Difference between revisions of "Team:Freiburg/Glossary"

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<div>
−
     <h4>Glossary</4>
+
     <h1>Glossary</h1>
 +
</div>
 +
<div>   
 +
    <p>
 +
    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.
 +
    </p>
 +
</div>
 
         <div class="table sectionedit2"><table class="inline">  
 
         <div class="table sectionedit2"><table class="inline">  
 
             <tr class="row0">
 
             <tr class="row0">
−
             <th class="col1 leftalign"> term </th><th class="col1 leftalign"> definition </th> </tr>
+
             <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 164: 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, foll-blown diseases after infection with HIV </td></tr>
+
             <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>
−
          <tr class="row5">
+
          <tr class="row5">
 +
            <td class="col1"> cell-free expression </td><td class="col0"> expression performed outside a cell by using cell-lysate and additional components </td></tr>
 +
<tr class="row6">
 
             <td class="col1"> CFP </td><td class="col0"> cyan fluorescent protein </td></tr>
 
             <td class="col1"> CFP </td><td class="col0"> cyan fluorescent protein </td></tr>
−
          <tr class="row6">
+
          <tr class="row7">
−
             <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>
+
            <td class="col1"> chlamydia </td><td class="col0"> sexually transmittable disease, transmitted by the bacterium <i>Chlamydia trachomatis</i> </td></tr>
−
          <tr class="row7">
+
<tr class="col8">
−
             <td class="col1"> </td><td class="col0"> </td></tr>
+
             <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="row8">
+
          <tr class="row9">
−
             <td class="col1"> </td><td class="col0"> </td></tr>
+
          <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="row9">
+
          <tr class="row10">
−
             <td class="col1"> </td><td class="col0"> </td></tr>
+
             <td class="col1"> Cy3 </td><td class="col0"> Cyanine 3, fluorescent dye used particularly in biomedical imaging </td></tr>
−
          <tr class="row10">
+
<tr class="row11">
−
             <td class="col1"> </td><td class="col0"> </td></tr>
+
             <td class="col1"> DE3 </td><td class="col0"> nomenclature of <a href="https://2015.igem.org/Team:Freiburg/Project/Coli_Strains"target="_blank"><i>E.coli</i> strains</a>, meaning it contains a T7 RNA-polymerase for general protein expression </td></tr>
−
 
+
          <tr class="row12">
 +
          <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/Protocols/Cellfex">protocol</a> </td></tr>
 +
<tr class="row13">
 +
             <td class="col1"> DMSO </td><td class="col0"> dimethylsulfoxid, added to PCR reactions </td></tr>
 +
          <tr class="row14">
 +
             <td class="col1"> dNTP </td><td class="col0"> deoxynucleotidetriphosphate, component of DNA and therefore added to PCR reaction mixes </td></tr>
 +
          <tr class="row15">
 +
            <td class="col1"> Dot Blot </td><td class="col0"> 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) </td></tr>
 +
          <tr class="row16">
 +
            <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 </a> </td></tr>
 +
          <tr class="row17">
 +
            <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">
 +
            <td class="col1"> GFP </td><td class="col0"> green fluorescent protein </td></tr>
 +
          <tr class="row19">
 +
            <td class="col1"> Gibson Assembly </td><td class="col0"> 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 <a href="https://2015.igem.org/Team:Freiburg/Project/Classic_vs_Gibson"> here </a> </td></tr>
 +
          <tr class="row20">
 +
            <td class="col1"> glycoprotein </td><td class="col0"> surface protein with oligosaccharide chains covalently bound to the polypeptide; also present on virus surfaces and often provoking an immunogenic response in humans </td></tr>
 +
          <tr class="row21">
 +
            <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">
 +
            <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">
 +
            <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>
 +
<tr class="row24">
 +
            <td class="col1"> Her2 protein </td><td class="col0"> biomarker for breast cancer </td></tr>
 +
          <tr class="row25">
 +
            <td class="col1"> His-tag </td><td class="col0"> tag consisting of several histidine residues binding to Ni-NTA and often used for protein purification and specific binding to surfaces </td></tr>
 +
          <tr class="row26">
 +
            <td class="col1"> HIV </td><td class="col0"> Human Immunodeficiency Virus, causes AIDS </td></tr>
 +
          <tr class="row27">
 +
            <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">
 +
            <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">
 +
            <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">
 +
            <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>
 +
          <tr class="row31">
 +
            <td class="col1"> LB </td><td class="col0"> Lyria-Bertani-medium, a nutritionally rich medium, primarily used for growing bacteria </td></tr>
 +
          <tr class="row32">
 +
          <td class="col1"> LOC </td><td class="col0"> Lab-on-a-Chip system, microarray based device for immunodiagnosis </td></tr>
 +
<tr class="row33">
 +
            <td class="col1"> Mg(OAc)<sub>2</sub> </td><td class="col0"> magnesium acetate, used to supplement our cell-free expression mix</td></tr>
 +
          <tr class="row34">
 +
            <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>
 +
          <tr class="row35">
 +
            <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">
 +
            <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">
 +
            <td class="col1"> o/n </td><td class="col0"> overnight, used in the labjournals as abbreviation </td></tr>
 +
          <tr class="row38">
 +
            <td class="col1"> OD </td><td class="col0"> optical density, used to determine approximate cell density in a solution </td></tr>
 +
          <tr class="row39">
 +
            <td class="col1"> PCR </td><td class="col0"> polymerase chain reaction, used to amplify DNA fragments using specific primers </td></tr>
 +
          <tr class="row40">
 +
            <td class="col1"> PDE </td><td class="col0"> partial differential equation </td></tr>
 +
          <tr class="row41">
 +
            <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">
 +
            <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>
 +
          <tr class="row44">
 +
            <td class="col1"> pET22b+ </td><td class="col0"> commonly used plasmid for protein overexpression in bacteria </td></tr>
 +
          <tr class="row45">
 +
            <td class="col1"> pJet </td><td class="col0"> blunt-end cloning vector </td> </tr>
 +
          <tr class="row46">
 +
            <td class="col1"> plasmid </td><td class="col0"> small, circular DNA molecule </td></tr>
 +
          <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>
 +
<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>
 +
          <tr class="row50">
 +
            <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">
 +
            <td class="col1"> RT </td><td class="col0"> room temperature, abbreviation used in the labjournal </td></tr>
 +
          <tr class="row52">
 +
            <td class="col1"> RV </td><td class="col0"> Rubella Virus, causes German measles </td></tr>
 +
          <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>
 +
<tr class="row55">
 +
            <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">
 +
            <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">
 +
            <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>
 +
<tr class="row59">
 +
            <td class="col1"> turboYFP </td><td class="col0"> enhanced version of the yellow fluorescent protein </td></tr>
 +
          <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>
  
  
−
</table></div>
+
</table>
 +
</div>
  
 
</div>
 
</div>

Latest revision as of 02:13, 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 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