Difference between revisions of "Team:Freiburg/Glossary"
| Line 41: | Line 41: | ||
<div class="table sectionedit2"><table class="inline"> | <div class="table sectionedit2"><table class="inline"> | ||
<tr class="row0"> | <tr class="row0"> | ||
| − | <th class="col1 leftalign"> | + | <th class="col1 leftalign"> Derm </th><th class="col1 leftalign"> Definition </th> </tr> |
<tr class="row1"> | <tr class="row1"> | ||
<td class="col1"> 5’UTR </td><td class="col0"> an untranslated region at the 5’ end of the RNA sequence that enhances translation </td></tr> | <td class="col1"> 5’UTR </td><td class="col0"> an untranslated region at the 5’ end of the RNA sequence that enhances translation </td></tr> | ||
| Line 47: | Line 47: | ||
<td class="col1"> affibody </td><td class="col0"> antibody mimetic, small protein engineered to bind to a large number of target proteins or peptides with high affinity, imitating monoclonal antibodies </td></tr> | <td class="col1"> affibody </td><td class="col0"> antibody mimetic, small protein engineered to bind to a large number of target proteins or peptides with high affinity, imitating monoclonal antibodies </td></tr> | ||
<tr class="row3"> | <tr class="row3"> | ||
| − | <td class="col1"> AIDS </td><td class="col0"> Acquired Immune Deficiency Syndrome, full-blown | + | <td class="col1"> AIDS </td><td class="col0"> Acquired Immune Deficiency Syndrome, full-blown disease after infection with HIV </td></tr> |
<tr class="row4"> | <tr class="row4"> | ||
<td class="col1"> APTES </td><td class="col0"> 3-aminopropyltriethoxysilane, a silane we used to link PDITC to the hydroxyl groups on the plasma activated glass slide of our protein array </td></tr> | <td class="col1"> APTES </td><td class="col0"> 3-aminopropyltriethoxysilane, a silane we used to link PDITC to the hydroxyl groups on the plasma activated glass slide of our protein array </td></tr> | ||
| Line 57: | Line 57: | ||
<td class="col1"> chlamydia </td><td class="col0"> sexually transmittable disease, transmitted by the bacterium <i>Chlamydia trachomatis</i> </td></tr> | <td class="col1"> chlamydia </td><td class="col0"> sexually transmittable disease, transmitted by the bacterium <i>Chlamydia trachomatis</i> </td></tr> | ||
<tr class="col8"> | <tr class="col8"> | ||
| − | <td class="col1"> classical cloning </td><td class="col0"> insertion of a DNA fragment for example into a plasmid backbone via restriction enzymes; each fragment has to be inserted separately | + | <td class="col1"> classical cloning </td><td class="col0"> 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 <a href="https://2015.igem.org/Team:Freiburg/Project/Classic_vs_Gibson"> here </a> </td></tr> |
<tr class="row9"> | <tr class="row9"> | ||
| − | <td class="col1"> CrPV IRES </td><td class="col0"> Cricket Paralysis Virus internal ribosome entry site, forming a specific secondary structure allowing the entry of ribosomes in | + | <td class="col1"> CrPV IRES </td><td class="col0"> Cricket Paralysis Virus internal ribosome entry site, forming a specific secondary structure allowing the entry of ribosomes in eukaryotes </td></tr> |
<tr class="row10"> | <tr class="row10"> | ||
<td class="col1"> Cy3 </td><td class="col0"> Cyanine 3, fluorescent dye used particularly in biomedical imaging </td></tr> | <td class="col1"> Cy3 </td><td class="col0"> Cyanine 3, fluorescent dye used particularly in biomedical imaging </td></tr> | ||
| Line 67: | Line 67: | ||
<td class="col1"> DiaMIX </td><td class="col0"> the cell-free expression mix we produced ourselves, also providing the <a href="https://2015.igem.org/Team:Freiburg/Protocol#cell-free_protocol">protocol</a> </td></tr> | <td class="col1"> DiaMIX </td><td class="col0"> the cell-free expression mix we produced ourselves, also providing the <a href="https://2015.igem.org/Team:Freiburg/Protocol#cell-free_protocol">protocol</a> </td></tr> | ||
<tr class="row13"> | <tr class="row13"> | ||
| − | <td class="col1"> DMSO </td><td class="col0"> | + | <td class="col1"> DMSO </td><td class="col0"> dimethylsulfoxid, added to PCR reactions </td></tr> |
<tr class="row14"> | <tr class="row14"> | ||
<td class="col1"> dNTP </td><td class="col0"> deoxynucleotidetriphosphate, component of DNA and therefore added to PCR reaction mixes </td></tr> | <td class="col1"> dNTP </td><td class="col0"> deoxynucleotidetriphosphate, component of DNA and therefore added to PCR reaction mixes </td></tr> | ||
| Line 75: | Line 75: | ||
<td class="col1"> ELISA </td><td class="col0"> enzyme-linked immunosorbent assay, antigens are immobilized in a 96-well plate, antibody-antigen-interaction is detected; find more information <a href="https://2015.igem.org/Team:Freiburg/Project/Diagnostics"> here </a> </td></tr> | <td class="col1"> ELISA </td><td class="col0"> enzyme-linked immunosorbent assay, antigens are immobilized in a 96-well plate, antibody-antigen-interaction is detected; find more information <a href="https://2015.igem.org/Team:Freiburg/Project/Diagnostics"> here </a> </td></tr> | ||
