Genetics

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Intron

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any nucleotide sequence in a gene that is taken out via RNA splicing while thefinal RNA product is being made. They are also known as the non-protein-codingsegments imbedded within DNA.

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Exon

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any protein coding nucleotide sequence that is left in a given gene after RNAsplicing occurs and the introns are removed. Exons are covalently bonded to one anotherto form mRNA.

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In Silico

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is an expression used to mean "performed on computer or via computersimulation”

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Mitochondrial DNA

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Contains 37 genes, all of which are essential for normalmitochondrial function. Thirteen of these genes provide instructions for makingenzymes involved in oxidative phosphorylation.

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Shine-Dalgarno (SD) sequence

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a ribosomal binding site, located upstream of the startcodon AUG, which helps recruit ribosomes in order to begin protein synthesis byguiding and aligning the ribosome with the start codon.

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ORF (open reading frame)

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a continuous stretch of DNA that encodes the protein-coding portion of the gene or transcript. It beiginswith a start codon (usually ATG,which encodes for methionine) and ends with a stop codon (no amino acid is encoded)..It normally does not contain termination codons other than the final stop codon whichdenotes the end of the ORF. Also referred to as the “coding sequence” or CDS.

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Phylogenetic tree:

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a hypothesis of the evolutionary relationships between populationsof organisms (as opposed to individuals in a pedigree) within a given taxon, which canbe as broad as all life or as specific as the class Aves (birds).

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Concatenated

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linked together in a chain or series

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Genome annotation:

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The process of attaching biological information to sequences.Identifies portions of the genome that do not code for proteins, identifies elements on thegenome, a process called gene prediction, attaches biological information to theseelements

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Contigs

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A contig is a series of overlapping DNA sequences used to make a physicalmap that reconstructs the original DNA sequence of a chromosome or a region of achromosome. A contig can also refer to one of the DNA sequences used in making sucha map.

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Transformed/transformation

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Transformation is the process by which competentbacteria becomes alters by incorporating exogenous DNA into the bacteria through thecell membrane.

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Bacteriophage

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any group of viruses that infect bacteria. Also sometimes called aphage or bacterial virus

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Endonuclease

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an enzyme that breaks down a nucleotide chain into two or moreshorter chains by cleaving the internal covalent bonds linking nucleotides

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Mutagenesis:

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a process by which the genetic information of an organism is changed ina stable manner, resulting in a mutation that may occur simultaneously in nature, or asa result of exposure to mutagens

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Suppression

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results when one mutation counteracts the effect of another mutation togive a wild‐type phenotype.

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Transposons

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is a small piece of DNA thatinserts itself into another place in the genome by either cutting itself out of the genome,or making a copy of itself and then “pasting” it into the genome.

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Horizontal transfer:

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The transmission of DNA between genomes; also called lateral gene transfer.

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Flanking Region

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The DNA sequences extending on either side of a specific locus orgene. 3' flanking region: A region of DNA which is NOT copied into the mature mRNA,but which is present adjacent to 3' end of the gene 5' flanking region: A region of DNA which is NOT transcribed into RNA, but rather isadjacent to 5' end of the gene. Also called the” leader sequence.”The 5’ flanking region contains the promoter, and may also contain enhancers or otherprotein binding sites.

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Mito-ribosomes

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Ribosomes that are created in the mitochondria and therefore found inall eukaryotes, are especially small and aid in the creation of proteins.

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Hairpin RNA

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a sequence of RNA that makes a tight hairpin turn which can be used tosilence target genes through RNA interference.

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Translational bypassing:

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is a unique phenomenon of a bacteriophage wherein thebacterial ribosome produces a single polypeptide chain from a discontinuous openreading frame (an ORF that has a “stop” codon inside the ORF)

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Byp (translational bypassing elements):

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A set of intracellular elements that promotesefficient and accurate bypassing of RNA sequences in translation. This includes“matching takeoff and landing codons, a stop codon, and both a hairpin RNA secondarystructure directly downstream of the takeoff site, and a Shine–Dalgarno (SD) sequence afew nucleotides upstream of the landing codon.”

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Hop Element (Ribosome Bypass):

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This is a specific sequence of nucleic acids in phageT4 that allows the peptidyltRNA complex during protein translation to slide down themRNA messaging sequence from one to potentially dozens of nucleotides downstreamand resume protein chain elongation and the process of protein translation ultimately nottranslating the skipped nucleic acid sequence.

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superwobble

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When a single tRNA species, which contains a U in the wobble posistion,is capable of reading all four nucleotides in the third codon position.

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Electrophoresis:

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is a technique used in laboratories in order to separate macromoleculesbased on size. The technique applies a negative charge so proteins move towards apositive charge. This is used for both DNA and RNA analysis.

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Liquid chromatography tandem mass spectrometry (LC-MS/MS):

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an instrumentused to separate substences in solution (liquid chromatography) then analyze thefractions in order to determine their identities (mass spectrometry).

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Sanger sequencing:

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Fred Sanger developed the first technique for sequencing DNA.DNA is replicated in the presence of chemically altered versions of the A, C, G, and Tbases: dideoxynucleotides (ddNTPs: chain-elongating inhibitors of DNA polymerase,used in Sanger method for DNA sequencing). Sanger sequencing is typically done on a gel. These bases stop the replication processwhen they are incorporated into the growing strand of DNA, resulting in varying lengthsof short DNA. These short DNA strands are ordered by size, and by reading the endletters from the shortest to the longest piece, the whole sequence of the original DNA isrevealed.

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Covariance:

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the measure of how changes in one variable affect the changes inanother variable, if at all.

