Glossary

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Aptamer: Short synthetic single stranded DNA or RNA sequences that have an affinity to molecules such as proteins, chemical compounds, cells, and microorganisms.
BSL-2 (Biosafety Level 2): Under this biosafety level any agent that poses a moderate hazard to the environment or moderate human disease requires work in a contained lab space.
Capsid: Protein exterior that protects viral DNA as it is transported from one cell to another during an infection.
Cascade complex (TniQ-Cascade): Cascade is a protein complex composed of Cas6, Cas7, and Cas8. In the INTEGRATE system, Cascade also associates with transposase protein TniQ to form the TniQ-Cascade complex. This TniQ-Cascade complex is guided to a target locus by a 32 nt. crRNA (Vo et al.)
ccdA antitoxin: gene for the ccdA protein that binds to the ccdB toxin and prevents toxicity
ccdB toxin: toxin protein that kills cells lacking the ccdA antitoxin. In cloning, plasmids containing ccdB can be selected against in strains lacking the antitoxin, and successfully cloned plasmids can be selected fo
Clonetegration: A two-plasmid system designed to integrate a gene into a specific site in the genome. Created by St-Pierre et al., 2013.
Conjugation: Method of horizontal gene transfer between two bacteria. Plasmids are transferred from donor cells (F+, F', or HFR cells) to recipient cells (F-).
Colorimetric μPAD: A microfluidic paper-based analytical device used for the development of rapid point-of-care tests.
crRNA: CRISPR RNA that is complementary to a target and guides the CRISPR complex to target sequnce.
Destination Vector: Cloning vector that is equipped with the BfuA1 sites needed for Golden Gate cloning.
F+ Cells: Cells that contain the conjugative Fertility plasmid, produce pili, and are conjugative donors.
F' Cells: Cells that had the F plasmid integrated into their genome due to HFR, but the F plasmid and some extra bits of genomic DNA were exised and recircularized into an episome. They still produce pili and are conjugative donors.
F- Cells: Cells that do not contain the conjugative Fertility plasmid nor produce pili, and so are conjugative repcipients.
Flippase: Protein that flips out DNA between two FRT sites. Used in Clontegration to remove the integration module from the E. coli chromosome.
Fluorescently-labeled RNA reporters: RNA strands with a fluorophore and a quencher attatched to either end. When the RNA sequence is cleaved, the quencher molecule floats away from the fluorophore, allowing it to observable flouresce.
Gb3 Receptor: Glycolipid globotriaosylceramide (Gb3) is a membrane protein that is highly expressed in the intestinal lining of mammalian cells. It acts as the receptor for the B subunit of the Shiga toxin.
Gene Block: A synthetically-made fragment of a gene.
HFR Cells: Cells that have the F plasmid integrated into their genome due to high frequency of recombination (HFR).
Helper Phage: C a bacteriophage or plasmid designed to carry all the necessary genes for particle formation when using phagemid vectors
Hemolytic Uremic Syndrome: A condition that affects the blood and blood vessels. It results in the destruction of blood platelets (cells involved in clotting), a low red blood cell count (anemia) and kidney failure due to damage to the very small blood vessels of the kidneys.
Hepatitis Delta Virus Ribozyme (HDVR): Self cleaving RNA molecule that generates a 2', 3'-cyclic phosphate on the 3' end of the sequence that is cut off form the ribozyme.
Hammerhead Ribozyme (HHR): Self cleaving RNA molecule that generates a 5' hydroxyl on the 5' end of the sequence that is cut off from the main ribozyme structure.
His Tag: sequences of histidine residues attached to recombinant proteins that can bind to several times of immobilized ions, allowing for protein purification.
INTEGRATE: In this system, a CRISPR RNA guides the TniQ-Cascade complex to a specific sequence of DNA, and transposase proteins TnsA, B, and C catalyze donor DNA integration ~50 bp downstream of the target. The donor DNA is defined by L and R transposon flanks, which are used by the transposases in this cut-and-paste system. Single plasmid CRISPR-guided DNA integration system developed by [1] Vo et al., “CRISPR RNA-guided integrases for high-efficiency, multiplexed bacterial genome engineering,” Nat Biotechnol, vol. 39, no. 4, pp. 480–489, Apr. 2021, doi: 10.1038/s41587-020-00745-y.
