B bacillus subtilis - breeding line

bacillus subtilis: a rod shaped, nonpathogenic bacterium commonly found in the soil. This gram-positive microbe has had its genome studied in microbiology as well as in genetic engineering studies. Often, Bacillus subtilis is used as a host in recombinant DNA experiments because of its ability to secrete proteins. [Source: Biotechnology Industry Organization, www.bio.org]

bacillus thuringiensis (Bt): a bacterium naturally living in soil that generates an endotoxin lethal to insects (including genera Dipetera, Coleoptera, and Lepidoptera among others). The endotoxin released is deadly due to the increased pH and activation of peptides that create pores in the insect’s gut initiated by the toxin. This combination causes the destruction of cells inside the target, leading to the insect’s death. Currently, researchers are attempting to integrate the baterium’s insect toxins into plant DNA in order to create crops resistant to different insect species. [Source: Biotechnology Industry Organization, www.bio.org]

backcross: a cross between one animal type that is heterozygous for alleles obtained from two parental strains and a second animal type from one of those parental strains. The term is often used by itself to describe the two-generation breeding protocol of an outcross followed by abackcross used frequently in linkage analysis. [Source: NHBLI/NCBI Glossary]

bacteriophage: a virus that infects, replicates within, and often destroys bacteria. Bacteriophages consist of a protein coat (or capsid) that holds genetic information inside (either DNA or RNA). The bacteriophage binds to specific bacteria and then injects its genetic material inside. The host’s transcriptional and translational machinery then synthesizes new bacteriophages using the injected material. Often, phage lysozymes, compounds that can cause bacteria to rupture, are released so that the new bacteriophages can infect other bacteria. Currently, bacteriophages are utilized in recombinant DNA studies and have been used to examine structure and regulation of genes. [Source: Biotechnology Industry Organization, www.bio.org]

bacterium: a group of small, single-celled, prokaryotic microorganisms that can live as a parasite (survival depends on another organism) or as an independent life form. Bacteria can vary in size and shape (rod, sphere, spiral, etc.), reproduce by cellular division, and utilize different forms of motility. Their nutritional sources also vary widely, as bacteria can live off of organic or inorganic sources and can live with or without oxygen present. The ability for bacteria to adapt to different environments and food sources allow them to survive in practically any location. [Source: Biotechnology Industry Organization, www.bio.org]

base: one of the molecules – adenine, guanine, cytosine, thymine, or uracil – which form part of the structure of DNA and RNA molecules. The order of bases in a DNA molecule determines the structure of proteins encoded by that DNA. See nucleotide.

base pair (bp): two complementary nucleotide bases joined together by chemical bonds. The two strands of the DNA molecule are held together in the shape of a double helix by the bonds between base pairs. The base adenine pairs with thymine, and guanine pairs with cytosine.

base sequence: the order of nucleotide bases in a DNA molecule. [Source: DOE Primer on Molecular Genetics]

base sequence analysis: a method, sometimes automated, for determining the base sequence. [Source: DOE Primer on Molecular Genetics]

bioactive: having an effect on a biological system.

bioassay: determination of the effectiveness of a compound (i.e. a drug, hormone, etc.) by measuring its effect on animals, tissues or cultures in comparison with a standard preparation. [Source: Biotechnology Industry Organization, www.bio.org]

bioaugmentation: increasing the activity of bacteria that break down pollutants by adding more of their kind. A technique used in bioremediation, a technique used to remove or neutralize contaminants in a particular environment using biological agents (plants, bacteria, or other living organisms). [Source: Biotechnology Industry Organization, www.bio.org]

biocatalyst: in bioprocessing, a substance, usually an enzyme, that activates or increases the rate of a chemical reaction in a living organism. Biocatalysts are currently used in industry in the production of high fructose corn syrup, semi-synthetic penicillins and cancer drugs. [Source: Biotechnology Industry Organization, www.bio.org]

biochemical: a product by or involving a chemical reaction in a living organism. Biochemistry is the application of chemistry to living beings. A few general research areas of biochemistry include analysis of the physical properties of biological molecules, the chemical interactions used to regulate metabolism, and the chemistry of the immune system. [Source: Biotechnology Industry Organization, www.bio.org]

biochemical stock: a variety or strain known to possess desirable biochemical traits. [Source: Agricultural Genome Information System, USDA]

biochip: an electronic device that uses organic molecules to form a semiconductor instead of silicon or germanium. Examples of possible applications for such technology include genotyping, DNA sequencing, and even retinal implantation to serve as an artificial retina for those who suffer from macular degeneration of the eye. See DNA chip technology.