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PCR (Polymerase chain reaction):

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technique used to amplify a single copy or a fewcopies of a piece of DNA across several orders of magnitude, generatingthousands to millions copies of a particular DNA sequence

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Anneal:

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The joining of single strands of DNA because of the pairing ofcomplementary bases. In PCR, primers anneal to complementary target DNAsequences during of the DNA (after DNA is made single stranded by heating)

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Random Hexamer Primers:

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a mixture of oligonucleotides representing all possible hexamer sequences.

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Amplicons

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a piece of DNA or RNA that is the source and/or product of natural orartificial amplification or replication events. It can be formed using various methodsincluding polymerase chain reactions (PCR), ligase chain reactions (LCR), or naturalgene duplication.

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Progenitor cell:

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a cell that is pluripotent (capable of becoming many different celltypes), but not totipotent (capable of becoming any cell type). That is, it has the abilityto differentiate into a specific type of cell, but is more limited than a stem cell. Relatively undifferentiated cell, which retains the ability to divide and cycle throughoutpostnatal life to reproduce cells that can specialize and take the place of those that die orare lost.

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Dedifferentiation:

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phenomenon where cells regress from a specialized function to asimpler state reminiscent of stem cells.

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Assymetric division

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two daughter cells with different cellular fates.Notably, stem cells divide asymmetrically to give rise to two distinct daughter cells:one copy of the original stem cell; the second daughter programmed to differentiate intoa non-stem cell fate.(In times of growth or regeneration, stem cells can also divide symmetrically, to producetwo identical copies of the original cell)

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Downregulation:

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lower expression (at RNA or protein levels) in one sample compared to another sample

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Upregulation:

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higher expression (at RNA or protein levels) in one sample compared to another sample

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Gain-of-function studies:

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utilizing a gain-of-function mutation or a gene, OR using a normal gene but manipulated to be expressed at a higher expression level than typically found in wildtype cells/organisms (overexpression )

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Cell cycle reentry:

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cells may exit from the active cell cycle in response to regulatory signals and pass into a nondividing phase called G0 phase. Cells may either remain in G0 phase forever, never enter G0 phase, or they can leave G0 phase later on after previously entering it. By leaving G0 phase, the cell reenters the active cell cycle (reenters G1 phase).

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Retinitis pigmentosa (RP)-

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a group of rare, genetic disorders that involve a breakdown and loss of cells in the retina, which is the light sensitive tissue that lines the back of the eye. Most likely the rods are the most damaged, affecting night vision, but cones can be damaged as well. No cure is currently known.

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Macular degeneration-

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an eye disease that progressively destroys the center of the retina - the macula - and impairs vision over time. It does not usually cause blindness, but impairs the ones central vision and therefore can affect ones ability to see straight and perform tasks such as driving or reading. There are various types of macular degeneration, but mostly affects people 60 years or older.

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electroporation:

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Application of electricity to produce temporary holes in cell membrane in order to introduce new DNA.

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Western blot:

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used to detect specific proteins in a sample of tissue homogenate or extract using electrophoresis to separate proteins by length of the polypeptide. -utilizes antibodies (polyclonal or monoclonal) to allow for the detection of a specific protein of interest -an antibody directed against a specific protein is called “anti-” the protein of interest

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polyacrylamide gels:

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Polyacrylamide is ideal for protein separations because it is chemically inert, electrically neutral, hydrophilic.

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Immunohistochemistry:

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a technique used to detect protein expression in tissue, to visualize spatial expression of which cells express a specific protein. Uses a thin section (slice) of tissue (tissue sections are usually made with a cryostat). Measures protein expression in a sample through the use of antibodies to a specific protein of interest.

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Morpholino :

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an oligonucleotide often used in observations of antisense gene expression similar to dsRNA and siren -- used to downregulate or knockdown expression of a gene

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BrdU:

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5-bromo-2-deoxyuridine (BrdU)- a nucleoside analogue BrdU is a uridine derivative and a structural analog of thymidine, and it can be incorporated into DNA during the synthesis phase of the cell cycle as a substitute for thymidine, thereby serving as a marker for proliferation.

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In situ hybridization:

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a technique used to detect RNA expression in tissue, to visualize spatial expression of which cells express a specific RNA. Uses a thin section (slice) of tissue (tissue sections are usually made with a cryostat). Measures protein expression in a sample through the use of labeled oligonucleotides to a specific RNA of interest.

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digoxigenin:

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a fluorescent label often attached to oligonucleotides, for use in in situ hybridizations.

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Target prediction algorithms:

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assist in the prediction of miRNA genes and their subsequent targets.

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Haplogroup:

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in molecular evolution, haplogroups, are a group of similar haplotypes sharing a common ancestor having the same single nucleotide polymorphism in all haplotypes.

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Admixture:

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when individuals from two or more previously separated populations begin interbreeding, which results in the introduction of new genetic lineages into a population.

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Bottleneck:

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sharp reduction in population size due to environmental events or human activities. This can reduce variation in the gene pool of a population.

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Principal components analysis (PCA):

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a statistical procedure to convert a set of observations of possibly correlated variables into a set of values of linearly uncorrelated variables called principal components. It is used to to explain the structure of variance in a data set. This helps in identifying which variables (or “components”) of individuals in a sample set have the most influence or effect on the outcome or observed events (or phenotypes).

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Outgroup:

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a group of organisms or a single species not part of the group under consideration. It is used for comparison when analyzing phylogenetic relationships.

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Genetic Drift:

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The change in frequency of a gene variant in a population due to a random sampling of organisms.

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Coverage:

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is the average number of “reads” representing a given nucleotide in the reconstructed sequence. A high coverage in shotgun sequencing is desired because it can overcome errors in base calling and assembly.

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AMS radiocarbon dated:

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Accelerator Mass Spectrometry Radiocarbon Dating - A technique to measure radiocarbon in samples.