Team:Freiburg/Glossary
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 navigating through our information pages and labjournals.
| Derm | 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, full-blown disease 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 |
| cell-free expression | expression performed outside a cell by using cell-lysate and additional components |
| CFP | cyan fluorescent protein |
| chlamydia | sexually transmittable disease, transmitted by the bacterium Chlamydia trachomatis |
| 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 |
| CrPV IRES | Cricket Paralysis Virus internal ribosome entry site, forming a specific secondary structure allowing the entry of ribosomes in eukaryotes |
| 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 |
| DiaMIX | the cell-free expression mix we produced ourselves, also providing the protocol |
| 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 |
| fluorophore | chemical compound that can emit light when excited with light of a certain wavelength |
| 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 |
| gonorrhea | sexually transmittable disease, also known as tripper, transmitted via the bacterium Neisseria gonorrhoeae |
| HA-tag | tag derived from the human influenza hemagglutinin and extensively used as a general epitope tag in expression vectors |
| HEPES-KOH | 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid potassium hydroxide, component in a buffer widely used in cell culture |
| Her2 protein | biomarker for breast cancer |
| His-tag | tag consisting of several histidine residues binding to Ni-NTA and often used for protein purification and specific binding to surfaces |
| 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 |
| IRES | internal ribosome entry site, forming a specific secondary structure allowing the entry of ribosomes in prokaryotes |
| iRIf | imaging Reflectometric Interference, label-free detection method for protein-protein interactions; mode of operation and further information can be found here |
| LB | Lyria-Bertani-medium, a nutritionally rich medium, primarily used for growing bacteria |
| LOC | Lab-on-a-Chip system, microarray based device for immunodiagnosis |
| Mg(OAc)2 | magnesium acetate, used to supplement our cell-free expression mix |
| microfluidic chamber | small compartment in a microfluidic device through which liquids in μL range can be rinsed |
| microfluidics | system through which very small volumes of liquids can be channeled and processed |
| Ni-NTA | nickel-nitrolotriacetic acid, chelate used for protein purification via a His-tag or as a surface for immobilization of His-tagged proteins |
| o/n | overnight, used in the labjournals 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 |
| PDE | partial differential equation |
| 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 part of the DiaCHIP forming the basis to immobilize DNA fragments as a 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 |
| POC | Point-of-Care diagnostics, diagnostic devices that can be used at home or even on the bedside of a patient |
| pOP | plasmid for Overexpression of Proteins, new plasmid backbone we submitted to the iGEM Registry, find out all the details here |
| Quotient picture | received by dividing the pixel intensity of each pixel in a picture taken before a particular step by the corresponding pixel intensity in a picture taken after the step, important for the evaluation of the iRIf measurements |
| RT | room temperature, abbreviation used in the labjournal |
| 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 |
| shine dalgarno sequence | sequence in bacterial mRNA that is recognized as a part of the ribosomal binding site |
| Spy-catcher | protein that forms a covalent bond with the Spy-tag, a system we tried 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 |
| trichomoniasis | sexually transmittable disease, transmitted via the flagellate Trichomonas vaginalis |
| 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 |
