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Revision as of 22:13, 12 September 2015

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Glossary

This glossary is meant to help you with the understanding of our whole website and therefore of our project. We provide you with a short overview of the most important terms, techniques, devices and abbreviations you might encounter while combing through our information pages and labjournals.

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