTS such as PLANT GUMS and PLANT RESINS.Proteins: 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.Soybeans: An annual legume. The SEEDS of this plant are edible and used to produce a variety of SOY FOODS.Fibroblasts: Connective tissue cells which secrete an extracellular matrix rich in collagen and other macromolecules.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.Plant Infertility: The failure of PLANTS to complete fertilization and obtain seed (SEEDS) as a result of defective POLLEN or ovules, or other aberrations. (Dict. of Plant Genet. and Mol. Biol., 1998)GlucuronidaseGene 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.Disease Resistance: The capacity of an organism to defend itself against pathological processes or the agents of those processes. This most often involves innate immunity whereby the organism responds to pathogens in a generic way. The term disease resistance is used most frequently when referring to plants.Poaceae: A large family of narrow-leaved herbaceous grasses of the order Cyperales, subclass Commelinidae, class Liliopsida (monocotyledons). Food grains (EDIBLE GRAIN) come from members of this family. RHINITIS, ALLERGIC, SEASONAL can be induced by POLLEN of many of the grasses.Mice, Knockout: Strains of mice in which certain GENES of their GENOMES have been disrupted, or "knocked-out". To produce knockouts, using RECOMBINANT DNA technology, the normal DNA sequence of the gene being studied is altered to prevent synthesis of a normal gene product. Cloned cells in which this DNA alteration is successful are then injected into mouse EMBRYOS to produce chimeric mice. The chimeric mice are then bred to yield a strain in which all the cells of the mouse contain the disrupted gene. Knockout mice are used as EXPERIMENTAL ANIMAL MODELS for diseases (DISEASE MODELS, ANIMAL) and to clarify the functions of the genes.

Loss-of-function mutations in the rice homeobox gene OSH15 affect the architecture of internodes resulting in dwarf plants. (1/14262)

The rice homeobox gene OSH15 (Oryza sativa homeobox) is a member of the knotted1-type homeobox gene family. We report here on the identification and characterization of a loss-of-function mutation in OSH15 from a library of retrotransposon-tagged lines of rice. Based on the phenotype and map position, we have identified three independent deletion alleles of the locus among conventional morphological mutants. All of these recessive mutations, which are considered to be null alleles, exhibit defects in internode elongation. Introduction of a 14 kbp genomic DNA fragment that includes all exons, introns and 5'- and 3'- flanking sequences of OSH15 complemented the defects in internode elongation, confirming that they were caused by the loss-of-function of OSH15. Internodes of the mutants had abnormal-shaped epidermal and hypodermal cells and showed an unusual arrangement of small vascular bundles. These mutations demonstrate a role for OSH15 in the development of rice internodes. This is the first evidence that the knotted1-type homeobox genes have roles other than shoot apical meristem formation and/or maintenance in plant development.  (+info)

Enhanced resistance to bacterial diseases of transgenic tobacco plants overexpressing sarcotoxin IA, a bactericidal peptide of insect. (2/14262)

Sarcotoxin IA is a bactericidal peptide of 39 amino acids found in the common flesh fly, Sarcophaga peregrina. Many agronomically important bacteria in Japan are killed by this peptide at sub-micro molar levels, and the growth of tobacco and rice suspension cultured cells is not inhibited with less than 25 microM. Transgenic tobacco plants which overexpress the peptide, i.e. over 250 pmol per gram of fresh leaf, under the control of a high expression constitutive promoter showed enhanced resistance to the pathogens for wild fire disease (Pseudomonas syringae pv. tabaci) and bacterial soft rot disease (Erwinia carotovora subsp. carotovora).  (+info)

Male gametic cell-specific gene expression in flowering plants. (3/14262)

The role of the male gamete-the sperm cell-in the process of fertilization is to recognize, adhere to, and fuse with the female gamete. These highly specialized functions are expected to be controlled by activation of a unique set of genes. However, male gametic cells traditionally have been regarded as transcriptionally quiescent because of highly condensed chromatin and a very reduced amount of cytoplasm. Here, we provide evidence for male gamete-specific gene expression in flowering plants. We identified and characterized a gene, LGC1, which was shown to be expressed exclusively in the male gametic cells. The gene product of LGC1 was localized at the surface of male gametic cells, suggesting a possible role in sperm-egg interactions. These findings represent an important step toward defining the molecular mechanisms of male gamete development and the cellular processes involved in fertilization of flowering plants.  (+info)

