DAPI (4',6-Diamidino-2-Phenylindole): A highly specific and sensitive fluoresceing DNA stain used in epifluorescent microscopy to observe structures containing DNA. DAPI specifically binds to double stranded DNA, and when excited with light the DAPI-DNA complex fluoresces a bright blue (Porter & Feig 1980).
De novo: Literally, 'from new' as opposed to inherited.
Decomposer: heterotrophic; microorganisms (usually bacteria and fungi) that break down nonliving organic matter and release nutrients which are then available for reuse by autotrophs
Decomposition: The biochemical process where biological materials are broken down into smaller particles and eventually into basic chemical compounds and elements. See also decomposer.
Deep scattering layer (DSL): layer of organisms that move away from the surface at night; the layer scatters or returns vertically directed sound pulses
Degeneracy: A feature of the genetic code that more than one nucleotide triplet codes for the same amino acid. The same applies to the termination signal which is encoded by three different stop codons.
Demersal fish: fish living near and on the bottom
Demersal: Refers to swimming animals that live near the bottom of an ocean, river, or lake. Often refers to eggs that are denser than water and sink to the bottom after being laid.
Denaturation: Reversible disruption of hydrogen bonds between nucleotides converting a double-stranded DNA molecule to single-stranded molecules. Heating or strong alkali treatment result in denaturation of DNA.
Deposit feeder: An animal that ingests small organisms, organic particles, and detritus from soft sediments, or filters organisms and detritus from such substrates.
Derived: Describes a character state that is present in one or more subclades, but not all, of a clade under consideration. A derived character state is inferred to be a modified version of the primitive condition of that character, and to have arisen later in the evolution of the clade. For example, "presence of hair" is a primitive character state for all mammals, whereas the "hairlessness" of whales is a derived state for one subclade within the Mammalia.
Desiccate: To dry completely.
Desiccation: Drying, or loss of moisture.
Desmokont: A dinoflagellate cell type in which two dissimilar flagella emerge from the anterior part of the cell; e.g. Prorocentrum sp. This morphological type does not have a cingulum or a sulcus.
Detritivore: An organism that eats small fragments of partially decomposed organic material (detritus) and its associated micro flora.
detritus any loose material, especially decomposed, broken, and dead organic materials
Detritus: Dead organic matter of plant or animal. See also detrivore.
Devonian Period: A geologic period in the Phanerozoic Eon (410 to 360 Mya).
diameter - With the exception of the Prorocentroids, the maximum cell width measured between the lateral extremes of the cingular flanges (Balech 1995).
Diarrhetic Shellfish Poisoning (DSP): A human gastrointestinal disease caused by the ingestion of toxic marine shellfish (filter-feeding bivalves) from cold and warm temperate regions of the Atlantic and Pacific Oceans (Steidinger 1993). Shellfish can accumulate and store large quantities of red tide dinoflagellate toxins without apparent harm to themselves (Steidinger & Baden 1984). Symptoms include diarrhea, nausea and vomiting lasting a few days. No human deaths have been reported (Hallegraeff 1995).
Diatom: Single-celled protistan algae of the class Bacillariophyceae that have intricate siliceous shells composed to two halves. They range in size from about 10 to 200 microns. Diatoms sometimes remain attached after cellular divisions, forming chains or colonies. These are the most numerous and important group of phytoplankters in the oceans, and form the primary food base for marine ecosystems.
Dicentric chromosome: One chromosome having two centromeres.
Diel: Refers to a 24-hour activity cycle based on daily periods of light and dark.
Dikaryotic: A cell that contains two separate haploid nuclei (n+n) which is different from being haploid (n) or diploid (2n). Naturally seen in fungal heterokaryons. Dikaryosis is a significant genetic peculiarity of the fungi.
Dimorphism: A condition where a population has two distinct physical forms (morphs). In sexual dimorphism, secondary sexual characteristics are markedly different (e.g., size, color, and behavior).
Dinoflagellate:A planktonic photosynthetic, unicellular algae that typically has two flagella, one being in a groove around the cell and the other extending from the center of the cell.
Dinokont: A dinoflagellate cell type in which two flagella are inserted ventrally; one flagellum is transverse and housed in a cingulum and the other is longitudinal and housed in a sulcus. A dinokont dinoflagellate can be a thecate species (with thecal plates) or an athecate species (without thecal plates)(Steidinger & Tangen 1996).
Dinophysoid: Group of dinokont type dinoflagellates. Members of this group are the only thecate dinoflagellates fundamentally divisible into two lateral halves and have an anterior cingulum and a narrow sulcus. They are laterally compressed, and their shapes in lateral view are essential for genus and species identification (Taylor et al. 1995).
Diploblast: A lower invertebrate such as jelly fish that are composed of two tissue layers (ectoderm and endoderm) and lacking the third layer (mesoderm) present in higher invertebrates and vertebrates.
Diplohaplobiontic: A lifecycle that alternates between the diploid and haploid stages of the organism.
Diploid: A cell that has a nucleus with two sets of chromosomes (2N).
Diploid number (2n): The full complement of chromosomes in a somatic cell (or a sex cell before meiosis). In humans, the diploid number is 46.
Disjunction: Separation of homologous chromosomes during anaphase of mitotic or meiotic divisions (see also nondisjunction).
Dispersal: The spreading of individuals throughout suitable habitat within or outside the population range. In a more restricted sense, the movement of young animals away from their point of origin to locations where they will live at maturity.
Disposable soma theory: A theory on the evolution of ageing and death suggesting that organisms derive little benefit from investing resources in increasing their lifespan beyond a certain point. It originated from the economic phenomenon that manufacturers invest minimum in durability.
Disruptive selection: Selection against the middle range of variation causing an increase in the frequency of a trait showing the extreme ranges of its variation. Disruptive selection might cause one species to evolve into two.
