Team:Debrecen-Hungary/parts
From 2010.igem.org
Ophir Keret (Talk | contribs) (→Gal4-NHR8 Chimeric nuclear receptor) |
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Our lipid detecting tool kit comprosis of 19 basic parts (11 ligand binding domains, 3 DNA binding domains and 5 other basic parts),9 composite chimeric receptors and 3 plasmid expression vectors and associated intermediates. Amongst our kit, parts of various speicies of the animalia kingdom may be found. The composite receptors are proof of concept that the basic parts acctually work. The bulk of the data (sequance, sub domains, 3d structure, ligand affinity and more..) can be found in the parts registry. | Our lipid detecting tool kit comprosis of 19 basic parts (11 ligand binding domains, 3 DNA binding domains and 5 other basic parts),9 composite chimeric receptors and 3 plasmid expression vectors and associated intermediates. Amongst our kit, parts of various speicies of the animalia kingdom may be found. The composite receptors are proof of concept that the basic parts acctually work. The bulk of the data (sequance, sub domains, 3d structure, ligand affinity and more..) can be found in the parts registry. | ||
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==Ligand binding domains - Basic Parts == | ==Ligand binding domains - Basic Parts == | ||
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===[http://partsregistry.org/wiki/index.php?title=Part:BBa_K364314 Nuclear hormone receptor 8 (C. Elegans)] === | ===[http://partsregistry.org/wiki/index.php?title=Part:BBa_K364314 Nuclear hormone receptor 8 (C. Elegans)] === | ||
- | + | The nhr-8 gene encodes a nuclear hormone receptor homolog; nhr-8 (ok186) mutants have abnormally low resistance to the toxins colchicine and chloroquine. NHR-8 functions in the nematode xenobiotic defense system. | |
[http://partsregistry.org/wiki/index.php?title=Part:BBa_K364314 Go to the official parts registry page for this part] | [http://partsregistry.org/wiki/index.php?title=Part:BBa_K364314 Go to the official parts registry page for this part] | ||
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=== [http://partsregistry.org/wiki/index.php?title=Part:BBa_K364315 Nuclear hormone receptor 23 (C. Elegans)] === | === [http://partsregistry.org/wiki/index.php?title=Part:BBa_K364315 Nuclear hormone receptor 23 (C. Elegans)] === | ||
- | + | The nhr-23 gene encodes a nuclear hormone receptor homolog that is required in all larval molts. NHR-23 is highly similar to Drosophila DHR3, an ecdysone-inducible gene product involved in metamorphosis. The NHR-23 protein is nuclear, and is present in all blastomeres during early embryogenesis. During later stages of morphogenesis, NHR-23 is restricted to epidermal cells. The expression of nhr-23 cycles between stages of larval development: during each intermolt period, levels of nhr-23 transcripts are 2-5 times greater than levels at each molt. Furthermore NHR-23 binds the DRS-type hormone response sequence in vitro. | |
[http://partsregistry.org/wiki/index.php?title=Part:BBa_K364315 Go to the official parts registry page for this part] | [http://partsregistry.org/wiki/index.php?title=Part:BBa_K364315 Go to the official parts registry page for this part] | ||
=== [http://partsregistry.org/wiki/index.php?title=Part:BBa_K364316 Nuclear hormone receptor 25 (C. Elegans)] === | === [http://partsregistry.org/wiki/index.php?title=Part:BBa_K364316 Nuclear hormone receptor 25 (C. Elegans)] === | ||
- | + | The nhr-25 encodes a nuclear hormone receptor orthologous to Drosophila Ftz-F1. NHR-25 is required for embryogenesis, molting, vulval and gonadal development, and hypodermal expression of acn-1. The nhr-25 is expressed in gonads and loaded into embryos as a maternal transcript. The nhr-25 is zygotically expressed in progeny of the E cell, and then in hypodermis and gut. The role of NHR-25 in molting may be evolutionarily conserved between nematodes and arthopods. | |
[http://partsregistry.org/wiki/index.php?title=Part:BBa_K364316 Go to the official parts registry page for this part] | [http://partsregistry.org/wiki/index.php?title=Part:BBa_K364316 Go to the official parts registry page for this part] | ||
=== [http://partsregistry.org/wiki/index.php?title=Part:BBa_K364317 Nuclear hormone receptor 31 (C. Elegans)] === | === [http://partsregistry.org/wiki/index.php?title=Part:BBa_K364317 Nuclear hormone receptor 31 (C. Elegans)] === | ||