<tr class="row17"> | <tr class="row17"> | ||
| − | <td class="col1"> fluorophore </td><td class="col0">chemical compound that can emit light when | + | <td class="col1"> fluorophore </td><td class="col0">chemical compound that can emit light when excited with light of a certain wavelength </td></tr> |
<tr class="row18"> | <tr class="row18"> | ||
<td class="col1"> GFP </td><td class="col0"> green fluorescent protein </td></tr> | <td class="col1"> GFP </td><td class="col0"> green fluorescent protein </td></tr> | ||
| Line 85: | Line 85: | ||
<td class="col1"> gonorrhea </td><td class="col0"> sexually transmittable disease, also known as tripper, transmitted via the bacterium <i>Neisseria gonorrhoeae</i> </td></tr> | <td class="col1"> gonorrhea </td><td class="col0"> sexually transmittable disease, also known as tripper, transmitted via the bacterium <i>Neisseria gonorrhoeae</i> </td></tr> | ||
<tr class="row22"> | <tr class="row22"> | ||
| − | <td class="col1"> HA-tag </td><td class="col0"> tag derived from the human influenza hemagglutinin and extensively used as a general epitope tag in expression vectors | + | <td class="col1"> HA-tag </td><td class="col0"> tag derived from the human influenza hemagglutinin and extensively used as a general epitope tag in expression vectors </td></tr> |
<tr class="row23"> | <tr class="row23"> | ||
<td class="col1"> HEPES-KOH </td><td class="col0"> 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid potassium hydroxide, component in a buffer widely used in cell culture </td></tr> | <td class="col1"> HEPES-KOH </td><td class="col0"> 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid potassium hydroxide, component in a buffer widely used in cell culture </td></tr> | ||
| Line 97: | Line 97: | ||
<td class="col1"> HSV-1 </td><td class="col0"> Herpes Simplex Virus type 1, also known as Human Herpes Virus type 3 </td></tr> | <td class="col1"> HSV-1 </td><td class="col0"> Herpes Simplex Virus type 1, also known as Human Herpes Virus type 3 </td></tr> | ||
<tr class="row28"> | <tr class="row28"> | ||
| − | <td class="col1"> IPTG </td><td class="col0"> | + | <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> |
<tr class="row29"> | <tr class="row29"> | ||
| − | <td class="col1"> IRES </td><td class="col0"> internal ribosome entry site, forming a specific secondary structure allowing the entry of ribosomes in | + | <td class="col1"> IRES </td><td class="col0"> internal ribosome entry site, forming a specific secondary structure allowing the entry of ribosomes in prokaryotes </td></tr> |
<tr class="row30"> | <tr class="row30"> | ||
<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 <a href="https://2015.igem.org/Team:Freiburg/Project/iRIf">here</a> </td></tr> | <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 <a href="https://2015.igem.org/Team:Freiburg/Project/iRIf">here</a> </td></tr> | ||
| Line 113: | Line 113: | ||
<td class="col1"> microfluidics </td><td class="col0"> system through which very small volumes of liquids can be channeled and processed</td></tr> | <td class="col1"> microfluidics </td><td class="col0"> system through which very small volumes of liquids can be channeled and processed</td></tr> | ||
<tr class="row36"> | <tr class="row36"> | ||
| − | <td class="col1"> Ni-NTA </td><td class="col0"> nickel-nitrolotriacetic acid, chelate used for protein purification via a His-tag or as surface for immobilization of His-tagged proteins </td></tr> | + | <td class="col1"> Ni-NTA </td><td class="col0"> nickel-nitrolotriacetic acid, chelate used for protein purification via a His-tag or as a surface for immobilization of His-tagged proteins </td></tr> |
<tr class="row37"> | <tr class="row37"> | ||
<td class="col1"> o/n </td><td class="col0"> overnight, used in the labjournals as abbreviation </td></tr> | <td class="col1"> o/n </td><td class="col0"> overnight, used in the labjournals as abbreviation </td></tr> | ||
| Line 121: | Line 121: | ||
<td class="col1"> PCR </td><td class="col0"> polymerase chain reaction, used to amplify DNA fragments using specific primers </td></tr> | <td class="col1"> PCR </td><td class="col0"> polymerase chain reaction, used to amplify DNA fragments using specific primers </td></tr> | ||
<tr class="row40"> | <tr class="row40"> | ||
| − | <td class="col1"> | + | <td class="col1"> PDE </td><td class="col0"> partial differential equation </td></tr> |
<tr class="row41"> | <tr class="row41"> | ||
| − | <td class="col1"> | + | <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> |
<tr class="row42"> | <tr class="row42"> | ||
| + | <td class="col1"> PDMS </td><td class="col0"> polydimethylsiloxane, in our project part of the DiaCHIP forming the basis to immobilize DNA fragments as a template for cell-free expression </td></tr> | ||
