Glossary of Terms

A

Ac transposon
Activator transposon , used to disrupt and characterize genes in maize. (see also)

Agrobacterium tumefaciens
A common soil bacterium. Agrobacterium has a special plasmid that causes tumors in infected plants. This plasmid can be modified so that it introduces a desired gene into a plant instead of causing a tumor.

algae
An informal grouping of certain single- and multi-celled plants, often found in aquatic habitats. The group known as the algae is now considered to be an informal, rather than taxonomic classification, given the diversity within the group.

AM (arbuscular mycorrhizal) fungi
A fungi that forms symbiotic bonds with the roots of many plants, supplying minerals such as phosphorus in exchange for carbon. (see also)

amino acids
A group of chemicals best known as the building blocks of proteins. Plants and many microbes can make their own amino acids, while animals need certain essential amino acids in their diets. (see also)

antibody
A protein that is produced in response to an antigen (often another protein from a virus or bacterium). It is able to attach tightly to the antigen. (see also)

antioxidant
A substance that slows the rate of oxidation reactions, often by binding metal ions that catalyze such reactions, or by neutralizing free radicals. Some antioxidants, such as beta-carotene, protect cells by inhibiting reactions that damage DNA.

apoptosis
Another name for programmed cell death. Apoptosis may be signaled by the nuclei or by external stimuli in normally functioning human and animal cells. Apoptosis may be triggered when abnormal cellular conditions (such as viral infection) are detected or when the developmental program of the cell dictates. (see also)

Arabidopsis thaliana
A small plant in the mustard family. Arabidopsis is an extremely common model organism in plant research because it has a small, simple genome and a short life cycle. (see also)

B

bacteria
One-celled simple organisms, varieties of which live in nearly every environment on Earth. Some bacteria are pathogens, but most are not. (see also)

baculovirus
A family of viruses that infect certain insects. They are used to biologically control insects and also have been developed as expression vectors for research and industrial applications. (see also)

bioinformatics
A rapidly developing branch of biology that derives knowledge from computer analysis of biological data. Bioinformatics is highly interdisciplinary, using techniques from statistics, mathematics, chemistry, biochemistry, physics, and linguistics.

biolistics
A genetic engineering technique where particles are accelerated to deliver genetic material directly into the cells of a plant.

biotechnology
Methods of using plants, animals, or microbes, either wholly or in part, to make or modify a product or change an existing species.

C

Cabbage Looper
Scientific name: Trichoplusia ni (Huebner) (Insecta: Lepidoptera: Noctuidae) The larvae of these brown moths are important agricultural pests.

carotenoid
A group of plant pigments that includes beta-carotene and lycopene. (see also)

cell
The smallest structural unit of living organisms that is able to grow and reproduce independently. (see also)

Chlamydomonas reinhardtii
A green algae. (see also)

chloroplast
A circular molecule of DNA found in all photosynthetic plants which codes for the function of photosynthesis. (see also: 1, 2)

chromosome
Threadlike structure made of DNA and associated proteins. Chromosomes, which contain genes, are found in the nucleus. (see also)

cytoplasm
The watery substance inside a cell, containing numerous substances such as salts, enzymes, and carbohydrates. Organelles are suspended in the cytoplasm. (see also)

D

DNA
Short for Deoxyribonucleic acid. Genetic information in DNA is coded in sequences of four nucleic acids, adenine, cytosine, guanine and thymine, which are connected with a “backbone” of sugar and phosphate molecules. Strands of DNA pair to complementary strands to form the famous double helix. In the nucleus, most DNA is found coiled around proteins called histones, forming compact structures called chromosomes. Each gene is a section of DNA that occupies a specific place on a particular chromosome. (see also)

DNA Fingerprinting (or DNA typing)
A technique for identifying individual organisms based upon the uniqueness of their DNA pattern. The technique has applications in forensics, anthropology, conservation biology, and ecological research.