Novel genes induced during an arbuscular mycorrhizal (AM) symbiosis formed between Medicago truncatula and Glomus versiforme. (4/14262)

Many terrestrial plant species are able to form symbiotic associations with arbuscular mycorrhizal fungi. Here we have identified three cDNA clones representing genes whose expression is induced during the arbuscular mycorrhizal symbiosis formed between Medicago truncatula and an arbuscular mycorrhizal fungus, Glomus versiforme. The three clones represent M. truncatula genes and encode novel proteins: a xyloglucan endotransglycosylase-related protein, a putative arabinogalactan protein (AGP), and a putative homologue of the mammalian p110 subunit of initiation factor 3 (eIF3). These genes show little or no expression in M. truncatula roots prior to formation of the symbiosis and are significantly induced following colonization by G. versiforme. The genes are not induced in roots in response to increases in phosphate. This suggests that induction of expression during the symbiosis is due to the interaction with the fungus and is not a secondary effect of improved phosphate nutrition. In situ hybridization revealed that the putative AGP is expressed specifically in cortical cells containing arbuscules. The identification of two mycorrhiza-induced genes encoding proteins predicted to be involved in cell wall structure is consistent with previous electron microscopy data that indicated major alterations in the extracellular matrix of the cortical cells following colonization by mycorrhizal fungi.  (+info)

A novel 53-kDa nodulin of the symbiosome membrane of soybean nodules, controlled by Bradyrhizobium japonicum. (5/14262)

A nodule-specific 53-kDa protein (GmNOD53b) of the symbiosome membrane from soybean was isolated and its LysC digestion products were microsequenced. cDNA clones of this novel nodulin, obtained from cDNA library screening with an RT-PCR (reverse-transcriptase polymerase chain reaction)-generated hybridization probe exhibited no homology to proteins identified so far. The expression of GmNOD53b coincides with the onset of nitrogen fixation. Therefore, it is a late nodulin. Among other changes, the GmNOD53b is significantly reduced in nodules infected with the Bradyrhizobium japonicum mutant 184 on the protein level as well as on the level of mRNA expression, compared with the wild-type infected nodules. The reduction of GmNOD53b mRNA is related to an inactivation of the sipF gene in B. japonicum 184, coding for a functionally active signal peptidase.  (+info)

The auxin-insensitive bodenlos mutation affects primary root formation and apical-basal patterning in the Arabidopsis embryo. (6/14262)

In Arabidopsis embryogenesis, the primary root meristem originates from descendants of both the apical and the basal daughter cell of the zygote. We have isolated a mutant of a new gene named BODENLOS (BDL) in which the primary root meristem is not formed whereas post-embryonic roots develop and bdl seedlings give rise to fertile adult plants. Some bdl seedlings lacked not only the root but also the hypocotyl, thus resembling monopteros (mp) seedlings. In addition, bdl seedlings were insensitive to the auxin analogue 2,4-D, as determined by comparison with auxin resistant1 (axr1) seedlings. bdl embryos deviated from normal development as early as the two-cell stage at which the apical daughter cell of the zygote had divided horizontally instead of vertically. Subsequently, the uppermost derivative of the basal daughter cell, which is normally destined to become the hypophysis, divided abnormally and failed to generate the quiescent centre of the root meristem and the central root cap. We also analysed double mutants. bdl mp embryos closely resembled the two single mutants, bdl and mp, at early stages, while bdl mp seedlings essentially consisted of hypocotyl but did form primary leaves. bdl axr1 embryos approached the mp phenotype at later stages, and bdl axr1 seedlings resembled mp seedlings. Our results suggest that BDL is involved in auxin-mediated processes of apical-basal patterning in the Arabidopsis embryo.  (+info)

NADH-glutamate synthase in alfalfa root nodules. Genetic regulation and cellular expression. (7/14262)

