0 0 0: Biotechnology glossary for those with some background in
biology and physical chemistry or chemical engineers. Also intended for
those, such as securities analysts, who need to reference such terminology
quickly despite having attained some proficiency in the field. In other
words, this glossary is not really intended for amateurs. Originally stored
as a searchable Unix "man" (manual or online help) file.
14-3-3 PROTEINS: 14-3-3 proteins are a family of proteins that
recognize and bind to phosphoserine in specific contexts. 14-3-3 proteins,
e.g. bind to the C-terminus of the serine 376-dephosphorylated p53, and by
this possibly activate its DNA binding ability and transcriptional
activity. 14-3-3 proteins also bind to phosphorylated Bad and prevent it from
inhibiting Bcl-2. Transcription of the 14-3-3 proteins 14-3-3-sigma and RAD3
is activated by p53 following DNA damage. RAD3 results in the inactivation of
cdc25 and thus G2 arrest, whereas 14-3-3-sigma is important for maintaining
G2 arrest by sequestering phosphorylated Cdc2-cyclin B1 from the nucleus into
the cytosol
3'-HYDROXYL END: The hydroxyl group that is attached to the 3' carbon
atom of the sugar (ribose or deoxyribose) of the terminal nucleotide of a
nucleic acid molecule.
5'-PHOSPHATE END: The phosphate group that is attached to the 5'
carbon atom of the sugar (ribose or deoxyribose) of the terminal nucleotide
of a nucleic acid molecule.
5'CAP: located at the 5' end of the mRNA molecule, the cap helps
inhibit degredation and enhances translation
ACC: In plants, 1-aminocyclopropane-l-carboxylate (ACC) is the
immediate precursor of ethylene. ACC deaminase: A bacterial enzyme that can
cleave ACC to ammonia and a-ketobutyrate. ACC oxidase: A plant enzyme that
catalyzes the oxidation of ACC to ethylene. Formerly called ethylene-forming
enzyme. ACC synthase: A plant enzyme that catalyzes the synthesis of ACC
from S-adenosylmethionine. Its activity is stimulated by indoleacetic acid.
ACCEPTOR SPLICE SITE: The boundary between the 3' end of an intron
and the 5' end of the adjacent exon.
ACETATE (ACETIC ACID): CH3-COOH. When in water, the hydrogen is
released as H+ to give CH3-COO-. This causes an increase in the concentration
of H+ in the water, making the solution more acidic.
ACETOBACTER: Bacteria which are strict anaerobes and produce acetate
(CH3COOH) from hydrogen and carbon dioxide (CO2).
ACETYL GROUP: -CH2-CH3. Often, biological reactions involve the
transfer of two carbons of this form.
ACETYL-CoA: A compound comprised of an acetyl group (-CH2-CH3) and
coenzyme A.
ACHIRAL: not chiral. A compound (or object) that is
superimposible on its mirror image. For example CH4.
ACID-ALCOHOL FAST REACTION: A way of dyeing cells in which
carbolfuschin remains bound to cells (Mycobacterium) when washed with
acid-alcohol, leaving the cells stained.
ACINETOBACTER: Known for their 'twitching motility'; these organisms
jump from spot to spot (and are otherwise uninteresting, Gram-negative
cocci).
ACINUS: A pyknosis inducing factor was identified as Acinus
('apoptotic chromatin condensation inducer in the nucleus'), which is
the precursor of an active chromatin condensating factor. Acinus is
cleaved by caspase-3.
ACTIN: A major protein component of skeletal muscle.
ACTINOMYCES: These bacteria form branching filaments as they
reproduce, and mostly anaerobic.
ACTIVATION ENERGY: The energy required to cause a reaction to proceed
ACYL CARRIER PROTEIN: A low-molecular-weight protein that forms
part of a larger complex for either fatty acid or
polyketide biosynthesis.
ADAPTIVE RADIATION: The evolution of new species or subspecies to
fill unoccupied ecological niches.
ADAPTOR: (1) A synthetic double-stranded oligonucleotide that is
blunt ended at one end and at the other has a nucleotide extension that can
base pair with a cohesive end created by cleavage of a DNA molecule with a
specific type II restriction endonuclease. After blunt-end ligation of the
adaptor to the ends of a target DNA molecule, the construct can be cloned
into a vector by using the cohesive ends of the adaptor. (2) A synthetic
single-stranded oligonucleotide that, after self- hybridization, produces a
molecule with cohesive ends and an internal restriction endonuclease
site. When the adaptor is inserted into a cloning vector by means of the
cohesive ends, the internal sequence provides a new restriction endonuclease
site.
ADDITION REACTIONS: reactions in which an unsaturated system
is saturated or part saturated by the addition of a molecule across
the multiple bond.
ADENINE: a purine base that codes for heredity information in
RNA and DNA
ADHESION MOLECULE: These are chemicals on cell surfaces
(Proteins or Phospholipids) that enable cells to stick or bind
together. These are important on the surface of placental cells to
allow them to attach to the uterus and to allow the placental cells to
join together to make the placenta.
ADIPOSE: of or relating to animal fat
ADP (ADENOSINE DIPHOSPHATE): A nucleotide (DNA monomer) which also
acts in the cell (along with ATP, which is ADP + phosphate) as the primary
cellular energy.
AFFERENT: going towards, ie. conveying impulses towards a
nerve center such as a brain
AGAROSE GEL ELECTROPHORESIS: A matrix composed of a highly purified
form of agar that is used to separate larger DNA and RNA molecules ranging
20,000 nucleotides.
AGGLUTINATION: The aggregation of particulate antigen by
antibodies. Agglutination applies to red blood cells as well as to
bacteria and inert particles covered with antigen.
AGONIST: A substance capable of binding to a molecular target
on the surface of a cell to initiate or enhance a biological response.
AGROBACTERIUM TUMEFACIENS. A common soil bacterium that causes crown
gall disease by transferring some of its DNA to the plant host. By altering
Agrobacterium so that it no longer causes the disease but is still able to
transfer DNA, we may they then use this altered Agrobacterium to ferry
desirable genes into plants.
AICD: Activation Induced Cell Death; Apoptosis of active
lymphocytes that have to be removed after an immune response.
AIF. Apoptosis Inducing Factor, a 57 kDa flavoprotein with
homology to bacterial oxidoreductases: AIF is located in the
mitochondria but it translocates to the nucleus when apoptosis is
induced: AIF induces chromatin condensation in isolated nuclei and
large-scale fragmentation of DNA; AIF also induces dissipation of the
mitochondrial transmembrane potential and exposure of
phosphatidylserine in the plasma membrane. It induces purified
mitochondria to release the apoptogenic proteins cytochrome c and
caspase-9. Bcl-2 can prevent the release of AIF from the mitochondrion
but does not affect its apoptogenic activity
AKT: Akt is a serine-threonine kinase that is implicated in
apoptosis suppression induced by Ras, growth factor receptors,
neurotrophin receptors and oncogenes. Akt phosphorylates and therfore
inactivates pro-Caspase-9 at Ser(196). Akt itself is activated by the
PI3K second messenger.
ALCALIGENES EUTROPHUS: One of the most studied hydrogen bacteria
(i.e. able to oxidize hydrogen to water for energy) and also autotrophic
(able to grow on CO2). Also able to grow on fructose and to denitrify.
ALGIN: any of a various of colloidal substances derived from
marine brown algae and used especially as thickeners or emulsifiers
ALGINATE: A polysaccharide polymer produced by different seaweeds
and bacteria that is comprised Of P-D-mannuronate
and a-L-guluronate.
ALKALOID: organic substances occurring naturally, which are
basic, forming salts with acids. The basic group is usually an amino
function.
ALLELE: Alternative form of a genetic locus; a single allele for each
locus is inherited separately from each parent (e.g., at a locus for eye
color the allele might result in blue or brown eyes).
ALLELIC EXCLUSION: The ability of heterozygous lymphoid cells
to produce only one allelic form of antigen-specific receptor when
they have the genetic endowment to produce both. Genes other than
those for the specific receptors are usually expressed codominantly.
ALLELIC FREQUENCY: The ratio of the occurrence of one particular
allele at a locus to the occurrence of all of the alleles of the locus in a
large number of individuals of a population.
ALLERGY: This is a condition that involve an immunity in the
body against a variety of things that can come into the body including
grasses, pollens, molds, etc. The immunity that results is a special
one involving an antibody called IgE. This antibody when it combines
with the allergen (pollen, mold, antibiotics) causes the immune system
to make inflammation that can result in itching, asthma, red eyes etc.
ALLOANTIBODY: An antibody in an individual that is directed
against another individual of the same species. Blocking antibodies
produced during pregnancy are antibodies of this type.
ALLOANTIGEN: This is the chemical that induces the immune
response in the woman during pregnancy. The alloantigen is provided by
the father to the baby's placenta.
ALLOGENETIC: The allelic variation seen among members of the same
species.
ALLOIMMUNITY: A condition characterized by a specific antibody
reaction to another human being. Recognition is usually mediated by
small polypeptide chains on the cell membrane. Rh sensitivity is set
up by this type of immunity.
ALLOMETRY EQUATION: Most lines of relative growth conform to y = bxa
where y and x are the two variates being compared, b and a are constants. The
value of a, the allometric exponent, is 1 one the growth is isometric;
allometry is said to be positive when a>1 and negative when a<1.
ALLOPOLYPLOIDY: a polyploid individual having a chromosomal
set derived more or less complete from different species
ALLOSTERIC REGULATION: A catalysis-regulating process in which the
binding of a small effector molecule to one site on an enzyme affects the
activity at another site of the enzyme.
ALLYL GROUP: a group containing 3 carbon atoms and a double
bond [C1=C2-C3, where C3 is called the allyliuc position or allylic
carbon atom].
ALLYLIC REARRANGEMENT: the migration of a double bond in a
3-carbon system from carbon atoms one and two to carbon atoms two and
three, e.g. C1=C2-C3-X X-C1-C2=C3
ALPHA-HELIX Common secondary structure of proteins in which the
linear sequence of amino acids is folded into a spiral that is stabilized by
hydrogen bonds between the carboxyl oxygen of each peptide bond.
ALTERNATION OF GENERATIONS. a life cycle alternating between a
diploid (=sporophytic) and haploid (=gametophytic) generation as found
in certain protists and plants.
ALTERNATIVE SPLICING: Cell-specific removal of an exon(s) during
processing of a primary transcript that leads to a functional mRNA.
ALTERNATIVE mRNA SPLICING. The inclusion or exclusion of different
exons to form different mRNA transcripts:
AMINO ACID: H2N-HCR-COOH The R represents an organic side
group. There are 26 standard (frequently found) amino acids. In water, these
molecules dissociate into the form H3N+-HCR-COO-. The acid form shows the
proclivity for two amino acids to associate by bringing together the
oppositely charged species (NH3+ and COO-). When these species react to give
off water, a peptide bond (-NH-CO-) is formed. Amino acids joined by peptide
bond are called polypeptides, or proteins.
AMINOACYL SITE: The portion of a ribosome where the
anticodon-codon interaction takes place during translation. Also
called an A site.
AMINOACYL-tRNA: A charged tRNA; a tRNA with its specific amino
acid attached to its 3' end.
AMNIOTIC EGG. a vertebrate egg with a shell which contains
large nutrient and water stores and a number of specialized
membranes: Found only in the reptiles, birds and monotremes.
AMP (ADENOSINE MONOPHOSPHATE): A nucleotide (DNA monomer) which also
acts in the cell as an indicator of cellular energy; this has a single
phosphate group, so it's at a (relatively) low energy level, and excessive
AMP in a cell indicates the cell is at a low energy state.
AMPICILLIN (beta-lactamase). An antibiotic derived from penicillin
that prevents bacterial growth by interfering with cell wall synthesis.
AMPLICON: A herpes simplex virus type I plasmid vector.
AMYLASE. a complex of enzymes which break down starches into
sugars
AMYLOLYTIC: Agents that are capable of breaking down starch into
sugars.
ANA (Antinuclear Antibody). This test checks for problems
similar to lupus and rheumatoid arthritis or other similar
immunological diseases which are associated with pregnancy losses or
infertility: This test becomes weakly positive in women with
infertility and in women with recurrent pregnancy losses: This
antibody causes inflammation in the body or in the uterus when a baby
attaches: It is usually reported as ANA positive with at titer of 1:40
or higher with a speckled pattern: This pattern is not typical of
lupus or rheumatoid arthritis or other immunological disorders.
ANABOLISM: Reactions within an organism which produce cellular
components.
ANAEROBIC RESPIRATION: The generation of cellular energy (i.e. ATP or
NADH) by the flow of electrons from a non-O2 donor (e.g. SO4, NO3, Fe2+).
ANAGENESIS. evolutionary change producing a single lineage in
which one taxon replaces another without branching
ANAPHYLATOXIN: Substance capable of releasing histamine from
mast cells.
ANAPHYLAXIS: Immediate hypersensitivity response to antigenic
challenge, mediated by IgE and mast cells. (Allergic reaction)
ANEUPLOIDY: having a chromosome number that is not an exact
multiple of the usual chromosome number
ANGIOSPERM: a division of vascular plants with ovules and
seeds enclosed in an ovary
ANKYRIN REPEATS: As has been studied in erythrocytes, the
polypeptide ankyrin binds both to transmembrane proteins and to
spectrin, and by this links the plasma membrane to the
cytoskeleton. Repeats of homologous ankyrin sequences have been found
in all IkB family members. It is the interaction between ankyrin
repeats of IkB and regions of the RHD of Rel/NF-kB proteins that
prevents nuclear translocation of Rel/NF-kB protein dimers.
ANNEALING: The process of heating (denaturing step) and slowly
cooling (renaturing step) double-stranded DNA to allow the formation of
hybrid DNA or DNA-RNA molecules.
ANOIKIS. Anoikis is the term for detachment-induced cell
death: cells undero apoptosis upon disruption of the cell-matrix
interactions. Involved are interactions between integrins and proteins
of the extracellular matrix, as well as RGD peptides.
ANOMERS: the specific term used to describe carbohydrate
stereoisomers differing only in configuration at the hemi-acetal
carbon atom.
ANT: Adenine Nucleotide Translocator, a member of the PT pore.
ANTAGONIST: A substance that blocks the ability of a given
agonist to bind to its molecular target so as to prevent or reduce a
biological response.
ANTHERIDIUM: the male reproductive organ (gametangium) in
which gametes develop
ANTI-DNA/HISTONE ANTIBODY: If a woman reacts to the broken
down DNA (histones) and it is a speckled pattern, then she is showing
a reaction to her own embryos.
ANTI-IDIOTYPE ANTIBODY: An antibody that has the properties of an
antigen.
ANTI-SENSE TECHNOLOGY: The use of an RNA molecule to block
gene expression by interfering with protein production.
ANTIBODY (Immunoglobulin,Ig,Ab): produced in response to antigen, or
foreign, immunity-inducing body.
ANTIBODY-DEPENDENT, CELL-MEDIATED CYTOTOXICITY (ADCC): A
phenomenon in which target cells, coated with antibody, are destroyed
by specialized killer cells (NK cells and macrophages), which bear
receptors for the Fc portion of the coating antibody (Fc
receptors). These receptors allow the killer cells to bind to the
anti-body-coated target.
ANTICODON: A nucleotide base triplet in a transfer RNA molecule that
pairs with a complementary base triplet, or codon, in a messenger RNA
molecule.
ANTIGEN PROCESSING: Large molecules are broken down
(processed) within macrophages into peptides and presented within the
groove of MHC molecules.
ANTIGEN RECEPTOR: The specific antigen-binding receptor on T
or B lymphocytes; these receptors are transcribed and translated from
rearrangements of V genes.
ANTIGEN-BINDING SITE: The part of an immunoglobulin molecule
that binds antigen specifically.
ANTIGEN-PRESENTING CELL (APC): A specialized type of cell,
bearing cell surface class II MHC (major histocompatibility complex)
molecules, involved in processing and presentation of antigen to
inducer, or helper , T cells. Examples: macrophage, dendritic cells.
ANTIGEN: Any foreign material that is specifically bound by
specific antibody or specific lymphocytes; also used loosely to
describe materials used for immunization. Antigens may also be
immunogens if they are able to trigger an immune response, or haptens
if not.
ANTIGENIC SWITCHING: The altering of a microorganism's surface
antigens through genetic rearrangement, to elude detection by the host's
immune system.
ANTIPARALLEL: parallel, but oppositely directed or oriented
such as DNA
ANTISENSE RNA: A complementary RNA sequence that binds to a naturally
occurring (sense) mRNA molecule, thus blocking its translation.
ANTISENSE: The in vivo treatment of a genetic disease by blocking
translation of a protein with a DNA or an RNA sequence that is complementary
to a specific mRNA.
ANTISERUM: The fluid portion of the blood that contains the antibodies
of an immunized organism.
APA (Antiphospholipid Antibody): These are antibodies in the
blood that attach to phospholipids that are structures on the surfaces
of all cells. A positive APA test indicates that the woman's blood
clots too fast cutting off blood flow to the baby. These antibodies
can also cause the placenta to attach too weakly to the uterus. The
usual treatment is baby aspirin and heparin (a blood thinner). Heparin
is given as an injection. Both medications are started before
pregnancy during the cycle of conception; these are the least
controversial of all the treatments for infertility or recurrent
pregnancy losses.
APAF-1: Apoptotic Protease Activating Factor 1: Mammalian
CED-4 homolog.
APAFs: Apoptotic Protease Activating Factors.
APICAL DOMINANCE: inhibition of the growth of lateral buds by
the terminal bud of a shoot. Responsible for primary growth.
APICAL MERISTEM: a region of active mitosis at the stem tip or
near the root tip. The meristem responsible for primary growth.
APOMIXIS: reproduction involving specialized generative
tissues, but not dependent on fertilization. Example: dandelion
APOMORPHIC CHARACTER: a derived phenotype that evolved after a
branch diverged from the phylogentic tree
APOPLAST: the nonliving pathway formed by the extracellular
matrix of plant cell walls
APOPTOSIS: The term 'apoptosis' describes the molecular and
morphological processes leading to controlled cellular
self-destruction. Frequently, the terms 'apoptosis' and 'programmed
cell death' are used as synonyms.
APTAMER: A synthetic nucleic acid that binds to a protein that
normally does not bind to a nucleic acid.
ARABIDOPSIS THALIANA: A small member of the mustard family (kitchen
cress). It has a very small genome (130-140 Mbp), five chromosomes and
contains almost no repetitive DNA. Its genome will be completely sequenced by
the end of 2000. It is a plant model system of choice because of the
additional advantages of short generation time (about five weeks), high seed
production (up to 40,000 seeds per plant) and natural self-pollination (as
opposed to natural cross-pollination in maize). It has five small
chromosomes.
ARCHAEBACTERIA: a taxon of primitive bacteria including
methane producing forms, red halophilic forms, and others that favor
harsh acidic environments. These may be closely related to eukaryotes.
ARCHEGONIUM: the flask shaped female sex organ of bryophytes
and early vascular plants; it holds and protects the egg
ARCHENTERON: the cavity of gastrula forming a primitive gut
ARCHEZOA: a recently proposed kingdom characterized by a
primitive level of organization in that these organisms have two
haploid nuclei but lack other cellular organelles. An example is
Giardia spp.
ARF: Alternative Reading Frame (also called p14ARF within the
p16INK4A locus. ARF is a tumor suppressor which regulates p53
stability, possibly by interacting with p53 and MDM2.
AROMATIC: an aromatic molecule or ion possesses aromaticity.
Aromaticity is the special property of planar (or nearly planar)
cyclic, conjugated systems having (4n+2) conjugated pi electrons. The
delocalisation of the (4n+2) pi electrons gives them special
stability. For benzene, the most common aromatic system (n = 1,
therefore 6 pi electrons), the aromaticity confers the characteristic
reactivity of electrophilic substitution.
ARS: Autonomously replicating sequence. ARS is the origin of
replication in yeast.
ARTHROBACTER: arthro is Greek, meaning 'joint' (like elbow). Common
soil organism, coccus shaped, and after budding, the two daughters form a
'V'.
ASK1: Apoptosis Signal Regulating Kinase 1; ASK1 is a MAP3k
which leads to JNK activation; ASK1 interacts with DAXX.
ASYMMETRIC INDUCTION: a term applied to the selective
synthesis of one diastereomeric form of a compound resulting from the
influence of an existing chiral centre adjacent to the developing
asymmetric carbon atom. This usually arises because, for steric
reasons, the incoming atom or group does not have equal access to both
sides of the molecule.
ATM: ATM is the gene mutated in ataxia-telangiectasia (AT)
patients. AT is an autosomal recessive disease characterized by high
cancer predisposition, radiation sensitivity, increased chromosome
breakage, and other physiological symptoms. Cells from AT patients
show reduced and delayed accumulation of p53 protein and its
transactivational activity in response to ionizing radiation. ATM is
one of the major upstream regulators of the p53 response to
radiation-induced damage, possibly by regulating the phosphorylation
status of p53.
ATOPY: A term used by allergists to describe IgE-mediated
anaphylactic responses in humans, usually genetically determined.
ATP (ADENOSINE TRIPHOSPHATE): A nucleotide (DNA monomer) which acts
in the cell (along with ATP, which is ADP + phosphate) as the primary
cellular energy source - energy from hydrolysis of the phosphate bond
(yielding phosphate and ADP) is coupled to other reactions.
ATP-dependence: There are ATP-dependent steps in the apoptotic
process, and it was reported that ATP levels might determine the cell
death fate by apoptosis or necrosis Known ATP-dependent steps are the
activation of caspase-9 by Apaf-1/cyto c and more downstream the
active nuclear transport mechanism
ATTENUATED VACCINE: A virulent organism that has been modified to
produce a less virulent form but nevertheless retains the ability to elicit
antibodies against the virulent form.
AUTOIMMUNITY (autoallergy): A condition characterized by a
specific antibody (antiphospholipid antibody or antibodies to DNA) or
cells (such as Natural Killer Cells) which react with molecules or
constituents of the body's own tissue and cause disease such as
Rheumatoid arthritis and lupus.
AUTOLOGOUS: Cells that are taken from an individual, and somehow
manipulated before being infused back into the original donor.
AUTONOMOUS REPLICATING SEQUENCE (ARS): Any cloned DNA sequence that
initiates and supports extrachromosomal replication of a DNA molecule in a
host cell; often used in yeast cells.
AUTOPOLYPLOIDY: an individual or strain whose chromosome
complement consists of more than two complete copies of the genome of
a single ancestral species
AUTORADIOGRAPHY: A technique that captures the image formed in a
photographic emulsion as a result of the emission of either light or
radioactivity from a labeled component that is placed next to unexposed film.
AUTOSOMAL DOMINANT: A trait that is expressed in an individual
who is heterozygous for a particular gene when the mutant allele is on
one of the autosomes.
AUTOSOMAL MODIFIER GENE: A gene that modifies the action of
the autosomes.
AUTOSOMAL RECESSIVE: A trait that is expressed in an
individual who is homozygous for a particular gene.
AUTOSOMES: All members of a chromosome set except the sex
chromosomes.
AUTOTROPHIC ORGANISM: one that obtains organic food molecules
by using energy from the sun or form the oxidation of inorganic
substances to make organic substances from inorganic ones
AUXOTROPH: A strain which is mutated so that it requires some growth
factor which the parent strain does not require.
AVIDITY: The summation of multiple affinities, for example
when a polyvalent antibody binds to a polyvalent antigen.
AXOLOTL (Ambystoma mexicanum): Literally meaning water monster (in
Aztec), axolotl is a salamander (amphibian) extensively used in the
evolutionary immunogenetic studies.
AZOTOBACTER VINELANDII: Aerobically fixes nitrogen and forms cysts.
AZOTOBACTER: Bacteria which fix nitrogen (N2) aerobically
(Gram-negative, obligately aerobic rods.)
B LYMPHOCYTE (B CELL): The precursors of antibody-forming plasma
cells; these cells carry immunoglobulin and class II MHC (major
histocompatibility complex) antigens on their surfaces. Derived from bone
marrow cells.
BACILLUS LICHENIFORMIS: A denitrifying soil bacterium - grows on
organics, uses nitrate (NO3) as an electron acceptor instead of oxygen
(i.e. anaerobic metabolism), producing nitrogen (N2) and carbon dioxide
(CO2).
BACILLUS SUBTILIS: studied as 'a typical Gram-positive
bacterium'. Most of the work on endospore formation has used
this organism.
BACILLUS THURINGIENSIS: a naturally occurring bacterium with
pesticidal properties. Bacillus thuringiensis produces a protein (Bt
toxin) that is toxic only to certain insect larvae that consume it.
BACILLUS: Latin, for 'little rod'. Aerobic bacteria which form
endospores (bacterial spores, since form inside bacteria).
BACKCROSS: Crossing an organism with one of its parent organisms.
BACMID: A shuttle vector based on the AcMNPV genome that can be
propagated in both E. coli and insect cells.
BACTERIAL ARTIFICIAL CHROMOSOME (BAC): A vector system based on the
Escherichia coli F factor plasmid that is used for cloning large (100- to
300-kb) DNA inserts.
BACTERIOPHAGE: A form of virus which attacks bacteria. First observed
by d'Herrelle
BACTERIOSTATIC: An effect in which bacteria are prevented from
growing.
BACTERIUM: A single-celled, microscopic prokaryotic organism: a
single cell organism without a distinct nucleus.
BACTEROIDES: 'little rod'. Inhabitants of the intestinal tract of
warm-blooded animals, found more frequently when animals eat lots of meat
(may be big protein digesters.)
BALANCED TRANSLOCATION: A rearrangement translocation with no
apparent loss or gain of chromosomal material, resulting in a
clinically normal but genetically "abnormal" person.
BANDING: The differential staining of a chromosome by a
variety of techniques that results in a specific pattern of positively
and negatively stained bands for each chromosomal pair.
BARR BODY: Also called sex-chromatin body which represents the
inactivated X chromosome in the nucleus of somatic mammalian cells. Normally
only seen in female cells and not in male cells. One Barr body is seen in
the cells of 46,XX and 47,XXY individuals, and none in the cells of 45,X and
46,XY individuals.