E

ecosystem
Interactions between living and non-living parts of the plant and animal communities and the flow of materials and energy between those parts.

endogenous
Originating from within an organism (not in response to external signals).

endosymbiosis
The theory that complex, eukaryotic organisms arose when free-living bacteria became trapped in larger cells and forged a symbiotic relationship. These trapped bacteria are thought to have evolved into chloroplasts and mitochondria, which still have their own DNA. (see also: 1, 2)

environmental stress
Stress in plants caused by the presence of unfavorable external factors, such as drought, air pollutants or low temperature.

enzyme
A protein or RNA molecule that facilitates or accelerates certain chemical reactions in biological systems.

ethylene
Gaseous plant hormone involved in numerous aspects of growth, development, and response including ripening, cell death, and response to stress and disease. (see also)

etiolation
Growth without light. Etiolated plants are generally pale, with long shoots and reduced roots and leaves. (see also)

eukaryote
An organism whose genetic material is kept in the nucleus of its cells. Eukaryotes include all organisms except bacteria. (see also)

evolution
The process by which organisms become better adapted to their environments over many generations. Selective pressure makes individuals with certain traits more likely to live longer and produce more offspring, thus shaping species over time. Evolution provides a conceptual framework for biologists, who assume that structures or behaviors must have come about because they conferred some advantage to the organism. (see also)

expression
The physical manifestation of the information contained in a gene.

F

fruit
Structure formed from the mature ovary of a flower, usually after fertilization. Fruits protect and spread seed from the plant. (see also)

fungi
Eukaryotic organisms that are neither plants nor animals, but are members of the kingdom Fungi. Fungi may have either one or multiple cells. They cannot photosynthesize, and often live as parasites or feed on dead organic matter. (see also)

fusion proteins
1. Proteins created by genetically joining two separate proteins or their gene coding sequences
2. Proteins that function to fuse membranes.(see also)

G

gamete
A reproductive cell, such as ova or spermatozoa. When two gametes fuse they form a zygote.

GE Foods
Abbreviation for food produced through genetic engineering.

gene
Section of DNA or RNA responsible for a certain function, such as coding for one protein or RNA molecule. Each gene influences the inheritance and development of some characteristic. Different forms of the same gene are known as alleles. (see also)

gene mapping
Determining the relative locations of genes on a chromosome.

gene regulation
The way in which a cell controls when, where, and how much a gene will be expressed. For example, conditions in a cell may set off a chain reaction, ultimately causing a protein to bind to a certain stretch of DNA. The interaction between DNA and protein causes more or fewer copies of the gene to be made, so that the cell responds appropriately to the change in conditions.

gene silencing
Blocking the expression of a gene, usually by preventing its transcription or translation. Silencing helps researchers find out the function of a gene.

gene splicing
Taking segments of DNA from one organism and putting them into the DNA of another organism. Synonymous with recombinant DNA technology.

genetic code
The way genetic information is stored in living organisms.

genetic engineering
A biotechnological process in which the traits or characteristics of an organism are changed by transferring individual genes from one species to another or modifying genes within a species.

genetic map
A map of the relative positions of genetic loci on a chromosome, determined on the basis of how often the loci are inherited together. Distance is measured in centimorgans (cM).

genetically modified organism (GMO)
An organism that has been modified using either traditional plant breeding techniques or genetic engineering techniques of gene transfer. In popular usage, the term "genetically modified organism", or GMO, refers only to an organism produced through genetic engineering. (see also)

genetics
The study of heredity of how differences between individuals are transmitted from one generation to next and how information in the genes is used in the development and functioning in the adult organism. (see also)

genome
All the genetic material in the chromosomes of a particular organism; its size is generally given as its total number of base pairs. (see also)

genomics
The scientific study of genes and their role in an organism’s structure, growth, health, and disease; for example, how the approximately 3000 genes in a given strain of bacteria contribute to the shape, function, and development of the whole organism. It is also the term now applied to the data and information derived from genome sequencing. (see also)

genotype
The specific genetic makeup of an organism, as contrasted with the actual characteristics of an organism.

glycoprotein
A protein containing a linked sugar or polysaccharide. Glycoproteins are most commonly the receptor molecules on the outer surfaces of cells and the proteins secreted from eukaryotic cells.

green fluorescent protein
A protein found in a jellyfish that fluoresces, or glows green, when UV light shines on it. GFP can function as a biological marker when attached to other proteins. The structure of the protein is cylindrical with the glowing component, an amino acid complex called a fluorophore, in the middle.