- | + | The nhr-31 encodes one of over 200 C. elegans nuclear receptors. The nhr-31 activity is required for proper growth, development, and function of the excretory cell. In regulating excretory cell development, NHR-31 appears to function by controlling the expression of genes encoding subunits of the vacuolar ATPase. An nhr-31::gfp promoter fusion is expressed at high levels in the excretory cell beginning at embryogenesis and continuing through adulthood, with lower levels of expression seen in the intestine and unidentified tail cells. | |
[http://partsregistry.org/wiki/index.php?title=Part:BBa_K364317 Go to the official parts registry page for this part] | [http://partsregistry.org/wiki/index.php?title=Part:BBa_K364317 Go to the official parts registry page for this part] | ||
=== [http://partsregistry.org/wiki/index.php?title=Part:BBa_K364321 Nuclear hormone receptor 64(C. Elegans)] === | === [http://partsregistry.org/wiki/index.php?title=Part:BBa_K364321 Nuclear hormone receptor 64(C. Elegans)] === | ||
- | NHR-64 | + | The nhr-64 encodes a conserved nuclear receptor that is a member of the NR2 subfamily of nuclear receptors that contains Drosophila and human HNF4 (mutations in human HNF4A are associated with Type I MODY (maturity-onset diabetes of the young)). By homology, NHR-64 is predicted to function as a transcription factor that may activate or repress transcription in response to a hormonal signal. However, as loss of nhr-64 activity via RNAi does not result in any obvious abnormalities, the precise role of NHR-64 in C. elegans development and/or behavior is not yet known. The nhr-64 is broadly expressed and detected in anterior and posterior neurons, the ventral nerve cord, the pharynx, gut, and hypodermis. |
[http://partsregistry.org/wiki/index.php?title=Part:BBa_K364321 Go to the official parts registry page for this part] | [http://partsregistry.org/wiki/index.php?title=Part:BBa_K364321 Go to the official parts registry page for this part] | ||
=== [http://partsregistry.org/wiki/index.php?title=Part:BBa_K364318 Nuclear hormone receptor 80 (C. Elegans)] === | === [http://partsregistry.org/wiki/index.php?title=Part:BBa_K364318 Nuclear hormone receptor 80 (C. Elegans)] === | ||
- | + | The nhr-80 encodes a nuclear hormone receptor, expressed in the intestine, that regulates expression of the delta-9 desaturases FAT-5/-6/-7, and thus regulates fatty acid metabolism. The nhr-80 is specific to nematodes, being a divergent ortholog of HNF4 with many paralogs in C. elegans. | |
[http://partsregistry.org/wiki/index.php?title=Part:BBa_K364318 Go to the official parts registry page for this part] | [http://partsregistry.org/wiki/index.php?title=Part:BBa_K364318 Go to the official parts registry page for this part] | ||
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ER-α is a 17β-estradiol-activated steroid receptor member of the nuclear receptor superfamily of transcription factors. It has a variety of central physiological roles, including those involved in maintenance of the reproductive, cardiovascular, musculoskeletal and central nervous systems. ER-α is expressed at low to moderate levels in major physiological systems (central nervous system (CNS), endocrine, metabolic, gastrointestinal, immune, reproductive, cardiovascular, respiratory and structural), with peaks of expression in the pituitary, ovary, uterus and vas deferens. ER-α dysfunction is associated with cancer, cardiovascular system defects, hematological system defects, immune and inflammation diseases, metabolic defects, reproductive defects. | ER-α is a 17β-estradiol-activated steroid receptor member of the nuclear receptor superfamily of transcription factors. It has a variety of central physiological roles, including those involved in maintenance of the reproductive, cardiovascular, musculoskeletal and central nervous systems. ER-α is expressed at low to moderate levels in major physiological systems (central nervous system (CNS), endocrine, metabolic, gastrointestinal, immune, reproductive, cardiovascular, respiratory and structural), with peaks of expression in the pituitary, ovary, uterus and vas deferens. ER-α dysfunction is associated with cancer, cardiovascular system defects, hematological system defects, immune and inflammation diseases, metabolic defects, reproductive defects. | ||
[http://partsregistry.org/wiki/index.php?title=Part:BBa_K364309 Go to the official parts registry page for this part] | [http://partsregistry.org/wiki/index.php?title=Part:BBa_K364309 Go to the official parts registry page for this part] | ||
