RNA InterferencePick a Gene, Make a Mutant!
A cell of the immune system, which circulates through the blood, bone marrow, and spleen, and plays an important role in antimicrobial defense.
A gelatinous substance used to grow, or culture, microorganisms. Agar provides the microorganisms a surface to grow on and contains nutrients.
A protein in the immune system that recognizes a specific target, or antigen, on a foreign molecule, allowing these two structures to bind together with precision.
A chromosome for which there is an equal number of copies in males and females -- that is, a chromosome that is not a sex chromosome.
A protein which, by binding to an operator sequence, promotes transcription of a gene.
The "genetic code" in a DNA molecule is written in four bases -- adenine (A), cytosine (C), guanine (G) and thymine (T) -- that are arrayed along each strand of the twisted, two-stranded molecule (the famous "double helix"). Each base is chemically tuned to pair, via hydrogen bonds, with a corresponding base on the opposite strand -- A with T, G with C. The size of an organism's genome is usually given by the number of base pairs.
A technique for analyzing interactions of proteins with DNA, consisting of chromosomal immunoprecipitation, followed by massively parallel DNA sequencing.
The combination of DNA and proteins found in the nucleus of a cell, which makes up chromosomes. Chromatin helps fold DNA so it will fit into the cell and is involved in both gene expression and DNA replication.
A structure of coiled DNA and proteins that organizes the genetic material in the cell's nucleus.
The scientific term for cells becoming more specialized throughout development.
DNA encodes the genetic blueprint of an organsim. This genetic material is composed of deoxyribonucleotides -- individual units combining a sugar, a base, and a phosphate group -- that each have different chemical properties, and are referred to by the different base names adenine (A), cytosine (C), guanine (G) and thymine (T). Combinations of these bases "spell out" the code of a given gene.
Proteins with a specific or general affinity for DNA.
The process of determining the specific order of nucleotide bases in a DNA molecule.
Biological molecules (mainly proteins) that catalyze, or increase the rate of, a chemical reaction
The study of changes in gene expression resulting from mechanisms other than changes in the underlying DNA sequence.
The class of organisms, composed of one or more cells, containing a membrane-enclosed nucleus and packaging its DNA with histones in a nucleosome array. Eukaryotic cells typically have complex organelles, such as mitochondria.
An exon is a contiguous segment of a gene found both in the initial transcript and in the final product; the introns are those segments found in the initial transcript which are removed during processing, and so are not found in the finished product.
In molecular biology, a gene is the molecular unit of inheritance for a single function or phenotype -- or, more precisely, the full sequence of bases within a section of the genome that is necessary and sufficient for the synthesis of a functional product. Usually that product is a polypeptide (a section of a protein), but in some cases it is an RNA molecule.
The full complement of genetic information recorded in the chromosomal DNA (or, for some organisms, RNA).
Within a genome sequencing project, annotation is the process of identifying biologically relevant elements within the genome sequence (e.g., genes), and adding information to the sequence on how those elements function.
The specific genetic encoding, or allele of a gene, that leads to an observable characteristic in an organism.
Green Fluorescent Protein (GFP)
A protein first isolated from the jellyfish Aequorea victoria that exhibits bright green fluorescence when exposed to ultraviolet blue light. The GFP gene can be introduced into organisms and used by scientists to "see" gene expression.
An organism containing both male and female reproductive organs within the same individual.
The small, basic proteins used to package the DNA in chromatin. The core histones (H2A, H2B, H3, and H4) are highly conserved over evolution, while histone H1 is more variable.
Histone Code Hypothesis
The hypothesis that combinations of chemical modifications to histone proteins in the chromatin form a complex, separate mechanism for regulating transcription and, thus, gene expression.
An enzyme that removes acetyl groups from the ends of histone proteins.
A gene found in an organism that shares an ancestral sequence with that of another organism. Homologs are often identified based on the retention of shared genetic or protein-level identities between two different species that share a common evolutionary history.
High-Occupancy Target (HOT) Region
Genomic regions where 15 or more independent transcription factors bind.
The process of isolating and concentrating a specific protein of interest by trapping an antibody that binds to that protein, using any of a number of lab techniques.
The intermediate developmental stages that an insect (such as Drosophila) undergoes between molts until it reaches sexual maturity.
The full complement of metabolites -- small molecules produced by cellular or organismal metabolism -- that characterize a cell, cell population, tissue, or organism.
Post-transcriptional regulators that bind to complementary sequences on target messenger RNAs, usually leading to gene silencing.
A non-human species used in experimental biology to study biological processes that might illuminate workings of the same processes in other organisms, for which the same experiments might be infeasible or unethical.
Molting, or ecdysis, is the periodic shedding of the outer skeleton, or exoskeleton, that accompanies the growth of most arthropods, including insects.
The form and structure of an organism.
Next-Generation Sequencing (NGS)
A family of techniques for DNA sequencing that rely on massively parallel processing of many millions of DNA fragments, followed by analysis and re-assembly of those fragments using computer techniques.
A unit of length equal to one billionth of a meter.
The basic unit of DNA packaging, consisting of DNA wound around histones.