NADH-dependent glutamate synthase (NADH-GOGAT; EC is a key enzyme in primary nitrogen assimilation in alfalfa (Medicago sativa L.) root nodules. Here we report that in alfalfa, a single gene, probably with multiple alleles, encodes for NADH-GOGAT. In situ hybridizations were performed to assess the location of NADH-GOGAT transcript in alfalfa root nodules. In wild-type cv Saranac nodules the NADH-GOGAT gene is predominantly expressed in infected cells. Nodules devoid of bacteroids (empty) induced by Sinorhizobium meliloti 7154 had no NADH-GOGAT transcript detectable by in situ hybridization, suggesting that the presence of the bacteroid may be important for NADH-GOGAT expression. The pattern of expression of NADH-GOGAT shifted during root nodule development. Until d 9 after planting, all infected cells appeared to express NADH-GOGAT. By d 19, a gradient of expression from high in the early symbiotic zone to low in the late symbiotic zone was observed. In 33-d-old nodules expression was seen in only a few cell layers in the early symbiotic zone. This pattern of expression was also observed for the nifH transcript but not for leghemoglobin. The promoter of NADH-GOGAT was evaluated in transgenic alfalfa plants carrying chimeric beta-glucuronidase promoter fusions. The results suggest that there are at least four regulatory elements. The region responsible for expression in the infected cell zone contains an 88-bp direct repeat.  (+info)

A single limit dextrinase gene is expressed both in the developing endosperm and in germinated grains of barley. (8/14262)

The single gene encoding limit dextrinase (pullulan 6-glucanohydrolase; EC in barley (Hordeum vulgare) has 26 introns that range in size from 93 to 822 base pairs. The mature polypeptide encoded by the gene has 884 amino acid residues and a calculated molecular mass of 97,417 D. Limit dextrinase mRNA is abundant in gibberellic acid-treated aleurone layers and in germinated grain. Gibberellic acid response elements were found in the promoter region of the gene. These observations suggest that the enzyme participates in starch hydrolysis during endosperm mobilization in germinated grain. The mRNA encoding the enzyme is present at lower levels in the developing endosperm of immature grain, a location consistent with a role for limit dextrinase in starch synthesis. Enzyme activity was also detected in developing grain. The limit dextrinase has a presequence typical of transit peptides that target nascent polypeptides to amyloplasts, but this would not be expected to direct secretion of the mature enzyme from aleurone cells in germinated grain. It remains to be discovered how the enzyme is released from the aleurone and whether another enzyme, possibly of the isoamylase group, might be equally important for starch hydrolysis in germinated grain.  (+info)