BASAL METABOLIC RATE (BMR): The number of kilocalories a
resting, endothermic animal requires to maintain minimum function.
BASE ANALOGUE: A substance that can mimic the chemical
behavior of 1 of the 4 DNA bases.
BASE PAIR (bp): A pair of complementary nitrogenous bases in a DNA
molecule--adenine-thymine and guanine-cytosine. Also, the unit of measurement
for DNA sequences.
BASOPHIL: A polymorphonuclear leukocyte., whose basophils
granules contain heparin, histamine and other vasoactive
amines. Within tissues, these cells are known as mast cells q.v.
BATCH FERMENTATION: A process in which cells or microorganisms are
grown for a limited time. At the beginning of the fermentation, an inoculum
is introduced into fresh medium, and no addition or removal of medium is done
for the duration of the process.
BCL-10: The Bcl-10 gene was identified and found to be mutated
in cases of low-grade MALT lymphoma. Bcl-10 contains a N-terminal
CARD, and it confered weak pro-apoptotic effect in 293 cells. In a
MALT lymphoma a truncated Bcl-2 without CARD was identified which
failed to induce apoptosis. Bcl-10 also activates NF-kB
BCL-2: First identified member of the Bcl-2 family; as an
oncogene with anti-apoptotic activity Bcl-2 is involved in cancer,
e.g. B cell lymphoma.
BCL-XL: Member of the Bcl-2 family; closely related Bcl-2
homolog.
BENCE-JONES PROTEIN: Dimers of immunoglobulin light chains in
the urine of patients with multiple myeloma.
BENZENE: C6H6 This molecule has a distributed double bond, drawn as a
circle inside a hexagon. The way that the carbons are connected means that
the three double bonds are shared around the ring (like -C=C-C= shifting
to =C-C=C-).
BETA-DNA: The normal form of DNA found in biological systems, which
exists as a right-handed helix.
BETAINE: A low-molecular-weight compound that acts as a methyl
group donor for methionine biosynthesis.
BH1, BH2, BH3, and BH4: Bcl-2 homology domains, which are
found in members of the Bcl-2 family.
BID: BID is a protein which is cleaved by Caspase-8 into
truncated BID (tBID). tBID translocates to the mitochondria where it
mediates the release of cytochrome c.
BILE: a fluid released from the gall bladder into the small
intestine that contains detergents to emulsify fats
BINARY VECTOR SYSTEM: A two-plasmid system in Agrobacterium for
transferring a T-DNA region that carries cloned genes into plant cells. The
virulence genes are on one plasmid, and the engineered T-DNA region is on the
other plasmid.
BIOLISTICS: Delivery of DNA to cells and organelles by means of
DNA-coated pellets that are fired under pressure at high speed.
BIR: BIR is an approximately 70 amino acid motif which is a
common structural feature of all IAP family members. The BIR motif is
present in one to three copies, and it may be necessary and sufficient
for the anti-apoptotic effect of IAPs.
BIVALENT: A pair of homologous chromosomes in association as
seen at metaphase of the first meiotic division.
BLASTOPORE: During early animal development the opening which
remains following gastrulation. In protostomes the blastopore becomes
the mouth; in deuterstomes, the anus.
BLASTULA: During early animal development, the hollow ball of
cells which marks the end of cleavage.
BLOCKING ANTIBODY: A functional term for an antibody molecule
capable of blocking the interaction of antigen with other antibodies
or with cells.
BLUNT (FLUSH) END: The end of a DNA duplex molecule in which neither
strand extends beyond the other.
BLUNT-END CUT: To cleave phosphodiester bonds in the backbone of
duplex DNA between the corresponding nucleotide pairs on opposite
strands. This cleavage process produces no nucleoticle extensions on either
strand.
BLUNT-END LIGATION: Joining (ligation) of the nucleotides that are at
the ends of two DNA duplex molecules, neither of which has an extension.
BMI-1: Bmi-1 was first isolated as an oncogene that cooperates
with c-myc in the generation of mouse lymphomas. It is a
transcriptional repressor, which e.g. downregulates the expression of
the ink4a tumor suppressor genes, p16 and p19ARF, and by this
regulates progression into S-phase
BOHR SHIFT: the decrease in oxygen affinity of a respiratory
pigment in response to decreased blood pH resulting from increased
carbon dioxide in the blood.
BREWER'S YEAST: Saccharoniyces cerevisiae.
BRUSH BORDER: the microscopic finger-like projections on the
epithelial cells lining the lumen of the small intestine which are
involved in final digestion and absorption of nutrients
C (CARBOXY) TERMINUS: The last amino acid of a protein.
C-DNA LIBRARY: a collection of cDNA's, each of which has been
inserted in a DNA vector (e.g. a circular DNA plasmid) and
replicated in a bacterium such as E. coli. The bacteria maintain a
ready pool of the cDNA's and can be cultured to make copies of the
library for many experiments. A population of bacteria containing
a single inserted cDNA is called a clone. To extract a cDNA from
the library, the insert from the corresponding clone can be
amplified using PCR primed off the vector sequences connected
to the ends of the cDNA.
CAAT BOX: A highly conserved DNA sequence found about 75 bp 5' to the
site of transcription in eukaryotic genes. Its specific (trans-acting)
transcription factor is CTF-1 (NF-1) (see also TATA / Goldberg-Hogness box).
CAD: Caspase Activated DNase, 40 kDa, is an apoptosis-specific
endonuclease that cleaves DNA into the observed olignucleosomal
fragments. CAD is a cytoplasmic protein containing a NLS, and it is
normally associated with its inhibitor ICAD. The CAD/ICAD complex is
inactive, but during apoptosis Caspase-3 cleaves ICAD, CAD enters the
nucleus and degrades chromosomal DNA. ICAD is not just inhibitor but
also chaperone for CAD, since active CAD is only expressed in presence
of ICAD.
CAG/CTG repeats: Abbreviation for cytosine-adenine-guanine
triplet nucleotide and cytosine-thymine- guanine triplet nucleotide
repeats; they are associated with unstable mutations.
CALLUS: A cluster of undifferentiated plant cells that have
the capacity to regenerate a whole plant in some species.
CALMODULIN: An intracellular protein which binds calcium and
promotes a specific cellular event, such as protein kinase
activity. Example. Calmodulin often acts as a second messenger for a
plant hormone.
CANONICAL STRUCTURES: any of two or more hypothetical
structures of resonance theory which can be written for a molecule
simply by rearranging the valence electrons of the molecule.
CAP SITE: The site of initiation of transcription.
CAP: A modified nucleotide added to the 5' end of a growing
mRNA chain, apparently required for normal processing, stability, and
the translation of mRNA.
CAPSID: A structure that is composed of the coat protein(s) of a
virus and is external to the viral nucleic acids. The capsid
often determines the shape of the virus.
CAPSID: the outer protein coat of a virus.
CARCINOEMBRYONIC ANTIGEN (CEA): Antigen present during
embryonic development which normally disappears but reappears in
malignant tissue.
CARCINOMA: A malignant tumor derived from epithelial tissue, which
forms the skin and outer cell layers of internal organs.
CARD: CAspase Recruitment Domains (CARDs) have been proposed
to mediate the recruitment of caspases. CARDs are found in several
caspases, e.g. CED-3, Caspase-1, Caspase-2, Caspase-8 and Caspase-9,
but also Apaf-1. The DEDs are a specific example for CARDs.
CARDIOLIPIN: This is a phospholipid. Some individuals make an
antibody to cardiolipin and this causes the blood to clot too
quickly. Patients who lose pregnancies through miscarriage sometimes
have a false positive test for syphilis because they have antibodies
to cardiolipin that were manufactured when the pregnancy miscarried.
CASPASES: Cystein Aspartate-specific Proteases: Caspases form
a proteolytic network that is of central importance in the initiation
and execution of the apoptotic program.
CAT ASSAY: Reporter gene assay used to measure activity of a
promoter under different conditions, such as to define elements of a
promoter or to study signals that activate an intact
enhancer/promoter. CAT is the abbreviation for the enzyme,
chloramphenicol acetyl transferase, the activity of which is measured
in the assay.
CATABOLISM: Reactions within an organism which produce cellular
energy.
CATALYTIC ANTIBODY (abzyme): An antibody selected for its ability to
catalyze a chemical reaction by binding to and stabilizing the transition
state intermediate.
CATALYTIC REFORMING: the process of improving the octane
number of straight-run gasoline by increasing the proportion of
aromatic and branched chain alkanes. [Catalysts employed are either
molybdenum-aluminium oxides or platinum based.]
CATALYTIC RNA (ribozyme): A natural or synthetic RNA molecule that
cuts an RNA substrate.
CBP/p300: CBP/p300 (CBBP = CREB-binding protein) is a histone
acetyltransferase. CBP can be phosphorylated by the cyclinE-Cdk2
complex, and by this CBP is activated. The CBP enzymatic activity
might result in the activation of S-phase-gene expression and might
contribute to G1/S transition. CBP is also target of the transforming
protein E1A which binds to CBP: bound E1A renders CPB constitutively
active. CBP is a co-activator for E2F and the RelA protein and it is a
coactivator for p53-dependent transactivation and- repression.
CD (cluster of differentiation) numbers are now used to
identify cell surface antigens that can be distinguished by monoclonal
antibodies. Some of these (e.g. CD25,35. 71) are clear-cut functional
molecules. and several (e.g. CD3,4, 8) are also widely used as markers
of particular cell types. The list below shows the major cell type on
which they are found and (in brackets) the function where known. It
represents the consensus at the last International Workshop (1993).
CD no. Cell type CD no. Cell type CD no. Cell type
1 thymocytes, APC 41 platelets 83 dendritic, act T,B
2 T, NK (LFA3R) 42 platelets 84 B, T, mac, leukaemia
3 T 43 myeloid 85 B, plasma cells, mono
4 T hlpr,some mac 44 myeloid, RBC 86 B, mono
5 some T, B 45 all leucocytes 87 myeloid
6 T, some B 46 all leucocytes 88 myeloid (C5aR)
7 T, NK 47 (all cells) 89 T, B, myeloid (Fc alpha R)
8 T cytotoxic 48 all leucocytes 90 thymocytes, brain ('Thy-I')
9 pre-B, mycloid 49a-f all leucyt/adhsn91 mono, mac (alpha2MR)
10 pre-B,leukaemia 50 all leucyt/lCAM392 many cells
11a adhesn (LFA 1) 51 endo, B, mac 93 myeloid
11b adhesion (CR3) 52 leucocytes 94 NK, T
11c adhesion (CR4) 53 all leucocytes 95 B, T
12 myeloid 54 act,TB,mac/ICAM196 act, NK, T
13 myeloid, endo 55 leucocytes 97 act, T, B
14 mono,mac/(LBPR) 56 NK (NCAM) 98 T, B, NK, platelets
15 myeloid 57 NK, some T,B 99 T,B, myeloid
16 myeloid,NK(FCR3)58 leucocyts (LFA3)100 T, B, NK, myeloid
17 myeloid,platelet59 leucocytes 101 T, NK, myeloid
18 as CD11 60 platelet,some T 102 endo (ICAM-2)
19 B 61 platelet(w CD41)103 T (intestinal)
20 B (Ca channel) 62 platelets 104 endo, epi
21 B (CR2l EBVR) 63 platlt, leucyt 105 endo
22 B 64 mono,mac(FCR1) 106 endo(VCAM-1)
23 B, mycloid(FCeR)65 myeloid 107 NK, endo
24 B. granulocyte 66 granulocytes 108 T, NK, endo
25 act,T,B,mac/IL2Ralpha 67 granulocytes 109 mono, endo
26 act,T,B,mac 68 mac 115 mono, mac (MCSFR)
27 T, some B 69 act,T,B,NK, mac 116 mono, mac (GM-CSFR)
28 some T, B 70 act,T,B 117 haemopoietic (SCFR)
29 most cells/adhsn71 prlfrtgcel(TF R)118 act, T
30 act, T, B 72 B 119 many cells (IFNgammaR)
31 myeloid,B,pltlts73 B, some T 120 many (TNFR)
32 myeloid,B(FCR2) 74 B,som mono,mac/Ii 121 T, B (IL-1R)
33 myeloid 75 B, some T 122 T, NK (lL-2Rbeta)
34 stem cells 76 B, NK, some T 124 TB, (IL-4R)
35 mycloid, B(CR1) 77 act, B 126 many (IL-6R)
36 mono,pltlts/LDLR78 B 127 many (IL-7R)
37 B, some T 79alpha,beta B 128 T, myeloid (IL-8R)
38 act,T,B,thymocyt80 act, B, T, mono 130 many (IL-6R-associated)
39 B,act T 81 B,T,NK,mono
40 B, IDC 82 B, T, NK, mono, epi, endo
act: activated;APC: antigen-presenting cell; alpha-2M: alpha-2
macroglobulin; CR: complement receptor; EBV:Epstein-Barr virus; endo:
endothelial cell; epi, epithelium; FCR: Fc receptor; I/V/N-CAM:
intercellular/vascular/neural adhesion molecule; IDC: interdigitating
cell; Ii: MHC invariant chain; IL-2R (etc.): IL-2 receptor; LBP:
lipopolysaccharide-binding protein; LFA leucocyte function antigen;
LDL: low-density lipoprotein; mac: macrophage; mono: monocyte; NK:
natural killer cell; RBC, red blood cell: SCF: stem cell factor; TF:
transferrin
CD4 T Helper Cell: This is a T lymphocyte that helps activate
CD3 cells in an immunity response by producing cytokines that cause
proliferation, differentiation and growth of other cells necessary for
completing the immune reaction. These are usually high normal in women
with infertility and recurrent pregnancy losses.
CD40: CD40 is involved in regulating T-cell-dependent B-cell
activation. Besides on B cells, macrophages and dendritic cells, CD40
is found on endothelial cells nd fibroblasts where it appears to
regulate inflammatory cytokine production (e.g via NF-kB) and cell
adhesion. There is also evidence for CD40 being involved in
regulating normal epithelial cell growth and differentiation, and CD40
might have an impact on the growth and sensitivity to apoptosis of
carcinoma cells.
CDC25: Cdc25 is an essential regulator of mitosis: it is a
nuclear phosphatase which normally dephosphorylates and activates its
substrate, the cyclin B/Cdc2 kinase. Dephosphorylation of cyclinB/Cdc2
initiates mitosis. Upon DNA damage, Cdc25 is phosphorylated by the
Chk1 serine/threonine kinase and subsequently sequestered into the
cytosol by Rad24: cyclinB/Cdc2 remains inactivated and the cell cycle
is arrested in the G2 phase.
CDNA (cDNA) CLONE: A double-stranded DNA molecule that is carried in
a vector and was synthesized in vitro from an mRNA sequence by using reverse
transcriptase and DNA polymerase.
CDNA (cDNA) LIBRARY: A collection of cDNA clones that were generated
in vitro from the mRNA sequences of a single tissue or cell population.
CDNA: cDNA: Complementary DNA; created using reverse
transcriptase, cDNA is a complement of mRNA, and can be inserted into
expression vectors to synthesize foreign proteins in cells.
CED-3: CED-3 is the C.elegans caspase; besides CED-4 and CED-9
it plays a central role in C.elegans apoptosis.
CED-4: CED-4 activates CED-3 in C.elegans, and it is regulated
by CED-9. Its mammalian homolog is Apaf-1
CED-9: CED-9 is a pro-survival member of the Bcl-2 family: it
is a crucial regulator of apoptosis in C.elegans.
CELL-MEDIATED CYTOTOXICITY (CMC): Killing (lysis) of a target
cell by an effector lymphocyte.
CELL-MEDIATED IMMUNITY (CMI): Immune reaction mediated by T
cells; in contrast to humoral immunity, which is antibody
mediated. Also referred to as delayed-type hypersensitivity.
CELLULAR ONCOGENE (proto-oncogene): A normal gene that when mutated
or improperly expressed contributes to the development of cancer.
CENTIMORGAN: A unit of genetic distance between two gene loci,
abbreviated cM. Named after T. H. Morgan (1866-1945), who studied Drosophila
melanogaster genetics. In humans, 1 cM is approximately 106 base pairs of
DNA.
CENTROMERE: The central portion of the chromosome to which the
spindle fibers attach during mitotic and meiotic division.
CEPH FAMILY PANEL: A set of about 65 two- or three-generation
families with siblingships of eight or more that are used for the genetic
mapping of the human genome. The blood cells from members of these families
that provide the source of DNA for genotyping are maintained by the Fondation
Jean Dausset Centre d'Etude Polymorphisme Humain in Paris, France.
CEPHEM-TYPE ANTIBIOTIC: An antibiotic that shares the basic
chemical structure of cephalosporin.
CG ISLAND: Unmethylated cytosine-guanine sequences that are
often found near the 5' ends of some genes.
CHAGAS' DISEASE: A parasitic disease caused by the protozoan
Trypanosoma cruzi.
CHAIN TERMINATION MUTATION: A mutation that generates a stop
codon, thus preventing further synthesis of the polypeptide chain.
CHAPERONE: Any protein that binds to an unfolded or partially folded
target protein to prevent misfolding, aggegation, and/or degradation of
it. Chaperones also facilitate the target protein's proper folding.
CHARGED (AMINO ACYL) tRNA: A transfer RNA molecule that is coupled to
its specific amino acid.
CHEMIOSMOSIS: The use of a chemical gradient (generally hydrogen
ions) across the cell wall to drive some other process or reaction. For
example, an ADP (low energy) may be converted to ATP (high energy) using the
potential available from allowing a hydrogen ion (H+) into the cell, where
the hydrogen ion concentration (which we also call pH) is lower (meaning pH
is higher).
CHEMIOSMOTIC PUMP: a membrane pump which actively transports
protons to establish an energy gradient which is then used to drive
some other cellular process, such as hormone, ion, or sucrose
transport
CHEMOKINES: Small, secreted proteins that mediate inflammation
by inducing chemotaxis (movement of a cell) and activation of a
variety of inflammatory cells.
CHEMOSTAT: A continuous growth system for cultures; CSTR (continuous
stirred-tank reactor)
CHEMOTAXIS: Migration of cells along a concentration gradient
of an attractant.
CHEMOTAXIS: Motion either up or down a chemical gradient
(i.e. towards or away from higher concentrations of the chemical.)
CHIMERA: Usually, a plant or animal that has populations of cells
with different genotypes. Sometimes it refers to a recombinant DNA molecule
that contains sequences from different organisms.
CHIRALITY: a term which may be applied to any asymmetric
object or molecule. The property of non-identity of an object with its
mirror image.
CHITIN: A polysaccharide of an amino sugar found in cell walls
of some protists and fungi and in the exoskeletons of arthropods.
CHITINASE: An enzyme produced by plants in response to infection by
fungal pathogens that hydrolyzes the chitin components in fungal cell
walls. Some bacteria also produce chitinase.
CHLORAMPHENICOL: An antibiotic that interferes with protein
synthesis.
CHOANOFLAGELLATE: a simple colonial organism in which
individual cells are flagellated and which exhibits elemental division
of labor. A type of collared, flagellated cell characteristic of the
choanoflagellates and also present in sponges.
CHORIONIC VILLUS SAMPLING (CVS): A procedure in which a small
sample of cells are taken from the placenta through a small catheter
placed up through the vagina and the cervix. This is done earlier in
pregnancy than amniocentesis and is used to test for chromosomal and
other biochemical abnormalities that may affect the health and well
being of the baby.
CHROMATID: Each of the two daughter strands of a duplicated
chromosome joined at the centromere during mitosis and meiosis.
CHROMATOGRAPHY: A series of related techniques for the
separation of a mixture of compounds by their distribution between two
phases. In gas-liquid chromatography the distribution is between a
gaseous and a liquid phase. In column chromatography the distribution
is between a liquid and a solid phase.
CHROMOGENIC SUBSTRATE: A compound or substance that contains a
color-forming group.
CHROMOSOMAL INTEGRATION SITE: A chromosomal location where foreign
DNA can be integrated, often without impairing any essential function in the
host organism.
CHROMOSOME JUMPING: A technique that allows two segments of duplex
DNA that are separated by thousands of base pairs (about 200 kb) to be cloned
together. After subcIoning, each segment can be used as a probe to identify
cloned DNA sequences that, at the chromosome level, are roughly 200 kb apart.
CHROMOSOME WALKING: A technique that identifies overlapping cloned
sequences that are about 40 kb long that form one continuous segment of a
chromosome.
CHROMOSOME WALKING: Working from a flanking DNA marker, overlapping
clones are successively identified that span a chromosomal region of
interest.
CHROMOSOME: A single DNA molecule, a tightly coiled strant of DNA,
condensed into a compact structure in vivo by complexing with accessory
histones or histone-like proteins. Chromosomes exist in pairs in higher
eukaryotes.
CHYLOMICRON: a protein coated sphere containing fats which is
synthesized by the small intestine. Chylomicrons are transported to
the liver via the lacteal and closed circulation
CIS-ACTING GENE: A gene acting on or co-operating with another gene
on the same chromosome.
CISTRON: A DNA sequence that codes for a specific polypeptide; a gene.
CITRIC ACID CYCLE (TRICARBOXYLIC ACID (TCA) CYCLE, KREBS CYCLE): A
metabolic pathway in which pyruvate (HOOC-CO-CH3) is converted to carbon
dioxide (CO2) with the coupled generation of ATP from ADP and NADH from
NAD. In most organisms, the primary part of catabolism (energy generation)
CLADISTICS: an approach that classifies taxa according to the
time when branches appear along the phylogenetic tree.
CLEAVE (cut,digest): To break phosphodiester bonds of duplex DNA,
usually with a type II restriction endonuclease.
CLOSTRIDIUM BUTYRICUM: Used to produce butyric acid,
butanol, acetate, acetone and ethanol from amino acids in
fermentation.
CLOSTRIDIUM PASTEURIANUM: An anaerobic nitrogen
fixer. Studied extensively for its ability to fix nitrogen, and
considered to be responsible for much of the nitrogen fixation which
occurs in soil.
CLOSTRIDIUM: Strict (obligate) anaerobes which are Gram-positive,
spore-forming rods. Some will produce butyric acid, acetone, and butanol.
CO-ORDINATE BOND: The linkage of two atoms by a pair of
electrons both electrons being provided by one of the atoms, the
donor. Coordinate bonds are covalent bonds.
COAT PROTEIN (capsid): The coating of a protein that enclosed the
nucleic acid core of a virus.
COCCUS (plural: COCCI): bacteria which are spherical
CODING TRIPLET: A set of three contiguous nucleotides of the
nontranscribed DNA strand of the coding region of a
structural gene that is complementary to a transcribed triplet.
CODOMINANCE: The expression of both alleles in a heterozygous
individual, e.g., presence of both hemoglobin A and S on
electrophoresis in an individual heterozygote for sickle-cell disease.
CODON OPTIMIZATION: An experimental strategy in which codons within a
cloned gene that are not the ones generally used by the host cell translation
system are changed to the preferred codons without changing the amino acids
of the synthesized protein.
CODON: A group of three nucleotides that specifies addition of one of
the 20 amino acids during translation of an mRNA into a polypeptide. Strings
of codons form genes and strings of genes form chromosomes.
COEFFICIENT OF RELATEDNESS: r = n(0.5)L where n is the alternative
routes between the related individuals along which a particular allele can be
inherited; L is the number of meiosis or generation links.
COENZYME: A compound which is involved in a reaction but is not part
of the enzyme catalyzing the reaction. These tend to be relatively low
molecular weight, and act as carriers of an agent (reduction capacity as in
ATP, or an acetyl group as in Acetyl-CoA (CoA stands for Coenzyme A)).
COHESIVE ENDS: Complementary single-strand extensions on the ends of
duplex DNA molecules.
COINTEGRATE VECTOR SYSTEM: A two-plasmid system for transferring
cloned genes to plant cells. The cloning vector has a T-DNA segment that
contains cloned genes. After introduction into Agrobacterium, the cloning
vector DNA undergoes homologous recombination with a resident disarmed Ti
plasmid to form a single plasmid carrying the genetic information for
transferring the genetically engineered T-DNA region to plant cells.
COLIFORM: Gram-negative, non-spore forming rods which produce gas and
lactose during fermentation
COMPETENCY: An ephemeral state, induced by treatment with cold
cations, during which bacterial cells are capable of uptaking foreign DNA.
COMPLEMENT RECEPTOR: A structure found on erythrocytes,
lymphocytes, neutrophils, monocytes and macrophages that binds C3
fragments.
COMPLEMENT: The complement of a nucleic acid sequence replaces each
base by its complementary base: adenine (A) by thymidine (T), cytosine (C) by
guanine (G), and vice versa. In RNA, adenine is paired not with thymidine but
with uracil (U). By convention, DNA and RNA molecules have a consistent
orientation (5' to 3') which is used in writing their sequences. To preserve
this orientation, the complement of a sequence is written backwards compared
to the original. For example, an RNA sequence ACGGUACU has the DNA complement
AGTACCGT.
COMPLEMENTARITY-DETERMINING REGION (CDR): A part of the variable (V)
regions of light and heavy antibody chains that makes contact with the
antigen. The amino acid sequences of CDRs are highly variable from one
antibody of the same class to another.
COMPLEMENTARY DNA (cDNA): A double-stranded DNA complement of an mRNA
sequence; synthesized in vitro by reverse transcriptase and DNA polymerase.
COMPLEMENTARY HOMOPOLYMERIC TAILING: The process of adding
complementary nucleotide extensions to different DNA molecules-e.g., dG
(deoxyguanosine) to the 3'-hydroxyl ends of one DNA molecule and dC
(deoxycytidine) to the 3'- hydroxyl ends of another DNA molecule-to
facilitate, after mixing, the joining of the two DNA molecules by base
pairing between the complementary extensions. Also called dG-dC tailing,
dA-dT tailing.
CONCATEMER: A DNA segment composed of repeated sequences linked end
to end.