The null hypothesis generally corresponds to what we expect if nothing "interesting" is happening. If you flip a coin many times, and generally get roughly 50% heads and 50% tails, that is consistent with the null hypothesis that the coin is fair. If you flip a coin many times and get 99% heads, the coin may be unfair, and hence you may have cause to reject the null hypothesis that it is fair.
A gene that has similar sequence in each species in which it's found because the species have a common ancestor during evolutionary time. For example, the alcohol dehydrogenase and Malic Enzyme 1 genes are similar in both Drosophila melanogaster and Homo sapiens. Normally, orthologous genes have the same function in each species in which they are found; therefore, studying the function of a gene in a model organism can provide good evidence for the function of the orthologous gene in humans
A shallow cylindrical dish, made of glass or plastic, used to grow, or culture, cells, bacteria, and other microorganisms.
The observable characteristics or traits of an organism, resulting from the interaction of the expression of the organism's genes with the influence of environmental factors.
A type of nonverbal communication, usually a chemical or hormone secreted by an animal, which often influences the behavior of other members of the same species. Pheromones are used to establish territory and attract mates.
Giant chromosomes formed by some cells that undergo multiple rounds of DNA replication without actual cell division. The salivary glands of Drosophila contain examples of such chromosomes. Their size makes them especially convenient for work in the lab.
Any of a variety of additional changes to a protein after translation that can modify its behavior and thus affect in gene expression.
A scientific term for offspring.
The class of single-cell organisms, including the eubacteria and archaea, that lack a true membrane-limited nucleus and other organelles.
Biological compounds made up of one or more polypeptides (a chain of amino acids) typically folded into a 3-D form. The sequence of amino acids in a protein is defined by the sequence of a gene.
A variety of processes used to isolate a particular protein from a biological tissue or culture, and thereby to allow the further characterization of the protein's structure and function.
The full complement of proteins expressed by a genome, cell, tissue, or organism.
A protein which, by binding to an operator sequence, prevents transcription of a gene.
A genome sequence assembled from the experimentally obtained sequences of a number of individuals in a species, designed to serve as a representative example of the "typical" gene sequence of that species.
Segments of DNA where transcription factors bind preferentially.
An enzyme that uses RNA as a template to transcribe single-stranded DNA -- thereby reversing the more familiar information flow from DNA to RNA. In addition to its use in the lab, RT has been extensively studied in retroviruses (particularly HIV) that have an RNA genome but must produce double-stranded DNA that becomes integrated into the host cell genome as part of their replication cycle.
The complex molecules that catalyze protein synthesis within the cell.
RNA is composed of nucleotides, just like DNA -- three major differences between the two: (1) RNA contains the sugar ribose, while DNA contains the slightly different sugar deoxyribose (2) RNA has the nucleobase uracil, while DNA contains thymine; (3) unlike DNA, most RNA molecules are single-stranded.
RNA Interference (RNAi)
The silencing or reduction of RNA expression (which generally correspondes to protein production) for a given gene in a cell or organism. It occurs as a natural process within living cells, but is also a powerful technique for studies of gene expression in the lab.
RNA Polymerase I, II, and III
Enzymes in eukaryotic cells that manage the synthesis of a strand of RNA based on the sequence encoded in the DNA.
A high-throughput technique for sequencing an organism's "transcriptome" -- the RNA transcribed from the genome under investigation.
The sequence of a small fragment of DNA, obtained as part of a high-throughput sequencing experiment.
A pair of chromosomes, usually designated X or Y, in the germ cells of most animals and some plants, that combine to determine the sex and sex-linked characteristics of an individual.
Small Interfering RNA (siRNA)
Short, 20-to-25-nucleotide, double-stranded RNA fragments that interfere with the expression of a specific gene.
Single-nucleotide polymorphism (SNP)
A difference in a single base pair in a given gene sequence, between two or more individuals, or between an individual and a reference genome, that is associated with a difference in phenotype or expressed trait.
The state of equilibrium or inactivity, analogous to hibernation.
During transcription, a DNA sequence is read by RNA polymerase and a complementary RNA copy of the DNA sequence is created.
A consensus sequence, TATA(A/T)A, found about 25 base pairs upstream from the start site of a group of eukaryotic genes encoding messenger RNA -- often those that can be transcribed at a high rate. The TATA box binds the TATA box binding protein (TBP), a subunit of TFIID, initiating the process of RNA polymerase II assembly at the promoter in vitro, and plays a key role as a recognition sequence for RNA polymerase II in eukaryotic organisms.
A protein that binds to a DNA sequence and controls (increases or decreases) the rate of transcription (the flow of genetic information from DNA to RNA).
The full complement of RNA molecules produced in a given cell or cell population.
Transcription Preinitiation Complex
A group of proteins necessary for the start of protein transcription in eukaryotic organisms.
The process in which RNA, produced during transcription, is decoded to produce an amino acid chain (polypeptide) that will then fold into an active protein.
Slang term for the domain of classic lab experiments handling actual and analyzing actual biological materials, as opposed to experiments and work performed using computer analysis.
This is the typical or most common form, appearance, or strain of an organism that exists in the wild, as opposed to the lab. It can also refer to the normal, non-mutated form of a gene that's common in nature.
The earliest developmental stage of the embryo, occurring when two gamete cells are joined by means of sexual reproduction.