bioconversion: chemical restructuring of organic materials, like plants or waste products, into useable substances by using a biological agent. The biocatalyst used to modify the chemical could be an enzyme, bacteria, or some other microorganism. For example, paper residuals can be modified using bioconversion so that it creates a fertilizer or soil amendment.

bioinformatics: the science of informatics as applied to biological research. Informatics is the management and analysis of data using advanced computing techniques. Bioinformatics is particularly important as an adjunct to genomics research, because of the large amount of complex data this research generates.

biosensor technology: Biosensor technology couples knowledge of biology with advances in microelectronics. A biosensor is composed of a biological component, such as a cell or antibody, linked to a tiny transducer. Biosensors are detecting devices that rely on the specificity of cells and molecules to identify and measure substances at extremely low concentrations. When the substance of interest collides with the biological component, the transducer produces a digital electronic signal proportional to the concentration of the substance. Biosensors can measure the nutritional value, freshness and safety of food, provide emergency room physicians with bedside measures of vital blood components, and locate and measure environmental pollutants. [Source: Biotechnology Industry Organization, www.bio.org]

biotechnology: the application of biological research techniques to the development of products which improve human health, animal health, and agriculture.

blood cells: blood is a fluid body tissue responsible for the transport of food and waste. Blood contains two types of cells; red blood cells (erythrocytes) which transport oxygen and carbon dioxide and white blood cells (leukocytes), which are responsible for a wide range of immunological functions.

bone marrow: soft tissue contained within the large central cavity of a bone as well as within other internal spaces. Bone marrow is responsible for the formation of blood cells. Such marrow is called “red marrow”. As organisms mature, red marrow is replaced by a fatty tissue that does not produce blood cells. That fatty tissue is called “yellow marrow”.

Bovine Spongiform Encephalopathy (BSE): (a.k.a. Mad Cow Disease) a degenerative disease of brain tissue (“encephalopathy”). BSE is caused by prions and results in the deposition of amyloid tissue thatcauses a breakdown of brain tissue leaving the infected brain with a “spongy” (“spongiform”) appearance.

BRCA1 and BRCA2: two genes which normally help to restrain cell growth, but which can contain certain genetic mutations associated with the development of breast and ovarian cancer. Note, however, that inherited BRCA1 and BRCA2 mutations are thought to account for less than 10% of all breast and ovarian cancers. Recent evidence suggests that somatic cell genetic mutations (i.e., non-inherited genetic mutations) in these two genes may also play a role in the development of cancer.

breeding line: plant specimens of high quality that are kept to produce offspring. [Source: Agricultural Genome Information System, USDA]

A acclimatization - avuncular relationship

acclimatization: the manner in which an organism adapts to a new environment or to a change in the old. For microbes, these physiological modifications often involve enzymatic changes (changes that modify proteins that speed up biochemical reactions). These modifications allow the organism to utilize a new nutrient source for survival. [Source: Biotechnology Industry Organization, www.bio.org]

acquired genetic mutation: see somatic cell genetic mutation

additive genetic effects: the effects of alleles at two different loci are additive when their combined effect is equal to the sum of their individual effects. Additive effects are most easily understood in the context of continuous (quantitative) traits. Consider a disease in which two loci, locus 1 with alleles A and a, and locus 1 with alleles B and b, contribute to the phenotype. If each allele represented by a capital letter contributes a score of 2 to the phenotype, and each allele represented by a small letter contributes a score of 3 to the phenotype, then if the alleles at loci 1 and 2 are additive, the resultant pheno-types for the possible genotypes are as follows: AABB – 8; AABb – 9; Aabb – 11; AaBB – 10; AaBb – 10; Aabb – 11; aaBB -10; aaBb – 9; aabb – 12. [Source: NHBLI/NCBI Glossary]

adjuvant: a substance that, in the presence of a drug, speeds up or improves the effectiveness of the medicine. The term is also used to identify a substance that is added to a vaccine so that a smaller dose of the vaccine is needed to induce an antibody response (i.e. an immune system response). The adjuvant accomplishes this by (1) preventing antigens from leaving the area where the immune response is occurring, and (2) by increasing the rate of multiplication of the lymphocytes. [Source: Biotechnology Industry Organization, www.bio.org.]