H

hepatitis B (hbv)
This disease is caused by DNA viruses in the family Hepadnaviridae and is much more serious than hepatitis A. Hepatitis B has a long incubation period (around three months) and can cause severe liver damage and even death. It is typically spread by blood or body fluid contact, such as through hypodermic needles or sexual intercourse.

host
An organism that is home to a parasite.

hypersensitive response
The process by which a plant, detecting a pathogen, kills the cells at the site of infection in order to contain the pathogen.

I

immune response
The reaction of the body as a whole (not just the immune system, as in an immune reaction) to the presence of an antigen, which includes making antibodies, developing immunity, developing hypersensitivity to the antigen, and developing tolerance.

in vitro
“In glass”—describes biological processes that occur outside a living organism, in a laboratory. For example, scientists may study the rate at which enzymes catalyze reactions in vitro.

in vivo
Describes biological processes that occur in a living organism.

insect
An animal of the class Insecta, in the phylum Arthropoda. Generally, insects have three-segment bodies (head, thorax, and abdomen) with one pair of antennae attached to the first segment (the head) and three pairs of legs and two pairs of wings attached to the middle segment (the thorax). Most insects live on land (though there are species that live in freshwater environments and in saltwater marshes). Note: centipedes, millipedes, spiders, and mites are not insects (though they are arthropods). (see also)

K

knock-out
An organism in which a certain gene has been disabled (“knocked out”) in some way. Knock outs are used to deduce the function of the missing gene.

L

lipoxygenase (LOX) proteins
A family of proteins that play a role in immune response. (see also)

lycopene
A red carotenoid associated with a decreased risk of digestive system and prostate cancers. An antioxidant, lycopene is found in fruits such as tomato and watermelon.

M

maize
Corn, Zea mays. (see also: 1, 2)

Medicago truncatula
Common name: Barrel Medic. A model organism in the legume family. Like other legumes, Medicago truncatula forms symbiosis with bacteria and fungi in the soil. It is often used to study these interactions. (see also)

metabolite
A substance involved in metabolism, being either synthesized during metabolism or taken in from the environment.

microarrays
Tool for large-scale analysis of gene expression, enabling the activities of hundreds of thousands of genes to be monitored simultaneously. By comparing microarrays from different samples, scientists find clues about which genes are involved in certain processes, such as stages of development or response to disease. (see also)

mitochondrion
The “powerhouse” of the cell, where sugar and oxygen react to produce usable energy. Plural: mitochondria. (see also).

model organism
A living thing used commonly in scientific research, usually with the hope that principles discovered in the model organism will have broad applicability for understanding other species. Examples include Escherichia coli, fruit flies, mice, and Arabidopsis thaliana.

mRNA
Messenger RNA, generally used to relay genetic information from DNA in the nucleus to ribosomes in the cytoplasm, where it is used to make proteins.

mutagenesis
Producing changes in an organism’s DNA in order to study the effect of disrupting certain genes, or to try to produce a desired trait.

mutant
Refers to an organism, population, gene, or chromosome, etc. which differs from the corresponding wild type by one or more changes to its DNA.

N

NBS-LRR proteins
Short for Nucleotide Binding Site and Leucine Rich Repeat domains. One part of these proteins binds to (“recognizes”) a molecule that indicates a pathogen is present. This recognition triggers a change in another part of the protein, which signals the cell to respond to the invader. (see also)

Nicotiana
A genus of plants in the Solanaceae family. Nicotiana tabacum (commercial tobacco) and Nicotiana benthamiana are used as model organisms, especially for gene silencing experiments.

nitric oxide (NO)
A gaseous signaling molecule with multiple roles in plants and animals. Also, an air pollutant produced by burning fossil fuels.

