Difference between revisions of "Team:Freiburg/Glossary"

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             <td class="col1"> IPTG </td><td class="col0"> Isopropylthiogalactopyranosid, allolactose analogue used to induce the lacI system in cells; often used to induce protein overexpression in bacteria </td></tr>
 
             <td class="col1"> IPTG </td><td class="col0"> Isopropylthiogalactopyranosid, allolactose analogue used to induce the lacI system in cells; often used to induce protein overexpression in bacteria </td></tr>
 
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             <td class="col1"> iRIf </td><td class="col0"> imaging Reflectometric Interference, label-free detection method for protein-protein interactions; mode of operation and further information can be found LINK ZU IRIF!!! </td></tr>
 
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             <td class="col1"> LB </td><td class="col0"> lysogeny broth, a nutritionally rich medium, which is primarily used for growing bacteria </td></tr>
 
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             <td class="col1"> MgOAc </td><td class="col0"> magnesium acetate, used for ?????? </td></tr>
 
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             <td class="col1"> </td><td class="col0"> </td></tr>
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             <td class="col1"> microfluidic chamber </td><td class="col0"> small compartment in a microfluidic device through which liquids in μL range can be rinsed </td></tr>
 
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             <td class="col1"> </td><td class="col0">  </td></tr>
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             <td class="col1"> microfluidics </td><td class="col0">  </td></tr>
 
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             <td class="col1"> Ni-NTA </td><td class="col0"> Nickel-Nitrolotriacetic acid, chelate used for protein purification via a His-tag </td></tr>
 
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            <td class="col1"> o/n </td><td class="col0"> overnight, used in the labbook as abbreviation </td></tr>
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            <td class="col1"> OD </td><td class="col0"> optical density, used to determine approximate cell density in a solution </td></tr>
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            <td class="col1"> PCR </td><td class="col0"> polymerase chain reaction, used to amplify DNA fragments using specific primers </td></tr>
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            <td class="col1"> PDITC </td><td class="col0"> 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 </td></tr>
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            <td class="col1"> PDMS </td><td class="col0"> Polydimethylsiloxane, in our project used to immobilize DNA fragments as template for cell-free expression </td></tr>
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            <td class="col1"> pelB </td><td class="col0"> signal sequence for periplasmic translocation of a protein </td></tr>
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            <td class="col1"> pET22b(+) </td><td class="col0"> commonly used plasmid for protein overexpression in bacteria </td></tr>
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            <td class="col1"> pJet </td><td class="col0"> pET22b(+) </td></tr>
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            <td class="col1"> plasmid </td><td class="col0"> small, circular DNA molecule </td></tr>
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            <td class="col1"> PMSF </td><td class="col0"> Phenylmethylsulfonylfluorid, small organic molecule that specifically inhibits serine proteases to prevent protein degradation in a disrupted cell </td></tr>
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            <td class="col1"> pOP </td><td class="col0"> plasmid for Overexpression of Proteins, new plasmid backbone we submitted to the iGEM Registry, find out all the details <a href="https://2015.igem.org/Team:Freiburg/Project/pOP-vector"> here </a> </td></tr>
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Revision as of 16:22, 12 September 2015

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Glossary

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 pET22b(+)
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