aerobic: requiring Oxygen (O2) for survival or growth. A good example of an aerobic organism is the human being. [Source: Biotechnology Industry Organization, www.bio.org]

affected relative pair: a general term describing a set of individuals related by blood, each of whom is affected with the trait in question. The most common types of affected relative pairs include affected sibling pairs, affected cousin pairs, and affected avuncular pairs. [Source: NHBLI/NCBI Glossary]

allele: one of a number of different forms of a gene. Each person inherits two alleles for each gene, one allele from each parent. These alleles may be the same or may be different from one another.

allograft: a transplant process wherein a tissue or organ is taken from one individual (donor) and placed into another (recipient). Both donor and recipient are members of the same species. Rejection of the transplanted material is a problem since the donor and recipient do not have the same genetic make up, unlike affected relative pairs. Matching surface antigens and other factors between donor and recipient and the use of anti-rejection drugs can significantly lessen the chance of rejection. Also known as a homograft.

Alzheimer’s disease: a disease characterized by, among other things, progressive loss of memory. The development of Alzheimer’s disease is thought to be associated at least in part with possessing certain alleles of the gene, which encodes apolipoprotein E.

amino acid: one of twenty different molecules that combine to form proteins. The sequence of amino acids in a protein determines the protein’s structure and function.

amplification: an increase in the number of copies of a specific DNA fragment. Polymerase Chain Reaction (PCR) is a cheap and easy technique used to amplify DNA strands by heating and cooling a medium that includes the strand to be copied, DNA polymerase, two 20-base primers, and an excess of nucleotides. Once a copy is made of the original sequence it can be used to generate subsequent copies, thus creating more and more DNA templates that can be used for duplication. [Source: Biotechnology Industry Organization, www.bio.org]

anaerobic: requiring little or no Oxygen (O2) for survival or growth. For instance, there are certain fungi and bacteria types that flourish in conditions that lack the presence of oxygen. [Source: Biotechnology Industry Organization, www.bio.org]

analyte: the substance which a laboratory test aims to detect. In cholesterol testing, for example, the analyte is cholesterol. In genetic testing, the analyte could be, for example, a specific allele or genetic mutation.

antibiotics: a group of chemical substances used to kill or inhibit the growth of certain microorganisms (bacteria, fungi, etc.) Antibiotics are widely used to prevent or treat the spread of infectious disease. They can be produced naturally, using microorganisms, where antibiotics are formed as a metabolic byproduct in bacteria or fungi, or synthetically. [Source: Biotechnology Industry Organization, www.bio.org]

antibody: a protein produced by the immune system in humans and higher animals, which binds to a specific antigen. When antibodies bind to corresponding antigens they set in motion a process to eliminate the antigens.

anticipation: the phenomenon whereby disease severity increases with each passing generation. Since disease severity is often difficult to measure, anticipation is frequently measured in terms of patient-reported age-of-onset of the disorder. For example, in a disease showing anticipation, a child may have earlier onset than their parent who has earlier onset than their grandparent. [Source: NHBLI/NCBI Glossary]

anticodon: a specific three-nucleotide sequence in transfer RNA that is complementary to a codon (a three-nucleotide sequence in messenger RNA) that specifies an amino acid in protein synthesis. When a codon and anticodon bond (because they are complementary strands) the amino acid attached to the transfer RNA is able to connect to the growing amino acid strand, which eventually forms a protein. [Source: Biotechnology Industry Organization, www.bio.org]

antigen: a foreign substance that, when introduced into the body, can stimulate an immune response.

antihemophilic factors: a family of blood plasma proteins that is necessary for the blood-clotting process. This group includes factor VIII, which in most cases of hemophilia, is found to be deficient. When the skin surrounding a body is cut or otherwise disrupted a cascade of these antihemophilic factors, or “clotting factors,” are initiated near the problem site. Certain clotting factors cause platelets in the blood to become “sticky” which attach to the wounded site and, in turn block the exit of blood from the body. The clotting factors also induce the binding of fibrin molecules to create an insoluble meshwork clot preventing blood loss. [Source: Biotechnology Industry Organization, www.bio.org]

antisense: a piece of nucleic acid, typically created in the lab, which has a sequence exactly opposite to an mRNA molecule made by the body. mRNA molecules made by the body serve as templates for the synthesis of protein (see transcription). Since the “antisense” mRNA molecule binds tightly to its mirror image, it can prevent a particular protein from being made.