CONCATEMER: A tandem array of repeating unit-length DNA elements.
CONFIGURATIONAL ISOMERS: a series of compounds which have the
same constitution and bonding of atoms but which differ in their
atomic spatial arrangement. Stereoisomers.
CONJUGATION: (1) The joining of two bacteria cells when genetic
material is transferred from one bacterium to another. (2) Sequence of
alternating double (or triple) and single bonds. e.g. C=C-C=C and
C=C-C=O. Conjugation can also be relayed by the participation of lone pairs
of electrons or vacant orbitals.
CONSTANT REGION (C REGION): The invariant carboxyl-terminal
portion of an antibody molecule, as distinct from the variable region
which is at the amino-terminal of the chain.
CONSTITUTIVE PROMOTER: An unregulated promoter that allows for
continual transcription of its associated gene.
CONTIG: A series of contiguous, overlapping, cloned DNA
fragments.
CONTIGUOUS (contig) MAP. The alignment of sequence data from large,
adjacent regions of the genome to produce a continuous nucleotide sequence
across a chromosomal region.
COOMBS' TEST: A test named for its originator, R.R.A. Coombs,
used to detect non-agglutinating antibodies on red blood cells by
addition of an anti-immunoglobulin antibody.
COPY NUMBER: The number of copies of a transgene integrated
into a host genome; used to describe transgenic animals.
COREPRESSOR: A low-molecular-weight compound that combines with an
inactive repressor protein to form a complex that binds to an operator region
and prevents transcription.
CORYNEBACTERIUM: Bacteria characterized by their shape - frequently
have a swollen end, giving a club shape, and after budding, the two daughters
form a 'V'.
COS (cos) ENDS: The 12-base, single-strand, complementary extensions
of bacteriophage A DNA.
COSEGREGATION: When two genetic conditions appear to be inherited
together.
COSMID: A vector that uses the cos end sequences of bacteriophage A
and in vitro bacteriophage packaging to form, after injection of the vector
into a host cell, a plasmid that can carry as much as 45 kb of insert DNA.
COSUPPRESSION: The transformation of a plant with a gene in the sense
orientation that the plant already possesses. This results in the down
regulation of both the endogenous and introduced genes. Also called sense
suppression.
COTRANSFECTION: The introduction of two different DNA molecules into
a eukaryotic cell. In baculovirus expression systems, the procedure by which
the baculovirus and the transfer vector are simultaneously introduced into
insect cells in culture.
COUPLING: The phase state in which either two dominant or two
recessive versions of two different genes occur on the same chromosome. Also
called cis configuration.
CPG (CpG) ISLANDS: Clusters of GC-rich regions that precede many
transcribed vertebrate genes.
CREB: cAMP-responsive element binding protein.
CRMA: Cytokine response-modifier protein produced by cowpox virus:
CrmA is a caspase-inhibitor for ICE family members, inhibits preferentially
Caspase-1 but also Caspase-8; CrmA shows homology to serpins, a family of
serine protease inhibitors. Cyclophilin D Cyp D is a cyclosporin A binding
protein and is located in the mitochondrial membrane; it is part of the PT
pore.
CROSS-HYBRIDIZATION: The hydrogen bonding of a single-stranded DNA
sequence that is partially but not entirely complementary to a single-stranded
substrate. Often, this involves hybridizing a DNA probe for a specific DNA
sequence to the homologous sequences of different species.
CROSS-REACTIVITY: The ability of an antibody, specific for one
antigen, to react with a second antigen; a measure of relatedness
between two different antigenic substances.
CROSSING OVER: Reciprocal breaking and rejoining of homologous
chromosomes in meiotic prophase I that results in exchange of
chromosomal segments.
CYANOBACTERIA: Photosynthetic, oxygen-producing bacteria, some
of which are capable of nitrogen-fixation (previously known as
"blue-green algae").
CYCLIC AMP (cyclic adenosine monophosphate). A second messenger that
regulates many intracellular reactions by transducing signals from
extracellular growth factors to cellular metabolic pathways.
CYTOCHROME: Electron carriers in the electron chain (the mechanism
which transport electrons across the cell membrane), made of proteins
containing iron sites.
CYTOKINE: These are hormones produced by white blood cells
(lymphocytes) that communicate with other cells of the immune system,
recruiting them to perform more aggressive roles in the fighting off of
infection or in the rejection of something from the body such as a baby, a
kidney or a bone marrow transplant. Soluble substances secreted by cells,
which have a variety of effects on other cells, e.g. Interleukin 1 (Il-1).
CYTOKININ: A plant hormone that stimulates cell division.
CYTOPLASM: The part of the cell inside the plasma membrane (inner
wall membrane) but excluding the nucleus (which is only found in eucaryotes).
CYTOSINE: One of the organic bases found in either DNA or RNA.
CYTOTOXIC (CYTOLYTIC) T CELL: Cell that kills target cells
bearing appropriate antigen within the groove of an MHC class I
molecule that is identical to that of the T cell.
CYTOTROPHOBLAST: This is a specialized cell of the placenta
(also a trophoblast) whose function is to attach the baby to the
mother's uterus. It provides the anchor. It grows deeply into the
lining of the uterus (decidua) and firmly attaches the placenta for
the duration of pregnancy.
CpG Island: Repetitive CpG doublets occurring in a sea of DNA
sequences low in CpG residues. Usually associated with
transcription-initiation regions of genes transcribed at low rates that do
not contain a TATA box. The CpG-rich stretch of 20-50 nucleotides occurs
within the first 100-200 bases upstream of the start site region (where
promoter-proximal elements reside). A trans-acting transcription factor
called SP1 recognizes the CpG islands (see also Htf islands). In vertebrates,
many of the nontranscribed genes (and the genes on the inactivated X
chromosome) have a 5-methyl group on the C residue in CpG dinucleotides in
transcription-control regions.
D GENE: A small segment of immunoglobulin heavy-chain and
T-cell receptor DNA, coding for the third hypervariable region of most
receptors.
DALTON: A unit of measurement equal to the mass of a hydrogen atom,
1.67E-24 gram/L (Avogadro's number).
DCC: DCC is a candidate tumor suppressor gene which is mutated
in cases of colonic carcinoma. DCC encodes a receptor for netrin-1 a
molecule involved in axon guidance. DCC induces apoptosis in the
absence of netrin-1 but blocks apoptosis when bound to netrin-1. DCC
is cleaved by Caspase-3 at Asp1290 and this cleavage seems to be
required for DCC's apoptotic activity.
DD: Death Domain: homologous cytoplasmic domain of Death
Receptors; by using their DDs, activated death receptors recruit
adaptor molecules like FADD, TRADD or DAXX, which eventually mediate
the apoptotic signal to the apoptotic machinery.
DEATH PHASE: The final growth phase, during which nutrients have been
depleted and the waste products become toxic and cell number decreases.
DED: Death Effector Domain: the DED is a specific example of a
more global homophilic interaction domain termed CARD, which is found
in several caspases with large prodomains. Specific for the DED is,
that it is also part of the adaptor protein FADD/MORT 1.
DELAYED TYPE HYPERSENSITIVITY (DTH): A T cell-mediated
reaction to antigen, which takes 24-48 hours to develop fully, and
which involves release of lymphokines and recruitment of monocytes and
macrophages. Also called c cell-mediated immunity.
DELETION: Loss of part or a whole chromosome or loss of DNA
nucleotide bases.
DELOCALIZATION: electron systems in which bonding electrons
are not localised between two atoms as for a single bond but are
spread (delocalized) over the whole group. e.g pi-bond electrons, in
particular the delocalised pi-electrons associated with aromatic
molecules.
DELTAPSI (deltaPsi): Mitochondrial inner transmembrane potential
DENATURE: To induce structural alterations that disrupt the
biological activity of a molecule. Often refers to breaking hydrogen bonds
between base pairs in double-stranded nucleic acid molecules to produce in
single-stranded polynucleotides or altering the secondary and tertiary
structure of a protein, destroying its activity.
DENITRIFY: To convert nitrate (NO3) to ammonia (NH3)
DENSITY GRADIENT CENTRIFUGATION: High-speed centrifugation in which
molecules "float" at a point where their density equals that in a gradient of
cesium chloride or sucrose.
DEOXYRIBOSE: The 5-carbon sugar component of DNA.
DESULFO-: named for sulfur. Anaerobic organisms which reduce sulfate
(SO3) or sulfur (elemental, to sulfide (H2S)) to get their energy.
DEXTROROTATORY: the phenomenon in which plane polarised light
is turned in a clockwise direction.
DFF45: DNA Fragmentation Factor (45 kDa), human homolog to
ICAD (from mouse). It is an inhibitor of a specific endonuclease
which cleaves DNA to oligonuceosomal fragments as one of the main
features of the apoptotic preocess.
DIAMINOPIMELIC ACID: The immediate precursor to L-lysine in bacteria
and plants, and a component of some bacterial cell walls.
DIASTEREOMERS (DIASTEREOISOMERS): stereoisomeric structures
which are not enantiomers (mirror images) of one another. Often
applied to systems which differ only in the configuration at one
carbon atom, e.g. meso- and d- or l-tartaric acids are
diastereoisomeric.
DIAUXIC GROWTH: A pattern of growth observed in batch studies in
which two growth compounds are available. The more favored compound (giving a
higher growth rate) is used first, and then the second compound is used,
resulting in a lower rate of growth.
DIAZOTROPH: An organism that can fix nitrogen.
DICENTRIC: Refers to an aberrant chromosome that contains 2
centromeres.
DICISTRONIC VECTOR: A mammalian cloning vector that is specially
designed to carry two functional genes.
DIDEOXYNUCLEOTIDE (ddNTP): A deoxynucleotide that lacks a 3' hydroxyl
group, and is thus unable to form a 3'-5' phosphodiester bond necessary for
chain elongation.
DIHEDRAL ANGLE: the angle between groups attached on adjacent
carbon atoms when viewed in a Newman projection.
DIHYDROFOLATE REDUCTASE: An enzyme that catalyzes the formation of
tetrahydrofolic acid.
DIKARYONS: A fungal mycelium that possesses two separate
haploid nuclei per cell which eventually fuse to form a diploid
nucleus. A unique fungal characteristic.
DIPLOBLASTIC: having two layers, an endoderm and an
exoderm. Example: Hydra
DIPLOID. The number of chromosomes in most somatic cells,
which is double the number found in the gametes (the haploid
number). In humans, the diploid chromosome number is 46.
DIRECTIONAL CLONING. DNA insert and vector molecules are digested
with two different restriction enzymes to create noncomplementary sticky ends
at either end of each restriction fragment. This allows the insert to be
ligated to the vector in a specific orientation and prevents the vector from
recircularizing.
DISACCHARIDE. A double sugar, consisting of two
monosaccharides joined by dehydration synthesis. Example: fructose
DISC. Death Inducing Signaling Complex.
DISCORDANT. A twin pair (or set of individuals) in which one
member exhibits a certain trait and the other does not.
DISPROPORTIONATION: a process in which a compound of one
oxidation state changes to compounds two or more oxidation states
e.g. 2Cu+ --> Cu + Cu2+
DISSOCIATION CONSTANT: the measure of the extent of
dissociation, measured by the dissociation constant K. For the
process: AB = A + B, K = ([A][B])/[AB]
DISSYMMETRIC: chiral
DITHIOTHREITOL: A low-molecular-weight thiol-containing reducing
agent. It is added to buffers in low concentrations to prevent protein
sulfhydryl groups from being oxidized. At higher concentrations, it is used
to reduce disulfide linkages in proteins.
DIZYGOTIC. The product of fertilization of 2 separate eggs by
2 separate sperm; nonidentical twin pair.
DNA CODON: A set of three contiguous deoxyribonucleotide pairs of the
coding region of a structural gene where the bases of one strand are
transcribed into a codon.
DNA LIGASE. An enzyme that rejoins cut pieces of DNA.
DNA POLYMERASE: An enzyme that links an incoming deoxyribonucleotide,
which is determined by complementarity to a deoxyribonucleotide in a template
DNA strand, with a phosphodiester bond to the X-hydroxyl group of the last
incorporated nucleotide of the growing strand during replication.
DNA POLYMORPHISM. One of two or more alternate forms (alleles) of a
chromosomal locus that differ in nucleotide sequence or have variable numbers
of repeated nucleotide units.
DNA PROBE. A molecule that has been labeled with a radioactive
isotope, dye or enzyme and is used to locate a particular portion of a
DNA molecule.
DNA REARRANGEMENTS. Recombination of DNA segments, eg, in
cells of the immune system, the variable (V), diversity (D), and
joining (J) regions somatically rearrange to generate functional
antibody genes.
DNA-PK. DNA-dependent Protein Kinase. DNA-PK is a substrate
for caspases (-3) and is activated upon DNA damage. One of its
substrates is p53.
DNASE I: An enzyme that degrades DNA, used to remove DNA from RNA
preparations and from cell free extracts. Also called deoxyribonuclease 1.
DOMAIN. A compact segment of an immunoglobulin molecule, made
up of about 110 amino acids around an S-S bond, and encoded by a
unique segment of DNA, surrounded by nontranslated sequences.
DONOR SITE. Guanine-thymidine sequence that defines the splice
site at the 5' end of an intron.
DOUBLE FERTILIZATION. A mechanism of fertilization in
angiosperms, in which two sperm cells unite with two cells in the
embryo sac to form the zygote and endosperm.
DOUBLE-STRANDED COMPLEMENTARY DNA (dscDNA). A duplex DNA molecule
copied from a cDNA template.
DOWN SYNDROME. This is a genetic disorder caused by the
presence of an extra chromosome 21. (Called trisomy 21). Affected
children have mental retardation and characteristic features of the
body, face and limbs. Affected children also have many medical
problems such has heart defects.
DOWNSTREAM. The region extending in a 3' direction from a gene.
DQ ALPHA. These are HLA antenna present on certain white blood
cells (lymphocytes). They are part of the white blood cell type of an
individual. When couples are compatible for these factors (share the
same DQ numbers), it is an unfavorable combination for pregnancy.
These tests give you back two numbers for each member of the couple.
In a normal pregnancy the father's DNA in the baby signals the
mother's body to protect the developing embryo. If the father's DNA is
too closely matched to the mother's, there is a good chance that the
embryo created by them cannot differentiate itself from the mother's
body. The mother's body then rejects the embryo because it cannot
identify and protect the embryo as a baby.
DQ BETA. The DQ antennae have an alpha limb (chain) and beta
limb (chain). If a man is DQ alpha 2 (0201) and DQ beta 2 (0201) and
the sperm carrying this information fertilizes the egg, the embryo
will be a blighted ovum. Donor sperm is considered in this situation.
DR ANTIGENS. MHC class II molecules found on B cells and
antigen-presenting cells of humans.
DRD. DED-Recruiting Domain; a domain of modest homology to the
DED domain, DRD was found in FLASH, which binds to the DEDs of DADD
and caspase-8.
E1A. E1A is a transforming viral protein produced by
adenovirus. E1A forces cells through the restriction point of the cell
cycle into the S phase by forming complexes with Rb and CBP/p300. By
binding Rb it activates E2F, and by binding CBP it activates its
histone acetyltransferase activity, both inducing S-phase-gene
expression. E1A has transforming activity only when cell proliferation
is not blocked, e.g. by p53. E1A stimulated proliferation normally
would trigger p53-dependent cell cycle arrest what results in
apoptosis. For that reason, adenovirus additionally expresses E1B
which blocks p53 function.
E1B. E1B (55 kDa) is an adenovirus oncogene, which blocks the
function of p53. E1B shares sequence and functional homology with Bcl-2
E1B19K. Anti-apoptotic adenovirus protein, which indirectly
prevents Fas-mediated activation of caspase-8, possibly by its
interaction with FLASH.
E2F. E2F is a key transcription factor for S-phase-gene
induction. E2F is strictly regulated during the cell cycle: it is
inactive when bound in a complex with the Rb protein.
E6 and E7. Viral onogenes produced by papillomavirus: E6
inactivates Rb, while E7 inactivates p53.
ECLIPSED: a conformation in which substituents on two attached
saturated carbon atoms overlap when viewed as a Newman projection.
ECTOTHERM. An animal that must use an external energy source
to regulate its body temperature. Cold-blooded.
EFFECTOR CELLS: Cells of the immune system that degrade antigens.
EFFECTOR: A low-molecular-weight compound that modifies the
function of a regulatory protein.
ELECTRON CHAIN: The mechanism which transports electrons across the
cell membrane, establishing the proton-motive force. Often, this chain
converts ATP to ADP while moving hydrogen ions out of the cell.
ELECTRON DONOR: The compound which is oxidized during metabolism
ELECTROPHILIC SUBSTITUTION: an overall reaction in which an
electrophile binds to a substrate with the expulsion of another
electrophile. The most common example is the electrophilic
substitution of a proton by another electrophile, such as a nitronium
ion, on an aromatic substrate such as benzene.
ELECTROPORATION. Application of a short, high-voltage electric
pulse to cells in the presence of DNA to permit DNA to enter the
cells.
ELISA (enzyme-linked immunosorbent assay). This is a
laboratory test method to analyze blood for the presence and the
amount of antibodies in the woman to DNA, phospholipids, and other
things. The test tubes are coated with the substance such as the
phospholipid. Then the serum to be tested is added. If there are
antibodies in the serum against the phospholipid, they attach and in
the process of attachment a color (dye) is released that turns the
fluid in the test tube a different color. The intensity of the color
tells you how high the immunity is (how much antibody is present).
ELONGATION: Sequential addition of one monomer at a time to a
polymer.
EMBRYONIC STEM CELLS: Cells of an early embryo that can give rise to
all differentiated cells, including germ line cells.
EMSA. Electrophoretic Mobility Shift Assay
ENANTIOMERS: a pair of isomers which are related as mirror
images of one another. e.g. isomers differing only in the
configuration about the chiral atoms.
ENCAPSIDATION. Process by which a virus' nucleic acid is enclosed in
a capsid.
ENCODE: To specify, after decoding by transcription and translation,
the sequence of amino acids in a protein.
ENDOMETRIOSIS. A disease condition of women when the tissue that
normally lines the uterus each month preparing for a baby (endometrium) leaks
out of the uterus inside the body cavity and begins to grow (and menstruate)
in locations such as the ovaries, fallopian tubes, bowel, bladder and
abdominal cavity. This causes pain, inflammation, scar tissue, and
autoimmunity response in the woman that may make it difficult for her to
become pregnant.
ENDONUCLEASE. Enzyme that cleaves bonds between nucleotides of
single- or double-stranded DNA or of RNA at specific sequences of
nucleotides.
ENDOPHYTE. A plant that lives inside another.
ENDOPROTEASE: An enzyme that cleaves the peptide bonds between amino
acids within a protein. Cleavage is usually at one or more specific sites.
ENDOSKELETON. A hard skeleton present beneath soft external
tissues, such as the spicules of sponges, the plates of echinoderms,
and the internal skeleton of all vertebrates.
ENDOSYMBIOSIS. a hypothesis that the creation of the
eukaryotic cell resulted from the symbiotic inclusion of prokaryotes
into a host cell
ENDOTHERM. An animal that uses its own metabolic energy to
maintain a constant body temperature, such as in a bird, mammal and
some insects.
ENDOTOXIN: A component of the cell wall of gram-negative bacteria
that elicits, in humans, an inflammatory response and fever.
ENOLASE: An enzyme that catalyzes the conversion of
2-phosphoglycerate to phosphoenolpyruvate.
ENOYLREDUCTASE. An enzyme involved in the synthesis of polyketicle
antibiotics.
ENTEROBACTER AEROGENES: A coliform (Gram-negative,
non-spore forming rods which produce gas and lactose during
fermentation) bacterium which is not usually found in the intestine.
ENTEROGASTRONE. a hormone secreted by the wall of the small
intestine which slows stomach digestion and emptying
ENTHALPY: a thermodynamic state function, generally measured
in kilojoules per mole. In chemical reactions the enthalpy change
(deltaH) is related to changes in the free energy (deltaG) and entropy
(deltaS) by the equation: deltaG = deltaH - T.deltaS
ENTROPY: a thermodynamic quantity which is a measure of the degree of
disorder within any system. The greater the degree of order the higher the
entropy; for an increase in entropy S is positive. Entropy has the units of
joules per degree K per mole.
ENV GENE. Encodes capsule or envelope protein of a retrovirus.
ENZYME-LINKED IMMUNOSORBENT ASSAY (ELISA): A primary antibody is
bound to the target molecule; a secondary antibody, which binds to the
primary antibody, is added later, and has attached to it an enzyme that can
convert a colorless substrate into a colored product. If the target molecule
is not present in the sample, washing steps will remove both antibodies and
no colored product will be produced.
ENZYMES. Proteins that control the various steps in all chemical
reactions. Biocatalysts. End in -ase.
EOSINOPHIL CHEMOTACTIC FACTOR OF ANAPHYLAXIS (ECF-A): A
substrate released from mast cells during anaphylaxis which attracts
eosinophils.
EOSINOPHIL. A polymorphonuclear leukocyte with large
eosinophilic (i.e. red) cytoplasmic granules.
EPB virus. Epstein-Barr virus
EPIGENETIC. A factor that changes the phenotype without
changing the genotype.
EPIMERIZATION: a process in which the configuration about one
chiral centre of a compound, containing more than one chiral atom, is
inverted to give the opposite configuration. The term epimers is
often used to describe two related compounds which differ only in the
configuration about one chiral atom.
EPISOME. A plasmid that can exist either independently in the
cytoplasm or as an integrated part of the genome of its bacterial
host.
EPISTASIS. The influence of a gene on the expression of another
(non-allelic) gene.
EPITOPE: A specific chemical domain on an antigen that is
recognized by an antibody. Each epitope on a molecule such as
a protein elicits the synthesis of a different antibody.
EPOXIDATION: the addition of an oxygen bridge across a double
bond to give an oxirane. Achieved by use of a peracid or, in a few
cases, by use of a catalyst and oxygen.
EQUILIBRIUM CONSTANT: according to the law of mass action, for
any reversible chemical reaction: aA + bB = cC + dD, the equilibrium
constant (K)is defined as: K = ([C]c[D]d)/([A]a[B]b)
EQUIVALENCE ZONE. In a precipitin reaction, the region in
which the concentration of antigen and antibody leads to maximal
precipitation.
ERYTHROMYCIN: An antibiotic produced by Streptomyces
ES. Embryonic Stem cells
ESCHERICHIA COLI. A commensal bacterium inhabiting the human colon
that is widely used in biology, both as a simple model of cell biochemical
function and as a host for molecular cloning experiments.
ESCHERICIA: Inhabitants of the intestinal tract of warm-blooded
animals, grow on a wide variety of carbon and energy sources.
ETHIDIUM BROMIDE. A fluorescent dye used to stain DNA and RNA. The
dye fluoresces when exposed to UV light. Carcinogenic to touch.
ETHYLENE: A gaseous compound that acts as a plant hormone. It is
important in fruit ripening, flower senescence, seed
germination, rooting of cuttings, root elongation, and the
response of the plant to environmental stress.
EUBACTERIA: One of the two kingdoms of bacteria. Bacteria in this
kingdom have ester-linked lipids (CH2-O-CO-) and a single form of RNA
polymerase consisting of four subunits. The lineage of prokaryotes that
includes the cyanobacteria and other contemporary bacteria, but excludes the
archaebacteria (=Archea), such as the halophiles and thermophiles.
EUKARYOTES: Organisms, including animals, plants, fungi, and some
algae, that have (1) chromosomes enclosed within a membrane-bounded nucleus
and (2) functional organelles, such as mitochondria and chloroplasts, in the
cytoplasm of their cells.
EXCISION: The natural or in vitro enzymatic release (removal) of a
DNA segment from a chromosome or cloning vector.
EXCITED STATE: the state of an atom, molecule or group when it
has absorbed energy and become excited to a higher energy state as
compared to the normal ground state. The excited state may be
electronic, vibrational, rotational, etc.
EXOCYTOSIS. The cellular secretion of macromolecules by the
fusion of vesicles with the plasma membrane.
EXON TRAPPING: A protocol for the isolation of exons from genomic
clones. Genomic DNA (I to 6 kb) is cloned into an
intron that is flanked by two exons (artificial gene) in a
vector. When an exon is present in the cloned DNA, reverse
transcriptase polymerase chain reaction (RT-PCR) shows that the
mRNA from the artificial gene is longer than expected.
The cloned DNA can be amplified, subcIoned, and characterized.
Also called exon entrapment, exon amplification.
EXON. A DNA sequence that is ultimately translated into protein.
EXONUCLEASE III (ExoIII, exodeoxyribonuclease III): An Escherichia
coli enzyme that removes nucleotides from the 3'hydroxyl ends of
double-stranded DNA.
EXONUCLEASE. An enzyme that cleaves nucleotide chains at their
terminal bonds only.
EXOPOLYSACCHARIDE: A high-molecular-weight polymer that is composed
of sugar residues and is secreted by a microorganism into the surrounding
environment.
EXPONENTIAL PHASE: A growth phase observed during batch growth in
which the rate of growth is described by an exponential equation (dX/dt =
kXt, so that X(t) = X(0) exp(kt)). (The entire process, however, is a
sigmoidal, hyperbolic tangent)
EXPRESSED SEQUENCE TAG (EST). a sequence from a transcribed
mRNA for a possibly unknown gene. Individual EST's are neither
especially informative nor highly accurate; however, they are easy
to collect in large numbers. A database of EST's can be helpful
for picking protein-coding sequences out of a long stretch of DNA,
or for providing a larger context for very short sequences, such
as the small pieces of protein sequence obtainable by mass
spectrometry. EST's are compiled by the National Center for
Biotechnology Information in a database called dbEST.
EXPRESSION VECTORS. Sequences of DNA into which cDNA fragments
are inserted to encourage cells to more efficiently transcribe desired
cDNA sequences.
EXTENSION (protruding end, sticky end, overhang, cohesive end): A
single-stranded DNA region consisting of one or more nucleotides at the end
of a strand of duplex DNA. (3' extension on the 3'-hydroxyl end; 5'extension
on the 5'-phosphate).