Lambda Integrase: An enzyme that transfers the lambda phage's viral DNA from the cytoplasm into the host cell's chromosome.
Lambda Repressor: Protein produced by lambda phage that keeps the integrated viral genome into the lysogenic phase so it does not kill the cell or spread to other cells.
mCherry: A member of the mFruits family of monomeric red fluorescent proteins, used in our proof of concept.
Non-homologous end joining (NHEJ): A repair pathway that repairs double stranded DNA breaks by ligating the broken fragments together directly. This pathway does not require a homologous repair template.
Non-specific RNase Activity: Cleavage of any RNA strand no matter what the sequence is.
Oligonucleotide: A polynucleotide whose molecules contain a relatively small number of nucleotides.
Origin of Replication: A sequence of DNA on a plasmid where replication starts.
Origin of transfer (oriT): A short nucleotide sequence (~500 bp) that is needed for the start of DNA transfer during bacterial conjugation.
Payload: A term used to describe the DNA sequence that is carried by the INTEGRATE machinery and inserted into the bacterial chromosome at the target site for the purpose of disrupting the target gene
Phage: Another name for a bacteriophage, or a virus that infects only bacteria.
Phage Origin of Replication (ori): DNA sequence recognized by phage packing machinery in order to pack a copy of a plasmid into the phage capsid.
Phagemid: An engineered plasmid that contains a phage ori of replication that allows it to be packaged into a bacteriophage capside in place of the viral genome.
Pili: Ahairlike structure on the surface of prokaryotic cells. There are numerous forms of pili that have diverse functions in cellular adhesion and mobility, mediating various cell-to-cell interactions, and DNA uptake. Type IV pili specifically connect two cells, draw them together, and facilitate DNA transfer.
Pseudovirion: Particles derived bacteriophages that are constructed in vitro by providing a lab strain of bacteria with two plasmids: a helper phage and the phagemid.
qPCR: Qualitative PCR amplifies a gene of interest using primers, just like regular PCR, but it also measures the amount of DNA amplified.
Recombinase: Enzyme that catalyzes directionally sensitive DNA exchange between short nucleotide target sites. These nucelotide target sites are specific for each recombinase.
Relaxosome: Protein complex encoded by tra genes. Responsible for nicking one strand of a double stranded conjugatable or mobilizable plasmid at their oriT, and unwinding the strand for transfer to the recipient cell.
Resistance Gene: Gene that encodes for resistance to an antibiotic, such as Kanamycin. Resistance genes are used as a selectable marker to verify that a desired plasmid is in a cell.
Ribosomal binding site (RBS): Sequence of nucleic acids at the 5’ end of a messenger RNA sequence that is recognized by ribosomes in order to begin transcription.
SEIR Compartment Model: A model frequently used in epidemiology which shows the transmission dynamics of an infectious agent througha population. Each compartment represents a group of individuals in a certain state along the infection cycle: Susceptible, exposed, infected, and recovered.
Shiga toxin-producing E. coli (STEC): Strains of the bacterium Escherichia coli that produce either Shiga toxin or Shiga-like toxin.
Spacer: Short region of DNA that is homologous to some other DNA, often of an infectious phage or plasmid. Spacers found between repeated sequences serve as the guide for bacterial CRISPR immune systems.
Stx2: Shiga toxin 2 (Stx2) is found on the bacterial chromosome of pathogenentic E. coli strains. This gene was thought to have originated from a lysogenic bacteriophage and encodes a protein that has been associated with hemorrhagic colitis, hemolytic uremic syndrome and other severe disease conditions.
SELEX: Systematic Evolution of Ligands by Exponential Enrichment is a well established method for generating aptamers in vitro.
Transfer (tra) genes: Genes that code for proteins involved in DNA transfer during conjugation.
Transconjugant: A cell that has recieved a plasmid of interest through conjugation.
Transposase: An enzyme that binds to the ends of a transposon, and catalyzes its movement to another location in a genome.
2’, 3’-cyclic phosphate (A>p) end: RNA molecules terminated with this structure have their 3’ phosphate bound to the 2’ carbon on the ribose, rather than just bound to the 3’ end.

Team:UCSC/Glossary

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