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+ | <html><br><a name="DBD"></a><br></html> | ||
==DNA binding domains - Basic Parts== | ==DNA binding domains - Basic Parts== | ||
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Estrogen receptor refers to a group of receptors that are activated by the hormone 17β-estradiol[1] (estrogen) , which is a member of the nuclear hormone family of intracellular receptors. The main function of the estrogen receptor is as a DNA-binding transcription factor that regulates gene expression. | Estrogen receptor refers to a group of receptors that are activated by the hormone 17β-estradiol[1] (estrogen) , which is a member of the nuclear hormone family of intracellular receptors. The main function of the estrogen receptor is as a DNA-binding transcription factor that regulates gene expression. | ||
[http://partsregistry.org/wiki/index.php?title=Part:BBa_K364307 Go to the official parts registry page for this part] | [http://partsregistry.org/wiki/index.php?title=Part:BBa_K364307 Go to the official parts registry page for this part] | ||
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+ | <html><br><a name="other"></a><br></html> | ||
==Other Basic Parts== | ==Other Basic Parts== | ||
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=== [http://partsregistry.org/wiki/index.php?title=Part:BBa_K364328 Gal4-DAF12 Chimeric nuclear receptor] === | === [http://partsregistry.org/wiki/index.php?title=Part:BBa_K364328 Gal4-DAF12 Chimeric nuclear receptor] === | ||
- | Artificial eukaryotic TF made of Gal4 DBD (DNA Binding Domain) and C. elegans | + | Artificial eukaryotic TF made of Gal4 DBD (DNA Binding Domain) and C. elegans nuclear receptor LBD (Ligand Binding Domain) DAF-12. |
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This composite artificial transcription factor will activate any reporter or any gene in general that has a UAS (Upper Activating Sequence) 3' of it's promoter. The usual binding sites of reporters, contain multiple UAS elements. In order to have a POPS output, the LBD has to recruit activators in the cell. This can be initiated by ligand binding or by recruiting a protein that has a fused strong activator like the VP activator. | This composite artificial transcription factor will activate any reporter or any gene in general that has a UAS (Upper Activating Sequence) 3' of it's promoter. The usual binding sites of reporters, contain multiple UAS elements. In order to have a POPS output, the LBD has to recruit activators in the cell. This can be initiated by ligand binding or by recruiting a protein that has a fused strong activator like the VP activator. | ||
[http://partsregistry.org/wiki/index.php?title=Part:BBa_K364328 Go to the official parts registry page for this part] | [http://partsregistry.org/wiki/index.php?title=Part:BBa_K364328 Go to the official parts registry page for this part] | ||
=== [http://partsregistry.org/wiki/index.php?title=Part:BBa_K364320 Gal4-NHR8 Chimeric nuclear receptor] === | === [http://partsregistry.org/wiki/index.php?title=Part:BBa_K364320 Gal4-NHR8 Chimeric nuclear receptor] === | ||
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- | Artificial eukaryotic TF made of Gal4 DBD (DNA Binding Domain) and C. elegans orphan nuclear receptor LBD (Ligand Binding Domain) . This composite artificial transcription factor will activate any reporter or any gene in general that has a UAS (Upper Activating Sequence) 3' of it's promoter. The usual binding sites of reporters, contain multiple UAS elements. In order to have a POPS output, the LBD has to recruit activators in the cell. This can be initiated by ligand binding or by recruiting a protein that has a fused strong activator like the VP activator. | + | Artificial eukaryotic TF made of Gal4 DBD (DNA Binding Domain) and C. elegans orphan nuclear receptor LBD (Ligand Binding Domain). |
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+ | This composite artificial transcription factor will activate any reporter or any gene in general that has a UAS (Upper Activating Sequence) 3' of it's promoter. The usual binding sites of reporters, contain multiple UAS elements. In order to have a POPS output, the LBD has to recruit activators in the cell. This can be initiated by ligand binding or by recruiting a protein that has a fused strong activator like the VP activator. | ||