EXTRACELLULAR MATRIX: The organized carbohydrate and protein
structure that is secreted by animal cells when they are
part of a tissue.
F(ab')2. A fragment of an antibody containing two
antigen-binding sites generated by cleavage of the antibody molecule
with the enzyme pepsin which cuts at the hinge region C-terminally to
the inter-H-chain disulphide bond.
F1 HYBRIDS. The first generation of animals generated from 2
different inbred strains. These animals are genetically identical to
one another but different from either inbred parent.
F2 HYBRIDS. The progeny produced from matings between F1
animals. These animals are different from one another and will contain
different mixtures of the genetic variations that were present in the
original inbred progenitors.
FADD. Fas-Associating protein with Death Domain (also called
MORT 1).
FATTY ACIDS: Molecules having a hydrophobic section (usually a chain
of (-CH2-)) and an end with a carboxylic acid (-COOH) which is
hydrophilic. One example of fatty acids are the components of soap which make
it possible to dissolve oils in water.
FERMENTATION: Breakdown of carbon compounds by cells or organisms to
ATP without using molecular oxygen.
FERREDOXIN: An iron-sulfur protein that acts as an electron
carrier.
FIBERS. A lignified cell type that reinforces the xylem of
angiosperms and functions in mechanical support; slender, tapered
sclerenchyma cells that usually form bundles.
FIBRINOLYSINS. These are special proteins in the blood of all
normal persons that help blood clots that formed dissolve.
FISCHER PROJECTION: a convention for drawing carbon chains so
that the relative 3-dimensional stereochemistry of the carbon atoms is
relatively easy portrayed on a 2-dimensional drawing.
FISH (FLUORESCENCE IN SITU HYBRIDIZATION): A physical mapping
approach that uses fluorescein tags to detect hybridization of probes with
metaphase chromosomes and with the lesscondensed somatic interphase
chromatin.
FLANKING REGION. The DNA sequences extending on either side of a
specific locus or gene.
FLASH. FLice-ASsociated Huge protein (220 kDa): FLASH is a
component of the DISC; it contains a motif structurally related to
CED-4/Apaf-1 and two tandem-repeated DED homologous domains (DRDs)
which mediate its interaction with caspase-8 and FADD. FLASH
self-associates through its CED-4-homologous domains (in analogy to
CED-4/Apaf-1). FLASH is required for the activation of Caspase-8
during Fas-meditated apoptosis. Overexpression of FLASH deletion
mutants inhibited Fas- and TNF-mediated apoptosis. FLASH also
interacts with the anti-apoptotic adenovirus protein E1B19K
FLAVOBACTERIUM: Known for moving by gliding (not wiggling); a
psychrophilic (cold-loving) organism.
FLAVONOID: A member of a class of plant phenolic compounds containing
two aromatic rings connected by a 3-carbon bridge.
FLICE. also called MACH or Caspase-8.
FLIP. FLICE Inhibitor Protein; inhibitor of Death Receptor
induced apoptosis; aliases for FLIP are among others Casper, Usurpin,
CASH.
FLOW CYTOMETRY. This is a laboratory method where blood is
placed into a machine that separates blood cells by size, shape,
density and epitope (antennae) on their surface. The immunophenotype
assay and the NK assay are tested by using this machine. Each cell in
the machine passes a laser eye and the reflected light is analyzed by
the machine. Each type of cell reflects light differently. An NK ( CD
56+) cell gives a different reflection than a B cell (CD 19+).
FLOW CYTOMETRY: Analysis of biological material by detection of the
lightabsorbing or fluorescing properties of cells or subcellular fractions
(i.e., chromosomes) passing in a narrow stream through a laser beam. An
absorbance or fluorescence profile of the sample is produced. Automated
sorting devices, used to fractionate samples, sort successive droplets of the
analyzed stream into different fractions depending on the fluorescence
emitted by each droplet.
FLOW KARYOTYPING: Use of flow cytometry to analyze and separate
chromosomes on the basis of their DNA content.
FLUORESCEIN: A fluorescent dye often used to label antibodies so
that they may be visualized after they have reacted with
antigens in cells.
FLUOROGRAPHY: Detection of the emission of light on X-ray film
from a labeled source.
FOLLICLE STIMULATING HORMONE (FSH). This brain hormone is
produced in the pituitary gland deep in the brain. It is responsible
for making the ovary grow and produce eggs. It is also important in
telling the ovary when to release the egg (ovulate) and when to begin
the production of estrogen by the ovary. In the male FSH does a
similar thing to the testicles. It stimulates them to produce and to
release the sperm to the site where they are ready to be ejaculated.
FOOTPRINTING. (DNA footprinting) Assay used to study
DNAbinding proteins.
FOUR-CUTTER: A type II restriction endonuclease that binds and
cleaves DNA at sites that contain four nucleotide pairs.
FRAGMENTATION. a method of asexual reproduction in the fungi
where a hypha breaks apart to form two new mycelia. In plants, a
method of asexual reproduction.
FRAMESHIFT MUTATION: In chromosomal DNA, an insertion or deletion of
base pairs that changes the reading frame of a gene.
FREE ENERGY (deltaG): a thermodynamic state function; the free
energy change (deltaG) in any reaction is related to the enthalpy and
entropy: deltaG = deltaH - T*deltaS
FREUND'S COMPLETE ADJUVANT. A water-in-oil emulsion that
contains an immunogen, an emulsifying agent, and killed mycobacteria
which enhance the immune response to the immunogen; termed
"incomplete" Freund's adjuvant if mycobacteria are not included.
FRONTIER ORBITAL SYMMETRY: the theory that the site and rates
of reaction depend on the geometries, sign of the wave function and
relative energies of the highest occupied molecular orbital (HOMO) of
one molecule and the lowest unoccupied molecular orbital (LUMO) of the
other.
FUNGUS: Eucaryotes which do not contain chlorophyll (that is, which
aren't algae). There are three primary fungal groups: yeast, molds, and
mushrooms
FUSION PROTEIN: The product of two or more coding sequences from
different genes that have been cloned together and that, after translation,
form a single polypeptide sequence. Also called hybrid protein, chimeric
protein.
Fab. Fragment of antibody containing the antigen-binding site,
generated by cleavage of the antibody with the enzyme papain, which
cuts at the hinge region N-terminally to the inter-H-chain disulphide
bond and generates two Fab fragments from one antibody molecule.
Fc receptor (FcR). A receptor on a cell surface with specific
binding affinity for the Fc portion of an antibody molecule. Fc
receptors are found on many types of cells.
Fc. Fragment of antibody without antigen-binding sites,
generated by cleavage with papain; the Fc fragment contains the
C-terminal domains of the heavy immunoglobulin chains.
G CAP: The 5'-terminal methylated guanine nucleotide that is
present on many eukaryotic mRNAs; it is joined, after
transcription, to the mRNA in a 5'-to-5' linkage.
G Proteins. A class of intracellular proteins that bind to the
internal surface of receptors and are involved in the signal
transduction process.
GAMETE: A cell with a haploid chromosome content. In animals,
sperm or egg; in plants, pollen or ovum.
GASTRIN. a hormone secreted by the wall of mammalian stomach
which activates digestive processes in the stomach
GATA-1. GATA-1 is a gene regulatory protein that is found in
red blood cells and contributes to cell-type specific expression of
the á-globin gene and for the maturation of erythroblasts. Absence of
GATA-1 leads to apoptosis and to a block in maturation. GATA-1
upregulates the expression of Bcl-XL and was found to be cleaved in a
caspase-dependent manner upon activation of death receptors on the
surface of erythroid cells, or alternatively, following deprivation of
erythropoietin. Thus, GABA-1 appears to be involved in a complex
regulation system determining the red blood cell's fate:
differentiation, reversible maturation arrest or death
GAUCHE: a conformational isomer in which the groups are
neither eclipsed nor trans to one another. Often taken as the
conformation where the dihedral angle between the groups is 60'.
GEL ELECTROPHORESIS: a DNA separation technique that is very
important in DNA sequencing. Standard sequencing procedures involve cloning
DNA fragments into special sequencing cloning vectors that carry tiny pieces
of DNA. The next step is to determine the base sequence of the tiny fragments
by a special procedure that generates a series of even tinier DNA fragments
that differ in size by only one base. These nested fragments are separated by
gel electrophoresis, in which the DNA pieces are added to a gelatinous
solution, allowing the fragments to work their way down through the
gel. Smaller pieces move faster and will reach the bottom first. Movement
through the gel is hastened by applying an electrical field to the gel.
GEL-SHIFT ASSAY. An assay used to detect specific protein
binding to DNA. Such binding creates complexes that migrate more
slowly during gel electrophoresis than free DNA. Also known as
mobility-shift assay.
GENETIC POLYMORPHISM: When two or more alleles of a locus in a
population of individuals occur at a frequency greater than one per cent.
GEOMETRICAL ISOMERISM: a term describing isomerism owing to
the presence of restricted rotation about a bond. The major example
is (Z) and (E) isomers of unsymmetrically substituted alkenes.
GLD MUTATION. gld = generalized lymphoproliferative disease;
spontaneous loss-of-function mutation in the FasL gene of mice. Leads
to accumulation of lymphocytes.
GLYCOGEN. the storage carbohydrate of animals; in mammals it
is found in high concentration in the muscles and in the liver
GLYCOLYSIS: The splitting of sugar into smaller organic acids,
yielding cellular energy.
GLYCOSYLATION: The covalent addition of sugar or sugar-related
molecules to proteins or polynucleotides.
GRAM-NEGATIVE: Cells which stain red when Gram-stained This arises
from the inability of iodine to bind to the cell's peptidoglycan (rigid layer
comprised of sugar and amino acid residues) because it is covered by another
layer of wall (the outer wall, made of lipopolysacharide and proteins.)
GRAM-POSITIVE: Cells which stain purple when Gram-stained This arises
from the binding of iodine to the cell's peptidoglycan (rigid layer comprised
of sugar and amino acid residues.)
GROWTH PHASE (curve). The characteristic periods in the growth of a
bacterial culture, as indicated by the shape of a graph of viable cell number
versus time.
GUANINE: One of the organic bases found in either DNA or RNA.
H-2 complex. The major histocompatibility complex situated on
chromosome 17 of the mouse; contains subregions K, I and D.
HAPLOID CELL. A cell containing only one set, or half the usual
(diploid) number, of chromosomes.
HAPLOTYPE: The alleles of the loci of a chromosome.
HAPTEN. A compound, usually of low molecular weight, that is
not itself immunogenic but that, after conjugation to a carrier
protein or cells, becomes immunogenic and induces antibody, which can
bind the hapten alone in the absence of carrier.
HARD AND SOFT ACIDS AND BASES: a classification of acids and
bases depending on their polarizability. Hard bases include fluoride
ions; soft bases include triphenylphosphine. Hard acids include Na+,
whilst an example of a soft, polarisable acid is Pt2+; hard-hard and
soft-soft interactions are favoured. Hardness and softness can be
described in terms of the HOMO and LUMO interactions.
HEAT SHOCK PROTEINS: The proteins synthesized in the nearly
universal response of organisms to environmental stress
such as high temperature.
HEAVY CHAIN (H chain). The larger of the two types of chains
that comprise a normal immunoglobulin or antibody molecule.
HELPER PLASMID: A plasmid that provides a function(s) to another
plasmid in the same cell. Some helper plasmids are used to mobilize
nonconjugative plasmids from a donor cell into a recipient cell.
HELPER T CELLS. A class of T cells which help trigger B cells
to make antibody against thymus-dependent antigens. Helper T cells
also help generate cytotoxic T cells.
HERITABILITY. the proportion of the total phenotypic variance that is
attributable to genetic causes:
h2 = genetic variance / total phenotypic variance
Natural selection tends to reduce heritability because strong
(directional or stabilizing) selection leads to reduced variation.
HETEROCHROMATIN. Dark-stained regions of chromosomes thought to be
for the most part genetically inactive.
HETERODUPLEX. A double-stranded DNA (dsDNA) molecule or DNA-RNA
hybrid, where each strand is of a different origin.
HETEROGENEOUS NUCLEAR RNA (hnRNA). The name originally given to large
RNA molecules found in the nucleus, which are now known to be unedited mRNA
transcripts, or pre-mRNAs.
HETEROLOGOUS PROBE: A DNA probe that is derived from one organism
and used to screen for a similar DNA sequence in a
clone bank derived from another organism.
HETEROLYTIC REACTION: a reaction in which a covalent bond is
broken with unequal sharing of the electrons from the bond.
HETEROPHILE ANTIGEN. A cross-reacting antigen that appears in
widely ranging species such as humans and bacteria.
HETEROPLASMY. The existence of more than 1 mitochondrial type
in the cells of an individual, i.e., the presence of both normal and
mutant mt DNA in a single individual.
HETEROPLOID. An individual with an abnormal number of
chromosomes (as compared to euploid, which is the normal number of
chromosomes).
HETEROTETRAMER. A molecule consisting of 4 subunits, at least
1 of which differs from the others.
HIGH THROUGHPUT SCREENING. The process of using automated
assays to search through large numbers of substances for desired
activity, resulting in less costly and faster systematic processes.
HINGE REGION. A flexible, open segment of an antibody molecule
that allows bending of the molecule. The hinge region is located
between Fab and Fc and is susceptible to enzymatic cleavage.
HISTOCOMPATIBILITY. Literally, the ability of tissues to get
along; in immunology, it means identity in all transplantation
antigens. These antigens, in turn, are collectively referred to as
histocompatibility antigens.
HLA (Human Leukocyte Antigen). These are molecules on the
surface of human cells that determine a person's white blood cell
type. Ten numbers make up this system. There are two A numbers, two B
numbers, two C numbers, two DR numbers and two DQ numbers. One number
at each locus (A,B,C, DR and DQ) comes from your mother the other one
comes from your father. Couples with infertility and recurrent
pregnancy losses share too many DR and DQ HLA factors. They are too
compatible. This is referred to as the unlucky match for a successful
pregnancy to occur.
HOLOENZYME: A catalytically active enzyme containing all of the
necessary cofactors and subunits.
HOMEOBOX: A short stretch of nucleotides whose base sequence is
virtually identical in all the genes that contain it. It has been found in
many organisms from fruit flies to human beings. In the fruit fly, a homeobox
appears to determine when particular groups of genes are expressed during
development.
HOMODIMER: A protein with two identical polypeptide chains.
HOMOLOGOUS CHROMOSOMES. Chromosomes that have the same linear
arrangement of genes--a pair of matching chromosomes in a diploid
organism.
HOMOLOGOUS RECOMBINATION. The exchange of DNA fragments between two
DNA molecules or chromatids of paired chromosomes (during crossing over) at
the site of identical nucleotide sequences.
HOMOLOGY. a similarity in a characteristic due to a shared ancestry
HOMOLYTIC REACTION: a reaction in which a covalent bond is
broken with equal sharing of the electrons from the bond.
HOMOMER: A protein with two or more identical protein chains. Also
called homomeric polypeptide, homomeric protein.
HOMOPLASMY. The presence of a single population of mt DNA in
the cells of a single individual. This is normal.
HOMOPOLYMER: A nucleic acid strand that is composed of one kind of
nucleotide.
HOMOTETRAMER. A molecule consisting of 4 identical subunits.
HOUSE-KEEPING GENES. Genes which are constitutively expressed in most
cells because they provide basic functions.
HPA-II (HpaII) TINY FRAGMENTS (HTF): Small DNA fragments that are
generated from a genomic clone after treatment with the restriction
endonuclease HpalI, which cleaves within the CpG islands.
HUMAN ARTIFICIAL CHROMOSOME (HAC): A chromosome that is assembled
from telomere, centromere, and human genomic DNA sequences.
HUMAN CHORIONIC GONADOTROPIN (hCG). A hormone that increases
early in pregnancy. It is produced by the cells of the placenta that
attach the baby to the uterus. Its detection is the basis of all
pregnancy tests. It is also used as a drug given to the woman to time
ovulation. Once this drug, is given the woman predictably ovulates in
36-40 hours.
HUMAN GROWTH HORMONE (HGH, somatotrophin). A protein produced in the
pituitary gland that stimulates the liver to produce somatomedins, which
stimulate growth of bone and muscle.
HUMAN MINISATELLITE DNA: Human DNA that is noncoding and generally
G+C rich and contains tandem repeats of short (9- to 40-base-pair) stretches
of DNA.
HUMEGON. This drug is used to stimulate ovulation. It contains
biologically active FSH an LH. Humegon and hCG are given sequentially
for induction of ovulation. It, like Pergonal, is also used in men to
treat testicular dysfunction.
HUMORAL IMMUNE RESPONSE: The production of antibody by B cells of the
immune system in response to the presence of a foreign antigen.
HYBRID CELL. A cell formed by fusion of 2 cells of different
origin in which the 2 nuclei have merged into 1. Can be cloned to
produce hybrid cell lines.
HYBRID GENE: The combination of two genes or the parts of two genes
in the correct reading frame that encodes a single protein that has amino
acid sequences from both genes.
HYBRID SELECTION: A protocol for determining which genomic clones
hybridize to a cDNA or mRNA molecule.
HYBRIDIZATION: (1) The pairing of two polynucleotide strands, often
from different sources, by hydrogen bonding between complementary
nucleotides. (2) The process whereby atomic orbitals of different type but
similar energies are combined to form a set of equivalent hybid
orbitals. These hybrid orbitals do not exist in the atoms but only in the
formation of molecular orbitals by combining atomic orbitals from different
atoms.
HYBRIDOMA: The product of the fusion of a myeloma cell with an
antibody-producing lymphocyte. This cell combination (hybridoma) can continue
to divide in cell culture and secrete a single type of antibody.
HYDROBORATION: the cis-addition of B-H bonds across double (or
triple) carbon-carbon bonds.
HYDROGEN UPTAKE POSITIVE (HUP): A term describing a microorganism
that is capable of assimilating hydrogen gas.
HYDROGENOLYSIS: the cleaving of a chemical bond by hydrogen.
Generally carried out in the presence of a hydrogenation catalyst.
HYDROLYSIS: the addition of the elements of water to a
substance, often with the partition of the substance into two parts,
such as in the hydrolysis of an ester to an acid and an alcohol.
HYDROPHILIC: Describing compounds which are highly soluble in
water. Generally, such compounds have a charge or are polar (having a
dipole).
HYDROPHOBIC; Describing compounds with a lower water solubility (and
high solubility in oils). Typically, these are neutral compounds. On a
molecular thermodynamic level, hydrophobic compounds would like to be in
among water molecules, but not as much as other water molecules would like to
be in the same place; hydrophilic compounds would like to be in with water
molecules more than other water molecules.
HYPERVARIABLE REGIONS. Portions of the light and heavy
immunoglobulin chains that are highly variable in amino acid sequence
from one immunoglobulin molecule to another, and that, together,
constitute the antigen-binding site of an antibody molecule. Also,
portions of the T-cell receptor which constitute the antigen-binding
site.
HYPHA (plural. HYPHAE). A single fungal filament;
Collectively, the hyphae make up the mycelium.
HYPOCOTYL. the portion of an early developing plant which is
below the cotelydon (s) (=seed leaf) but above the root system. Its
elongation helps the young plant to break away from the ground.
HYPOTHALAMUS. This is a thumb-sized gland near the base of the
brain that controls the pituitary gland. It releases messages called
releasing hormones that stimulate the pituitary gland to release its
hormones (FSH and LH) in the proper amounts to achieve ovulation. In
some women the hypothalamus is dysfunctional and infertility results.
HYSTEROSALPINIGOGRAM (HSG). This is an x-ray test that
involves the injection of a liquid dye into the uterus and into the
tubes. It allows the doctor to see the size and the shape of the
uterus, whether there are any abnormalities and whether the tubes are
open to take the sperm to the egg and to deliver the fertilized egg
into the uterus.
IAPs. Inhibitor of Apoptosis Proteins: a family of proteins
with antiapoptotic effect, probably by inhibiting Caspase-3 and -7.
ICAD. Inhibitor of CAD (Caspase-activated DNase), identified
in mouse cells, ICAD is homologous to human DFF45. ICAD binds to CAD,
and inhibits its DNase activity. Active Caspase-3 cleaves ICAD and by
this activates CAD what results in oligonucleosomal DNA cleavage. ICAD
is not just inhibitor of CAD but probably also chaperone for CAD,
since active CAD is only expressed in presence of ICAD.
ICE NUCLEATION PROTEIN: A protein around which ice crystals form.
ICE-MINUS BACTERIA: Bacteria that do not synthesize ice nucleation
proteins.
IDIOTYPE. The combined antigenic determinants (idiotopes)
found on antibodies of an individual that are directed at a particular
antigen; such antigenic determinants are found only in the variable
region.
IFN-gamma. Interferon-gamma; cytokine with antiviral effect
produced by cytotoxic CD8+ T lymphocytes and CD4+ Th1 cells but not by
Th2 lymphocytes. It inhibits proliferation of T2h cells, activates
macrophage functions and regulates antibody production of B
lymphocytes.
IKAP. IKK-complex-Associated Protein is a scaffold component
of the heigh molecular weight IKK complexes. Like NEMO/IKK-gamma, IKAP
binds to IKKs directly, but it also binds to NIK. It might direct the
assembly or disassembly of IKK complexes in response to signalling,
and control deactivation of the kinase complex after stimulation.
IKKs. Two IkB kinases (IKKs) have been cloned : IKK-alpha and
-beta. They are the only kinases known to phospphorylate IkB-alpha at
the same residues that are modified in response to agents that
activate NF-kB. IKKs are part of multi-protein complexes (800 kDa)
which include the IKK-alpha and -beta, NEMO/IKK-gamma, IKAP and NIK.
IL (Interleukin). This is a generic term for cytokines
produced by white blood cells when they are activated and in the
process of killing or rejecting something such as an embryo, a kidney
transplant or an infection. CD3-IL2 Receptor + cells are T cells in
the process of rejection in the body. They should be below 5% of the
total T cells in the immunophenotype testing.
IMMEDIATE-EARLY GENE: A viral gene that is expressed promptly after
infection.
IMMORTALIZING ONCOGENE. A gene that upon transfection enables a
primary cell to grow indefinitely in culture.
IMMUNE RESPONSE (Ir) GENE. A gene controlling an immune
response to a particular antigen; most genes of this type are in the
MHC (major histocompatibility complex), and the term is rarely used to
describe other types of Ir genes outside the MHC.
IMMUNOAFFINITY CHROMATOGRAPHY: A purification technique in which an
antibody is bound to a matrix and is subsequently used to bind a specific
protein and separate it from a complex mixture.
IMMUNOGEN (ANTIGEN, Ag): induces antibody response.
IMMUNOGLOBULIN (Ig). A general term for all antibody
molecules. Each Ig unit is made up of two heavy chains and two light
chains and has two antigen- binding sites.
IMMUNOGLOBULIN CLASS. There are five different classes or
families of antibodies (immunoglobulins). IgM is the first antibody
produced when an immune response is initiated. It lives in the blood
system. IgG lives in the lymphatic system and is made by IgM. IgA
lives in the organs and protects them. IgD which is present as a
memory antibody in the blood once a person is immune or immunized. IgE
is the antibody that causes allergies and asthma. It is present
throughout the body.
IMMUNOGLOBULIN FOLD. The immunoglobulin fold is one of the
most versatile and widely-used structural units of proteins. The
immunoglobulin fold was originally characterized as the globular
modules that form the homology domains of immunoglobulins. Its
secondary structure consists of a barrel that is composed of a three-
and a four-stranded antiparallel beta-sheet which are linked by a
disulfide bond.
IMMUNOTHERAPEUTIC PROCEDURE: The use of an antibody or a fusion
protein containing the antigen binding site of an antibody to treat a disease
and enhance the well-being of a patient.
IMMUNOTOXIN: A fusion protein that has separate domains with antibody
and toxin activity. The antibody portion of the molecule facilitates binding
to a target molecule or cell, and the toxin inactivates the target molecule
or kills the cell.
IN SITU HYBRIDIZATION: Use of a DNA or RNA probe to detect the
presence of the complementary DNA sequence in cloned bacterial or cultured
eukaryotic cells.
IN VITRO TRANSLATION: Protein synthesis that is directed by either
purified DNA with bacterial extracts or mRNA with wheat germ or rabbit
reticulocyte extracts that provide ribosomes, tRNAs, and protein synthesis
factors. The reaction mixture is often supplemented with ATP, GTP, and amino
acids.
INBRED MOUSE STRAIN. A strain of mice that has been maintained
by successive brother to sister matings over many generations, e.g.,
BALB/c and C57BL/6 mice strains.
INBREEDING DEPRESSION. Reduction in offspring fitness resulting from
mating between blood relatives.
INCLUSION BODY: A protein that is overproduced in a recombinant
bacterium and forms a crystalline array inside the
bacterial cell.
INCOMPATIBILITY GROUP: A classification scheme indicating which
plasmids can coexist within a single cell. Plasmids must belong to different
incompatibility groups to coexist within the same cell. Plasmids that belong
to the same incompatibility group are unstable when placed into the same
cell. A plasmid cloning vector should always belong to an incompatibility
group different from that of the host bacterium's endogenous; plasmids.
INCOMPLETE DOMINANCE. A condition where a heterozygous off- spring
has a phenotype that is distinctly different from, and intermediate to, the
parental phenotypes.
INCOMPLETE PENETRANCE: When some individuals in a population have a
specific genotype that causes an abnormality but are not affected.
INDEPENDENT ASSORTMENT: The formation of all possible gene
combinations in gametes with genes on different chromosomes, followed by the
random joining of male and female gametes. Also called Mendel's second law of
inheritance.
INDUCER. A molecule that induces the expression of a gene.
INITIATION CODON: The codon AUG, which specifies the first amino acid
(methionine [N-formylmethionine in prokaryotes]) of a protein. Also called
initiator, translational start codon, translational initiation signal.