| + | <tr class="row43"> | ||
<td class="col1"> pelB </td><td class="col0"> signal sequence for periplasmic translocation of a protein </td></tr> | <td class="col1"> pelB </td><td class="col0"> signal sequence for periplasmic translocation of a protein </td></tr> | ||
| − | |||
| − | |||
<tr class="row44"> | <tr class="row44"> | ||
| − | <td class="col1"> | + | <td class="col1"> pET22b+ </td><td class="col0"> commonly used plasmid for protein overexpression in bacteria </td></tr> |
<tr class="row45"> | <tr class="row45"> | ||
| − | <td class="col1"> | + | <td class="col1"> pJet </td><td class="col0"> blunt-end cloning vector </td> </tr> |
<tr class="row46"> | <tr class="row46"> | ||
| − | <td class="col1"> | + | <td class="col1"> plasmid </td><td class="col0"> small, circular DNA molecule </td></tr> |
<tr class="row47"> | <tr class="row47"> | ||
| + | <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> | ||
| + | <tr class="row48"> | ||
<td class="col1"> POC </td><td class="col0"> Point-of-Care diagnostics, diagnostic devices that can be used at home or even on the bedside of a patient </td></tr> | <td class="col1"> POC </td><td class="col0"> Point-of-Care diagnostics, diagnostic devices that can be used at home or even on the bedside of a patient </td></tr> | ||
| − | + | <tr class="row49"> | |
<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> | <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> | ||
| − | |||
| − | |||
<tr class="row50"> | <tr class="row50"> | ||
| − | <td class="col1"> | + | <td class="col1"> Quotient picture </td><td class="col0"> 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 </td></tr> |
<tr class="row51"> | <tr class="row51"> | ||
| − | <td class="col1"> | + | <td class="col1"> RT </td><td class="col0"> room temperature, abbreviation used in the labjournal </td></tr> |
<tr class="row52"> | <tr class="row52"> | ||
| − | <td class="col1"> | + | <td class="col1"> RV </td><td class="col0"> Rubella Virus, causes German measles </td></tr> |
<tr class="row53"> | <tr class="row53"> | ||
| + | <td class="col1"> SDS-PAGE </td><td class="col0"> sodium dodecyl sulfate polyacrylamide gel electrophoresis, used to separate and analyze proteins according to their molecular mass within an electric field </td></tr> | ||
| + | <tr class="row54"> | ||
<td class="col1"> shine dalgarno sequence </td><td class="col0"> sequence in bacterial mRNA that is recognized as a part of the ribosomal binding site </td></tr> | <td class="col1"> shine dalgarno sequence </td><td class="col0"> sequence in bacterial mRNA that is recognized as a part of the ribosomal binding site </td></tr> | ||
| − | + | <tr class="row55"> | |
| − | <td class="col1"> | + | <td class="col1"> Spy-catcher </td><td class="col0"> protein that forms a covalent bond with the Spy-tag, a system we tried to establish a specific surface for the protein microarray </td></tr> |
| − | + | ||
| − | + | ||
<tr class="row56"> | <tr class="row56"> | ||
| − | <td class="col1"> | + | <td class="col1"> Spy-tag </td><td class="col0"> tag that can be genetically fused to proteins for subsequent covalent bonding with the Spy-catcher </td></tr> |
<tr class="row57"> | <tr class="row57"> | ||
| + | <td class="col1"> TAE </td><td class="col0"> TRIS-acetic acid-EDTA mix used in buffers for gel electrophoresis </td></tr> | ||
| + | <tr class="row58"> | ||
<td class="col1"> trichomoniasis </td><td class="col0"> sexually transmittable disease, transmitted via the flagellate <i>Trichomonas vaginalis</i> </td></tr> | <td class="col1"> trichomoniasis </td><td class="col0"> sexually transmittable disease, transmitted via the flagellate <i>Trichomonas vaginalis</i> </td></tr> | ||
| − | + | <tr class="row59"> | |
<td class="col1"> turboYFP </td><td class="col0"> enhanced version of the yellow fluorescent protein </td></tr> | <td class="col1"> turboYFP </td><td class="col0"> enhanced version of the yellow fluorescent protein </td></tr> | ||
| − | |||
| − | |||
<tr class="row60"> | <tr class="row60"> | ||
| + | <td class="col1"> VZV </td><td class="col0"> Varicella Zoster Virus, also known as Human Herpes Virus type 6, causes chickenpox </td></tr> | ||
| + | <tr class="row61"> | ||
<td class="col1"> Western Blot </td><td class="col0"> analytical technique used to detect specific proteins by using specific antibodies after separation of proteins by gel electrophoresis </td></tr> | <td class="col1"> Western Blot </td><td class="col0"> analytical technique used to detect specific proteins by using specific antibodies after separation of proteins by gel electrophoresis </td></tr> | ||
Revision as of 00:18, 19 September 2015
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.
| 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; find more information here |
| 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 |