antisense oligonucleotide: a short string of nucleotides that can bond to messenger RNA (mRNA) and block the process of gene expression. [Source: NHBLI/NCBI Glossary]

antiserum: a serum, the liquid portion of the blood without cells, that contains antibodies that are developed to combat specific antigens such as viruses, bacteria, etc. Antibodies can be acquired from an animal that has either been infected with a microorganism that has the antigen or has been injected with the antigen directly into the body. Antisera are used to confer passive immunity to many diseases. [Source: Biotechnology Industry Organization, www.bio.org]

apolipoprotein E (Apo E): certain alleles of the gene which encodes the protein apolipoprotein E have been reported to be associated with the development of heart disease and Alzheimer’s disease.

apoptosis: the process which, when functioning normally, programs cells to self-destruct at an appropriate moment in an organism’s life-cycle. If the apoptotic process malfunctions in a cell, uncontrolled cell growth may result, which can contribute to the development of cancer. Such disruption of apoptosis may be associated with an inherited genetic mutation or a somatic cell genetic mutation.

application (patent): a nonprovisional utility patent application must include a specification, including a claim or claims; drawings, when necessary; an oath or declaration; and the prescribed filing fee. [Source: “Glossary,” USPTO Website www.uspto.org, accessed 1 February 2002.]

artificial insemination: a process whereby semen is placed within a female’s uterus by artificial means i.e. other than sexual intercourse. This process is usually accomplished by placing the semen in a syringe and then using the syringe to deposit the semen at the mouth of the uterus. Sperm cells within the semen then travel to and fertilize waiting egg cells. This process is used to treat some forms of human infertility. Artificial insemination is a common practice in the production of domestic livestock. Compare with invitro fertilization, invivo fetilization.

ascertainment: the scheme by which individuals are selected, identified, and recruited for participation in a research study. [Source: NHBLI/NCBI Glossary]

assay: the examination of a compound or mixture in order to determine the amount of a certain component present (like finding out how many eggs are in a cake). An assay can also be used to describe the potency of a given drug when used in a pharmacological context. In toxicology, the term is used to describe a procedure where living cells (i.e. a cell culture) are used to determine the presence of a given chemical, while in virology an assay is used to establish the effectiveness of a virus on a particular host. [Source: Biotechnology Industry Organization, www.bio.org]

association: in human genetic linkage studies, association studies frequently involve the comparison of allele frequencies for a marker locus between a disease population and in a control population. When statistically significant differences in the frequency of an allele(s) are found between a disease and control population, the disease and allele(s) are said to be in association. [Source: NHBLI/NCBI Glossary]

attenuated: weakened; with reference to microbiology or virology, to decrease the effectiveness, or virulence, of a pathogen. When a vaccine is attenuated, it means that it contains a weakened virus. This procedure is commonly used to induce active immunity in the body without causing illness. [Source: Biotechnology Industry Organization, www.bio.org]

autograft: tissue taken from one part of an individual organism’s body and then moved or transplanted to another location within that same organism. Rejection is rarely (if ever) a problem since the donor and recipient are the same individual. Skin transplants are a common example. Autografts are also used when bone marrow is harvested from an individual and stored for later use. This marrow tissue is transplanted back into the donor to replace tissue destroyed during chemotherapy.

autoimmune disease: a disease whereby an individual’s immune system mounts an attack on a portion of its own tissues. Tissues undergoing such an attack can be destroyed in the process. Rheumatoid arthritis is an example of an autoimmune disease.

autoradiography: a technique that uses X-ray film to visualize radioactively labeled molecules or fragments of molecules; used in analyzing length and number of DNA fragments after they are separated by gel electrophoresis. [Source: DOE Primer on Molecular Genetics]

autosomal recessive disorder: see autosome and recessive allele.

autosome: any chromosome that is not involved in determining an organism’s sex. Humans have 22 pairs of autosomes in each cell.

avuncular relationship: the nieces and nephews (or aunts and uncles) of individuals are related in an avuncular fashion. [Source: NHBLI/NCBI Glossary]