INITIATION COMPLEX: The fMet-tRNA'Fet-mRNA-small ribosomal
subunit-large ribosomal subunit combination in prokaryotes or the Met-tRNA
let-mRNA-small ribosomal subunit-large ribosomal subunit combination in
eukaryotes that is ready for the elongation phase of translation.
INITIATOR tRNA: The fMet-tRNA'Fet in prokaryotes and Met-tRNA Met in
eukaryotes that starts translation.
INOSITOL LIPID. A membrane-anchored phospholipid that transduces
hormonal signals by stimulating the release of any of several chemical
messengers.
INTEGRATION-EXCISION (I/E) REGION: The portion of bacteriophage A DNA
that enables bacteriophage A DNA to be inserted into a specific site in the
Escherichia coli chromosome and excised from this site.
INTERFERON. A protein produced naturally by the cells of our
bodies. It increases the resistance of surrounding cells to attacks by
viruses. One type of interferon, alpha interferon, is effective
against certain types of cancer. Others may prove effective in
treating autoimmune diseases.
INTERNAL RIBOSOMAL ENTRY SITE: A nontranslated sequence following a
coding region of a polycistronic RNA that binds to a small ribosomal subunit
and forms an initiation-of-translation complex.
INTERPHASE: The period in the cell cycle when DNA is replicated in
the nucleus; followed by mitosis.
INTROGRESSION. Backcrossing of hybrids of two plant populations to
introduce new genes into a wild population.
INTRON (INTERVENING SEQUENCE): Segment of gene transcribed but then
excised from primary transcript during processing to a functional RNA
molecule.
INVERSION. A structural rearrangement of a chromosome in which
2 breaks occur, followed by the reinsertion of the chromosome segment
but in reversed order. It may be either paracentric, i.e., it does not
include the centromere, or pericentric, i.e., it does include the
centromere.
ION CHANNEL: An integral protein, within a cell membrane, that
facilitates selective ion transport.
IPTG (Isopropylthiogalactopyranoside): an inducer of the lac
(lactose) operon. In recombinant DNA technology, IPTG is often used to induce
cloned genes that are under the control of the lac repressor-lac promoter
system.
ISOCHROMOSOME. A structural chromosome rearrangement caused by
the division of a chromosome along an axis perpendicular to the usual
axis of division; results in chromosomes with either 2 short arms or 2
long arms.
ISODISOMY. The presence of 2 identical homologues of a
transmitted chromosome from only 1 of the parents. junk DNA with no
apparent function.
ISOGRAFT. A tissue transplanted between two genetically
identical individuals.
ISOHEMAGGLUTININS. Antibodies to major red blood cell antigens
present normally as a result of inapparent immunization by
cross-reactive antigens in bacteria, food, etc.
ISOTYPE SWITCH. The shift of a B cell or its progeny from the
secretion of antibody of one isotype or class of antibody with the
same V regions but a different heavy- chain constant region and,
hence, a different isotype (class switch).
ISOTYPES. Classes of antibody that differ in the constant
region of their heavy chain (Fc portion); distinguishable also on the
basis of reaction with antisera raised in another species. These
differences also result in different biological activities of the
antibodies.
IVIg (Intravenous Immunoglobulin G Infusion). This gamma
globulin preparation is made just like Rhogam, the gamma globulin that
is given to Rh negative women during pregnancy. It is made from pooled
blood that is washed and processed (it comes out clear in the end). It
takes approximately 2-4 hours to administer in the vein. The first
dose in given preconception in a doctor's office. The next doses if
they are needed in women with the highest levels of Natural Killer
Cells, are given by a nurse in the home. Before it is administered,
the nurse will give the patient an injection of Benadryl to avoid an
allergic reaction (this makes the patient very sleepy). Some common
reactions include: headaches, joint pain, flu like symptoms and
occasionally fever. The Natural Killer test is done again 7-10 days
afterwards to make sure it is working and enough IVIg has been given.
Ia. "Immune response-associated" proteins, found on B cells
and antigen-presenting cells of mice; an old term now replaced with
MHC (major histocompatibility complex) class II molecules.
IgG (Immunoglobulin G). This is a protein in the blood
produced by B lymphocytes (CD19+). It is an antibody that is present
primarily in the lymph system. It is produced by IgM (Immunoglobulin)
that resides in the blood. One IgM produces five IgG antibody
molecules in a balanced system. It is a Y shaped molecule consisting
of two heavy and two light chains, each having variable and constant
regions. The variable regions determine the fit with the antigen that
initiated the response like a key-in-lock situation.
IkB-proteins. IkB-proteins (IkB-alpha, beta, and epsilon) are
inhibitor proteins of NF-kB, which keep cytosolic NF-kB under tight
control by binding to NF-kB and blocking its transport into the
nucleus. For NF-kB activation, IkB-alpha is phosphorylated by IKKs at
two serine residues what results in the binding of ubiquitin to and
degradation of IkB-alpha by the proteasome.
J chain (joining chain). A polypeptide involved in the
polymerization of immunoglobulin molecules IgM and IgA.
J gene. A gene segment coding for the J or joining segment in
immunoglobulin DNA; V genes translocate to J segments in L chains, and
to D and J segments in H chains. Also, codes for a portion of the
T-cell receptor.
K cell. An effector lymphocyte with Fc receptors which allow
it to bind to and kill antibody-coated target cells.
KANAMYCIN. An antibiotic of the aminoglycoside family that poisons
translation by binding to the ribosomes.
KARYORRHEXIS. fragmentation of nucleus during apoptosis.
KARYOTYPE. All of the chromosomes in a cell or an individual
organism, visible through a microsope during cell division.
KETOSYNTHASE: A low-molecular-weight enzyme involved as part of a
larger complex in polyketide biosynthesis.
KILLER T CELL. A T cell with a particular immune specificity
and an endogenously produced receptor for antigen, capable of
specifically killing its target cell after attachment to the target
cell by this receptor. Also called cytotoxic T cell.
KILOBASE PAIR (kb,kbp, 1000 base pairs): unit of length of DNA.
KINASES. Enzymes which phosphorylate proteins.
KINETOCHORE. A structure at the centromere to which the
spindle fibers are attached.
KLEBSIELLA: Named for T.A.E. Klebs (who isolated the cause of
diphtheria). Another enteric bacterium (gastric tract inhabitant), but
produces butanediol.
KLENOW FRAGMENT: A product of proteolytic digestion of the DNA
polymerase I from E. coli that retains both polymerase and 3'-exonuclease
activities but not 5'-exonuclease activity.
KNOCKOUT: The targeted disruption of a gene by homologous
recombination.
LAC OPERON. A structural unit in the E.coli genome that consists of
three structural genes (encoding different enzymes involved in sugar
metabolism) transcribed together and their common promoter and operator
genes. Provides a good model for studying the interactions between promoters
and repressors.
LACTEAL. a blind-ended tube which forms the basic element of
the lymphatic system; in the digestive system of mammals, lacteals
transport fats from the small intestine to the closed circulatory
system
LACTOBACILLUS: named for milk. These are often found in dairy
products (fermenters of food)
LAG PHASE. The initial growth phase, during which cell number remains
relatively constant prior to rapid growth.
LAGGING STRAND OF DNA. The new strand of a DNA replicating in
the 3' to 5' direction. It is synthesized in short fragments in the
5'to 3' direction that are subsequently joined together.
LATERAL MERISTEM. A continuous cylinder of meristematic cells
surrounding the xylem and pith that produces secondary xylem and
phloem. Responsible for secondary growth.
LCAO: a method for the calculation of molecular orbitals from
a linear combination of atomic orbitals.
LEUKOCYTE ANTIBODY DETECTION (Cross Match). A close DQ Alpha
match will be indicated by this test. Low numbers on this test tell
the doctor you need LIT (Lymphocyte Immune Therapy). This is an
immunization given to the woman made from the husband's white blood
cells. IVIg (Intravenous Gamma Globulin) is used by some doctors for
this problem. Others choose to put in more embryos to increase the
chances of having an embryo that will be accepted because it is too
compatible to the mother's DNA. The immunization is made from the
husband's or a donor's white blood cells (lymphocytes). A donor is
used for the woman if the couple's DQ alpha numbers are very close.
The immunization is known to be working when the woman's antibodies to
her husband's T and B lymphocytes climb to over 30% and the woman's
microcytotoxicity test becomes positive.
LEWIS ACID: an agent capable of accepoting a pair of electrons
to form a coordinate bond.
LICHEN: A symbiote of algae and fungus able to grow in extreme
conditions. The alga makes carbohydrates out of carbon dioxide, which are
used by the fungus to grow. The fungus extracts minerals and fixes nitrogen,
which are used by the alga to grow.
LIGAND. A molecule that can bind to a receptor and thereby
induce a signal in the cell, e.g., a hormone.
LIGASE (DNA ligase). An enzyme that catalyzes a condensation reaction
that links two DNA molecules via the formation of a phosphodiester bond
between the 3' hydroxyl and 5' phosphate of adjacent nucleotides.
LIGATE. The process of joining two or more DNA fragments.
LIGATION: Joining of two DNA molecules by the formation of
phosphodiester bonds. In vitro, this reaction is usually
catalyzed by the enzyme T4 DNA ligase.
LIGHT CHAIN (L chain). The light chain of immunoglobulin is a
structural feature that occurs in two forms: kappa and lambda.
LIGNOCELLULOSE: The combination of lignin, hemicellulose, and
cellulose that forms the structural framework of plant cell walls.
LINKAGE DISEQUILIBRIUM. The frequency, in a population of
linked genes, which is governed by factors other than change.
LINKAGE MAP. A chromosome map showing the relative positions
of genetic markers of a given species, as determined by linkage
analysis; not the same as a physical, or gene, map, which uses linkage
analysis, cytogenetic examination, and physical techniques to generate
the map.
LINKAGE PHASE. The arrangement of alleles of linked loci on
chromosomes.
LINKER DNA. A synthetic DNA that carries the recognition site
for a restriction enzyme and that can bind 2 DNA fragments. Also, the
stretch of DNA between 2 nucleosomes.
LINKER. A short, double-stranded oligonucleotide containing a
restriction endonuclease recognition site, which is ligated to the ends of a
DNA fragment.
LIPASE. an enzyme which digests fats
LIPOFECTION: Delivery into eukaryotic cells of DNA, RNA, or other
compounds that have been encapsulated in an
artificial phospholipid vesicle.
LIPOPOLYSACCHARIDE (LPS): A combination of sugars and fatty acids
which is found in the outer wall or slime layer of some bacteria. It has the
property of being partially soluble in water and also in oils.
LIPOSOME: A circular collection of lipid molecules in which the
hydrophobic portions of the molecule are facing inward;
a lipid vesicle with an aqueous interior that can carry nucleic
acids, drugs, or other therapeutic agents.
LISTERIA MONOCYTOGENES: Bacterium which causes listeriosis.
LIT (Lymphocyte Immunization Therapy). Lymphocyte immune
therapy is used in women with recurrent spontaneous abortions. This
immunization is made from the father-to-be's blood or sometimes from a
donor's blood. It is injected under the skin of the mother's
forearm. This is done twice, separated by one month. Testing to see
that it has worked is done one month after the second
treatment. Common reactions to this treatment include: swelling,
irritation, and itching at the injection site. Some women run a fever
after this treatment.
LITHOTROPH: An organism able to use inorganic compounds as an
electron acceptor. Thus, denitrifyers, sulfur bacteria, and iron bacteria are
lithotrophs; also lithotrophs tend to be anaerobes.
LOD (Z) SCORE: The logarithm of the ratio of the likelihood of the
odds that two loci are linked with a recombination fraction
equal to or greater than 0 and less than 0.5, to the likelihood
of the odds for independent assortment.
LOGARITHMIC PHASE. The steepest slope of the growth curve--the phase
of vigorous growth during which cell number doubles every 20-30 minutes.
LONE PAIR: a pair of electrons in a molecule which is not
shared by two of the constituent atoms.
LONG TERMINAL REPEATS (LTR): Similar blocks of genetic information
that are found at the ends of the genomes of retroviruses.
LONG-RANGE RESTRICTION MAPPING: Restriction enzymes are proteins that
cut DNA at precise locations. Restriction maps depict the positions on
chromosomes of restriction enzyme cutting sites. These are used as
biochemical "signposts", or markers of specific areas along the
chromosomes. The map will detail the positions on the DNA molecule that are
cut by particular restriction enzymes.
LOSS OF HETEROZYGOSITY. Describes a locus (or loci) at which a
deletion or other process has converted the locus from heterozygosity
to homozygosity or hemizygosity. Phenomenon can lead to cancers by
loss of tumor suppressor genes.
LPR MUTATION. lpr = Lymphoproliferation; spontaneous
loss-of-function mutation in the Fas gene of mice. Leads to
accumulation of lymphocytes.
LUMO: the lowest unoccupied molecular orbital in a molecule or
ion.
LUTEINIZING HORMONE (LH). This pituitary hormone works in
concert with FSH. FSH starts the development of the egg, and LH
finishes the development and starts progesterone production. FSH is
important to stimulate the cells of the follicle to produce
Estrogen. LH is important to stimulate the cells of the follicle that
produce Progesterone during the second half of the menstrual cycle. A
certain ratio of FSH to LH tells the ovary when to release the egg
(ovulation). In the male, LH stimulates the testicles to produce the
male hormone testosterone.
LYMPHOCYTE. This is a white blood cell that is in charge of
starting antigen specific immunity responses. There are many types of
lymphocytes in the immune family. These consist of T cells, B cells,
granulocytes, basophils, mast cells, eosiniophils, Natural Killer
Cells, etc. Each cell type has a CD designation. Small cell with
virtually no cytoplasm, found in blood, in all tissue, and in lymphoid
organs, such as lymph nodes, spleen, and Peyer's patches, and bears
antigen-specific receptors.
LYMPHOKINES. Soluble substances secreted by lymphocytes, which
have a variety of effects on lymphocytes and other cell types.
LYSOGENIC. A type or phase of the virus life cycle during which the
virus integrates into the host chromosome of the infected cell, often
remaining essentially dormant for some period of time.
LYSOGENY: A condition in which a bacteriophage genome (prophage)
survives within a host bacterium either as part of the host chromosome or as
part of an extrachromosomal element and does not initiate lytic functions.
LYTIC. A phase of the virus life cycle during which the virus
replicates within the host cell, releasing a new generation of viruses when
the infected cell lyses.
MACH. MORT 1 associated CED-3 homolog; also called FLICE or
Caspase-8.
MACROPHAGE. A type of white blood cell that ingests dead
tissue and cells and is involved in producing Interleukin 1.
MACRORESTRICTION MAP: Map depicting the order of and distance between
sites at which restriction enzymes cleave chromosomes.
MALT LYMPHOMAS. B cell lymphomas of Mucosa-Associated Lymphoid
Tissue, in most cases arising in the gastric mucosa, either as
low-grade or high-grade form. High-grade MALT lymphoma might result
from transformation of low-grade disease. There is an etological link
between low-grade gastric malt lymphoma and infection with
Helicobacter pilori. Cytogenetic studies of low-grade MALT lymphomas
identified abnormalities of chromosome 1p22, in particular
translocation t(1;14)(p22,q32): on 1p22 the gene Bcl-10 was cloned and
found to be mutated in MALT lymphomas but also in other tumor types
MALTOSE BINDING PROTEIN: An abundant bacterial protein located
within the periplasmic space and involved in the
uptake of maltose. Fusion with other proteins often results in
the fusion protein being secreted to the periplasm.
MAP UNIT: A measure of genetic distance between two linked genetic
loci; usually 1% recombination corresponds to one map unit.
MAP3K. Mitogen-Activated Protein kinase kinase kinase.
MARKOWNIKOW'S RULE: in the ionic addition of hydrogen halides to a
carbon-carbon double bond the halogen attaches itself to the carbon atom
bearing the least number of hydrogen atoms. The rule is useful in the
prediction of the major product from such reactions. Free radical reactions
proceed in the opposite sense, giving rise to anti-Markownikow addition.
MASS SPECTROMETRY: a form of spectrometry in which, generally,
high energy electrons are bombarded onto a sample and this generates
charged fragments of the parent substance; these ions are then focused
by electrostatic and magnetic fields to give a spectrum of the charged
fragments.
MAST CELL. Tissue located cell probably derived from
basophils. Possesses receptor for Fc of IgE. Participates in
MAXAM-GILBERT METHOD. A method for determining the exact
nucleotide sequence via a chemical degradation process.
MDM-2. The mdm-2 gene was identified by virtue of its
amplification in transformed mouse lines. Its overexpression was shown
to be tumourigenic. Homologous deletion of mdm-2 in mice is lethal at
early stages of embryogenesis but is completely rescued by additional
deletion of the p53 gene. By binding to p53, the mdm-2 gene product
MDM2 can target p53 for nuclear export and degradation. Moreover, it
can block transcriptional activity of p53. Interestingly, mdm-2 is a
transcriptional target of p53, what gives rise to a feedback loop
MEIOSIS: The process of two consecutive cell divisions in the diploid
progenitors of sex cells. Meiosis results in four rather than two daughter
cells, each with a haploid set of chromosomes.
MENDEL'S FIRST LAW (law of segregation). The two alleles received one
from each parent segregate independently in gamete formation, so that each
gamete receives one or the other with equal probability.
MENDEL'S SECOND LAW (law of recombination). Two characters determined
by two unlinked genes are recombined at random in gametic formation, so that
they segregate independently of each other, each according to the first
law. (Note that recombination here is not used to mean crossing-over in
meiosis).
MERISTEM. A plant cell line capable of continuous cell
division, such as cambium in the stem or pericycle in the root
MESOPHILE: A microorganism that is able to grow within the
temperature range of 20 to 50'C; optimal growth often
occurs at about 37C.
MESSENGER RNA (mRNA). The class of RNA molecules that copies the
genetic information from DNA, in the nucleus, and carries it to ribosomes, in
the cytoplasm, where it is translated into protein.
METACENTRIC CHROMOSOME. A chromosome with its centromere near the
centre. If the centromere is slightly off-centre, the chromosome is said to
be submetacentric (see also acrocentric and telocentric).
METALLOTHIONEIN. A protective protein that binds heavy metals, such
as cadmium and lead.
METAPHASE: A stage in mitosis or meiosis during which the
chromosomes are aligned along the equatorial plane of the cell.
METHYLATION. The addition of a methyl group (-CH3) to DNA. Methylated
DNA is inactivated and not transcribed. Most frequently occurs at CpG
doublets (see genomic imprinting and CpG islands).
METRODIN. This drug contains FSH. It is given in a sequential
manner with hCG for ovulation induction.
MHC (Major histocompatibility complex). A genetic system of
man that determines the antennae (cell surface molecules) on
lymphocytes that are responsible for antigen presentation to T
lymphocytes in the elicitation and the expression (the beginnings) of
an immune response. This genetic system is responsible for rapid
rejection of grafts between individuals that are not appropriately
matched. This system is responsible for the rejection of pregnancies
and embryos in individuals that are too closely matched at DR and DQ.
A cluster of genes on chromosome 6 in humans, encoding cell surface
molecules that are polymorphic and that code for antigens which lead
to rapid graft rejection between members of a single species which
differ at these loci. Several classes of protein such as MHC class I
and II proteins are encoded in this region. These in humans, are known
as 'Human leukocyte antigens' (HLA).
MHC CLASS I MOLECULE. A molecule encoded to genes of the MHC
which participates in antigen presentation to cytotoxic T (CD8+)
cells.
MHC CLASS II MOLECULE. A molecule encoded by genes of the MHC
which participates in antigen presentation to helper T (CD4+) cells.
MHC RESTRICTION. The ability of T lymphocytes to respond only
when they 'see' the appropriate antigen in association with "self" MHC
class I or class II proteins on the antigen presenting cells.
MICELLE. a very small globule of digested fatty acids,
glycerides, and glycerol which is found in the lumen of the small
intestine.
MICHAELIS CONSTANT: Dissociation constant that characterizes the
binding of an enzyme to a substrate. The lower the constant, the tighter the
binding of the enzyme to the substrate.
MICROBIAL MATS (biofilms). Layered groups or communities of microbial
populations.
MICROINJECTION. A means to introduce a solution of DNA, protein, or
other soluble material into a cell using a fine microcapillary pipet.
MIGRATION INHIBITION FACTOR (MIF). A lymphokine that inhibits
the motility of macrophages in culture.
MINIMAL PROMOTER. The minimal elements of a promoter,
including the TATA box and transcription initiation site, which is
inactive unless regulatory elements that enhance promoter activity are
placed upstream; used to test candidate sequences for enhancer
activity.
MINOR HISTOCOMPATIBILITY ANTIGENS. These antigens, encoded
outside the MHC, are numerous, but do not generate rapid graft
rejection or primary responses of T cells in vitro. They do not serve
as restricting elements in cell interactions.
MISSENSE MUTATION: A genetic mutation that changes a codon for one
amino acid into a codon specifying another amino acid.
MITOCHONDRIA. A small, intracellular, spherical to rod-shaped
cytoplasmic organelle, enclosed by Z membranous spaces; the inner membrane is
folded, forming a series of projections called cristae. Mitochondria are the
principal sites of ATP synthesis; they contain enzymes of the tricarboxylic
acid cycle and enzymes for fatty acid oxidation, oxidative phosphorylation,
and many other biochemical pathways. They contain their own nucleic acids and
ribosomes, replicate independently, and code for the synthesis of some of
their own proteins.
MITOGEN. A substance that stimulates the proliferation of many
different clones of lymphocytes.
MITOSIS. A process of cell division in eukaryotic cells
conventionally divided into the growth period (interphase) and four
stages: prophase, metaphase, anaphase, and telophase. The stages
conserve chromosome number by equally allocating replicated
chromosomes to each of the daughter cells.
MIXED LYMPHOCYTE REACTION (MLR). When lymphocytes from two
individuals are cultured together, a proliferative response is
generally observed, as the result of reactions of T cells of one
individual to MHC antigens on the other individual's cells.
MMPs. Matrix MetalloProteinases (MMPs) break down collagen and
other proteins that form connective tissue. This is important for cell
mobility, e.g. during embryonic development and for the migration of
immune cells or the cells necessary for wound healing to places where
they are needed. But overactivity of MMPs can be involved in disorders
such as arthritis and cancer. MMP-2 was found to be overexpressed in
metatstatic tumors, obviously helping the tumors to spread by
degrading collagen in basement membranes, which usually are a first
barrier for tumor cells during the metastatic process.
MOBILE ELEMENTS. DNA sequences that are capable of inserting
themselves into other locations in the genome.
MOBILITY-SHIFT ASSAY. An assay used to detect specific protein
binding to DNA. Such binding creates complexes that migrate more
slowly during gel electrophoresis than free DNA. Also known as
gel-shift assay.
MOBILIZING FUNCTIONS: The genes on a plasmid that facilitate the
transfer of either a nonconjugative or conjugative plasmid from one bacterium
to another.
MODIFIER GENE. A gene that alters the expression of a gene at
another locus.
MONOCLONAL ANTIBODY (MAb): A single type of antibody that is directed
against a specific epitope (antigenic determinant) and is produced by a
hybridoma cell line, which is formed by the fusion of a lymphocyte with a
myeloma cell. Some myeloma cells synthesize single antibodies
naturally.
MONOCYTE. Large circulating white cell, 2-10% of total white cells,
phagocytic, indented nucleus. Migrates to tissues, where it is known
as a macrophage.
MONOGENIC. Describing a single gene or mendelian trait.
MONOKINES. Soluble substances secreted by monocytes, which
have a variety of effects on other cells.
MONOPHYLETIC. A taxon (or taxa) derived from a single
ancestral line
MONOSOMY. An aneuploid condition in which a specific
chromosome is present in only single copy, giving the individual a
total of 45 chromosomes.
MONOZYGOTIC. Refers to twins derived from a single fertilized
egg.
MORPHOGEN. A protein present in embryonic tissues in a
concentration gradient that induces a developmental process.
MOSAIC. An individual or tissue with at least 2 cell lines
differing in genotype or karyotype, derived from a single zygote.
MRNA. mRNA: Messenger ribonucleic acid; the complementary
strand of RNA transcribed from DNA and translated by the ribosomes
into proteins.
MULTI-LOCUS PROBE. A probe that hybridizes to a number of different
sites in the genome of an organism.
MULTIGENIC. Many genes are involved in the expression of a
trait.
MULTIPOINT (MULTILOCUS) LINKAGE ANALYSIS: The determination of the
order and map distances of many loci on a chromosome at one time.
MURINE. Relating to mice or rats.
MYCELIUM: A mass of interwoven thread-like filaments of a fungus
or bacteria.
MYCOBACTERIUM: named after fungus (= myco, Latin). Primarily
characterized by their ability to be stained by the acid-alcohol fast
reaction
MYCORRHIZAE. Fungi that form symbiotic relationships with roots of
more developed plants.
MYELOMA. A tumour of plasma cells, generally secreting a
single species of immunoglobulin.
N (AMINO) TERMINUS: The first amino acid(s) of a protein.
NAD/NADH (NICOTINAMIDE ADENINE DINUCLEOTIDE): A compound used in some
cellular energy processes. NADH carries a greater reducing potential than
does ATP (One NADH can convert 3 ATDP to ATP), and so it is used for reducing
potential for high-energy metabolic conversions. The actual compound is one
AMP bonded to a nucleotide (nicotinamide) which is not a component of DNA or
RNA.
NEMO/IKK-gamma. NEMO (NF-kB Essential Modifier, found in
mouse) and its human homologue IKK-gamma are part of the IKK complex
and are essential in the acivation of NF-kB. They probably link IkB
kinases (IKKs) to upstream activators.
NEOMYCIN PHOSPHOTRANSFERASE: An enzyme that inactivates the
antibiotics neomycin and kanamycin. This enzyme is often used as a selective
marker for transgenic plants.
NEPHRIDIUM. A general term for an invertebrate excretory organ
as found in the segmented worms and mollusks
NEUROFIBROMIN. The protein product of the neurofibromatosis
type 1 gene.
NEUTROPHIL. A type of leukocyte (white blood cell) involved in
early inflammatory response.