  • Viruses that pack genetic material into stable infectious particles can incorporate some or all of their genes into their hosts' genomes, allowing remnants of infection to remain even after the viruses themselves have moved on. (
  • On a smaller scale, naked genetic elements such as bacterial plasmids and transposons, or jumping genes, often shuttle around and between genomes. (
  • Investigators will develop research on sequencing of genomes, identification of molecular markers and genes associated with agronomic characteristics of interest, production and evaluation of transgenic sugar cane, breeding and characterization of new cultivars, basic research on biology, genetics, biochemistry, plant physiology, regulatory networks of sugar cane and other model plants that may contribute to the development of research on bioenergy or that have biofuel potential. (
  • NOVOMIR is a program that is used for the identification of miRNA genes in plant genomes. (
  • Finding of miRNA genes either needs costly experimental approaches for example, genetics, which led to the detection of the first animal miRNAs cloning and sequencing of cDNA, or deep sequencing or computational prediction methods, which facilitate subsequent experimental verification or falsification. (
  • RNAi was applied to modulation of the metabolic gene concerning biosynthesis of petal color pigment in plant. (
  • The gene of chalcone synthase, the key enzyme of anthocyanin biosynthesis, in trenia (Torenia hybrida) was targeted. (
  • Functional analysis indicated that elevated levels, at harvest and during cold storage, of genes related to antioxidant systems and the biosynthesis of metabolites with antioxidant activity correlates with tolerance. (
  • By contrast, cold storage induced, in sensitivity to woolliness dependant manner, a gene expression program involving the biosynthesis of secondary cell wall and pectins. (
  • The work will be complemented by bioinformatic search for genes of AGP protein backbones and glycosyltransferases responsible for AGP biosynthesis (collaborations see below). (
  • We saw changes in the level of mRNA NAD + capping occurring in different plant tissues and in different developmental stages," says Gregory, senior author on the paper and an associate professor in the School of Arts & Sciences' Department of Biology. (
  • While teaching a class on RNA, Gregory had shared with his students a paper about a yeast version of the plant protein DX01, an enzyme now known to be responsible for removing NAD + from mRNA. (
  • The researchers first confirmed that DX01 acted similarly in plants as in mammals, removing the NAD + from mRNA transcripts. (
  • That's pretty neat becaue it looks like it's a strong regulator of RNA stability, so the plant can destabilize different sets of mRNA transcripts, depending on where this process is acting and what cue is being given. (
  • The plant nucleolus and mRNA biogenesis. (
  • Gene expression is subject to extensive regulation, including transcription, mRNA degradation, translation and protein degradation, each of which operates on a different temporal regime [ 12 - 14 ]. (
  • The aim of my research is to u nderstand how plants respond to abiotic stresses such as drought and high temperature and find ways to improve the growth and productivity of plants/crops under stress conditions. (
  • During periods of drought, researchers have found the turnip mosaic virus can switch from a hindrance to a help, altering its host's circadian clock so the plant loses less water. (
  • This study explores the effects of drought stress in plant virus evolution. (
  • Drought-evolved viruses conferred a significantly higher drought tolerance to infected plants. (
  • Chaves MM, Flexas J, Pinheiro C (2009) Photosynthesis under drought and salt stress: regulation mechanisms from whole plant to cell. (
  • Whole-plant and leaf gas-exchange measurements showed reduced transpiration in the mrp5 mutant compared to control, concomitant with an approximately 20% increase in instantaneous water-use efficiency, and mrp5 mutants had reduced water loss from excised leaves and were less wilty than wild-type plants under drought conditions (Klein et al. (
  • a genetic manipulation, is to reduce transpiration, then, under identical watering regimes, the mutant plant is actually experiencing less drought stress than the wild-type control plant. (
  • Thus, these experiments illustrate the fact that plants employ a diversity of mechanisms to achieve drought tolerance, only some of which involve alterations in stomatal regulation. (
  • Identifying genes that are involved in the plant response to drought stress will enable the development of new grape strains that are tolerant to drought. (
  • Objective: We cloned the VvibZIP14 gene from Vitis vinifera and analyzed its role in drought resistance. (
  • Transgenic plants showed improved resistance to drought stress and reduced electrolyte leakage compared to plants overexpressing empty vector, whereas chlorophyll content, photosystem II maximal photochemical efficiency, and net photosynthetic rate were higher. (
  • Catalase, peroxidase, and superoxide dismutase activities were also increased in VvibZIP14- overexpressing plants subjected to drought stress. (
  • We welcome papers on virion structure and assembly, viral genome replication and regulation of gene expression, genetic diversity and evolution, virus-cell interactions, cellular responses to infection, transformation and oncogenesis, gene delivery, viral pathogenesis and immunity, and vaccines and antiviral agents. (