[http://partsregistry.org/wiki/index.php?title=Part:BBa_K364320 Go to the official parts registry page for this part] | [http://partsregistry.org/wiki/index.php?title=Part:BBa_K364320 Go to the official parts registry page for this part] | ||
=== [http://partsregistry.org/wiki/index.php?title=Part:BBa_K364322 Gal4-NHR23 Chimeric nuclear receptor] === | === [http://partsregistry.org/wiki/index.php?title=Part:BBa_K364322 Gal4-NHR23 Chimeric nuclear receptor] === | ||
- | + | Artificial eukaryotic TF made of Gal4 DBD (DNA Binding Domain) and C. elegans orphan nuclear receptor LBD (Ligand Binding Domain). | |
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- | Artificial eukaryotic TF made of Gal4 DBD (DNA Binding Domain) and C. elegans orphan nuclear receptor LBD (Ligand Binding Domain) | + | |
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This composite artificial transcription factor will activate any reporter or any gene in general that has a UAS (Upper Activating Sequence) 3' of it's promoter. The usual binding sites of reporters, contain multiple UAS elements. In order to have a POPS output, the LBD has to recruit activators in the cell. This can be initiated by ligand binding or by recruiting a protein that has a fused strong activator like the VP activator. | This composite artificial transcription factor will activate any reporter or any gene in general that has a UAS (Upper Activating Sequence) 3' of it's promoter. The usual binding sites of reporters, contain multiple UAS elements. In order to have a POPS output, the LBD has to recruit activators in the cell. This can be initiated by ligand binding or by recruiting a protein that has a fused strong activator like the VP activator. | ||
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[http://partsregistry.org/wiki/index.php?title=Part:BBa_K364322 Go to the official parts registry page for this part] | [http://partsregistry.org/wiki/index.php?title=Part:BBa_K364322 Go to the official parts registry page for this part] | ||
=== [http://partsregistry.org/wiki/index.php?title=Part:BBa_K364323 Gal4-NHR31 Chimeric nuclear receptor] === | === [http://partsregistry.org/wiki/index.php?title=Part:BBa_K364323 Gal4-NHR31 Chimeric nuclear receptor] === | ||
- | + | Artificial eukaryotic TF made of Gal4 DBD (DNA Binding Domain) and C. elegans orphan nuclear receptor LBD (Ligand Binding Domain). | |
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- | Artificial eukaryotic TF made of Gal4 DBD (DNA Binding Domain) and C. elegans orphan nuclear receptor LBD (Ligand Binding Domain) | + | |
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This composite artificial transcription factor will activate any reporter or any gene in general that has a UAS (Upper Activating Sequence) 3' of it's promoter. The usual binding sites of reporters, contain multiple UAS elements. In order to have a POPS output, the LBD has to recruit activators in the cell. This can be initiated by ligand binding or by recruiting a protein that has a fused strong activator like the VP activator. | This composite artificial transcription factor will activate any reporter or any gene in general that has a UAS (Upper Activating Sequence) 3' of it's promoter. The usual binding sites of reporters, contain multiple UAS elements. In order to have a POPS output, the LBD has to recruit activators in the cell. This can be initiated by ligand binding or by recruiting a protein that has a fused strong activator like the VP activator. | ||
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[http://partsregistry.org/wiki/index.php?title=Part:BBa_K364323 Go to the official parts registry page for this part] | [http://partsregistry.org/wiki/index.php?title=Part:BBa_K364323 Go to the official parts registry page for this part] | ||
=== [http://partsregistry.org/wiki/index.php?title=Part:BBa_K364324 Gal4-NHR80 Chimeric nuclear receptor] === | === [http://partsregistry.org/wiki/index.php?title=Part:BBa_K364324 Gal4-NHR80 Chimeric nuclear receptor] === | ||
- | + | Artificial eukaryotic TF made of Gal4 DBD (DNA Binding Domain) and C. elegans orphan nuclear receptor LBD (Ligand Binding Domain). | |
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- | Artificial eukaryotic TF made of Gal4 DBD (DNA Binding Domain) and C. elegans orphan nuclear receptor LBD (Ligand Binding Domain) | + | |