NEWMAN PROJECTION: a projection obtained by viewing along a
carbon-carbon single (double) bond.
NF-kB. NF-kB is a transcription factor that coordinates the
activation of numerous genes in response to pathogenes and
pro-inflammatory cytokines. NF-kB is critical for proper immune
function, cell growth and survival, and anomalous activation is
associated with inflammatory and neoplastic diseases and viral
infection. NF-kB is activated by several exogeneous stimuli.
NGF RECEPTOR FAMILY. Nerve Growth Factor receptor family.
NICK TRANSLATION. A procedure for making a DNA probe in which a DNA
fragment is treated with DNase to produce single-stranded nicks, followed by
incorporation of radioactive nucleotides from the nicked sites by DNA
polymerase I.
NICK: break phosphodiester bond in backbone of one of
the strands of a duplex DNA molecule.
NICKED CIRCLE (relaxed circle). During extraction of plasmid DNA from
the bacterial cell, one strand of the DNA becomes nicked. This relaxes the
torsional strain needed to maintain supercoiling, producing the familiar form
of plasmid.
NIK. NF-kB-inducing kinase, which is activated by TRADD or
TRAFs upon TNFR- or IL-ligation. NIK is an essential component in the
phosphorylation of IKKs.
NITROCELLULOSE. A membrane used to immobilize DNA, RNA, or protein,
which can then be probed with a labeled sequence or antibody.
NITROGEN FIXATION: Conversion of atmospheric nitrogen to
ammonia. Biological nitrogen fixation is catalyzed by the enzyme nitrogenase,
which is found only in prokaryotes.
NITROGENOUS BASES. The purines (adenine and guanine) and pyrimidines
(thymine, cytosine, and uracil) that comprise DNA and RNA molecules.
NK cell. Naturally occurring, large, granular, lymphocyte-like
killer cells that kill various tumour cells; they may play a role in
resistance to tumours. Also, they participate in ADCC. They do not
exhibit antigenic specificity, and their number does not increase by
immunization.
NLS. Nuclear Localization Signals can be located almost
anywhere in the aminoacid sequence and generally consists of a short
sequence (4 to 8 aa) which is rich in the positively charged
aminoacids lysine and arginine and frequently contains proline.
NMDA RECEPTOR. The N-methyl-D-Aspartate receptor is a subtype
of glutamate-activated ionotropic channels, that is implicated in
synaptic mechanisms underlying learning, memory and the perception of
pain. It is also believed to be a target of the intravenous general
anaesthetic agent ketamine and possibly nitrous oxide. Also xenon was
reported to exert its anaethetic effects by inhibiting NMDA receptors.
NOD BOX: A DNA sequence that controls the transcriptional regulation
of Rhizobium nodulation genes.
NONDISJUNCTION. The failure of homologous chromosomes (in
mitosis or meiosis 1) or sister chromatics (in meiosis 11) to separate
properly into different progeny cells.
NONPENETRANCE. Lack of clinical expression of the mutant
phenotype in an individual with the appropriate genotype.
NORTHERN BLOTTING: Similar to Southern blotting, except that RNA that
has been separated by gel electrophoresis is transferred from a gel onto a
matrix such as a nitrocellulose or nylon membrane, and the presence of a
specific RNA molecule is detected by DNA-RNA hybridization.
NOTOCHORD. a stiff dorsal rod found in all chordates at some
devlopmental stage; the notochord is replaced by the vertebral column
in most chordates
NUCLEASE. A class of enzymes that degrades DNA and/or RNA molecules
by cleaving the phosphodiester bonds that link adjacent nucleotides. In
deoxyribonuclease (DNase), the substrate is DNA. In endonuclease, it cleaves
at internal sites in the substrate molecule. Exonuclease progressively
cleaves from the end of the substrate molecule. In ribonuclease (RNase), the
substrate is RNA. In the S1 nuclease, the substrate is single-stranded DNA or
RNA.
NUCLEIC ACIDS. The two nucleic acids, deoxyribonucleic acid (DNA) and
ribonucleic acid (RNA), are made up of long chains of molecules called
nucleotides.
NUCLEOPHILE: a substance which donates a pair of electrons in
the reaction considered.
NUCLEOPHILIC SUBSTITUTION: an overall reaction in which a
nucleophile reacts with a compound displacing another
nucleophile. Such reactions commonly occur in aliphatic chemistry. If
the reaction is unimolecular they are known as SN1 reactions; for
reactions which are bimolecular, they are known as SN2 reactions.
NUCLEOSIDE: A base (purine or pyrimidine) that is covalently
linked to a five-carbon (pentose) sugar.
NUCLEOTIDE: A nucleoside with one or more phosphate groups linked to
the 5' carbon of the pentose sugar. Ribose- containing nucleosides are often
called ribonucleoside monophosphate (NMP), ribonucleoside diphosphate (NDP),
or ribonucleoside triphosphate (NTP). When the nucleoside contains the sugar
deoxyribose, the nucleotides are called deoxyribonucleoside mono-, di-, or
triphosphates (dNMP, dNDP, or dNTP).
OLIGONUCLEOTIDE LIGATION ASSAY (OLA): A diagnostic technique for
determining the presence or absence of a specific
nucleotide pair within a target gene which indicates whether a
gene is wild type (normal) or mutant (defective).
OLIGONUCLEOTIDE: A short molecule (usually 6 to 100 nucleotides) of
singlestranded DNA. Oligonucleoticles are sometimes called
oligodeoxyribonucleotides or oligomers and are usually synthesized
chemically.
OLIGOPROBE. A short DNA probe whose hybridization is sensitive
to a single base mismatch.
ONCOGENE: A gene, one or more forms of which is associated with
cancer. Many oncogenes are involved, directly or indirectly, in controlling
the rate of cell growth.
OPEN READING FRAME (ORF). a DNA sequence which is believed, on the
basis of statistical evidence, to code for protein, but for which no matching
protein or mRNA is known. ORFs can often be confirmed by matching their
sequences to a database of known genes or EST's.
OPERATOR. A prokaryotic regulatory element that interacts with a
repressor to control the transcription of adjacent structural genes.
OPERON: A cluster of genes that are coordinately regulated.
OPINE: The condensation product of an amino acid with either a
keto acid or a sugar.
OPSONIN. A substance, usually antibody or complement
component, which coats a particle such as a bacterium and enhances
phagocytosis by phagocytic cells.
OPSONIZATION. Literally means "preparation for eating". The
coating of a bacterium with antibody and/or complement that leads to
enhanced phagocytosis of the bacterium by phagocytic cells.
OPTICAL ACTIVITY: the property of certain substances to rotate
plane polarized light. It is associated with asymmetry. Compounds
that possess a chiral carbon atom of all the same 'handedness' will
rotate plane polarized light. Isomers that rotate light in equal but
opposite directions are sometimes called 'optical isomers', although
the better term to use is 'enantiomers'.
ORGANELLES. Membrane-bound intracellular, cytoplasmic
structures having specialized functions, e.g., mitochondria, plastics,
Golgi apparatus, lysosomes.
ORGANOCHEMICAL NOMENCLATURE: The number of carbons and associated
names are: meth-: 1; eth-: 2; prop-: 3; but-: 4; -ane: no non-hydrogens; -ol:
alcohol; -diol: two alcohols; -anate, -oic acid: carboxylic acid (COOH);
-anone: ketone (C=O); -amine: NH2; -ene: carbonn-carbon double bond (C=C);
Phen-: benzyne; Phosphate: P(O4)2-; -ose: Sugar (CH2O)n; Deoxy sugars are
missing one OH group; Sulfate: SO42-; Sulfide: -SH; -ase: enzyme.
ORIGIN OF REPLICATION (ori): The nucleotide sequence at which DNA
synthesis is initiated.
OUTBRED MOUSE STRAINS. Strains of mice propagated by
nonstandardized matings. These mice retain substantial genetic
variability.
OVERLAPPING READING FRAMES. Start codons in different reading frames
generate different polypeptides from the same DNA sequence.
OXIDATION: a chemical process in which the proportion of
electronegative substituents in a compound is increased, or the charge
is made more positive, or the oxidation number is increased.
P-BR322. A derivation of ColE1, one of the first plasmid vectors
widely used.
P-UC. A widely used expression plasmid containing a -galactosidase
gene.
P1 ARTIFICIAL CHROMOSOME (PAC): A plasmid vector system based on
bacteriophage P1 that uses electroporation for introducing a vector with a
large DNA insert (100 to 300 kb) into Escherichia coli.
P1 CLONING SYSTEM: A plasmid vector system based on bacteriophage P1
that uses in vitro bacteriophage P1 packaging for introducing a vector with a
large DNA insert (80 to 100 kb) into Escherichia coli.
P1-DERIVED ARTIFICIAL CHROMOSOME (PAC): A vector used to clone DNA
fragments (100- to 300-kb insert size; average, 150 kb) in Escherichia coli
cells. Based on bacteriophage (a virus) P1 genome.
P14ARF. p14ARF (or just ARF) is a human tumor-suppressor gene
(the mouse homolog is p19ARF); it is activated by E2F-1 and stabilizes
p53. Abnormal proliferation (due to defect of Rb, expression of
oncogenes such as Ras, E1A, or Myc) results in deregulated E2F-1
activity, which induces p14ARF and stabilizes p53. This would lead to
cell-cycle arrest or apoptosis unless a second lesion occurred such as
mutation in p14ARF or p53 itself.
P16INK4A. p16INK4a is a tumor-suppressor which inhibits the
cyclin-dependent kinases 4 and 6. Its inhibitory effect results from
its binding to CDk4/6 and by this preventing the formation of the
Cdk4/6-cyclin D complex. INK4 inhibitors (p16INK4a and the related
p19INK4a) also distort the Cdk4/6 kinase catalytic cleft and interfere
with its ATP binding.
P35. Caspase-inhibitor from insect Baculovirus; inhibits ICE
family members with broader specificity than CrmA: it inhibits
Caspase-1 and caspase-3 equally well.
P53. p53 is a tumor-suppressor gene which codes for a
transcriptionally active protein involved in cell cycle arrest, DNA repair
and apoptosis. Almost 50% of human cancers contain a p53 missense mutation
-- including cancers of the breast, cervix, collon, lung, liver, prostate,
bladder, and skin -- and these cancers are more aggressive, more apt to
metastasize, and more often fatal. A number of tumor-promoting viruses and
environmental carcinogens act via p53. Carcinogenic aflatoxins produced by
fungi that contaminate foods such as corn and peanuts are known to alter one
specific amino acid in p53, while carcinogens in cigarette smoke also cause a
characteristic alteration. Strains of human papilloma virus (HPV) linked with
cervical cancer -- in particular HPV 16 and 18 -- produce proteins that
promote the destruction of p53. Two other DNA tumor viruses -- simian virus
40 and adenovirus -- also produce proteins that target p53, eliminate its
activity as a transcription factor, and initiate cell transformation. P53
knockout mice are highly susceptible to spontaneous tumor formation. Because
p53 suppresses abnormal cell proliferation, it may represent an important
mechanism for protection against cancer. p53 is induced by DNA damage or
stress (heat shock, viral infection) and results in G1 cell cycle arrest or
apoptosis. Several response genes (p21, mdm-2, GADD45, bax ...) have been
identified that are transcriptionally activated by p53, but p53 also can
repress transcription of genes with promoters lacking p53-binding sites
(e.g. hsp70, c-fos, c-jun, Rb, bcl-2..) In apoptosis, p53 may also have
transcription-independent functions. When a mutation in the p53 gene results
in the substitution of one amino acid for another, p53 loses its ability to
block abnormal cell growth. Indeed, some mutations produce a p53 molecule
that actually stimulates cell division and promotes cancer.
P73. p73 is a homologue of p53; p73 can induce cell cycle
arrest and apoptosis. It also transcriptionally induces the expression
of some (but not all) known p53 target genes such as p21.
PAC T.he artificial chromosome vector derived from the
temperate bacteriophage, P1, used for cloning 100- to 200-kb DNA
fragments.
PALINDROMIC SEQUENCES: Complementary DNA sequences that are the same
when each strand is read in the same direction (e.g., 5' to 3').
PALISADE PARENCHYMA. the major photosynthetic layer of a leaf
characterized by tightly packed columns of parenchymal cells just
beneath the upper dermal layer
PARACOCCUS DENITRIFICANS: A strong denitrifyer.
PARASPORAL CRYSTAL: Tightly packaged insect protoxin molecules that
are produced by strains of Bacillus thuringiensis during the formation of
resting spores.
PARATOPE. An antibody combining site that is complementary to
an epitope.
PARENCHYMA. the undifferentiated ground tissue in plants which
is capable of some mitotic activity, especially in wound-healing. This
tissue is also involved in storage of nutrient and in photosyntesis.
PARP. Poly(ADP-Ribose) Polymerase; PARP catalyses the
poly(ADP-ribosyl)ation (PARation) of nuclear proteins such as
histones, topoisomerases I and II, SV40T antigen, DNA polymerase
alpha, PCNA, and it also automodifies itself. PARP is activated
following DNA strand breakage during DNA repair. PARP also was
reported to modify p53 early during apoptosis and by this possibly
stabilizing p53. At later stages PARP is cleaved (= inactivated) by
caspase-3 and PAR is removed from p53, concomitant with the onset of
the execution phase of apoptosis. PARP-/- fibroblasts did not show
PARation and no signs of apoptosis after anti-Fas treatment,
suggesting an essential role for PARP and PARation in the early stages
of apoptosis
PARTIAL DIGEST: Treatment of a DNA sample with a type II restriction
endonuclease under conditions that result in a limited number of cuts in each
DNA molecule to yield many possible combinations of cleaved pieces in the
final sample.
PASSIVE IMMUNIZATION. Immunization by the administration of
preformed antibody into a nonimmune individual.
PBL. Peripheral Blood Lymphocyte.
PCD. Programmed Cell Death: the term programmed cell death is
usually reserved for physiological conditions during which disposal of
cells takes place, such as development and morphogenesis, clonal
selection of lymphocytes, and cell renewal in epithelia. On the
contrary, the term apoptosis indicates a form of active cell death
triggered by pathological conditions such as inflammation, cancer,
viral infections, or exposure to a wide variety of chemical and
physical stimuli.
PENETRANCE: A certain fraction, usually expressed as a percentage,
of individuals with a mutant gene(s) at a locus that show
the expected abnormal (mutant) phenotype.
PEP. Abbreviation for primer extension preamplification.
PEPSIN. enzymes secreted by the mammalian stomach lining which
assist in digestion of proteins
PEPTIDE BOND: The covalent bond between the free carboxyl group of
the a carbon of one amino acid and the free amino group of the a carbon of an
adjacent amino acid in a peptide or protein.
PEPTIDE EXPRESSION LIBRARY. A collection of peptide molecules
in which the amino acid sequences are varied and which are produced by
recombinant cells.
PEPTIDE FINGERPRINT. The chromatographic pattern of peptides
obtained after partial hydrolysis of a protein or peptide. The
technique also may be applied to DNA and RNA.
PEPTIDE: A short chain of amino acids that are linked with peptide
bonds.
PEPTIDOGLYCAN: A part of the cell wall which is a rigid layer
comprised of sugar and amino acid residues. The term actually refers to the
chemical structure of this wall.
PEPTIDYL (P) SITE: The portion of a ribosome where the tRNA with the
peptide chain participates in peptide bond formation with the aminoacyl-tRNA
during translation.
PEPTIDYL-tRNA: The tRNA that has a growing peptide chain attached to
it during translation.
PERGONAL. This is a drug used to stimulate ovulation. It
contains equal amounts of FSH and LH. It is administered by injection
and is used to stimulate the development of the follicle and the egg
in the ovary in women undergoing ovulation induction. This preparation
is also used in men with infertility due to primary or secondary
problems of sperm production to stimulate sperm production.
PERICYCLE. A layer of cells just inside the endodermis of a
root that may become meristematic and begin dividing again.
PERINATOLOGIST. This is an Obstetrician/Gynecologist who has
had extra training in maternal fetal medicine. They treat high risk
pregnant women and manage their pregnancies and deliveries.
PERIPLASM: The space (periplasmic space) between the cell
(cytoplasmic) membrane of a bacterium or fungus and the outer membrane or
cell wall.
PEROXISOMAL ENZYMES. Enzymes localized to the
peroxisomes. These enzymes are initially synthesized by the free
polyribosomes and then enter the cytoplasm and eventually are
localized to the peroxisomes. There are at least 40 enzymes. Some are
involved in the production and decomposition of hydrogen peroxide and
some are concerned with lipid and amino acid metabolism.
PEROXISOME. A subcellular organelle surrounded by a single
membrane containing at least 40 enzymes involved in energy production.
PHAGOCYTOSIS. The engulfment of a particle or a microorganism
by leukocytes.
PHARYNGEAL SLITS. the numerous openings between the throat
(=pharynx) and exterior which are present at some developmental stage
of all chordates.
PHASE STATE: The coupling or repulsion of two linked genes.
PHASE-KNOWN: A double heterozygous genotype that is known to be in
either a cis or trans configuration.
PHASE-UNKNOWN: The gene arrangement of a double heterozygous genotype
that is not known.
PHENETICS. An approach to taxonomy based on measurable
similarities and differences in phenotypic characters, but without
consideration of homology, analogy, or phylogeny. Numerical taxonomy,
where many, many characters are measured on all taxa, is a form of
phenetics.
PHENOCOPY: A nongenetic condition that closely resembles a genetic
disorder.
PHENOTYPE: An observable feature or set of traits that is
determined by a gene or combination of genes of an organism.
PHENYLKETONURIA (PKU): An autosomal recessive disorder in humans that
is due to the lack of the liver enzyme phenylalanine hydroxylase and that
causes phenylalanine to accumulate.
PHLOEM. the vascular tissue in plants which transports food
from the leaf to the roots. Phloem is living tissue
PHOSPHATASE. An enzyme that hydrolyzes esters of phosphoric acid,
removing a phosphate group.
PHOSPHODIESTER BOND. A bond in which a phosphate group joins adjacent
carbons through ester linkages. A condensation reaction between adjacent
nucleotides results in a phosphodiester bond between 3' and 5' carbons in DNA
and RNA.
PHOSPHOLIPID: Lipids consisting of a phosphate-containing group and
two fatty acids, each ester-linked to a glycerol
PHOSPHOROTHIOATE LINKAGE: The linkage between nucleotides after a
sulfur group replaces an available oxygen of a phosphodiester linkage.
PHOSPHORYLATION. The addition of a phosphate group to a compound.
PHOTOPERIODISM. the ability of organisms to read the
light:dark cycle when making seasonal adjustments
PHYTOCHROME. a light-sensitive pigment found within the plant
cell. Phytochromes are involved in a number of light-related events,
such as seasonal flowering, but are not considered hormones.
PHYTOHEMAGGLUTININ. Lectin isolated from the red bean used to
agglutinate red blood cells and stimulate lymphocytes to divide; used
in preparation of peripheral blood karyotypes.
PINOCYTOSIS. Ingestion of liquid or very small particles by
vesicle formation in a cell.
PITUITARY GLAND. A small hormone producing gland just beneath the
hypothalamus at the base of the brain. The hormones produced control
the ovaries, the thyroid and the adrenal glands of the woman. FSH, LH
and TSH are some of the hormones produced. Disorders of this gland
leads to irregular or absent ovulation in the female and abnormal or
absent sperm production in the male.
PLASMA CELL. End-stage differentiation of a B cell to an
antibody-producing cell.
PLASMID. A small circular piece of bacterial or yeast DNA which is
found in the cytoplasm and which is replicated independently of the rest of
the cell's genome. Plasmids are used to establish a transgenic strain.
typically carries one or more genes encoding antibiotic resistance
proteins. A store of ancient genetic material not well understood.
PLASMODESMATA. the pores between two plant cells which permit
cytoplasmic flow between adjacent cells. Plasmodesmata are not present
in animals cells.
PLASMOVIRUS; A combined retrovirus packaging-and-vector system
that is confined to a plasmid.
PLASTID: In plants, a double-membrane-bound organelle such as a
chloroplast.
PLATELET-DERIVED GROWTH FACTOR (PDGF). A protein, produced by
platelets and other cells, that strongly stimulates cell growth and
division and is involved in normal wound healing. The gene for PDGF is
identical to the proto-oncogene sis.
PLEIOTROPHY. The effect of a particular gene on several different
traits.
PML GENE. The PML gene was first identified as being
translocated (and fused with the retinoic acid receptor alpha,
RAR-alpha) in acute promyelocytic leukaemia (APL). PML encodes a cell
growth and tumor suppressor which was reported to be a mediator of
multiple apoptotic signals, including Fas, TNF-alpha, and interferons
type I and II. PML was reported to be required for caspase-1 and -3
activation upon exposure to these stimuli. PML also might be involved
in the expression of genes required for the formation of functional
MHC class I receptors: malfunction of PML thus may affect the
susceptibility of tumor cells to be recognized by T cells, what may
allow tumors to escape the immune system
POLLEN: Microspores of plants that carry male gametes.
POLY(A) POLYMERASE. Catalyzes the addition of adenine residues to the
3' end of pre-mRNAs to form the poly(A) tail.
POLYACRYLAMIDE GEL ELECTROPHORESIS. Electrophoresis through a matrix
composed of a synthetic polymer, used to separate proteins, small DNA, or RNA
molecules of up to 1000 nucleotides. Used in DNA sequencing.
POLYADENYLATION SIGNAL: A sequence that terminates transcription and
provides a recognition site at the end of an mRNA for the enzymatic addition
of adenine residues.
POLYADENYLATION. The addition of approximately 200 adenosine
residues at the 3' end of messenger RNAs, apparently involved in their
transport of the nucleus and stability.
POLYADENYLATION; POLY(A) TAILING: Addition of adenine residues to the
3' end of eukaryotic mRNAs. Adenine-rich 3'-terminal segment is called a
poly(A) tail.
POLYCISTRONIC RNA: An mRNA that encodes two or more proteins.
POLYCLONAL ACTIVATOR. A substance that induces activation of
many individual clones of either T or B cells.
POLYCLONAL ANTIBODY: A serum sample that contains antibodies that
bind to different antigenic determinants of one antigen.
POLYGENIC. Controlled by or associated with more than one gene.
POLYHYDROXYALKANOATE: Biodegradable polymers produced by
microorganisms as a carbon and energy storage material.
POLYKETIDE: A class of antibiotics Polyketide synthase. An enzyme
involved in the biosynthesis of polyketicle antibiotics.
POLYLINKER (MULTIPLE CLONING SITE): Synthetic DNA sequence that
contains a number of different restriction endonuclease sites.
POLYLINKER. A short DNA sequence containing several restriction
enzyme recognition sites that is contained in cloning vectors.
POLYMERASE (DNA). Synthesizes a double-stranded DNA molecule using a
primer and DNA as a template.
POLYMERASE CHAIN REACTION (PCR). a technique for making many copies
of a specific DNA sequence. The reaction is initiated using a pair of short
primer sequences which match the ends of the sequence to be
copied. Thereafter, each cycle of the reaction copies the sequence between
the primers. Primers can bind to the copies as well as the original sequence,
so the total number of copies increases exponentially with time.
POLYMORPHIC SITE (LOCUS): A chromosome location that has two or more
identifiable allelic DNA sequences that each occur with
a frequency of 1% (0.01) or greater in a large population.
POLYMORPHONUCLEAR LEUKOCYTE. White cell, granular
cytoplasm. Neutral staining (neutrophil) - most frequent,
phagocytic. Basophilic staining - basophil q.v. Eosinophilic
staining - eosinophil q.v.
POLYPEPTIDE (PROTEIN): Linear series of amino acids linked together
with peptide bonds.
POLYPLOID. A multiple of the haploid chromosome number that results
from chromosome replication without nuclear division.
POLYSACCHARIDE. A polymer composed of multiple units of
monosaccharide (simple sugar).
POLYSOMES (POLYRIBOSOMES). Structures composed of multiple
ribosomes attached to mRNA in the process of translation.
POLYVALENT VACCINE. A recombinant organism into which has been cloned
antigenic determinants from a number of different disease-causing
organisms.
POSITIONAL GENE CLONING: A strategy for isolating an unknown disease
gene. The disease gene is mapped to a chromosome site. A contig or genomic
clone that covers the site of the disease gene is tested for
exons. Examination of exons and mutation detection assays establish which
gene is the disease gene.
POSITIONAL-CANDIDATE GENE CLONING: A strategy for isolating an
unknown disease gene. The disease gene is mapped to a chromosome site. The
genes and expressed sequence tags that have been mapped to the same interval
(bin) as the disease gene become candidates for the disease gene. Examination
of exons and mutation detection assays establish which gene is the disease
gene.
POSITIVE-NEGATIVE SELECTION: A protocol that both selects for cells
that carry a DNA insert integrated at a specific targeted chromosomal
location (positive selection) and selects against cells that carry a DNA
insert integrated at a nontargeted chromosomal site (negative selection).
POSTTRANSLATIONAL MODIFICATION: The specific addition of phosphate
groups, sugars (glycosylation), or other molecules to a protein after it has
been synthesized.
PREDNISONE. This is a steroid that blocks inflammation of an
allergic reaction. A common reaction from this drug is bloating. It is
a drug that can cause many side effects. Ask your doctor many
questions about its many side effects.
PRIMARY LYMPHOID ORGANS. Organs in which the maturation of T
and B lymphocytes take place and antigen-specific receptors are first
acquired.
PRIMARY RESPONSES. The immune response to a first encounter
with antigen. The primary response is generally small, has a long
induction phase or lag period, consists primarily of IgM antibodies,
and generates immunologic memory.
PRIMER: A short oligonucleotide that hybridizes with a template
strand and provides a 3'-hydroxyl end for the initiation of nucleic acid
synthesis.
PRIMERWALKING: A method for sequencing long (>1 kb) cloned pieces of
DNA. The initial sequencing reaction reveals the sequence of the first few
hundred nucleotides of the cloned DNA. On the basis of these data, a primer
that contains about 20 nucleotides and is complementary to a sequence near
the end of sequenced DNA is synthesized and used for sequencing of the next
few hundred nucleotides of the cloned DNA. This procedure is repeated until
the complete nucleotide sequence of the cloned DNA is determined.