  • KEY MESSAGE: An anther-specific GRP gene, regulated by PhMYC2 , causes a significant reduction of male fertility when overexpressed in petunia, and its promoter is efficient in genetic engineering of male-sterile lines. (
  • We examined genetic interactions among three ABA response loci,ABI3, ABI4, and ABI5, by comparing phenotypes of mutants, ectopic expression lines, mutants carrying an ectopically expressed transgene, and the corresponding wild-type lines. (
  • It has become evident that invasive intervention in genetic makeup and the transfer of isolated genes cannot be equated with natural mechanisms of heredity and gene regulation. (
  • The basic difference between conventional cultivation and genetic engineering of plants is becoming more and more distinct in the light of current genome research. (
  • They advocate more extensive testing on the compounds and genetic stability of GE plants before they are released into the field and companies can apply for market authorisation. (
  • Their descriptions of gene pools define the limits to which plant breeders can exploit genetic diversity for cultivar development (Figure 1). (
  • The barley- Puccinia hordei (barley leaf rust) pathosystem is a model for investigating partial disease resistance in crop plants and genetic mapping of phenotypic resistance has identified several quantitative trait loci (QTL) for partial resistance. (
  • A total of 1,410 genes were identified as being significantly differentially expressed across the genome, of which 55 were accounted for by the genetic differences defined by QTL-NILs at Rphq 2 and Rphq 3. (
  • Genetic redundancy resulting from whole genome duplication is thought to facilitate evolutionary change through sub- and neo-functionalization among paralogous gene pairs. (
  • Topics: Crops -- Genetic engineering -- Congresses, Plant genetic engineering -- Congresses, Plant genetic. (
  • Plants of a given species will grow to a characteristic size, indicating an intrinsic and hence genetic control for organ size. (
  • Sangiovese berries before and after thinning at veraison using a genome-wide microarray representing all grapevine genes listed in the latest V1 gene prediction. (
  • An Agilent custom microarray consisting of 15,000 probes derived from barley consensus EST sequences was used to investigate genome-wide and QTL-specific differential expression of genes 18 hours post-inoculation (hpi) with Puccinia hordei . (
  • We observed genome-wide expansion of the circadian expression phase among retained paralogous pairs. (
  • Leonelli S, Davey R, Arnaud E, Parry G , Bastow R (2017) Data management and best practice for plant science. (
  • The biological species is portioned into two categories, (A) subspecies composed of agronomically used lines, and (B) subspecies, which consists of weedy or wild relatives of subspecies A. The secondary gene pool (GP-2) refers to all biological species, which cross with a different combinable species. (
  • Furthermore, involvement of AGPs during embryogenesis and in plant-microbe interactions have been shown for many land plant species and implicates that AGPs might also play a role in evolution of these processes. (
  • Despite their identification in hundreds of plant species, few miRNAs have been identified in the Asteraceae, a large family that comprises approximately one tenth of all flowering plants. (
  • The findings of this study might ultimately help in the understanding of miRNA-mediated gene regulation in important crop species. (
  • Since, azole and other current treatment of Candida infection often lead to proliferation of resistant Candida species, use of plant extract will be useful. (
  • These species form a hybrid zone, yet remain morphologically and ecologically distinct, despite active gene exchange. (
  • Maize is one of the most important crop species and serves also as a model plant for grass research. (
  • If herbicides are in fact a key factor shaping agricultural plant diversity, one would expect to see the signal of past herbicide impacts in the current plant community composition of an intensively farmed region, with common, successful species more tolerant to widely used herbicides than rare or declining species. (
  • In a new paper in Developmental Cell , a research team led by Penn biologists Brian Gregory and Xiang Yu identified a mechanism by which plants can conduct this agile regulation of gene expression. (
  • RNA-protein complexes play essential roles in the regulation of gene expression, by orchestrating the basic growth and maintenance of the cell as well as the complex developmental programs of multicellular eukaryotes. (
  • Microscopic studies on resistance levels in relation to the pathogen developmental phases has indicated plant cell wall penetration and haustorium formation by P. hordei as critical phases determining the success or failure of the infection [ 6 ]. (
  • In seed plants, the PD networks are highly dynamic and undergo drastic functional and structural changes controlling developmental processes, metabolic acclimatisation and pathogen responses. (
  • The Biomass Division will establish an integrated research and innovation network in sugar cane genomics, plant, insect and microorganism biochemistry, biotechnology and cultivar improvement. (
  • The Taproot is the podcast that digs beneath the surface to understand how scientific publications in plant biology are created. (
