Difference between revisions of "Team:Freiburg/Glossary"
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Revision as of 18:14, 12 September 2015
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Glossary4>
term | definition |
---|---|
5’UTR | an untranslated region at the 5’ end of the RNA sequence that enhances translation |
affibody | antibody mimetic, small protein engineered to bind to a large number of target proteins or peptides with high affinity, imitating monoclonal antibodies |
AIDS | Acquired Immune Deficiency Syndrome, foll-blown diseases after infection with HIV |
APTES | 3-aminopropyltriethoxysilane, a silane we used to link PDITC to the hydroxyl groups on the plasma activated glass slide of our protein array |
CFP | cyan fluorescent protein |
classical cloning | insertion of a DNA fragment for example into a plasmid backbone via restriction enzymes; each fragment has to be inserted separately. For differences to Gibson cloning see here |
Cy3 | Cyanine 3, fluorescent dye used particularly in biomedical imaging |
DE3 | nomenclature of E.coli strains, meaning it contains a T7 RNA-polymerase for general protein expression |
DMSO | Dimethylsulfoxid, added to PCR reactions |
dNTP | deoxynucleotidetriphosphate, component of DNA and therefore added to PCR reaction mixes |
Dot Blot | simplification of Northern, Southern or Western Blot in order to save time; proteins are not separated electrophoretically but simply spotted on a membrane and then detected via nucleotide probes (Northern and Southern Blot) or antibodies (Western Blot) |
ELISA | enzyme-linked immunosorbent assay, antigens are immobilized in a 96-well plate, antibody-antigen-interaction is detected; find more information here |
fluorophore | fluorescent chemical compound that can emit light upon light excitation; typically contains several combined aromatic groups or plane or cyclic molecules with several π bonds |
GFP | green fluorescent protein |
Gibson Assembly | combination of DNA fragments in an isothermal reaction without the need of restriction enzymes; more information and a comparison to classical cloning can be found here |
glycoprotein | surface protein with oligosaccharide chains covalently bound to the polypeptide; also present on virus surfaces and often provoking an immunogenic response in humans |
HA-tag | tag derived from the human influenza hemagglutinin and extensively used as a general epitope tag in expression vectors. |
Her2 protein | biomarker for breast cancer |
His6 | tag consisting of six histidine residues binding to Ni-NTA and often used for protein purification |
HIV | Human Immunodeficiency Virus, causes AIDS |
HSV-1 | Herpes Simplex Virus type 1, also known as Human Herpes Virus type 3 |
IPTG | Isopropylthiogalactopyranosid, allolactose analogue used to induce the lacI system in cells; often used to induce protein overexpression in bacteria |
iRIf | imaging Reflectometric Interference, label-free detection method for protein-protein interactions; mode of operation and further information can be found LINK ZU IRIF!!! |
LB | lysogeny broth, a nutritionally rich medium, which is primarily used for growing bacteria |
MgOAc | magnesium acetate, used for ?????? |
microfluidic chamber | small compartment in a microfluidic device through which liquids in μL range can be rinsed |
microfluidics | |
Ni-NTA | Nickel-Nitrolotriacetic acid, chelate used for protein purification via a His-tag |
o/n | overnight, used in the labbook as abbreviation |
OD | optical density, used to determine approximate cell density in a solution |
PCR | polymerase chain reaction, used to amplify DNA fragments using specific primers |
PDITC | p-Phenyldiisothiocyanate, used to link amino groups, in our project used to produce a surface to which proteins can bind, e.g. on a glass slide |
PDMS | Polydimethylsiloxane, in our project used to immobilize DNA fragments as template for cell-free expression |
pelB | signal sequence for periplasmic translocation of a protein |
pET22b(+) | commonly used plasmid for protein overexpression in bacteria |
pJet | blunt-end cloning vector |
plasmid | small, circular DNA molecule |
PMSF | Phenylmethylsulfonylfluorid, small organic molecule that specifically inhibits serine proteases to prevent protein degradation in a disrupted cell |
pOP | plasmid for Overexpression of Proteins, new plasmid backbone we submitted to the iGEM Registry, find out all the details here |
quotient picture | picture taken before a particular step subtracted from one taken after the step, important for the evaluation of the iRIf measurements |
RT | room temperature, abbreviation used in the labbook |
RV | Rubella Virus, causes German measles |
SDS-PAGE | sodium dodecyl sulfate polyacrylamide gel electrophoresis, used to separate and analyze proteins according to their molecular mass within an electric field |
Spy-catcher | protein that forms a covalent bond with the Spy-tag, system we tested to establish a specific surface for the protein microarray |
Spy-tag | tag that can be genetically fused to proteins for subsequent covalent bonding with the Spy-catcher |
TAE | TRIS-acetic acid-EDTA mix used in buffers for gel electrophoresis |
turboYFP | enhanced version of the yellow fluorescent protein |
VZV | Varicella Zoster Virus, also known as Human Herpes Virus type 6, causes chickenpox |
Western Blot | analytical technique used to detect specific proteins by using specific antibodies after separation of proteins by gel electrophoresis |