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This composite artificial transcription factor will activate any reporter or any gene in general that has a UAS (Upper Activating Sequence) 3' of it's promoter. The usual binding sites of reporters, contain multiple UAS elements. In order to have a POPS output, the LBD has to recruit activators in the cell. This can be initiated by ligand binding or by recruiting a protein that has a fused strong activator like the VP activator. | This composite artificial transcription factor will activate any reporter or any gene in general that has a UAS (Upper Activating Sequence) 3' of it's promoter. The usual binding sites of reporters, contain multiple UAS elements. In order to have a POPS output, the LBD has to recruit activators in the cell. This can be initiated by ligand binding or by recruiting a protein that has a fused strong activator like the VP activator. | ||
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[http://partsregistry.org/wiki/index.php?title=Part:BBa_K364324 Go to the official parts registry page for this part] | [http://partsregistry.org/wiki/index.php?title=Part:BBa_K364324 Go to the official parts registry page for this part] | ||
=== [http://partsregistry.org/wiki/index.php?title=Part:BBa_K364325 Gal4-PXR Chimeric nuclear receptor] === | === [http://partsregistry.org/wiki/index.php?title=Part:BBa_K364325 Gal4-PXR Chimeric nuclear receptor] === | ||
- | [http://partsregistry.org/wiki/index.php?title=Part:BBa_K364325 Go to the official parts registry page for this part] | + | Artificial eukaryotic TF made of Gal4 DBD (DNA Binding Domain) and H. sapiens nuclear receptor LBD (Ligand Binding Domain). |
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+ | This composite artificial transcription factor will activate any reporter or any gene in general that has a UAS (Upper Activating Sequence) 3' of it's promoter. The usual binding sites of reporters, contain multiple UAS elements. In order to have a POPS output, the LBD has to recruit activators in the cell. This can be initiated by ligand binding or by recruiting a protein that has a fused strong activator like the VP activator. [http://partsregistry.org/wiki/index.php?title=Part:BBa_K364325 Go to the official parts registry page for this part] | ||
=== [http://partsregistry.org/wiki/index.php?title=Part:BBa_K364326 Gal4-EcR Chimeric nuclear receptor] === | === [http://partsregistry.org/wiki/index.php?title=Part:BBa_K364326 Gal4-EcR Chimeric nuclear receptor] === | ||
+ | Artificial eukaryotic TF made of Gal4 DBD (DNA Binding Domain) and D. Melanogaster nuclear receptor LBD (Ligand Binding Domain). | ||
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+ | This composite artificial transcription factor will activate any reporter or any gene in general that has a UAS (Upper Activating Sequence) 3' of it's promoter. The usual binding sites of reporters, contain multiple UAS elements. In order to have a POPS output, the LBD has to recruit activators in the cell. This can be initiated by ligand binding or by recruiting a protein that has a fused strong activator like the VP activator. | ||
[http://partsregistry.org/wiki/index.php?title=Part:BBa_K364326 Go to the official parts registry page for this part] | [http://partsregistry.org/wiki/index.php?title=Part:BBa_K364326 Go to the official parts registry page for this part] | ||
=== [http://partsregistry.org/wiki/index.php?title=Part:BBa_K364327 Gal4-ER Chimeric nuclear receptor] === | === [http://partsregistry.org/wiki/index.php?title=Part:BBa_K364327 Gal4-ER Chimeric nuclear receptor] === | ||
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+ | Artificial eukaryotic TF made of Gal4 DBD (DNA Binding Domain) and H. Sapiens nuclear receptor LBD (Ligand Binding Domain). | ||
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+ | This composite artificial transcription factor will activate any reporter or any gene in general that has a UAS (Upper Activating Sequence) 3' of it's promoter. The usual binding sites of reporters, contain multiple UAS elements. In order to have a POPS output, the LBD has to recruit activators in the cell. This can be initiated by ligand binding or by recruiting a protein that has a fused strong activator like the VP activator. | ||
[http://partsregistry.org/wiki/index.php?title=Part:BBa_K364327 Go to the official parts registry page for this part] | [http://partsregistry.org/wiki/index.php?title=Part:BBa_K364327 Go to the official parts registry page for this part] | ||