  • Pursuing it, they found that the mutants had an abundance of small RNAs, molecules often associated with silencing the expression of other RNA molecules. (
  • Comparison of transcript levels in mature seeds of ABA-insensitive, ABA-hypersensitive, ABA-deficient, or heterochronic mutants indicates that ABI4 expression is altered in only two of the backgrounds, the ABA-insensitive mutantsabi1-1 and abi3-1. (
  • The fri mutation causes early flowering with reduced FLC expression similar to frl1, fes1, suf4 , and flx, which are mutants of FLC-specific regulators. (
  • Growth, photosynthetic activity, and potassium and sodium concentration in rice plants under salt stress. (
  • Plants with a mutation in the gene for an enzyme called DX01 (on right) were stunted in their growth compared to normal plants. (
  • At that time, his lab grew plants with a DX01 mutation and found that their growth was stunted, their leaves were pale green, their development was delayed, and they had defects in fertility. (
  • Plants lacking DX01 developed the problems Gregory had seen years earlier: stunted growth and development. (
  • Strain Mechanosensing Quantitatively Controls Diameter Growth and PtaZFP2 Gene Expression in Poplar. (
  • The basic leucine zipper (bZIP) family is one of the largest transcription factor (TF) families in plants, which play crucial roles in plant growth and development. (
  • Water is one of the main limiting factors of plant growth. (
  • Abiotic stresses reduce plant growth and crop productivity and, hence, are serious threats to agricultur e and, therefore, human well-being. (
  • To determine whetherABI4 is necessary and/or sufficient for ABA response, we assayed the effects of loss of ABI4 function and ectopicABI4 expression on growth and gene expression. (
  • Plant Structure, Growth, and Development 36. (
  • We also performed qRT-PCR analysis to investigate the differential expression pattern of five newly identified miRNAs during five different cotyledon growth stages in safflower. (
  • This could help to guide future work into targeting genes to improve crop growth and stress resilience. (
  • In contrast to uniform control, non-uniform salinity treatment improved plant growth and water use, with more water absorbed from the non- and low salinity side. (
  • Improved plant growth under non-uniform salinity was thus attributed to increased water use, reduced leaf Na(+) concentration, transport of excessive foliar Na(+) to the low salinity side, and enhanced Na(+) efflux from the low salinity root. (
  • Overexpression of an H+-PPase gene from Thellungiella halophila in cotton enhances salt tolerance and improves growth and photosynthetic performance. (
  • BB expression mirrors proliferative activity, yet the gene functions to limit proliferation, suggesting that it acts in an incoherent feedforward loop downstream of growth activators to prevent over-proliferation. (
  • the highest levels of expression were detected in the early stages of organ growth with high mitotic activity, and BB expression appeared to decline in concert with the decrease in cell divisions. (
  • This somewhat counterintuitive expression pattern suggests that BB functions as an intrinsic growth brake in an incoherent feedforward loop [ 5 ] during organ growth. (
  • According to this idea, BB expression would be induced by (a) factor(s) that also activate(s) cell proliferation, yet it in turn would counteract this growth stimulation. (
  • Furthermore, the Tnt1 U3 region, and especially the tandemly repeated BII boxes, contains several sequences similar to well-characterized motifs involved in the activation of several plant defense genes. (
  • Recent gain-of-function studies show that two tobacco MAPKs induce the expression of defense genes and cause cell death. (
  • There is no reason why these results cannot be extrapolated to other plants and crops. (
  • A better understanding of plant adaptation to low phosphate will open the way to increased phosphorus use efficiency by crops. (
  • Currently, plant breeders work to produce crops to feed the masses, or support the burdening need for fiber and fuel. (
  • Domestication of major crops included the selection of plants that did not naturally shed ripe fruits or seeds. (
  • Sexual recombination allows for alleles to be recombined in meiosis resulting in plants which can be selected with novel traits (Tracy, 2004). (
  • However, what does a plant breeder do if desired alleles are in distantly related plants? (
  • Results: We identified quantitative differences in a subset of core cold responsive genes that correlated with sensitivity or tolerance to CI at harvest and during cold storage, and also subsets of genes correlating specifically with high sensitivity to woolliness and browning. (
  • We applied quantitative Real-Time PCR (qRT-PCR) to confirm the expression of eight potential miRNAs in Carthamus tinctorius and Helianthus annuus. (
  • Methods: Gene expression was analyzed by quantitative real-time PCR. (
  • This work underlines the complexity involved in precise quantitative control of gene expression and lays the foundation for identifying important upstream regulators that determine BB expression levels and thus final organ size. (
  • Bogino P., Oliva M., Sorroche F., Giordano W. The role of bacterial biofilms and surface components in plant-bacterial associations. (
  • With the advent of new technologies in studies of plant transcriptomes and proteomes, now we have the tools necessary for fast and precise elucidation of desirable crop traits. (