Nucleopolyhedrovirus
A genus of viruses within the family of baculoviruses (Baculoviridae).

nucleus
The part of all eukaryotic cells where genetic information is stored. (see also)

O

organelle
A structure within a eukaryotic cell that has a specific function. Examples include nuclei, mitochondria, and (in plants) chloroplasts.

ozone (O₃)
An unstable, poisonous form of oxygen that is produced naturally in the ozone layer from atmospheric oxygen (O2) by electric discharge or exposure to ultraviolet radiation. Also produced in the lower atmosphere when light reacts with certain pollutants.

P

pathogen
An organism that causes disease. Examples include some viruses, bacteria, fungi, and parasites.

pathogenesis
The process of causing disease.

peptide
A chain of amino acids held together by peptide bonds. The word “peptide” is generally used to describe an amino acid chain that is shorter than a protein.

pharmaceuticals
Chemicals that have special uses in medicine.

phenotype
The observable characteristics of an organism; the product of both genes (genotype) and environment.

phosphate (PO₄^3-)
An important nutrient for plants. (see also: 1, 2)

phosphorylation
The addition of a phosphate group to a protein. Phosphorylation occurs in many important processes in the cell. For example, many enzymes are either activated or deactivated by phosphorylation, enabling the cell to control their activity.

photoreceptor
In plants, a molecule that detects light by undergoing a chemical change when light hits it.

photosynthesis
Process in which light energy is captured by chlorophyll and reacts with water and carbon dioxide to produce carbohydrate and oxygen. Occurs in plants, algae, cyanobacteria and lichens. (see also)

plant development
The life cycle sequence that occurs as a plant grows up from a seed.

plant hormone
Any of various hormones produced by plants that control or regulate germination, growth, metabolism, or other physiological activities. (see also)

plant pathology
The study of plant diseases.

plant-based vaccine
Vaccine in which one or more proteins from a virus or bacterium are produced in a plant tissue using recombinant DNA technology.

plasmid
Small, circular piece of DNA in a bacterium. Plasmids are separate from the bacterium’s main body of DNA, which is contained in a single chromosome. Plasmids can be passed between bacteria, and often encode a certain trait, such as antibiotic resistance.

plastid
A type of organelle within a plant cell. Chloroplasts are a type of plastid.

polymerase (DNA or RNA)
An enzyme that makes DNA or RNA from a DNA (or RNA) template.

Polymerase Chain Reaction (PCR)
Method of copying short DNA sequences millions of times in vitro.

potato
Solanum tuberosum, a plant cultivated for its starchy edible tubers.

prokaryote
Organism lacking a nucleus and other organelles. Prokaryotes include bacteria, and are usually single-celled.

promoter
A DNA region in front of or near the coding sequence of a gene. The promoter binds RNA polymerase and thus controls transcription of the gene.

protein
A complex biological molecule composed of a chain of amino acids. Proteins have many different functions: structure, movement, catalysis, transport, regulation of cellular processes, and response to stimuli. The information for making proteins is stored in the sequence of nucleotides in the genome. (see also)

proteomics
The scientific study of an organism’s proteins and their role in an organism’s structure, growth, and disease response. All biological processes involve changes in proteins, and total protein profile (the proteome) varies during the development of an organism and the progression and treatment of disease.

Pseudomonas syringae pv. tomato
The pathogen that causes bacterial speck disease in tomatoes. (see also)

Pto
A tomato gene that confers resistance to bacterial speck disease caused by Pseudomonas syringae pv. tomato. (see also)

Q

QTL Analysis
Studies aimed at mapping the limits or determining the relative importance or function of specific DNA sequences in a promoter.