Distribution: (1) A species distribution is the spatial pattern of its population or populations over its geographic range. See RANGE. (2) A population age distribution is the proportions of individuals in various age classes. (4) Within a population, individuals may be distributed evenly, randomly, or in groups throughout suitable habitat.
Disulfide bond(-S-S-): A covalent linkage between two cysteine residues in different parts of a protein or between two different proteins. Insulin (a small protein having two polypeptide chains) and immunoglobulin molecules, for example, have interchain and intrachain disulfide bonds. HLA molecules also have disulfide bonds. The C282Y mutation removes one of the disulfide bonds in the HLA class I-like HFE protein and abolishes its surface expression.
Diurnal: Refers to daylight activities, or organisms most active during daylight. See DIEL.
Divergent evolution: A kind of evolutionary change that results in increasing morphological difference between initially more similar lineages.
Diversity: Term used to describe numbers of taxa, or variation in morphology.
dn/ds ratio: In molecular phylogenetic studies, the ratio of the number of non-synonymous nucleotide substitutions to the number of synonymous nucleotide substitutions. In the case of functionally important (or otherwise constrained) genes, ds is expected to exceed dn (dn/ds <1). Because most amino acid changes will disrupt protein structure and those non-synonymous substitutions (dn) causing them will not be maintained. In a non-functional pseudogene, there will be no discrimination between them and equal numbers of dn and ds are expected (dn/ds=1). When natural selection is acting to favor changes at the amino acid level, it is predicted that dn will exceed ds, hence a high dn/ds ratio. In classical MHC loci, in the peptide binding regions (allele-specific sequences) because of heterozygote advantage/frequency- dependent selection, there is always a high dn/ds ratio (>1) whereas in the remainder of the gene dn/ds <1 (due to functional constrains). This suggests balancing selection is acting on peptide binding regions.
DNA (deoxyribonucleic acid): The large double-stranded molecule carrying the genetic code. It consists of four bases (adenine, guanine, cytosine and thymine), phosphate and ribose.
DNA binding motif: Common sites on different proteins which facilitate their binding to DNA. Examples are leucine zipper and zinc finger proteins. Any such protein is called DNA-binding protein.
DNA Polymerase: A group of enzymes mainly involved in copying a single-stranded DNA molecule to make its complementary strand. Eukaryotic DNA polymerases participate in chromosomal replication, repair, crossing-over and mitochondrial replication. To initiate replication, DNA polymerases require a priming RNA molecule. They extend the DNA using deoxyribonucleotide triphosphates (dNTP) as substrates and releasing pyrophosphates. The dNMPs are added to the 3' OH end of the growing strand (thus, DNA replication proceeds from 5' to 3' end).
DNA repair: Restoration of the correct nucleotide sequence of a DNA molecule that has acquired a mutation or modification. It includes proofreading by DNA polymerase (see helicase).
DNA: Deoxyribonucleic acid. The primary genetic material of a cell that makes up genes and chromosomes. See also genes, chromosome.
Domain: Region of a protein with a distinct tertiary structure and characteristic activity (for example, the membrane distal and membrane proximal domains of an MHC molecule).
Dominance: The property possessed by some alleles of determining the phenotype for any particular gene by masking the effects of the other allele (when heterozygous). Thus, homozygosity or heterozygosity for the dominant allele result in the same genotype in complete dominance (if red is dominant over white, the petals of a flower heterozygous for red and white would be red). Incomplete dominance appears as a blend of the phenotypes corresponding to the two alleles (like pink petals as opposed to red or white). In co-dominance, both alleles equally contribute to the phenotype (red and white petals occur together).
Dominant allele: An allele that masks an alternative allele when both are present (in heterozygous form) in an organisms (see recessive).
Dominant-negative mutation: A (heterozygous) dominant mutation on one allele blocking the activity of wild-type protein still encoded by the normal allele causing a loss-of-function phenotype. The phenotype is indistinguishable from that of homozygous dominant mutation. p53 mutations may act as dominant-negative (see also haploinsufficiency).
Dorsal: Of or relating to the back side of an organism. In dinokonts, opposite the ventral side (front side)
Dorsoventral: Extending along the axis joining the dorsal and ventral sides.
Dosage compensation: The phenomenon in women, who have two copies of genes on the X chromosome, of having the same level of the products of those genes as males (who have a single X chromosome). This is due to the process of inactivation of one of the X chromosomes in females (Lyonization). See Lyon's hypothesis.
Double fertilization: The union of one male gametophyte nucleus with the ovum nucleus and another male gametophyte nucleus with the polar nuclei to form the endosperm in seed plants. See also pollen grain.
Double heterozygote: An individual who is heterozygous at two loci under investigation.
Double stranded RNA (dsRNA): In eukaryotes, it is an accidental byproduct of transcriptional process. It may occur as the genome of certain viruses (such as reovirus) or may be produced during viral replication as a general marker for viral infection. It is believed that dsRNA is the toxic substance responsible for general symptoms of viral infection as it induces cytokine production. dsRNA is the major activator of the PKR enzyme which is the major agent of anti-viral innate immunity.
Downstream: The direction which RNA polymerase moves during transcription (5' to 3') and ribosomes moves during translation. By convention, the +1 position of a gene is the first transcribed nucleotide, nucleotides downstream from the +1 position are designated +2, +3, etc.
Drift evolution: A high rate of immunologically significant mutations in certain viruses. This results in drifting away from recognition by the immune system by antigenic change. Influenza virus, HIV and HCV constantly change their antigenic structure through drift evolution.
Drosophila melanogester: Common fruit fly. It contributed heavily to the study of genetics because of its ease and speed to breed. It contains only four pairs of chromosomes. Link to Drosophila website.