=== [http://partsregistry.org/wiki/index.php?title=Part:BBa_K364329 ER DBD-VDR hinge-ER LBD Chimeric nuclear receptor] === | === [http://partsregistry.org/wiki/index.php?title=Part:BBa_K364329 ER DBD-VDR hinge-ER LBD Chimeric nuclear receptor] === | ||
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+ | Artificial eukaryotic TF made of Estrogen receptor's DBD (DNA Binding Domain), a vitamin D3 receptor hinge domain and H. sapiens nuclear receptor LBD (Ligand Binding Domain). | ||
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+ | This composite artificial transcription factor will activate any reporter or any gene in general that has a UAS (Upper Activating Sequence) 3' of it's promoter. The usual binding sites of reporters, contain multiple UAS elements. In order to have a POPS output, the LBD has to recruit activators in the cell. This can be initiated by ligand binding or by recruiting a protein that has a fused strong activator like the VP activator. | ||
[http://partsregistry.org/wiki/index.php?title=Part:BBa_K364329 Go to the official parts registry page for this part] | [http://partsregistry.org/wiki/index.php?title=Part:BBa_K364329 Go to the official parts registry page for this part] | ||
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+ | <html><br><a name="composite"></a><br></html> | ||
== Eukaryotic expression vectors - Composite Parts == | == Eukaryotic expression vectors - Composite Parts == | ||
=== [http://partsregistry.org/wiki/index.php?title=Part:BBa_K364330 TRE-PolyA (intermediate part of the expression vector)] === | === [http://partsregistry.org/wiki/index.php?title=Part:BBa_K364330 TRE-PolyA (intermediate part of the expression vector)] === | ||
+ | Tetracycline Response Element - minimal CMV promoter - PolyA tail which is a fusion of two regulators. It is not possible to fuse coding sequences between them because of scar formation after the ligation but it can be a negative control for the expression vectors made by standard BioBrick parts from pSB1A3 (BBa_K364332, BBa_K364333). | ||
[http://partsregistry.org/wiki/index.php?title=Part:BBa_K364330 Go to the official parts registry page for this part] | [http://partsregistry.org/wiki/index.php?title=Part:BBa_K364330 Go to the official parts registry page for this part] | ||
=== [http://partsregistry.org/wiki/index.php?title=Part:BBa_K364332 TRE-Gal4-PXR-PolyA in PSB1A3 (expression vector)] === | === [http://partsregistry.org/wiki/index.php?title=Part:BBa_K364332 TRE-Gal4-PXR-PolyA in PSB1A3 (expression vector)] === | ||
+ | Expression vector from standard BioBrick parts, expressing Gal4 - human Pregnane X receptor LBD composite part. | ||
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+ | The Gal4-PXR Chimeric nuclear receptor is an artificial eukaryotic TF made of Gal4 DBD (DNA Binding Domain) and H. sapiens nuclear hormone receptor LBD (Ligand Binding Domain) which can be expressed by this expression vector. | ||
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+ | The minimal CMV promoter ensures a continuous expression of the chimeric construct, but furthermore it can be expressed in an inducible form using the Tetracyclin-controlled transcriptional activation system. | ||
[http://partsregistry.org/wiki/index.php?title=Part:BBa_K364332 Go to the official parts registry page for this part] | [http://partsregistry.org/wiki/index.php?title=Part:BBa_K364332 Go to the official parts registry page for this part] | ||
=== [http://partsregistry.org/wiki/index.php?title=Part:BBa_K364333 TRE-Gal4-EcR-PolyA in PSB1A3 (expression vector)]=== | === [http://partsregistry.org/wiki/index.php?title=Part:BBa_K364333 TRE-Gal4-EcR-PolyA in PSB1A3 (expression vector)]=== | ||
- | + | Expression vector from standard BioBrick parts, expressing Gal4 - Ecdysone receptor LBD composite part. | |
- | + | The Gal4-EcR Chimeric nuclear receptor is an artificial eukaryotic TF made of Gal4 DBD (DNA Binding Domain) and D. Melanogaster nuclear hormone receptor LBD (Ligand Binding Domain) which can be expressed by this expression vector. | |
- | = | + | The minimal CMV promoter ensures a continuous expression of the chimeric construct, but furthermore it can be expressed in an inducible form using the Tetracyclin-controlled transcriptional activation system. |
+ | [http://partsregistry.org/wiki/index.php?title=Part:BBa_K364333 Go to the official parts registry page for this part] | ||
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Latest revision as of 09:39, 26 October 2010
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