R

recombinant
1. An organism which, because of DNA recombination, contains a combination of alleles differing from either of its parents.
2. DNA that contains sequences from different sources, usually the result of in vitro laboratory procedures.
3. Individual gamete or chromosome resulting from recombination.

recombination
The creation of new DNA sequences by splicing together fragments of DNA from two or more sources. Recombination occurs naturally during the formation of gametes, when chromosomes from each of an organism’s parents trade segments of DNA. In genetic engineering, recombination is used to introduce genes to an organism.

replication (DNA)
The process by which copies are made of DNA. The two strands of the original DNA separate, and DNA polymerase builds a new strand on each with complementary nucleotides. (see also)

ripening
The maturation process in which fruit becomes desirable to seed dispersing organisms. (see also)

RNA
Short for Ribonucleic acid. A genetic molecule like DNA, RNA plays many roles in the cell, some of which are only beginning to be understood. RNA is composed of four nucleic acids, adenine, cytosine, guanine and uracil, which are connected with a “backbone” of sugar and phosphate molecules. RNA generally exists in single strands instead of in a double helix like DNA. In certain viruses, the genome is encoded in RNA rather than DNA. (see also)

S

salicylic acid (SA)
1. An organism which, because of DNA recombination, contains a combination of alleles differing from either of its parents.
2. DNA that contains sequences from different sources, usually the result of in vitro laboratory procedures.
3. Individual gamete or chromosome resulting from recombination.

signal transduction
The creation of new DNA sequences by splicing together fragments of DNA from two or more sources. Recombination occurs naturally during the formation of gametes, when chromosomes from each of an organism’s parents trade segments of DNA. In genetic engineering, recombination is used to introduce genes to an organism.

stable isotope
The process by which copies are made of DNA. The two strands of the original DNA separate, and DNA polymerase builds a new strand on each with complementary nucleotides. (see also)

starch
The maturation process in which fruit becomes desirable to seed dispersing organisms. (see also)

sugar
Short for Ribonucleic acid. A genetic molecule like DNA, RNA plays many roles in the cell, some of which are only beginning to be understood. RNA is composed of four nucleic acids, adenine, cytosine, guanine and uracil, which are connected with a “backbone” of sugar and phosphate molecules. RNA generally exists in single strands instead of in a double helix like DNA. In certain viruses, the genome is encoded in RNA rather than DNA. (see also)

symbiosis
Short for Ribonucleic acid. A genetic molecule like DNA, RNA plays many roles in the cell, some of which are only beginning to be understood. RNA is composed of four nucleic acids, adenine, cytosine, guanine and uracil, which are connected with a “backbone” of sugar and phosphate molecules. RNA generally exists in single strands instead of in a double helix like DNA. In certain viruses, the genome is encoded in RNA rather than DNA. (see also)

T

tissue culture
A technique for growing cells from multicellular organisms in a liquid or solid culture medium for research.

tobacco
See Nicotiana.

tomato
Lycopersicon esculentum, a plant cultivated for its edible fleshy, unusually red fruit. (see also)

transcription
The process by which an RNA polymerase produces single-stranded RNA complementary to one strand of the DNA, or rarely, RNA.

transformation
The introduction and integration of a piece of DNA into a cell.

transgene
The specific gene moved from one organism to another using recombinant DNA technology.

transgenic
Describes organisms with foreign DNA integrated into their genomes.

translation
The process by which ribosomes and specialized RNA synthesize a specific polypeptide using genetic information in messenger RNA.

transposon
A segment of DNA, usually in a prokaryote, that randomly inserts itself into a different part of a cell’s genome. Usually more than 5000 base pairs in length (though eukaryotic transposons are generally much shorter).

V

vaccine
A preparation of dead or weakened pathogens, or of certain proteins from pathogens, that is used to prime a potential host’s immune system to ward off the pathogen. (see also)

vectors
Plasmids, viruses or other vehicles used to insert desired genes into a host cell.

virology
The scientific study of viruses and viral infections.

virulence
The ability of a microbe to cause disease.

virus
A particle consisting of DNA or RNA, a protein capsid, and sometimes an outer envelope. Viruses are inactive until they infect a host, whether plant, animal, or bacteria. They then use the host to reproduce themselves. (see also)

virus budding (movement)
The pushing out and pinching off of virus particles from the surface of an infected cell. During this process of virus assembly, a virus may acquire a membranous envelope from the cell’s plasma membrane.

virus-induced gene silencing (VIGS)
A defense mechanism in which a plant infected by a virus destroys any RNA that is similar to double-stranded RNA introduced by the virus. As a result, the gene encoded in the targeted RNA cannot be translated into protein. (see also)