  • In the tertiary gene pool (GP-3) although crosses are possible with the crop of interest, hybrids are lethal or completely sterile. (
  • The quaternary gene pool (GP-4) does not allow any transfer of DNA between the crop of interest or other organism by mating and sexual recombination. (
  • In this case the process of transgenesis must be used to insert a DNA sequence from any biological or synthetic source known as a transgeneinto the crop plant of interest. (
  • The DNA can be chimeric where different segments e.g. the promoter, gene of interest and terminator can be taken from any source and put together in a functional manner so that the DNA cassette is expressed once transferred into the genome of the crop of interest. (
  • multiflorum) and Corn (Zea mays) Competition Vijay K. Nandula US Department of Agriculture-Agricultural Research Service (USDA-ARS), Crop Production Systems Research Email: vijay Book titles include Edible Plants, Edible Perennials, Edible Trees, and Woodland Gardening. (
  • Transposons seem to have been pivotal contributors to the evolution of adaptive immunity both in vertebrates and in microbes, which were only recently discovered to actually have a form of adaptive immunity-namely, the CRISPR-Cas (clustered regularly interspaced short palindromic repeats-CRISPR-associated genes) system that has triggered the development of a new generation of genome-manipulation tools. (
  • This playlist can be used to teach the eukaryotic regulation of gene expression and its role in the development of plants and animals. (
  • Against the backdrop of various political discussions on the further development of testing standards in the EU, the authors make concrete suggestions on how testing systems can be improved to generate more data on the quality and safety of genetically engineered plants. (
  • Parry G (2014) Components of the Nuclear Pore Complex play multiple roles in plant development. (
  • This included the enhanced modulation of genes that are normally regulated during berry development and the induction of a large set of genes that are not usually expressed. (
  • Long since the development of agriculture, humankind has desired to tailor plants to their liking so that they may better meet their needs. (
  • Jasmonic acid distribution and action in plants: regulation during development and response to biotic and abiotic stress. (
  • The invention of intercellular communication networks was a crucial step in plant evolution that enabled i) coordinated strategies to face the hazardous biotic and abiotic stresses occurring during the conquest of land and that allowed ii) the development of increasingly complex plant bodies with division of labour between spatially patterned, cooperative tissues and organs. (
  • Therefore, methylome analysis is an increasingly valuable research tool with a range of applications, including studies on gene regulation, cell differentiation, embryogenesis, aging, occurrence and development of disease, phenotypic diversity and evolution in plants and animals. (
  • This chapter provides information on anatomy and morphology, photoperiod and temperature regulation of development, dormancy, cold hardiness, photosynthesis and carbon allocation patterns, water relations, and plant nutrition of strawberries. (
  • This dramatic increase in the number of LFY-responsive cells compared to whole plants suggested that the tissue culture system could greatly facilitate the analysis of LFY-dependent gene regulation by genomic approaches. (
  • Available literature suggests that many genomic loci are epigenetically modified during reproductive phases of plant life cycle. (
  • Manipulation of a Senescence-Associated Gene Improves Fleshy Fruit Yield. (
  • Activation of retrotransposons by stresses and external changes is common in all eukaryotic systems, including plants. (
  • Advances in massively parallel sequencing platforms and approaches to capture ribosomal position with nucleotide resolution, i.e. ribosome profiling [ 16 ], precisely capture gene expression at the level of translation. (
  • Abscission consists in the detachment of entire vegetative and reproductive organs due to cell separation processes occurring at the abscission zones (AZs) at specific positions of the plant body. (
  • Overall, these results suggest that PhGRP, which is a male fertility-related gene that expresses specifically in anthers, is regulated by PhMYC2 and whose promoter can be used as an effective tool in the creation of male-sterile lines. (
  • There was a strong negative correlation between expression and methylation for IGFBP2, ITGA11, ESR1, and EPHB6, all of which have DMRs downstream from their promoter. (
  • In this study, we describe our plasmid vectors and transient gene expression system, drawing on examples of (i) assigning function to a heme thiolate (TH)-P450 gene, (ii) identifying a transcription factor target promoter, and (iii) exploring the role of RNA processing in dsRNA hairpin-induced RNA silencing. (
  • Thus, the floral induction system is suitable for the detection of low abundance transcripts whose expression is controlled in an LFY-dependent manner. (
  • This evolutionary comparative approach will reveal how the evolution of cell division and branching enabled the formation of the land plants. (
  • In addition, many tools take into account a phylogenetic conservation of the pre-miRNA structure and miRNA sequence, which limits the chance to detect non-conserved, evolutionary new miRNA genes. (

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