PROKARYOTES: Organisms, usually bacteria, that have neither a
membrane-bound nucleus enclosing their chromosomes nor functional organelles
such as mitochondria and chloroplasts.
PROMOTER. A region of DNA extending 150-300 bp upstream from the
transcription start site that contains binding sites for RNA polymerase and a
number of proteins that regulate the rate of transcription of the adjacent
gene.
PRONUCLEUS. Either of the two haploid gamete nuclei just prior to
their fusion in the fertilized ovum.
PROPHAGE: A repressed or inactive state of a bacteriophage genome
that is maintained in a bacterial host cell as part of the
chromosomal DNA.
PROTEASE INHIBITOR: A protein that can form a tight complex with a
protease and block its activity.
PROTEASE: An enzyme that hydrolyzes peptide bond linkages and
cleaves proteins into smaller peptides.
PROTECTING GROUP: a group that is used to protect a functional
group from unwanted reactions. After application the protecting group
can be removed to reveal the original functional group.
PROTEIN KINASE. An enzyme that adds phosphate groups to a protein
molecule at serine, threonine, or tyrosine residues.
PROTEINACEOUS INFECTIOUS PARTICLE (prion). A proposed pathogen
composed only of protein with no detectable nucleic acid and which is
responsible for Creutzfeldt-Jakob disease and kuru in humans and scrapie in
sheep.
PROTEOLYTIC. The ability to break down protein molecules.
PROTO-ONCOGENES. Normal genes that are found in normal
eukaryotic cells concerned with various aspects of cell division. If
amplified, mutated, rearranged, or picked up by a retrovirus, they may
give rise to oncogenes that can cause cancer.
PROTOPLAST: A bacterial, yeast, or plant cell that has had its
cell wall removed either chemically or enzymatically.
PSEUDOAUTOSOMAL REGION. The distal tip of the Y chromosome
short arm, which undergoes crossover with the distal tip of the X
chromosome short arm during meiosis in the male.
PSEUDOMONAS AERUGINOSA: One bacteria which can cause
diarrhea or infection by action of it's toxin, which kills skin cells.
Fluorescent.
PSEUDOMONAS AERUGINOSA: One bacteria which can cause diarrhea or
infection by action of it's toxin, which kills skin cells. Fluorescent.
PSEUDOMONAS FLUORESCENS: Non-pathogenic and fluorescent.
PSEUDOMONAS PUTIDA: Best known for growing on most any
organic compound, especially aromatics.
PSEUDOMONAS SACCHAROPHILA: A bacterium widely studied for metabolism
and metabolic enzymes.
PSEUDOMONAS SYRINGAE. The genetically engineered strain of this
bacteria lacks a cell-surface protein that helps ice crystals to form.
Spraying these bacteria on crops may prevent freezing-related damages.
PSEUDOMONAS: Motile, non-spore forming, straight or curved rods
(bacteria) which are heterotrophic aerobes (eat organics, and never ferment).
PSEUDOTYPE FORMATION (PHENOTYPIC MIXING): The packaging of the genome
of one virus in the envelope or capsid protein of another virus.
PSYCHROPHILE: can grow at temperatures as low as 0' to 5'C.
PT PORE. Permeability Transition pore; supposedly involved in
the loss of the mitochondrial transmembrane potential and the release
of cytochrome c into the cytosol. The PT pore includes VDAC, ANT and
cyclophilin D.
PTEN. PTEN is a tumor suppressor gene that codes for a
phosphatase; it dephosphorylates
phosphatidylinosyol-3,4,5-trisphosphate (PIP3) to PIP2. Thus PTEN
activity controls the PIP3 pathway and by this downregulates the
activity of involved kinases such as Akt/protein kinase B (PKB). PTEN
knockout in mice results in embryonic lethality, whereas Pten
heterozygous mice display hyperplastic/dysplastic features, features
typical for autoimmune disorders and high tumor incidence. AICD and
Fas-dependent apoptosis of peripheral T cells from Pten+/- mice is
impaired due to the disregulation of the PI3-kinase/Akt dependent
patheway
PULSED FIELD ELECTROPHORESIS. An electrophoretic technique
that allows the separation of relatively long (>5,000 kb) sequences of
DNA.
PURINE: Fusion of a pyrimidine and an imidazole ring, e.g.,
adenine or guanine.
PYKNOSIS. Pyknosis describes the observation of condensed
nuclei with clumped and condensed chromatin as a sign of cell
death. Pyknosis is often accompanied by 'karyorrhexis'. A pyknosis
inducing factor was identified as Acinus ('apoptotic chromatin
condensation inducer in the nucleus'), which is the precursor of an
active chromatin condensating factor. Acinus is cleaved by caspase-3
PYRIMIDINE: A nitrogen-containing, single-ring, basic compound that
occurs in nucleic acids. The pyrimidines in DNA are cytosine and thymine; in
RNA, cytosine and uracil.
PYROGEN: causes fever
Q-BANDING. The pattern of bright and dim fluorescent
crossbands seen on chromosomes under ultraviolet light after
quinacrine mustard staining.
QUASIDOMINANCE. The pattern of inheritance produced by the
mating of an affected homozygote with an individual heterozygous for
the same recessive trait so that homozygous affected members appear in
2 or more successive generations.
QUENCHER: The portion of a molecule that can quench fluorescence.
R,S CONVENTION: a formal non-ambiguous, nomenclature system
for the assignment of absolute configuration of structure to chiral
atoms, using the Cahn, Ingold and Prelog priority rules.
R-BANDING. A chromosome banding technique in which chromosomes
are heated in a phosphate buffer; produces dark and light bands in
patterns that are the reverse of those produced by G-banding.
RACEMIC MIXTURE, RACEMATE: an equimolar mixture of the two
enantiomeric isomers of a compound. [As a consequence of the equal
numbers of laevo- and dextro-rotatory molecules present in a racemate,
there is no net rotation of plane polarized light.]
RADICAL: a term applied to an atom or molecule having one or
more free valencies.
RADIOALLERGOSORBENT TEST (RAST). A solid-phase
radioimmunoassay for detecting IgE antibody specific for a particular
allergen.
RADIOIMMUNOASSAY (RIA). A widely used technique for
measurement of primary antigen-antibody interactions, and for the
determination of the level of important biological substances in mixed
samples. It takes advantage of the specificity of the antigen-antibody
interaction and the sensitivity that derives from measurement of
radioactively labelled materials.
RANDOM AMPLIFIED POLYMORPHIC DNA (RAPD): A diagnostic procedure in
which chromosomal DNA (usually from plants but sometimes from microorganisms
or animals) is characterized by the DNA fragments that are synthesized when
PCR is initiated after the addition of a single primer to the reaction
mixture.
RANDOM PRIMER METHOD: A protocol for labeling DNA in vitro. A sample
of random oligonucleotides containing all possible combinations of nucleotide
sequences is hybridized to a DNA probe. Then, in the presence of a DNA
polymerase and the four deoxyribonucleotides (one of which is labeled), the
3'-hydroxyl ends of the hybridized oligonucleotides provide initiation sites
for DNA synthesis that uses the separated strands of the probe DNA as a
template. This reaction produces labeled copies of portions of the probe DNA.
RAPID AMPLIFICATION OF cDNA ENDS (RACE): PCR used to generate
double-stranded DNA (cDNA) from the 3' end (3'RACE) or the 5' end (5'RACE) of
a specific mRNA.
READ-THROUGH: Transcription or translation that proceeds beyond
the normal stopping point because the transcription or
translation termination signal of a gene is absent or mutated.
READING FRAME. A series of triplet codons beginning from a specific
nucleotide. Depending on where one begins, each DNA strand contains three
different reading frames.
REAGIN. Allergist's term for IgE antibodies.
REC-A: recA catalyzes pairing of ssDNA with complementary dsDNA
(recombinase),forms D loop , requires ATP hydrolysis, helical filament of
recA around ssDNA, 6 recA monomers per turn, ssDNA is 50% more stretched out
than regular beta-DNA,; filament has POLARITY, allows movement in 1 direction
on dsDNA, movement requires ATP hydrolysis, 2 sites in recA, one binds ssDNA,
other binds complementary strand. recA also a key part of the SOS response:
DNA damage triggers an emergency response, group of >15 genes turned on
following DNA damage expression kept low by lexA repressor (binds to promoter
of each gene), when DNA damage occurs, get ssDNA, recA binds to it;
ssDNA::recA filament binds lexA molecules, bound lexA is induced to degrade
itself and other lexA molecules, reduces [lexA], can't bind to promoters of
the SOS genes, expression of SOS genes now goes ahead. The RecA protein, a
molecule of 38,000 Mr (125,126), is a multifunctional polypeptide directing a
number of activities, none of which is completely understood in detail. It's
central role in homologous recombination and DNA-damage repair has created
considerable interest. Widespread distribution and evolutionary conservation
of recA.
RECBCD: recBCD generates ssDNA needed for recombination, 325kd
complex which has nuclease + helicase activity, unwinding requires ATP,
unwinding faster than rewinding, so makes a loop behind recBCD; cleavage at
chi sequence, 8bp sequence, one chi every ~4.5kb on E. coli chromosome, makes
single-strand cut next to chi site, continues to unwind, topo I, ruvABC
involved in branch migration, ruvC is "resolvase", cleaves Holliday
intermediate.
RECESSIVE GENE: An allele that does not demonstrably contribute to
the phenotype in a heterozygote.
RECESSIVE(-acting) ONCOGENE, (anti-oncogene). A single copy of this
gene is sufficient to suppress cell proliferation; the loss of both copies of
the gene contributes to cancer formation.
RECOGNITION SEQUENCE (site). A nucleotide sequence--composed
typically of 4, 6, or 8 nucleotides--that is recognized by a restriction
endonuclease. Type II enzyrnes cut (and their corresponding modification
enzymes methylate) within or very near the recognition sequence.
RECOMBINANT DNA. Hybrid DNA produced in a test tube by joining
segments of DNA from natural or synthetic sources. These segments can
then be inserted into the genetic material of an organism to introduce
a novel function.
RECOMBINATION FRACTION. In linkage analysis, the fraction of
meiotic events that show a recombination between 2 loci.
RECOMBINATION FREQUENCY. The frequency at which crossing over occurs
between two chromosomal loci--the probability that two loci will become
unlinked during meiosis.
REDUCTION: chemical processes in which the proportion of more
electronegative substituents is decreased, or the charge is made more
negative, or the oxidation number is lowered.
REGULATORY GENE. A gene whose protein controls the activity of other
genes or metabolic pathways.
REGULATORY PROTEIN: A protein that plays a role in either turning
on or turning off transcription.
REL PROTEINS. Family of structurally Related proteins which are the
subunits of the NF-kB transcription factor. Five different Rel proteins (also
called Rel/NF-kB proteins) have been identified so far: p50, p52, p65, Rel-B,
and cRel. All those Rel proteins contain a conserved N-terminal region,
called the Rel Homology Domain (RHD).
RELAXED PLASMID. A plasmid that replicates independently of the main
bacterial chromosome and is present in 10-500 copies per cell.
RENATURE. The reannealing (hydrogen bonding) of single-stranded DNA
and/or RNA to form a duplex molecule.
REOVIRUS. The human reovirus is a double-stranded RNA
virus. Since reovirus infections are in general asymptomatic and
reovirus replication depends on an activated Ras signalling pathway it
may be useful in tumor therapy since many tumors display increased ras
activity. Indeed, reovirus was shown to selectively infect ras
overexpressing tumor cells and suppress tumor growth
REPLICA PLATING: The transfer of cells from bacterial colonies on
one petri plate to another petri plate; the locations of
the colonies that grow on the second plate correspond to those on
the original (master) petri plate.
REPLICATION FORK. The unwound region of the DNA double helix
in which replication takes place.
REPLICATION SEGREGATION. Refers to changes in the proportions
of mitochondrial DNA alleles as the mitochondria reproduce.
REPLICON. A unit of genetic material which behaves autonomously
during replication of DNA. In bacterias, a whole chromosome is a replicon. In
eukaryotes, chromosomes are divided into hundreds of replicons. Each replicon
contains a segment beginning with a binding site for RNA polymerase.
REPRESSOR. A DNA-binding protein in prokaryotes that blocks gene
transcription by binding to the operator.
REPRODUCTIVE IMMUNOPHENOTYPE. This checks for the presence of Natural
Killer Cells. In most cases, Natural Killer Cells are good because they
reduce the likelihood of developing cancer. In some cases excessive NK
activity can kill the embryo or interfere with the endocrine system that
produces hormones essential for pregnancy. At high Natural Killer Cell levels
IVIg is prescribed. IVIg is made from pooled blood and is processed and
washed so that it is free of HIV and other blood-borne illnesses (it comes
out clear after processing). At lower levels of Natural Killer Cells, some
doctors use prednisone, a steroid. These tests measure the following CD (Cell
Designation) levels: CD-3 (normal 63-86); CD-4 (normal 31-53); CD-8 (normal
17-35); CD-19 (normal 3-8); C56 (normal 3-12) these are the Natural Killer
Cells; CD3/IL2-R (normal 0-5); CD19/CD5 (normal 0-30), high numbers in this
category interfere with the reproductive hormones necessary for pregnancy.
REPULSION (TRANS CONFIGURATION): The phase state in which a dominant
version and a recessive version of two different genes occur on the same
chromosome.
RESOLUTION: the separation of a racemate into its two
enantiomers by means of some chiral agency.
RESONANCE: the representation of a compound by two or more
canonical structures in which the valence electrons are rearranged to
give structures of similar probability. [The actual structure is
considered to be a hybrid or the resonance forms.]
RESPIRATORY BURST. Oxygen dependent increase in metabolic
activity within phagocytic cells stimulated by bacteria or parasites,
to be microbicidal.
RESTRICTION DIGEST. The process in which DNA is exposed to
restriction enzymes (restriction endonuclease), causing it to be
cleaved into fragments of DNA called restriction fragments.
RESTRICTION ENDONUCLEASE (enzyme). A class of endonucleases that
cleaves DNA after recognizing a specific sequence, such as BamH1 (GGATCC),
EcoRI (GAATTC), and HindIII (AAGCTT). Type I. Cuts nonspecifically a distance
greater than 1000 bp from its recognition sequence and contains both
restriction and methylation activities. Type II. Cuts at or near a short,
and often symmetrical, recognition sequence. A separate enzyme methylates the
same recognition sequence. Type III. Cuts 24-26 bp downstream from a short,
asymmetrical recognition sequence. Requires ATP and contains both restriction
and methylation activities.
RESTRICTION ENZYMES. Bacterial enzymes that cleave DNA at very
specific locations.
RESTRICTION FRAGMENT LENGTH POLYMORPHISM (RFLP): The occurrence of
variations in the lengths of certain DNA fragments that are produced after
cleavage with a type II restriction endonuclease. The differences in DNA
lengths are due to the presence or absence of a specific restriction
endonuclease recognition site(s) and are detected by DNA hybridization with
DNA probes after separation by gel electrophoresis.
RESTRICTION MAP: The linear array of restriction endonuclease
sites on a DNA molecule.
RESTRICTION SITE: The sequence of nucleoticle pairs in duplex DNA
that is recognized by a type II restriction endonuclease. Sometimes called
restriction enzyme site, restriction endonuclease site, or recognition site.
RETICULOENDOTHELIAL SYSTEM. A network of phagocytic cells.
RETROVIRUS. A member of a class of RNA viruses that utilizes the
enzyme reverse transcriptase to reverse copy its genome into a DNA
intermediate, which integrates into the hostcell chromosome. Many naturally
occurring cancers of vertebrate animals are caused by retroviruses.
REVERSE TRANSCRIPTASE: An RNA-dependent DNA polymerase that uses an
RNA molecule as a template for the synthesis of a complementary DNA strand.
REVERSE TRANSCRIPTION-POLYMERASE CHAIN REACTION (RT-PCR): A two-step
protocol for synthesizing cDNA molecules. First, cDNA strands are synthesized
in vitro by reverse transcriptase with oligo(dT) as a primer and mRNA as the
template. Second, a specific cDNA strand is amplified by the polyrnerase
chain reaction (PCR), with one primer directed to a sequence of the first
cDNA strand and the other to a sequence of the complementary cDNA strand
(second strand) that is synthesized during the first PCR cycle.
REVERSIBLE PROCESS: a process in which the forward reaction
can reach an equilibrium with the reverse reaction.
RGD TRIPEPTIDE. Arginine-glycine-aspartate tripeptide motif
which can be found in proteins of the extracellular matrix. Integrins
link the intracellular cytoskeleton of cells with the extracellular
matrix by recognizing this RGD motif. Without attachment to the
extracellular matrix, cells normally undergo apoptosis
('anoikis'). Soluble RGD peptides induce apoptosis and might be used
as drugs against angiogenesis, inflammation and cancer mestastasis.
RHD. Rel Homology Domain (RHD), the conserved N-terminal
domain of Rel/NF-kB proteins. It contains the DNA-binding and
dimerization domains and the nuclear localization signal.
RHIZOBIA. Bacteria in a symbiotic relationship with leguminous plants
that results in nitrogen fixation.
RHODOSPIRILLUM RUBRUM: This bacterial strain is studied for
metabolism - it makes hydrogen when growing on light (it's a phototroph) with
organic and amino acids as C- and N-sources.
RHOGAM. The immunoglobulin, very similar to IVIg, that is
given to Rh negative women carrying Rh positive infants to prevent her
body from developing an immunity against the babies red blood cells.
RIBOSE: The 5-carbon sugar component of RNA.
RIBOSOMAL BINDING SITE (SHINE-DALGARNO SEQUENCE): Sequence of
nucleotides near the F-phosphate end of a bacterial mRNA that facilitates the
binding of the mRNA to the small ribosomal subunit.
RIBOSOMAL RNA (rRNA). The RNA component of the ribosome.
RIBOSOME-BINDING SITE. The region of an mRNA molecule that binds the
ribosome to initiate translation.
RIBOSOMES. Cytoplasmic organelles composed of ribosomal RNA
and protein, on which polypeptide synthesis from messenger RNA occurs.
RIBOZYME: An RNA molecule that has catalytic activity.
RIBULOSE BISPHOSPHATE CARBOXYLASE (Rubisco): Most abundant enzyme in
the world, it is found in all green plants and is responsible for the
fixation of carbon dioxide in photosynthesis.
RING CHROMOSOME. A structurally abnormal chromosome in which
the end of each chromosome arm has been deleted and the broken arms
have reunited to form a ring.
RNA (RIBONUCLEIC ACID): polynucleotide that has ribose as its pentose
sugar and uracil as one of its pyrimidines.
RNA POLYMERASE: An enzyme that links an incoming ribonucleotide,
which is determined by complementarity to a base in a template DNA strand,
with a phosphodiester bond to the 3'-hydroxyl group of the last incorporated
ribonucleotide of the growing RNA strand during transcription.
ROLLING CIRCLE: A mode of DNA replication that produces
concaterneric duplex DNA.
ROTAMERS: isomers formed by restricted rotation. [See also
conformational isomers.]
S1 NUCLEASE: An enzyme that specifically degrades single-stranded
DNA.
SACCHARIFACTION: Hydrolysis of polysaccharides, after
liquefaction, by glucoamylase to maltose and glucose.
SACCHAROMYCES: These are yeasts which feed on sugars.
SALMONELLA TYPHIMURIUM: Causes salmonella, but is not especially
virulent, and therefore is nice for research.
SALMONELLA: named after D. E. Salmon. Inhabitants of the intestinal
tract of warm-blooded animals, grow on a wide variety of carbon and energy
sources, cause diseases (pathogens).
SARA. Smad Anchor for Receptor Activation, an anchor protein
that recruits Smad2 and Smad3 to the TGF-beta receptor.
SATELLITE DNA. A portion of the DNA that differs enough in
base composition so that it forms a distinct band on cesium chloride
gradient centrifugation; usually contains highly repetitive DNA
sequences.
SATELLITE RNA (viroids). A small, self-splicing RNA molecule that
accompanies several plant viruses, including tobacco ringspot virus.
SATURATED: the term given to organic molecules which contain
no multiple bonds.
SAWHORSE PROJECTION: the sideways projection of a
carbon-carbon single bond and the attached substituents.
SCAFFOLD. The nuclear structure observed when histones are
experimentally removed from chromosomes. Thought to represent a
structural component of the nucleus and of chromosome.
SDS-PAGE: Sodium dodecyl sulfate-polyacrylamide gel
electrophoresis.
SECRETORY COMPONENT. A surface receptor on epithelial cells
lining mucosal surfaces which binds dimeric IgA and transports it
through the cell into mucosal secretions.
SEGREGATION. The separation of allelic genes at
meiosis. Because allelic genes occupy the same locus on homologous
chromosomes, they pass to different gametes.
SELECTABLE MARKER. A gene whose expression allows one to identify
cells that have been transforrned or transfected with a vector containing the
marker gene.
SEMICONSERVATIVE REPLICATION. During DNA duplication, each strand of
a parent DNA molecule is a template for the synthesis of its new
complementary strand. Thus, one half of a preexisting DNA molecule is
conserved during each round of replication.
SENESCENCE (AGING): The last stage in the postembryonic development
of multicellular organisms, during which loss of functions and degradation of
biological components occur.
SENSE MUTATION. A mutation that changes a termination (stop) codon
into one that codes for an amino acid. Such a mutation results in an
elongated protein.
SEQUENCE HYPOTHESIS. Francis Crick's seminal concept that genetic
information exists as a linear DNA code; DNA and protein sequence are
colinear.
SEQUENCE TAGGED SITE (STS): A short (200- to 500-bp) DNA sequence
that occurs once in the genome and is identified by PCR amplification.
SEQUENCE TAGGED SITE CONTENT MAPPING: Markers that are based on
unique polymerase chain reaction primers that are used to determine shared
sites among clones of a library, which in turn facilitates the assembly of a
contig.
SEROTYPE: Classification of an organism or protein on the basis of
its interaction with antibodies.
SERPINS. A family of serine protease inhibitors.
SHEAR: The sliding of one layer across another, with deformation
and fracturing in the direction parallel to the movement.
SHIGELLA: named for K. Shiga, who isolated a species which causes
dysentery. Just like Eschericia, they inhabit the intestinal tract of
warm-blooded animals, grow on a wide variety of carbon and energy sources,
but they are commonly pathogens.
SHORT TANDEM REPEAT (STR) : DNA sequence with a sequential repeating
set of two (di-), three (tri-), or four (tetra-) nucleotide pairs.
SHORT TANDEM REPEAT POLYMORPHISM (STRP): Two or more short tandem
repeats that differ from each other by the number of repeated nucleoticle
units with each allelic DNA sequence occurring at a frequency of 1% or more
in a large population. The difference in the lengths of allelic short tandem
repeats is detected by gel electrophoresis following the polymerase chain
reaction with primers that are complementary to unique DNA sequences that
flank a short tandem repeat.
SHORT TEMPLATE: A DNA strand that is synthesized during the
polymerase chain reaction and has a primer sequence at one
end and a sequence complementary to the second primer at the
other end.
SHUTTLE (BIFUNCTIONAL) VECTOR: A plasmid cloning vehicle, usually a
plasmid, that can replicate in two different organisms because it carries two
different origins of replication.
SIDEROPHORE: A low-molecular-weight substance that binds very
tightly to iron.
SIGMA FACTOR: An accessory bacterial protein(s) that directs the
binding of RNA polymerase to specific promoters.
SIGNAL SEQUENCE (LEADER PEPTIDE): Segment of about 15 to 30 amino
acids at the N terminus of a protein that enables the protein to be secreted
(pass through a cell membrane). The signal sequence is removed as the protein
is secreted.
SIGNAL TRANSDUCTION. The biochemical events that conduct the signal
of a hormone or growth factor from the cell exterior, through the cell
membrane, and into the cytoplasm. This involves a number of molecules,
including receptors, proteins, and messengers.
SILENCER. The cis regulatory element that reduces
transcription of a gene.
SINGLE-STRAND CONFORMATION ANALYSIS/POLYMORPHISM (SSCA,SSCP): A
mutation detection assay that is based on the conformation of single strands
of DNA (ssDNA). If there is a nucleotide difference between the DNA molecules
from two different sources, then following denaturation and gel
electrophoresis the locations of the single strands in the two lanes of the
gel will be different.
SIX-CUTTER: A type II restriction endonuclease that binds and cleaves
DNA at sites that contain six nucleotide pairs.
SIZE MARKERS: A set of macromolecules of known relative molecular
masses that are used to calculate the relative molecular masses of
electrophoretically fractionated macromolecules.
SKEWED X-INACTIVATION. A nonrandom pattern of inactivation of
1 of the X chromosomes in a female that can arise through a variety of
mechanisms. When this occurs, the active X chromosome may bear the
mutant allele and the female will show signs and symptoms of the
disease. The female is called a manifesting heterozygote or a carrier.
SLE. Systemic Lupus Erythematosus; autoimmune disease,
antinuclear antibodies against blood cells and other tissues lead to
the formation of soluble immune complexes which cause vascular
inflammations.
SLOW-REACTING SUBSTANCE OF ANAPHYLAXIS (SRS-A). A group of
leukotrienes released by mast cells during anaphylaxis which induces a
prolonged constriction of smooth muscle. This prolonged constriction
is not reversible by treatment with antihistamines.
SMAD/DPC4. Smads are pivotal to intracellular signalling by
members of the TGF-beta family. Smad2 and Smad3 are receptor-regulated
Smads that interact with, and become phosphorylated by, activated
type-I receptor kinases. The phosphorylated Smad then binds Smad4, and
this heteromeric complex is translocated to the nucleus where it
controls the transcription of target genes which are leading to
inhibition of proliferation in most normal cells. Smad was reported to
induce p21waf1 expression. Smad/DPC4 is a tumor suppressor gene which
is deleted or mutated in about 50% of pancreatic adenocarcinomas.
SMALL NUCLEAR RNA (snRNA). Short RNA transcripts of 100-300 bp that
associate with proteins to form small nuclear ribonucleoprotein particles
(snRNPs), which participate in RNA processing.
SODD. The Silencer of Death Domains (SODD) was isolated as a protein
that prevents constitutive activation of TNF-R1. It interacts with the Death
Domains of TNF-R1 and DR3 but not with those of Death Domain Receptors (DDRs)
such as TNF-R2, Fas, DR4, or DR5. It was demonstrated that SODD interacts
with a region of TNF-R1 that also interacts with TRADD. SODD and TNF-R1 are
pre-associated in non-stimulated cells, and upon TNF treatment this
SODD-TNF-R1 complex is rapidly disrupted. Overexpresion of SODD prevents
TNF-induced cell death and activation of NF-kB
SODIUM DODECYL SULFATE: An anionic detergent that denatures
proteins.
SOMATIC CELL HYBRID PANEL: A set of derived chromosome-specific
hybrid cell lines that each carry a different portion of a particular
chromosome. The members of such a panel have chromosomal deletions and, in
some cases, carry translocated chromosomes that retain a segment of a
particular chromosome. Ideally, the retained portions of the cell lines of a
panel cover the entire chromosome. Also called somatic cell hybrid mapping
panel, somatic cell deletion panel.
SOUTHERN BLOTTING: A technique for transferring denatured DNA
molecules that have been separated electrophoretically from a gel to a matrix
(such as a nitrocellulose or nylon membrane) on which a hybridization assay
can be performed.
SPARGER: A device that introduces air into a bioreactor in the form
of separate, fine streams.
SPLICE SITE: The nucleotides at (1) the end of an exon and the
beginning of an intron and (2) the end of an intron and the beginning of the
next exon that are required for the joining of two exons and removal of an
intron during the processing of a primary transcript to a functional mRNA.
SPORE. a haploid cell formed following meiosis which then
undergoes mitosis and gives rise to a haploid individual, such as the
gametophyte in green algae or plants. In fungi, a haploid spore gives
rise to a new mycelium.
SSCP. Abbreviation for single-strand conformation polymorphism.
SSOP. Sequence-specific oligonucleotide probe. Together with PCR-SSP,
commonly used to type classical MHC genes following amplification by PCR
reaction (see also serological typing).
SSP. Sequence-specific primer. PCR-SSP is a common method to type
classical MHC genes.
STABILITY CONSTANT: when a complex is formed between a metal
ion and an a ligand in solution, the equilibrium may be expressed by a
constant which is related to the free energy change for the process:
For: M + A = MA : - deltaG = RTlnK
STANDARD METABOLIC RATE (SMR). the number of kilocalories an
ectotherm requires to maintain minimum function at a defined
environmental temperature.
STAPHYLOCOCCUS: named for their appearance, like a bunch of
grapes (Greek, staphyl). They're Gram-positive, non-motile,
non-spore-forming and aerobic (but will ferment).
STATIONARY PHASE. The plateau of the growth curve after log growth,
during which cell number remains constant. New cells are produced at the same
rate as older cells die. The assymptotic maximum of the hyperbolic tangent.
STEADY STATE: In continuous fermentation, when the number of cells
that are removed with the outflow is exactly balanced by the number of newly
synthesized cells.
STEREOSPECIFIC REACTIONS: reactions in which bonds are broken
and made at a particular carbon atom and which lead to a single
stereoisomer. If the configuration is altered in the process the
reaction is said to involve inversion of configuration; if the
configuration remains the same the transformation occurs with
retention of configuration.
STERIC HINDRANCE: the phenomenon of physical blockage of a
particular site within a molecule by the presence of local atoms or
groups of atoms. [As a consequence of steric hindrance, a reaction at
a particular site will be impeded.]
STICKY END. aka COHESIVE END. Overhanging ends of a double-stranded
DNA molecule that are capable of hybridizing with complementary ends.
STR. Abbreviation for short tandem repeat. These often serve
as polymorphic markers.
STREPTOCOCCUS PNEUMONIAE: Naturally found benignly in the respiratory
system, but quite willing to turn pathogenic if your defenses are down,
causing all sorts of problems, but especially pneumonia (Streptococcal
pneumonia is often lethal).
STREPTOCOCCUS: Some of the bad-boy bacteria in this genus cause
various diseases, while some of the altar boy-bacteria are involved in making
buttermilk and other fermented foods [link to fermented foods]. They are
Gram-positive, non-motile, non-spore-forming and aerobic (but will ferment,
producing lactic acid.)
STREPTOCOCCUS: streptos is Greek for 'twisted', coccus is Greek for
'grain'. Some of the bad-boy bacteria in this genus cause various diseases,
while some of the altar boy-bacteria are involved in making buttermilk and
other fermented foods [link to fermented foods]. For the boring: they're
Gram-positive, non-motile, non-spore-forming and aerobic (but will ferment,
producing lactic acid.)
STREPTOMYCES: streptos is Greek for 'twisted', myces is Latin for
'fungus'. Not a bit related to Streptococcus! Form branching filaments as
they reproduce, and mostly noted for making antibiotics (Current favorites:
Chloramphenicol, Erythromycin, Neomycin, Nystatin, Streptomycin,
Tetracycline).
STRINGENCY. Reaction conditions--notably temperature, salt, and
pH--that dictate the annealing of single-stranded DNA/DNA, DNA/RNA, and
RNA/RNA hybrids. At high stringency, duplexes form only between strands with
perfect one-to-one complementarity; lower stringency allows annealing between
strands with some degree of mismatch between bases.
STRINGENT PLASMID. A plasmid that only replicates along with the main
bacterial chromosome and is present as a single copy, or at most several
copies, per cell.
STRP. short tandem repeat polymorphism.
STRUCTURAL ISOMERISM: isomers which differ in the order of
bonding of the constituent atoms.
SUBSTITUTION REACTIONS: reactions in which one atom or group
of atoms is replaced by another atom or group of atoms. [See
electrophilic substitutions and nucleophilic substitutions.]
SUBTILISIN: A proteolytic enzyme usually found in Bacillus
subtilis.
SUCROSE DENSITY GRADIENT CENTRIFUGATION: A procedure used to
fractionate mRNAs or DNA fragments on the basis of
size.
SUPERCOILED PLASMID. The predominant in vivo form of plasmid, in
which the plasmid is coiled around histone-like proteins. Supporting proteins
are stripped away during extraction from the bacterial cell, causing the
plasmid molecule to supercoil around itself in vitro.
SUPERCOILED/SUPERTWISTED DNA. A closed circular DNA molecule in which
the DNA molecule is further twisted on itself to form a more compact
molecule. Left-handed (negative) supercoiling leads to a loosening of the
strands of the double helix (underwinding). Positive supercoiling is not seen
in vivo. (gamma-DNA)
SUPERGENE. A group of neighboring genes on a chromosome that tend to
be inherited together and sometimes are functionally related.
SUPERNATANT. The soluble liquid of a sample after centrifugation or
precipitation of insoluble solids.
SUPPRESSION. A mechanism for producing a specific state of
immunologic unresponsiveness by the induction of suppressor T
cells. This type of unresponsiveness is passively transferable by
suppressor T cells or their soluble products.
SURVIVIN. Survivin is a member of the human IAPs. Elevated
survivin expression was reported in most human tumors. In HeLa cells,
survivin was found to be expressed in the G2/M phase of the cell cycle
in a cycle regulated manner and to associate with the microtubuli of
the mitotic spindle in a specific and saturable reaction. Disruption
of survivin-microtubuli interactions resulted in loss of
anti-apoptotic activity of survivin and increased caspase-3
activation. Survivin may be required to counteract a constitutive
pathway that induces apoptosis during mitosis
SV40 T. The Simian virus large T antigen is a single dual
purpose protein able to block both Rb and p53.
SYMPORT. a membrane-bound carrier molecule which
simultaneously transports two different solutes, such as a proton and
sucrose or proton and auxin
SYNAPSIS. The pairing of homologous chromosome pairs during prophase
of the first meiotic division, when crossing over occurs.
SYNCYTIOTROPHOBLAST. This is a specialized cell of the
placenta (also a trophoblast) which acts like a dialysis membrane
between the mothers blood and the babies blood, feeding the baby as
well as removing waste products from the babies blood.
SYNGENEIC. Refers to genetically identical members of the same
species.
T lymphocytes (T cells). White blood cells, produced in the
bone marrow, that aid B cells in making antibodies to fight bacterial
infections. They also are instrumental in rejection of foreign tissue,
and may be important in the body's defense against cancer. Undergoes
a developmental stage in the thymus.
T-DNA (t-DNA, transfer DNA, tumor-DNA). The transforming region of
DNA in the Ti plasmid of Agrobacterium tumefaciens.
T-RNA (t-RNA, transfer RNA). The class of small RNA molecules that
transfer amino acids to the ribosome during protein synthesis. See Transfer
RNA.
T-dependent antigen. An immunogen that is able to induce
antibody synthesis only in the presence of lymphokines released by
helper T cells.
T-independent antigen. An immunogen which induces antibody
synthesis in the absence of lymphokines released by T cells; the
antibodies are generally only of the IgM isotype.
T4 DNA LIGASE: An enzyme from bacteriophage T4-infected cells that
catalyzes the joining of duplex DNA molecules and repairs nicks in DNA
molecules. The enzyme joins a 5'-phosphate group to a 3'-hydroxyl group.
T4 DNA POLYMERASE END LABELING: DNA that has been cut with a
restriction endonuclease(s) is mixed with T4 DNA polymerase and one labeled
deoxyribonucleotide, The 3' exonuclease activity of the T4 DNA polymerase
removes deoxyribonucleotides from the 3' ends of the DNA fragments.
Immediately after a deoxyribonucleotide that is the same as the
deoxyribonucleotide in the reaction mixture is cleaved off, the T4 DNA
polymerase activity incorporates a labeled deoxyribonucleotide from the
reaction mixture. No further incorporation of deoxyribonucleotides occurs
because there is only one kind of deoxyribonucleotide in the reaction
mixture.
TAP1. Transporter Associated with antigen Processing 1 (is
induced by NF-kB). TAP belongs to the ABC family of ATP-dependent
transporters. It transports peptides (which have been processed in
the cytoplasm by the proteasome) into the ER, where the peptides are
assembled into ternary complexes wit the alpha and beta2-m chains of
the MHC1 for antigen presentation
TAQ POLYMERASE. A heat-stable DNA polymerase isolated from the
bacterium Therrnus aquaticus, used in PCR. Originally patented despite
occuring naturally in hot springs.
TATA BOX: The DNA sequence, to which RNA polymerase binds, that lies
upstream from the site of initiation of transcription and ensures that
transcription starts at a specified nucleotide. Also called a Pribnow box in
prokaryotes and a Hogness box in eukaryotes after the researchers who
discovered the function of the TATA box in prokaryotes and eukaryotes,
respectively.
TAUTOMERISM: a form of structural isomerism where the two
structures are interconvertible by means of the migration of a proton.
TCA CYCLE. The tricarboxylic acid cycle (also known as the Krebs
cycle). A major metabolic pathway involved in aerobic cellular respiration
(energy production) which takes place in the mitochondria of animal and plant
cells. Pyruvic acid produced during glycolysis is converted to acetyl CoA
which is then oxidized to CO2. The reducing power of the end products NADH
and FADH2 are used in the synthesis of ATP by oxidative phosphorylation.
TELOMERE. The end of a chromosome.
TEMPLATE STRAND: The polynucleotide strand that a polymerase uses
for determining the sequence of nucleofides during
the synthesis of a new nucleic acid strand.
TEMPLATE. An RNA or single-stranded DNA molecule upon which a
complementary nucleotide strand is synthesized.
TERMINATION CODON (TRANSLATIONAL STOP SIGNAL): A naturally occurring
codon that does not base pair with the anticodon of any tRNA. Generally, the
three codons in this class (UAA, UAG, and UGA) are used to terminate
translation, although in some rare instances one of these codons does code
for an amino acid.
TGF-BETA SUPERFAMILY. Members of the Transforming Growth
Factor beta family are cytokines that regulate the proliferation of
cells; often they inhibit the cellular proliferation of normal cells.
TH1 and TH2. Helper T cells; T cells that induce B cells to
make antibody responses to antigens. Activated helper T cells express
glycoprotein g39 which is a ligand for CD40 expressed on B cells:
interaction of g39 with CD40 results in B cell activation, what is
enhanced by cytokines and lymphokines expressed by T helper cells
(IL-2, IL-4, IL-5 ...). Th1 cells enhance microbicidal action of
monocytes and macrophages on intracellular microorganisms while Th2
cells diminish the potency of the cellular immune response initiated
by Th1 cells. Th1 cells diminish, to some extent, the priming of naive
T cells to develop into IL-4 producers.
THERMOPHILE: A microorganism that grows optimally at high
temperatures, usually above 50'C. Some thermophiles can
grow at temperatures of 90' to 100'C.
THIOBACILLUS DENITRIFICANS: Grows on carbon
dioxide, using sulfur as an electron donor, and nitrate as an electron
acceptor (i.e. S goes to SO4 while NO3 goes to NH3.) A very frugal
organism.
THIOBACILLUS: named for sulfur. These bacteria oxidize sulfur
(elemental), sulfides (H2S, and similar) and thiosulfate (S2O3) for energy.
THIOREDOXIN: A small protein that acts as an electron carrier.
THYMIDINE KINASE (tk). An enzyme that allows a cell to utilize an
alternate metabolic pathway for incorporating thymidine into DNA. Used as a
selectable marker to identify transfected eukaryotic cells.
THYMIDYLATE SYNTHASE: An enzyme that catalyzes the methylation of the
uracil moiety in dUMP to convert it to dTMP.
TI (Ti) PLASMID: A large extrachromosomal element that is found in
strains of Agrobacterium and is responsible for crown gall
formation.
TISSUE PLASMINOGEN ACTIVATOR (tPA): biotechnology thrombolytic
TITRE. The reciprocal of the last dilution of a titration
giving a measurable effect; e.g. if the last dilution giving
significant agglutination is 1:128, the titre is 128.
TNFR FAMILY. Tumor Necrosis Factor Receptor family is
important in mediating inflammation and cytotoxicity. Members of the
TNFR family are the Death Receptors on the cell surface which mediate
apoptosis upon stimulation by specific ligands.
TOLERANCE. Diminished or absent capacity to make a specific
response to an antigen, usually produced as a result of contact with
that antigen under nonimmunizing conditions.
TOSYLATION: a reaction which introduces the
toluene-4-sulphonyl group into a molecule. [Generally by reaction of
an alcohol with tosyl chloride to give the tosylate ester.]
TOTIPOTENT (PLURIPOTENT): When a cell is able to respond to any one
of a number of different stimuli and, subsequently, to develop into any one
of a number of differentiated cell types.
TOXOID. A nontoxic derivative of a toxin used as an immunogen
for the induction of antibodies capable of cross-reacting with the
toxin.
TPL-2 KINASE. TPL-2 kinase is homologous to NIK. TPL-2
interacts with the C-terminus of NF-kB p105 and mediates
phosphorylation of NF-kB p105 (probably not directly but by a
downstream kinase). Upon phosphorylation, NF-kB p105 is either totally
degraded or only partially degraded from its C-terminus by the
proteasome to yield the NF-kB p50 subunit; while the p105 levels are
clearly decreased by TPL-2 activity, the p50 levels remain quite
constant. The degradation of p105 presumably generates active NF-kB by
releasing associated NF-kB/Rel subunits from p105 which can
translocate into the nucleus
TRAFs. TNFR-associated factors
TRANSCAPSIDATION. The partial of full coating of the nucleic acid of
one virus with a coat protein of a differing virus.
TRANSCRIBED TRIPLET: A set of three contiguous nucleotides of the
transcribed DNA strand of the coding region of a structural gene that
determines a codon in the mRNA.
TRANSCRIPT MAPPING: Assigning gene transcripts, in the form of
cDNA clones or expressed sequence tags, to specific chromosome regions by
fluorescence in situ hybridization, hybridization, polyrnerase chain reaction
(PCR), analysis of somatic cell hybrid mapping panels, or other
strategies.
TRANSCRIPTION factor: A protein that facilitates RNA synthesis by
binding to a specific DNA sequence or another transcription factor that is
bound to a specific DNA sequence.
TRANSCRIPTION. The synthesis of mRNA using a DNA template.
TRANSDUCTION: The transfer of nonviral DNA by a virus to a cell.
TRANSFECTION. The uptake and expression of a foreign DNA sequence by
cultured eukaryotic cells. (eg after "punching" holes in cell wall with LiAc
- Lithium Acetate)
TRANSFORMATION. In prokaryotes, the natural or induced uptake and
expression of a foreign DNA sequence--typically a recombinant plasmid in
experimental systems. In higher eukaryotes, the conversion of cultured cells
to a malignant phenotype--typically through infection by a tumor virus or
transfection with an oncogene.
TRANSFORMING ONCOGENE. A gene that upon transfection converts a
previously immortalized cell to the malignant phenotype.
TRANSFORMING RETROVIRUS. A retrovirus carrying an additional
DNA sequence (often an oncogene) that confers the ability to transform
infected cells to malignant phenotype.
TRANSGENE: A gene from one source that has been incorporated into the
genome of another organism.
TRANSITION-STATE INTERMEDIATE. In a chemical reaction, an unstable
and high-energy configuration assumed by reactants on the way to making
products. Enzymes are thought to bind and stabilize the transition state,
thus lowering the energy of activation needed to drive the reaction to
completion.
TRANSLATION: The process of protein (polypeptide) synthesis in
which the amino acid sequence of a protein is determined
by mRNA mediated by tRNA molecules, and carried out on ribosomes.
TRANSLOCATION: (1) The movement of peptidyl-tRNA and mRNA from the
aminoacyl site to the peptidyl site on the ribosome during the elongation
phase of translation; this movement opens the aminoacyl site for the next
codon. (2) The transfer of chromosome material from one chromosome to
another. (3) The movement of compounds through a plant.
TRANSPOSASE: An enzyme that is encoded by a transposon gene and that
facilitates the insertion of the transposon into a new chromosomal site and
excision from a site.
TRANSPOSON (TRANSPOSABLE ELEMENT): A DNA sequence (mobile genetic
element) that can insert randomly into a chromosome, exit the site, and
relocate at another chromosomal site.
TRANSPOSON. A mobile genetic element that can move from one
location in the gene and reinsert at another site.
TRANSVAGINAL ULTRASOUND ASPIRATION. An ultrasound-guided
technique for egg retrieval. A long, thin needle is passed through the
vagina into the ovary. When the follicle is entered, suction is
applied to retrieve the eggs. It is also known as ultrasound-guided
egg aspiration and transvaginal egg retrieval.
TRANSVERSION. A mutation in which purine is substituted for
pyrimidine or vice versa.
TRIBRID PROTEIN: A fusion protein that has three segments, each
encoded by parts of different genes.
TRICHLOROETHYLENE: An organic compound, used as a solvent and
degreasing agent, that often persists in the environment.
TRICHODERMA: A fungus, most of which feed on plant pathogens.
TRIPARTITE MATING: A process in which conjugation is used to transfer
a plasmid vector to a target cell when the plasmid vector is not
self-mobilizable. When (1) cells that have a plasmid with conjugative and
mobilizing functions are mixed with (2) cells that carry the plasmid vector
and (3) target cells, mobilizing plasmids enter the cells with the plasmid
vector and mobilize the plasmid vector to enter into the target cells.
Following tripartite mating, the target cells with the plasmid vector are
separated from the other cell types in the mixture by various selection
procedures.
TRIPLET. A sequence of 3 nucleotides comprising a codon of a
nucleic acid and representing the code for an amino acid (triplet
code, codon).
TRIPLOBLASTIC. Possessing three germ layers: the endoderm,
mesoderm, and ectoderm. Most eumetazoa are triploblastic.
TROPHOBLAST. These are the cells of the embryo that become the
placenta and attach the baby to the mother's uterus. These cells
provide an armor of protection completely around the baby in the
uterus. They also serve to nourish the baby carrying food from the
mother's blood to the babies blood. These are the cells that are
biopsied during a chorionic villus biopsy (CVS) to determine if the
baby is genetically normal.
TRYPSIN. A proteolytic enzyme that hydrolyzes peptide bonds on the
carboxyl side of the amino acids arginine and lysine. Released in the
pancreatic juice which digests protein in the small intestine
TUMOR SUPPRESSOR PROTEINS. Tumor suppressor proteins protect cells
from uncontrolled proliferation and transformation into tumor cells. They
affect several cellular pathways, such as those controlling proliferation,
apoptosis, differentiation and genomic identity. The common definition of a
tumor suppressor gene requires the demonstration of mutations of both copies
of a candidate gene in tumors (Knudson's two-mutation criterion). P53 is an
example of a tumor-suppresser gene.
TUNEL. Terminal deoxyNucleotidyl (dUTP) transferase-mediated
End Labeling. In vivo apoptose assay for the detection of DNA
fragmentation in cells.
UBIQUITIN. A small protein that becomes covalently linked to a
protein targeted for degradation.
UNEQUAL CROSSING OVER. Crossing over between similar DNA
sequences that are misaligned, resulting in sequences with deletion or
duplication of DNA segments. A cause of a number of genetic variants,
e.g., -thalassemia and Lepore hemoglobin.
UPSTREAM: In molecular biology, the stretch of DNA base pairs
that lie in the 5' direction from the site of initiation of
transcription. Usually, the first transcribed base is designated
+1 and the upstream nucleofides are indicated with minus
signs, e.g., - 1, - 10. Also, to the 5' side of a particular gene
or sequence of nucleotides.
VALENCE ISOMERISATION: the isomerisation of molecules which
involve structural changes resulting only from a relocation of single
and double bonds. If a dynamic equilibrium is established between the
two isomers it is also referred to as valence tautomerism. An example
is the valence tautomerism of cyclo-octa-1,3,5-triene.]
VARIABLE SURFACE GLYCOPROTEIN (VSG). One of a battery of antigenic
determinants expressed by a microorganism to elude immune detection.
VDAC. The Voltage-Dependent Anion Channel is involved in the
mechanism of cytochrome c release from the mitochondrial intermembrane
space into the cytosol. VDAC was shown to interact with Bcl-XL, Bax
and Bax. Bcl-XL decreased the conductivity of VDAC, whereas Bax and
Bak increased the conducticity of VDAC. Bax and Bak also induced VDAC
to be permeable for cytochrome c. Moreover, mitochondria from
VDAC-deficient yeast did not release cyto c in presence of Bax, but
mitochondria from VDAC-deficient yeast reconstituted with the human
vdac gene released cyto c in presence of Bax VDAC might also interact
with ANT or other components of the PT pore.
VECTOR. The agent used to carry new DNA into a cell. Viruses
or plasmids are often used as vectors.
VINYL GROUP: the ethenyl group, -CH=CH2.
VIR GENES: A set of genes on a Ti plasmid that prepare the T-DNA
segment for transfer into a plant cell.
VIRION. a complete virus particle that consists of an RNA or
DNA core with a protein coat, sometimes with external envelopes. It is
the extracellular infective form of a virus.
VIROID. A plant pathogen that consists of a naked RNA molecule of
approximately 250-350 nucleotides, whose extensive base pairing results in a
nearly correct double helix.
VIRUS. An infectious particle composed of a protein capsule and a
nucleic acid core, which is dependent on a host organism for replication. A
double-stranded DNA copy of an RNA virus genome that is integrated into the
host chromosome during lysogenic infection.
W, Z CHROMOSOMES. Sex chromosomes in species (like snakes, birds,
moths) where the female is the heterogametic sex (WZ).
WALDEN INVERSION: a Walden inversion occurs at a tetrahedral
carbon atom during an SN2 reaction when the entry of the reagent and
the departure of the leaving group are synchronous. The result is an
inversion of configuration at the centre under attack.
WALKER'S A and B-BOX CONSENSUS SEQUENCES. Those sequences are
nucleotide binding sites, e.g. in Apaf-1.
WD-repeats. Loosely conserved set of sequences which is found
in many regulatory proteins, including beta-subunits of heterotrimeric
G proteins, the SREBP cleavage-activating protein, but also in Apaf-1.
WESTERN BLOTTING: Transfer of protein from a gel to a membrane.
Wild type A genetic term that denotes the most commonly observed
phenotype, or the normal state, in contrast to a
mutant condition.
WILD TYPE. The term used to indicate the normal allele (often
symbolized as +) or the normal phenotype.
X-AUTOSOME TRANSLOCATION. The reciprocal translocation between
the X chromosome and 1 of the autosomes.
X-LINKED DOMINANT. A trait that is manifested in the
heterozygous female as well as in the male who has the mutant allele
on 1 of the X chromosomes.
X-LINKED RECESSIVE. A disorder manifested exclusively in a
male who is a heterozygote or a homozygous female when the abnormal
gene is carried on the X chromosome. A female is usually a carrier if
she is heterozygous and transmits the disease to the son.
XENOPUS. An amphibian (frog) who shared a common ancestor with
mammals about 350 million years ago. The oldest species in which all three
regions of the MHC are known to be linked.
XYLOSE: A 5-carbon sugar that is a major constituent of
hemicellulose.
YEAST ARTIFICIAL CHROMOSOMES (YAC). An artificial chromosome created
from DNA, centromere and telomere of yeast chromosomes. Heavily used as
vector in cloning of very large (>1Mb) genomic fragments.
YEAST: A single-celled, usually rounded fungus.
Z-DNA. A region of DNA that is "flipped" into a lefthanded helix,
characterized by alternating purines and pyrimidines, and which may be the
target of a DNA-binding protein.
ZINC FINGER PROTEINS. Transcription-activator proteins
containing finger-like structures containing zinc atoms.
ZOO BLOT. A Southern blot containing conserved DNA sequences from
related genes of different species. It is taken as evidence that the
sequences are coding sequences from a specific gene. Hybridization of a
cloned human DNA sequence to DNA from various vertebrate organisms to
determine whether the cloned DNA is evolutionarily conserved.